Meta-analysis of Polyploid Cotton QTL Shows Unequal Contributions of Subgenomes to a Complex Network of Genes and Gene Clusters Implicated in Lint Fiber Development

PubMed Central

Rong, Junkang; Feltus, F. Alex; Waghmare, Vijay N.; Pierce, Gary J.; Chee, Peng W.; Draye, Xavier; Saranga, Yehoshua; Wright, Robert J.; Wilkins, Thea A.; May, O. Lloyd; Smith, C. Wayne; Gannaway, John R.; Wendel, Jonathan F.; Paterson, Andrew H.

2007-01-01

QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks. PMID:17565937

Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development.

PubMed

Rong, Junkang; Feltus, F Alex; Waghmare, Vijay N; Pierce, Gary J; Chee, Peng W; Draye, Xavier; Saranga, Yehoshua; Wright, Robert J; Wilkins, Thea A; May, O Lloyd; Smith, C Wayne; Gannaway, John R; Wendel, Jonathan F; Paterson, Andrew H

2007-08-01

QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks.

CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses.

PubMed

Zhang, Dong; Paterson, Andrew H

2017-01-01

Conventional biparental quantitative trait locus (QTL) mapping has led to some successes in the identification of causal genes in many organisms. QTL likelihood intervals not only provide "prior information" for finer-resolution approaches such as GWAS but also provide better statistical power than GWAS to detect variants with low/rare frequency in a natural population. Here, we describe a new element of an ongoing effort to provide online resources to facilitate study and improvement of the important Saccharinae clade. The primary goal of this new resource is the anchoring of published QTLs for this clade to the Sorghum genome. Genetic map alignments translate a wealth of genomic information from sorghum to Saccharum spp., Miscanthus spp., and other taxa. In addition, genome alignments facilitate comparison of the Saccharinae QTL sets to those of other taxa that enjoy comparable resources, exemplified herein by rice.

Genetics and Genomics of Social Behavior in a Chicken Model.

PubMed

Johnsson, Martin; Henriksen, Rie; Fogelholm, Jesper; Höglund, Andrey; Jensen, Per; Wright, Dominic

2018-05-01

The identification of genes affecting sociality can give insights into the maintenance and development of sociality and personality. In this study, we used the combination of an advanced intercross between wild and domestic chickens with a combined QTL and eQTL genetical genomics approach to identify genes for social reinstatement, a social and anxiety-related behavior. A total of 24 social reinstatement QTL were identified and overlaid with over 600 eQTL obtained from the same birds using hypothalamic tissue. Correlations between overlapping QTL and eQTL indicated five strong candidate genes, with the gene TTRAP being strongly significantly correlated with multiple aspects of social reinstatement behavior, as well as possessing a highly significant eQTL. Copyright © 2018 by the Genetics Society of America.

Educational Software for Mapping Quantitative Trait Loci (QTL)

ERIC Educational Resources Information Center

Helms, T. C.; Doetkott, C.

2007-01-01

This educational software was developed to aid teachers and students in their understanding of how the process of identifying the most likely quantitative trait loci (QTL) position is determined between two flanking DNA markers. The objective of the software that we developed was to: (1) show how a QTL is mapped to a position on a chromosome using…

Identification of trait-improving quantitative trait loci for grain yield components from a dent corn inbred line in an advanced backcross BC2F2 population and comparison with its F2:3 population in popcorn.

PubMed

Li, Y L; Niu, S Z; Dong, Y B; Cui, D Q; Wang, Y Z; Liu, Y Y; Wei, M G

2007-06-01

Normal maize germplasm could be used to improve the grain yield of popcorn inbreds. Our first objective was to locate genetic factors associated with trait variation and make first assessment on the efficiency of advanced backcross quantitative trait locus (AB-QTL) analysis for the identification and transfer of favorable QTL alleles for grain yield components from the dent corn inbred. A second objective was to compare the detection of QTL in the BC2F2 population with results using F(2:3) lines of the same parents. Two hundred and twenty selected BC2F2 families developed from a cross between Dan232 and an elite popcorn inbred N04 were evaluated for six grain yield components under two environments, and genotyped by means of 170 SSR markers. Using composite interval mapping (CIM), a total of 19 significant QTL were detected. Eighteen QTL had favorable alleles contributed by the dent corn parent Dan232. Sixteen of these favorable QTL alleles were not in the same or near marker intervals with QTL for popping characteristics. Six QTL were also detected in the F(2:3) population. Improved N04 could be developed from 210 and 208 families with higher grain weight per plant and/or 100-grain weight, respectively, and 35 families with the same or higher popping expansion volume than N04. In addition, near isogenic lines containing detected QTL (QTL-NILs) for grain weight per plant and/or 100-grain weight could be obtained from 12 families. Our study demonstrated that the AB-QTL method can be applied to identify and manipulate favorable QTL alleles from normal corn inbreds and combine QTL detection and popcorn breeding efficiently.

Multienvironment Quantitative Trait Loci Analysis for Photosynthate Acquisition, Accumulation, and Remobilization Traits in Common Bean Under Drought Stress

PubMed Central

Asfaw, Asrat; Blair, Matthew W.; Struik, Paul C.

2012-01-01

Many of the world’s common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers’ field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization to grain by using a recombinant inbred line population developed from the Mesoamerican intragenepool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress across two continents: Africa and South America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for 11 traits associated with drought tolerance. QTL were detected by both a mixed multienvironment model and by composite interval mapping for each environment using a linkage map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. In the multienvironment, mixed model, nine QTL were detected for 10 drought stress tolerance mechanism traits found on six of the 11 linkage groups. Significant QTL × environment interaction was observed for six of the nine QTL. QTL × environment interaction was of the cross-over type for three of the six significant QTL with contrasting effect of the parental alleles across different environments. In the composite interval mapping, we found 69 QTL in total. The majority of these were found for Palmira (47) or Awassa (18), with fewer in Malawi (4). Phenotypic variation explained by QTL in single environments ranged up to 37%, and the most consistent QTL were for Soil Plant Analysis Development (SPAD) leaf chlorophyll reading and pod partitioning traits. QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection. Our results indicate the relevance of QTL detection in the sites in which bean breeding will be undertaken and the importance of photosynthate accumulation as a trait for common bean drought tolerance. PMID:22670228

Multienvironment quantitative trait Loci analysis for photosynthate acquisition, accumulation, and remobilization traits in common bean under drought stress.

PubMed

Asfaw, Asrat; Blair, Matthew W; Struik, Paul C

2012-05-01

Many of the world's common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers' field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization to grain by using a recombinant inbred line population developed from the Mesoamerican intragenepool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress across two continents: Africa and South America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for 11 traits associated with drought tolerance. QTL were detected by both a mixed multienvironment model and by composite interval mapping for each environment using a linkage map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. In the multienvironment, mixed model, nine QTL were detected for 10 drought stress tolerance mechanism traits found on six of the 11 linkage groups. Significant QTL × environment interaction was observed for six of the nine QTL. QTL × environment interaction was of the cross-over type for three of the six significant QTL with contrasting effect of the parental alleles across different environments. In the composite interval mapping, we found 69 QTL in total. The majority of these were found for Palmira (47) or Awassa (18), with fewer in Malawi (4). Phenotypic variation explained by QTL in single environments ranged up to 37%, and the most consistent QTL were for Soil Plant Analysis Development (SPAD) leaf chlorophyll reading and pod partitioning traits. QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection. Our results indicate the relevance of QTL detection in the sites in which bean breeding will be undertaken and the importance of photosynthate accumulation as a trait for common bean drought tolerance.

Bias correction for estimated QTL effects using the penalized maximum likelihood method.

PubMed

Zhang, J; Yue, C; Zhang, Y-M

2012-04-01

A penalized maximum likelihood method has been proposed as an important approach to the detection of epistatic quantitative trait loci (QTL). However, this approach is not optimal in two special situations: (1) closely linked QTL with effects in opposite directions and (2) small-effect QTL, because the method produces downwardly biased estimates of QTL effects. The present study aims to correct the bias by using correction coefficients and shifting from the use of a uniform prior on the variance parameter of a QTL effect to that of a scaled inverse chi-square prior. The results of Monte Carlo simulation experiments show that the improved method increases the power from 25 to 88% in the detection of two closely linked QTL of equal size in opposite directions and from 60 to 80% in the identification of QTL with small effects (0.5% of the total phenotypic variance). We used the improved method to detect QTL responsible for the barley kernel weight trait using 145 doubled haploid lines developed in the North American Barley Genome Mapping Project. Application of the proposed method to other shrinkage estimation of QTL effects is discussed.

Mapping of epistatic quantitative trait loci in four-way crosses.

PubMed

He, Xiao-Hong; Qin, Hongde; Hu, Zhongli; Zhang, Tianzhen; Zhang, Yuan-Ming

2011-01-01

Four-way crosses (4WC) involving four different inbred lines often appear in plant and animal commercial breeding programs. Direct mapping of quantitative trait loci (QTL) in these commercial populations is both economical and practical. However, the existing statistical methods for mapping QTL in a 4WC population are built on the single-QTL genetic model. This simple genetic model fails to take into account QTL interactions, which play an important role in the genetic architecture of complex traits. In this paper, therefore, we attempted to develop a statistical method to detect epistatic QTL in 4WC population. Conditional probabilities of QTL genotypes, computed by the multi-point single locus method, were used to sample the genotypes of all putative QTL in the entire genome. The sampled genotypes were used to construct the design matrix for QTL effects. All QTL effects, including main and epistatic effects, were simultaneously estimated by the penalized maximum likelihood method. The proposed method was confirmed by a series of Monte Carlo simulation studies and real data analysis of cotton. The new method will provide novel tools for the genetic dissection of complex traits, construction of QTL networks, and analysis of heterosis.

Ensemble Learning of QTL Models Improves Prediction of Complex Traits

PubMed Central

Bian, Yang; Holland, James B.

2015-01-01

Quantitative trait locus (QTL) models can provide useful insights into trait genetic architecture because of their straightforward interpretability but are less useful for genetic prediction because of the difficulty in including the effects of numerous small effect loci without overfitting. Tight linkage between markers introduces near collinearity among marker genotypes, complicating the detection of QTL and estimation of QTL effects in linkage mapping, and this problem is exacerbated by very high density linkage maps. Here we developed a thinning and aggregating (TAGGING) method as a new ensemble learning approach to QTL mapping. TAGGING reduces collinearity problems by thinning dense linkage maps, maintains aspects of marker selection that characterize standard QTL mapping, and by ensembling, incorporates information from many more markers-trait associations than traditional QTL mapping. The objective of TAGGING was to improve prediction power compared with QTL mapping while also providing more specific insights into genetic architecture than genome-wide prediction models. TAGGING was compared with standard QTL mapping using cross validation of empirical data from the maize (Zea mays L.) nested association mapping population. TAGGING-assisted QTL mapping substantially improved prediction ability for both biparental and multifamily populations by reducing both the variance and bias in prediction. Furthermore, an ensemble model combining predictions from TAGGING-assisted QTL and infinitesimal models improved prediction abilities over the component models, indicating some complementarity between model assumptions and suggesting that some trait genetic architectures involve a mixture of a few major QTL and polygenic effects. PMID:26276383

Verification of QTL for Grain Starch Content and Its Genetic Correlation with Oil Content Using Two Connected RIL Populations in High-Oil Maize

PubMed Central

Yang, Guohu; Dong, Yongbin; Li, Yuling; Wang, Qilei; Shi, Qingling; Zhou, Qiang

2013-01-01

Grain oil content is negatively correlated with starch content in maize in general. In this study, 282 and 263 recombinant inbred lines (RIL) developed from two crosses between one high-oil maize inbred and two normal dent maize inbreds were evaluated for grain starch content and its correlation with oil content under four environments. Single-trait QTL for starch content in single-population and joint-population analysis, and multiple-trait QTL for both starch and oil content were detected, and compared with the result obtained in the two related F2∶3 populations. Totally, 20 single-population QTL for grain starch content were detected. No QTL was simultaneously detected across all ten cases. QTL at bins 5.03 and 9.03 were all detected in both populations and in 4 and 5 cases, respectively. Only 2 of the 16 joint-population QTL had significant effects in both populations. Three single-population QTL and 8 joint-population QTL at bins 1.03, 1.04–1.05, 3.05, 8.04–8.05, 9.03, and 9.05 could be considered as fine-mapped. Common QTL across F2∶3 and RIL generations were observed at bins 5.04, 8.04 and 8.05 in population 1 (Pop.1), and at bin 5.03 in population 2 (Pop.2). QTL at bins 3.02–3.03, 3.05, 8.04–8.05 and 9.03 should be focused in high-starch maize breeding. In multiple-trait QTL analysis, 17 starch-oil QTL were detected, 10 in Pop.1 and 7 in Pop.2. And 22 single-trait QTL failed to show significance in multiple-trait analysis, 13 QTL for starch content and 9 QTL for oil content. However, QTL at bins 1.03, 6.03–6.04 and 8.03–8.04 might increase grain starch content and/or grain oil content without reduction in another trait. Further research should be conducted to validate the effect of these QTL in the simultaneous improvement of grain starch and oil content in maize. PMID:23320103

Statistical properties of interval mapping methods on quantitative trait loci location: impact on QTL/eQTL analyses

PubMed Central

2012-01-01

Background Quantitative trait loci (QTL) detection on a huge amount of phenotypes, like eQTL detection on transcriptomic data, can be dramatically impaired by the statistical properties of interval mapping methods. One of these major outcomes is the high number of QTL detected at marker locations. The present study aims at identifying and specifying the sources of this bias, in particular in the case of analysis of data issued from outbred populations. Analytical developments were carried out in a backcross situation in order to specify the bias and to propose an algorithm to control it. The outbred population context was studied through simulated data sets in a wide range of situations. The likelihood ratio test was firstly analyzed under the "one QTL" hypothesis in a backcross population. Designs of sib families were then simulated and analyzed using the QTL Map software. On the basis of the theoretical results in backcross, parameters such as the population size, the density of the genetic map, the QTL effect and the true location of the QTL, were taken into account under the "no QTL" and the "one QTL" hypotheses. A combination of two non parametric tests - the Kolmogorov-Smirnov test and the Mann-Whitney-Wilcoxon test - was used in order to identify the parameters that affected the bias and to specify how much they influenced the estimation of QTL location. Results A theoretical expression of the bias of the estimated QTL location was obtained for a backcross type population. We demonstrated a common source of bias under the "no QTL" and the "one QTL" hypotheses and qualified the possible influence of several parameters. Simulation studies confirmed that the bias exists in outbred populations under both the hypotheses of "no QTL" and "one QTL" on a linkage group. The QTL location was systematically closer to marker locations than expected, particularly in the case of low QTL effect, small population size or low density of markers, i.e. designs with low power. Practical recommendations for experimental designs for QTL detection in outbred populations are given on the basis of this bias quantification. Furthermore, an original algorithm is proposed to adjust the location of a QTL, obtained with interval mapping, which co located with a marker. Conclusions Therefore, one should be attentive when one QTL is mapped at the location of one marker, especially under low power conditions. PMID:22520935

gQTL: A Web Application for QTL Analysis Using the Collaborative Cross Mouse Genetic Reference Population.

PubMed

Konganti, Kranti; Ehrlich, Andre; Rusyn, Ivan; Threadgill, David W

2018-06-07

Multi-parental recombinant inbred populations, such as the Collaborative Cross (CC) mouse genetic reference population, are increasingly being used for analysis of quantitative trait loci (QTL). However specialized analytic software for these complex populations is typically built in R that works only on command-line, which limits the utility of these powerful resources for many users. To overcome analytic limitations, we developed gQTL, a web accessible, simple graphical user interface application based on the DOQTL platform in R to perform QTL mapping using data from CC mice. Copyright © 2018, G3: Genes, Genomes, Genetics.

Composite Interval Mapping Based on Lattice Design for Error Control May Increase Power of Quantitative Trait Locus Detection.

PubMed

He, Jianbo; Li, Jijie; Huang, Zhongwen; Zhao, Tuanjie; Xing, Guangnan; Gai, Junyi; Guan, Rongzhan

2015-01-01

Experimental error control is very important in quantitative trait locus (QTL) mapping. Although numerous statistical methods have been developed for QTL mapping, a QTL detection model based on an appropriate experimental design that emphasizes error control has not been developed. Lattice design is very suitable for experiments with large sample sizes, which is usually required for accurate mapping of quantitative traits. However, the lack of a QTL mapping method based on lattice design dictates that the arithmetic mean or adjusted mean of each line of observations in the lattice design had to be used as a response variable, resulting in low QTL detection power. As an improvement, we developed a QTL mapping method termed composite interval mapping based on lattice design (CIMLD). In the lattice design, experimental errors are decomposed into random errors and block-within-replication errors. Four levels of block-within-replication errors were simulated to show the power of QTL detection under different error controls. The simulation results showed that the arithmetic mean method, which is equivalent to a method under random complete block design (RCBD), was very sensitive to the size of the block variance and with the increase of block variance, the power of QTL detection decreased from 51.3% to 9.4%. In contrast to the RCBD method, the power of CIMLD and the adjusted mean method did not change for different block variances. The CIMLD method showed 1.2- to 7.6-fold higher power of QTL detection than the arithmetic or adjusted mean methods. Our proposed method was applied to real soybean (Glycine max) data as an example and 10 QTLs for biomass were identified that explained 65.87% of the phenotypic variation, while only three and two QTLs were identified by arithmetic and adjusted mean methods, respectively.

Development of genic cleavage markers in association with seed glucosinolate content in canola.

PubMed

Fu, Ying; Lu, Kun; Qian, Lunwen; Mei, Jiaqin; Wei, Dayong; Peng, Xuhui; Xu, Xinfu; Li, Jiana; Frauen, Martin; Dreyer, Felix; Snowdon, Rod J; Qian, Wei

2015-06-01

The orthologues of Arabidopsis involved in seed glucosinolates metabolism within QTL confidence intervals were identified, and functional markers were developed to facilitate breeding for ultra-low glucosinolates in canola. Further reducing the content of seed glucosinolates will have a positive impact on the seed quality of canola (Brassica napus). In this study 43 quantitative trait loci (QTL) for seed glucosinolate (GSL) content in a low-GSL genetic background were mapped over seven environments in Germany and China in a doubled haploid population from a cross between two low-GSL oilseed rape parents with transgressive segregation. By anchoring these QTL to the reference genomes of B. rapa and B. oleracea, we identified 23 orthologues of Arabidopsis involved in GSL metabolism within the QTL confidence intervals. Sequence polymorphisms between the corresponding coding regions of the parental lines were used to develop cleaved amplified polymorphic site markers for two QTL-linked genes, ISOPROPYLMALATE DEHYDROGENASE1 and ADENOSINE 5'-PHOSPHOSULFATE REDUCTASE 3. The genic cleavage markers were mapped in the DH population into the corresponding intervals of QTL explaining 3.36-6.88 and 4.55-8.67 % of the phenotypic variation for seed GSL, respectively. The markers will facilitate breeding for ultra-low seed GSL content in canola.

Fine-mapping and validating qHTSF4.1 to increase spikelet fertility under heat stress at flowering in rice.

PubMed

Ye, Changrong; Tenorio, Fatima A; Redoña, Edilberto D; Morales-Cortezano, Portia S; Cabrega, Gleizl A; Jagadish, Krishna S V; Gregorio, Glenn B

2015-08-01

This study fine mapped and validated a QTL on rice chromosome 4 that increases spikelet fertility under high temperature (over 37 °C) at the flowering stage. Climate change has a negative effect on crop production and food security. Understanding the genetic mechanism of heat tolerance and developing heat-tolerant varieties is essential to cope with future global warming. Previously, we reported on a QTL (qHTSF4.1) from an IR64/N22 population responsible for rice spikelet fertility under high-temperature stress at the flowering stage. To further fine map and validate the effect of qHTSF4.1, PCR-based SNP markers were developed and used to genotype BC2F2, BC3F2, BC3F3, and BC5F2 populations from the same cross. The interval of the QTL was narrowed down to about 1.2 Mb; however, further recombination was not identified even with a large BC5F2 population that was subsequently developed and screened. The sequence in the QTL region is highly conserved and a large number of genes in the same gene family were observed to be clustered in the region. The QTL qHTSF4.1 consistently increased spikelet fertility in all of the backcross populations. This was confirmed using 24 rice varieties. Most of the rice varieties with the QTL showed a certain degree of heat tolerance under high-temperature conditions. In a BC5F2 population with clean background of IR64, QTL qHTSF4.1 increased spikelet fertility by about 15%. It could be an important source for enhancing heat tolerance in rice at the flowering stage. PCR-based SNP markers developed in this study can be used for QTL introgression and for pyramiding with other agronomically important QTLs/genes through marker-assisted selection.

New consistent QTL in pea associated with partial resistance to Aphanomyces euteiches in multiple field and controlled environments from France and the United States

USDA-ARS?s Scientific Manuscript database

Partial resistances, often controlled by QTL (Quantitative Trait Loci), are considered to be more durable than monogenic resistances. Prior to develop efficient breeding programs for polygenic resistance to pathogens, a higher understanding of genetic diversity and stability of resistance QTL in pla...

Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5’ accessions

PubMed Central

2012-01-01

Background Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for fire blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. Results When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90). In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with fire blight resistance. However, this QTL was not observed in the New Zealand or German populations. Conclusions The results suggest that the upper region of ‘Robusta 5’ linkage group 3 contains multiple genes contributing to fire blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative fire blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of fire blight resistance. PMID:22471693

Meta-QTL analysis of seed iron and zinc concentration and content in common bean (Phaseolus vulgaris L.).

PubMed

Izquierdo, Paulo; Astudillo, Carolina; Blair, Matthew W; Iqbal, Asif M; Raatz, Bodo; Cichy, Karen A

2018-05-11

Twelve meta-QTL for seed Fe and Zn concentration and/or content were identified from 87 QTL originating from seven population grown in sixteen field trials. These meta-QTL include 2 specific to iron, 2 specific to zinc and 8 that co-localize for iron and zinc concentrations and/or content. Common bean (Phaseolus vulgaris L.) is the most important legume for human consumption worldwide and it is an important source of microelements, especially iron and zinc. Bean biofortification breeding programs develop new varieties with high levels of Fe and Zn targeted for countries with human micronutrient deficiencies. Biofortification efforts thus far have relied on phenotypic selection of raw seed mineral concentrations in advanced generations. While numerous quantitative trait loci (QTL) studies have been conducted to identify genomic regions associated with increased Fe and Zn concentration in seeds, these results have yet to be employed for marker-assisted breeding. The objective of this study was to conduct a meta-analysis from seven QTL studies in Andean and Middle American intra- and inter-gene pool populations to identify the regions in the genome that control the Fe and Zn levels in seeds. Two meta-QTL specific to Fe and two meta-QTL specific to Zn were identified. Additionally, eight Meta QTL that co-localized for Fe and Zn concentration and/or content were identified across seven chromosomes. The Fe and Zn shared meta-QTL could be useful candidates for marker-assisted breeding to simultaneously increase seed Fe and Zn. The physical positions for 12 individual meta-QTL were identified and within five of the meta-QTL, candidate genes were identified from six gene families that have been associated with transport of iron and zinc in plants.

SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications

PubMed Central

Iquebal, Mir Asif; Jaiswal, Sarika; Angadi, U.B.; Sablok, Gaurav; Arora, Vasu; Kumar, Sunil; Rai, Anil; Kumar, Dinesh

2015-01-01

DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world’s first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of ‘mono’ repeat (76.82%) over ‘di’ repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change. Database URL: http://webapp.cabgrid.res.in/sbmdb/ PMID:26647370

SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.

PubMed

Iquebal, Mir Asif; Jaiswal, Sarika; Angadi, U B; Sablok, Gaurav; Arora, Vasu; Kumar, Sunil; Rai, Anil; Kumar, Dinesh

2015-01-01

DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world's first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of 'mono' repeat (76.82%) over 'di' repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change. Database URL: http://webapp.cabgrid.res.in/sbmdb/. © The Author(s) 2015. Published by Oxford University Press.

Mapping quantitative trait loci for traits defined as ratios.

PubMed

Yang, Runqing; Li, Jiahan; Xu, Shizhong

2008-03-01

Many traits are defined as ratios of two quantitative traits. Methods of QTL mapping for regular quantitative traits are not optimal when applied to ratios due to lack of normality for traits defined as ratios. We develop a new method of QTL mapping for traits defined as ratios. The new method uses a special linear combination of the two component traits, and thus takes advantage of the normal property of the new variable. Simulation study shows that the new method can substantially increase the statistical power of QTL detection relative to the method which treats ratios as regular quantitative traits. The new method also outperforms the method that uses Box-Cox transformed ratio as the phenotype. A real example of QTL mapping for relative growth rate in soybean demonstrates that the new method can detect more QTL than existing methods of QTL mapping for traits defined as ratios.

Molecular Mapping and Validation of a Major QTL Conferring Resistance to a Defoliating Isolate of Verticillium Wilt in Cotton (Gossypium hirsutum L.)

PubMed Central

Wei, Ze; Guo, Xian; Guo, Yuping; Zhang, Suqing; Zhao, Junsheng; Zhang, Guihua; Song, Xianliang; Sun, Xuezhen

2014-01-01

Verticillium wilt (VW) caused by Verticillium dahliae Kleb is one of the most destructive diseases of cotton. Development and use of a VW resistant variety is the most practical and effective way to manage this disease. Identification of highly resistant genes/QTL and the underlining genetic architecture is a prerequisite for developing a VW resistant variety. A major QTL qVW-c6-1 conferring resistance to the defoliating isolate V991 was identified on chromosome 6 in LHB22×JM11 F2∶3 population inoculated and grown in a greenhouse. This QTL was further validated in the LHB22×NNG F2∶3 population that was evaluated in an artificial disease nursery of V991 for two years and in its subsequent F4 population grown in a field severely infested by V991. The allele conferring resistance within the QTL qVW-c6-1 region originated from parent LHB22 and could explain 23.1–27.1% of phenotypic variation. Another resistance QTL qVW-c21-1 originated from the susceptible parent JM11 was mapped on chromosome 21, explaining 14.44% of phenotypic variation. The resistance QTL reported herein provides a useful tool for breeding a cotton variety with enhanced resistance to VW. PMID:24781706

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

PubMed Central

2010-01-01

Background The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content. Results A soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix® Soy GeneChip and high-throughput Illumina® whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region. Conclusions This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome. PMID:20199683

Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease

PubMed Central

Peters, James E.; Lyons, Paul A.; Lee, James C.; Richard, Arianne C.; Fortune, Mary D.; Newcombe, Paul J.; Richardson, Sylvia; Smith, Kenneth G. C.

2016-01-01

Genome-wide association studies (GWAS) have transformed our understanding of the genetics of complex traits such as autoimmune diseases, but how risk variants contribute to pathogenesis remains largely unknown. Identifying genetic variants that affect gene expression (expression quantitative trait loci, or eQTLs) is crucial to addressing this. eQTLs vary between tissues and following in vitro cellular activation, but have not been examined in the context of human inflammatory diseases. We performed eQTL mapping in five primary immune cell types from patients with active inflammatory bowel disease (n = 91), anti-neutrophil cytoplasmic antibody-associated vasculitis (n = 46) and healthy controls (n = 43), revealing eQTLs present only in the context of active inflammatory disease. Moreover, we show that following treatment a proportion of these eQTLs disappear. Through joint analysis of expression data from multiple cell types, we reveal that previous estimates of eQTL immune cell-type specificity are likely to have been exaggerated. Finally, by analysing gene expression data from multiple cell types, we find eQTLs not previously identified by database mining at 34 inflammatory bowel disease-associated loci. In summary, this parallel eQTL analysis in multiple leucocyte subsets from patients with active disease provides new insights into the genetic basis of immune-mediated diseases. PMID:27015630

Application of a new IBD-based QTL mapping method to common wheat breeding population: analysis of kernel hardness and dough strength.

PubMed

Crepieux, Sebastien; Lebreton, Claude; Flament, Pascal; Charmet, Gilles

2005-11-01

Mapping quantitative trait loci (QTL) in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the estimation of the effects highly depend on the choice of the two parental lines. Thus, the QTL found represent only a small part of the genetic architecture and can be of limited economical interest in marker-assisted selection. On the other hand, applied breeding programmes evaluate large numbers of progeny derived from multiple-related crosses for a wide range of agronomic traits. It is assumed that the development of statistical techniques to deal with pedigrees in existing plant populations would increase the relevance and cost effectiveness of QTL mapping in a breeding context. In this study, we applied a two-step IBD-based-variance component method to a real wheat breeding population, composed of 374 F6 lines derived from 80 different parents. Two bread wheat quality related traits were analysed by the method. Results obtained show very close agreement with major genes and QTL already known for those two traits. With this new QTL mapping strategy, inferences about QTL can be drawn across the breeding programme rather than being limited to the sample of progeny from a single cross and thus the use of the detected QTL in assisting breeding would be facilitated.

lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals.

PubMed

Ziyatdinov, Andrey; Vázquez-Santiago, Miquel; Brunel, Helena; Martinez-Perez, Angel; Aschard, Hugues; Soria, Jose Manuel

2018-02-27

Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by modeling such correlations as random effects in linear mixed models (LMMs). The R package lme4 is a well-established tool that implements major LMM features using sparse matrix methods; however, it is not fully adapted for QTL mapping association and linkage studies. In particular, two LMM features are lacking in the base version of lme4: the definition of random effects by custom covariance matrices; and parameter constraints, which are essential in advanced QTL models. Apart from applications in linkage studies of related individuals, such functionalities are of high interest for association studies in situations where multiple covariance matrices need to be modeled, a scenario not covered by many genome-wide association study (GWAS) software. To address the aforementioned limitations, we developed a new R package lme4qtl as an extension of lme4. First, lme4qtl contributes new models for genetic studies within a single tool integrated with lme4 and its companion packages. Second, lme4qtl offers a flexible framework for scenarios with multiple levels of relatedness and becomes efficient when covariance matrices are sparse. We showed the value of our package using real family-based data in the Genetic Analysis of Idiopathic Thrombophilia 2 (GAIT2) project. Our software lme4qtl enables QTL mapping models with a versatile structure of random effects and efficient computation for sparse covariances. lme4qtl is available at https://github.com/variani/lme4qtl .

Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico

PubMed Central

Maga, A. Murat; Navarro, Nicolas; Cunningham, Michael L.; Cox, Timothy C.

2015-01-01

We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl) and 30 QTL responsible for the skull shape (SSH.qtl). Size, sex, and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315 MB and contained 2476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest. PMID:25859222

Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea

PubMed Central

Das, Shouvik; Upadhyaya, Hari D.; Bajaj, Deepak; Kujur, Alice; Badoni, Saurabh; Laxmi; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. Laxmipathi; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

A rapid high-resolution genome-wide strategy for molecular mapping of major QTL(s)/gene(s) regulating important agronomic traits is vital for in-depth dissection of complex quantitative traits and genetic enhancement in chickpea. The present study for the first time employed a NGS-based whole-genome QTL-seq strategy to identify one major genomic region harbouring a robust 100-seed weight QTL using an intra-specific 221 chickpea mapping population (desi cv. ICC 7184 × desi cv. ICC 15061). The QTL-seq-derived major SW QTL (CaqSW1.1) was further validated by single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker-based traditional QTL mapping (47.6% R2 at higher LOD >19). This reflects the reliability and efficacy of QTL-seq as a strategy for rapid genome-wide scanning and fine mapping of major trait regulatory QTLs in chickpea. The use of QTL-seq and classical QTL mapping in combination narrowed down the 1.37 Mb (comprising 177 genes) major SW QTL (CaqSW1.1) region into a 35 kb genomic interval on desi chickpea chromosome 1 containing six genes. One coding SNP (G/A)-carrying constitutive photomorphogenic9 (COP9) signalosome complex subunit 8 (CSN8) gene of these exhibited seed-specific expression, including pronounced differential up-/down-regulation in low and high seed weight mapping parents and homozygous individuals during seed development. The coding SNP mined in this potential seed weight-governing candidate CSN8 gene was found to be present exclusively in all cultivated species/genotypes, but not in any wild species/genotypes of primary, secondary and tertiary gene pools. This indicates the effect of strong artificial and/or natural selection pressure on target SW locus during chickpea domestication. The proposed QTL-seq-driven integrated genome-wide strategy has potential to delineate major candidate gene(s) harbouring a robust trait regulatory QTL rapidly with optimal use of resources. This will further assist us to extrapolate the molecular mechanism underlying complex quantitative traits at a genome-wide scale leading to fast-paced marker-assisted genetic improvement in diverse crop plants, including chickpea. PMID:25922536

mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea

PubMed Central

Das, Shouvik; Singh, Mohar; Srivastava, Rishi; Bajaj, Deepak; Saxena, Maneesha S.; Rana, Jai C.; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

2016-01-01

The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8–10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (CaqaPN4.1: 867.8 kb and CaqaPN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (CaqbPN4.1: 637.5 kb and CaqbPN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby expediting genomics-assisted breeding and genetic enhancement of crop plants, including chickpea. PMID:26685680

Two distinct classes of QTL determine rust resistance in sorghum.

PubMed

Wang, Xuemin; Mace, Emma; Hunt, Colleen; Cruickshank, Alan; Henzell, Robert; Parkes, Heidi; Jordan, David

2014-12-31

Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits.

Comparative genome-wide mapping versus extreme pool-genotyping and development of diagnostic SNP markers linked to QTL for adult plant resistance to stripe rust in common wheat.

PubMed

Wu, Jianhui; Huang, Shuo; Zeng, Qingdong; Liu, Shengjie; Wang, Qilin; Mu, Jingmei; Yu, Shizhou; Han, Dejun; Kang, Zhensheng

2018-06-16

A major stripe rust resistance QTL on chromosome 4BL was localized to a 4.5-Mb interval using comparative QTL mapping methods and validated in 276 wheat genotypes by haplotype analysis. CYMMIT-derived wheat line P10103 was previously identified to have adult plant resistance (APR) to stripe rust in the greenhouse and field. The conventional approach for QTL mapping in common wheat is laborious. Here, we performed QTL detection of APR using a combination of genome-wide scanning and extreme pool-genotyping. SNP-based genetic maps were constructed using the Wheat55 K SNP array to genotype a recombinant inbred line (RIL) population derived from the cross Mingxian 169 × P10103. Five stable QTL were detected across multiple environments. A fter comparing SNP profiles from contrasting, extreme DNA pools of RILs six putative QTL were located to approximate chromosome positions. A major QTL on chromosome 4B was identified in F 2:4 contrasting pools from cross Zhengmai 9023 × P10103. A consensus QTL (LOD = 26-40, PVE = 42-55%), named QYr.nwafu-4BL, was defined and localized to a 4.5-Mb interval flanked by SNP markers AX-110963704 and AX-110519862 in chromosome arm 4BL. Based on stripe rust response, marker genotypes, pedigree analysis and mapping data, QYr.nwafu-4BL is likely to be a new APR QTL. The applicability of the SNP-based markers flanking QYr.nwafu-4BL was validated on a diversity panel of 276 wheat lines. The additional minor QTL on chromosomes 4A, 5A, 5B and 6A enhanced the level of resistance conferred by QYr.nwafu-4BL. Marker-assisted pyramiding of QYr.nwafu-4BL and other favorable minor QTL in new wheat cultivars should improve the level of APR to stripe rust.

QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population.

PubMed

Wang, Yuhui; VandenLangenberg, Kyle; Wen, Changlong; Wehner, Todd C; Weng, Yiqun

2018-03-01

Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized. The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line 'Coolgreen'. Phenotypic data on responses to natural DM and PM infection were collected in multi-year and multi-location replicated field trials. A high-density genetic map with 2780 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing and 55 microsatellite markers was developed, which revealed genomic regions with segregation distortion and mis-assemblies in the '9930' cucumber draft genome. QTL analysis identified 11 and 4 QTL for DM and PM resistances accounting for more than 73.5 and 63.0% total phenotypic variance, respectively. Among the 11 DM resistance QTL, dm5.1, dm5.2, and dm5.3 were major-effect contributing QTL, whereas dm1.1, dm2.1, and dm6.2 conferred susceptibility. Of the 4 QTL for PM resistance, pm5.1 was the major-effect QTL explaining 32.4% phenotypic variance and the minor-effect QTL pm6.1 contributed to disease susceptibility. Three PM QTL, pm2.1, pm5.1, and pm6.1, were co-localized with DM QTL dm2.1, dm5.2, and dm6.1, respectively, which was consistent with the observed linkage of PM and DM resistances in PI 197088. The genetic architecture of DM resistance in PI 197088 and another resistant line WI7120 (PI 330628) was compared, and the potential of using PI 197088 in cucumber breeding for downy and powdery mildew resistances is discussed.

Molecular mapping of QTL alleles of Brassica oleracea affecting days to flowering and photosensitivity in spring Brassica napus

PubMed Central

Bennett, Rick A.; Kebede, Berisso

2018-01-01

Earliness of flowering and maturity are important traits in spring Brassica napus canola–whether grown under long- or short-day condition. By use of a spring B. napus mapping population carrying the genome content of B. oleracea and testing this population under 10 to 18 h photoperiod and 18 to 20 0C (day) temperature conditions, we identified a major QTL on the chromosome C1 affecting flowering time without being influenced by photoperiod and temperature, and a major QTL on C9 affecting flowering time under a short photoperiod (10 h); in both cases, the QTL alleles reducing the number of days to flowering in B. napus were introgressed from the late flowering species B. oleracea. Additive effect of the C1 QTL allele at 14 to18 h photoperiod was 1.1 to 2.9 days; however, the same QTL allele exerted an additive effect of 6.2 days at 10 h photoperiod. Additive effect of the C9 QTL at 10 h photoperiod was 2.8 days. These two QTL also showed significant interaction in the control of flowering only under a short-day (10 h photoperiod) condition with an effect of 2.3 days. A few additional QTL were also detected on the chromosomes C2 and C8; however, none of these QTL could be detected under all photoperiod and temperature conditions. BLASTn search identified several putative flowering time genes on the chromosomes C1 and C9 and located the physical position of the QTL markers in the Brassica genome; however, only a few of these genes were found within the QTL region. Thus, the molecular markers and the genomic regions identified in this research could potentially be used in breeding for the development of early flowering photoinsensitive B. napus canola cultivars, as well as for identification of candidate genes involved in flowering time variation and photosensitivity. PMID:29320498

Molecular mapping of QTL alleles of Brassica oleracea affecting days to flowering and photosensitivity in spring Brassica napus.

PubMed

Rahman, Habibur; Bennett, Rick A; Kebede, Berisso

2018-01-01

Earliness of flowering and maturity are important traits in spring Brassica napus canola-whether grown under long- or short-day condition. By use of a spring B. napus mapping population carrying the genome content of B. oleracea and testing this population under 10 to 18 h photoperiod and 18 to 20 0C (day) temperature conditions, we identified a major QTL on the chromosome C1 affecting flowering time without being influenced by photoperiod and temperature, and a major QTL on C9 affecting flowering time under a short photoperiod (10 h); in both cases, the QTL alleles reducing the number of days to flowering in B. napus were introgressed from the late flowering species B. oleracea. Additive effect of the C1 QTL allele at 14 to18 h photoperiod was 1.1 to 2.9 days; however, the same QTL allele exerted an additive effect of 6.2 days at 10 h photoperiod. Additive effect of the C9 QTL at 10 h photoperiod was 2.8 days. These two QTL also showed significant interaction in the control of flowering only under a short-day (10 h photoperiod) condition with an effect of 2.3 days. A few additional QTL were also detected on the chromosomes C2 and C8; however, none of these QTL could be detected under all photoperiod and temperature conditions. BLASTn search identified several putative flowering time genes on the chromosomes C1 and C9 and located the physical position of the QTL markers in the Brassica genome; however, only a few of these genes were found within the QTL region. Thus, the molecular markers and the genomic regions identified in this research could potentially be used in breeding for the development of early flowering photoinsensitive B. napus canola cultivars, as well as for identification of candidate genes involved in flowering time variation and photosensitivity.

Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree-based QTL analysis

PubMed Central

Verma, Sujeet; Zurn, Jason D; Salinas, Natalia; Mathey, Megan M; Denoyes, Beatrice; Hancock, James F; Finn, Chad E; Bassil, Nahla V; Whitaker, Vance M

2017-01-01

The cultivated strawberry (Fragaria×ananassa) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis. In this study, breeder-specified traits were evaluated in the Eastern (Michigan) and Western (Oregon) United States for a common set of breeding populations during 2 years. Several QTLs were validated for soluble solids content (SSC), fruit weight (FWT), pH and titratable acidity (TA) using a pedigree-based QTL analysis approach. For fruit quality, a QTL for SSC on linkage group (LG) 6A, a QTL for FWT on LG 2BII, a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were detected. In addition, a large-effect QTL for flowering was detected at the distal end of LG 4A, coinciding with the FaPFRU locus. Marker haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal flowering. SNP probes in the FaPFRU region may help facilitate marker-assisted selection for this trait. PMID:29138689

Identification of aerenchyma formation-related QTL in barley that can be effective in breeding for waterlogging tolerance.

PubMed

Zhang, Xuechen; Zhou, Gaofeng; Shabala, Sergey; Koutoulis, Anthony; Shabala, Lana; Johnson, Peter; Li, Chengdao; Zhou, Meixue

2016-06-01

Aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilized approach for the selection of waterlogging tolerant barley genotypes. One major QTL for aerenchyma formation after 7 days of waterlogging treatment was identified and the newly developed markers explained 44 % of the phenotypic variance. This QTL can now be effectively used in barley breeding programs. Waterlogging is one of the important limiting conditions for crop yield and productivity. The main feature of waterlogged soils is oxygen deprivation, due to slow gas diffusion in water. Decreased oxygen content in waterlogged soils leads to the oxygen deficiency in plant tissues, resulting in reduced energy availability for plants. Rapidly induced aerenchyma formation is critical to maintaining adequate oxygen supply and overall waterlogging tolerance in barley. In this study, we have proved that quantifying aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilised approach for the selection of waterlogging tolerant barley genotypes, which is supported by measurements of redox potential (an indicator of anaerobic conditions). This protocol was also used to identify quantitative trait loci (QTL) in a doubled haploid population of barley from the cross between Yerong (tolerant) and Franklin (sensitive) genotypes. The QTL for aerenchyma formation and root porosity were at the same location as the waterlogging tolerance QTL. Seven new markers were developed and added onto this region on chromosome 4H. One major QTL for aerenchyma formation after 7 days waterlogging treatment explained 44.0 % of the phenotypic variance. This successful QTL for aerenchyma formation can be effectively used in the marker assisted selection to improve waterlogging tolerance in barley.

Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree-based QTL analysis.

PubMed

Verma, Sujeet; Zurn, Jason D; Salinas, Natalia; Mathey, Megan M; Denoyes, Beatrice; Hancock, James F; Finn, Chad E; Bassil, Nahla V; Whitaker, Vance M

2017-01-01

The cultivated strawberry ( Fragaria × ananassa ) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis. In this study, breeder-specified traits were evaluated in the Eastern (Michigan) and Western (Oregon) United States for a common set of breeding populations during 2 years. Several QTLs were validated for soluble solids content (SSC), fruit weight (FWT), pH and titratable acidity (TA) using a pedigree-based QTL analysis approach. For fruit quality, a QTL for SSC on linkage group (LG) 6A, a QTL for FWT on LG 2BII, a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were detected. In addition, a large-effect QTL for flowering was detected at the distal end of LG 4A, coinciding with the FaPFRU locus. Marker haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal flowering. SNP probes in the FaPFRU region may help facilitate marker-assisted selection for this trait.

Fourteen Years of R/qtl: Just Barely Sustainable

PubMed Central

Broman, Karl W.

2014-01-01

R/qtl is an R package for mapping quantitative trait loci (genetic loci that contribute to variation in quantitative traits) in experimental crosses. Its development began in 2000. There have been 38 software releases since 2001. The latest release contains 35k lines of R code and 24k lines of C code, plus 15k lines of code for the documentation. Challenges in the development and maintenance of the software are discussed. A key to the success of R/qtl is that it remains a central tool for the chief developer's own research work, and so its maintenance is of selfish importance. PMID:25364504

Quantitative trait Loci analysis using the false discovery rate.

PubMed

Benjamini, Yoav; Yekutieli, Daniel

2005-10-01

False discovery rate control has become an essential tool in any study that has a very large multiplicity problem. False discovery rate-controlling procedures have also been found to be very effective in QTL analysis, ensuring reproducible results with few falsely discovered linkages and offering increased power to discover QTL, although their acceptance has been slower than in microarray analysis, for example. The reason is partly because the methodological aspects of applying the false discovery rate to QTL mapping are not well developed. Our aim in this work is to lay a solid foundation for the use of the false discovery rate in QTL mapping. We review the false discovery rate criterion, the appropriate interpretation of the FDR, and alternative formulations of the FDR that appeared in the statistical and genetics literature. We discuss important features of the FDR approach, some stemming from new developments in FDR theory and methodology, which deem it especially useful in linkage analysis. We review false discovery rate-controlling procedures--the BH, the resampling procedure, and the adaptive two-stage procedure-and discuss the validity of these procedures in single- and multiple-trait QTL mapping. Finally we argue that the control of the false discovery rate has an important role in suggesting, indicating the significance of, and confirming QTL and present guidelines for its use.

Quantitative trait loci underlying resistance to sudden death syndrome (SDS) in MD96-5722 by 'Spencer' recombinant inbred line population of soybean.

PubMed

Anderson, J; Akond, M; Kassem, M A; Meksem, K; Kantartzi, S K

2015-04-01

The best way to protect yield loss of soybean [Glycine max (L.) Merr.] due to sudden death syndrome (SDS), caused by Fusarium virguliforme (Aoki, O'Donnel, Homma & Lattanzi), is the development and use of resistant lines. Mapping quantitative trait loci (QTL) linked to SDS help developing resistant soybean germplasm through molecular marker-assisted selection strategy. QTL for SDS presented herein are from a high-density SNP-based genetic linkage map of MD 96-5722 (a.k.a 'Monocacy') by 'Spencer' recombinant inbred line using SoySNP6K Illumina Infinium BeadChip genotyping array. Ninety-four F 5:7 lines were evaluated for 2 years (2010 and 2011) at two locations (Carbondale and Valmeyer) in southern Illinois, USA to identify QTL controlling SDS resistance using disease index (DX). Composite interval mapping identified 19 SDS controlling QTL which were mapped on 11 separate linkage group (LG) or chromosomes (Chr) out of 20 LG or Chr of soybean genome. Many of these significant QTL identified in one environment/year were confirmed in another year or environment, which suggests a common genetic effects and modes of the pathogen. These new QTL are useful sources for SDS resistance studies in soybean breeding, complementing previously reported loci.

Mapping of quantitative trait loci for grain yield and its components in a US popular winter wheat TAM 111 using 90K SNPs.

PubMed

Assanga, Silvano O; Fuentealba, Maria; Zhang, Guorong; Tan, ChorTee; Dhakal, Smit; Rudd, Jackie C; Ibrahim, Amir M H; Xue, Qingwu; Haley, Scott; Chen, Jianli; Chao, Shiaoman; Baker, Jason; Jessup, Kirk; Liu, Shuyu

2017-01-01

Stable quantitative trait loci (QTL) are important for deployment in marker assisted selection in wheat (Triticum aestivum L.) and other crops. We reported QTL discovery in wheat using a population of 217 recombinant inbred lines and multiple statistical approach including multi-environment, multi-trait and epistatic interactions analysis. We detected nine consistent QTL linked to different traits on chromosomes 1A, 2A, 2B, 5A, 5B, 6A, 6B and 7A. Grain yield QTL were detected on chromosomes 2B.1 and 5B across three or four models of GenStat, MapQTL, and QTLNetwork while the QTL on chromosomes 5A.1, 6A.2, and 7A.1 were only significant with yield from one or two models. The phenotypic variation explained (PVE) by the QTL on 2B.1 ranged from 3.3-25.1% based on single and multi-environment models in GenStat and was pleiotropic or co-located with maturity (days to heading) and yield related traits (test weight, thousand kernel weight, harvest index). The QTL on 5B at 211 cM had PVE range of 1.8-9.3% and had no significant pleiotropic effects. Other consistent QTL detected in this study were linked to yield related traits and agronomic traits. The QTL on 1A was consistent for the number of spikes m-2 across environments and all the four analysis models with a PVE range of 5.8-8.6%. QTL for kernels spike-1 were found in chromosomes 1A, 2A.1, 2B.1, 6A.2, and 7A.1 with PVE ranged from 5.6-12.8% while QTL for thousand kernel weight were located on chromosomes 1A, 2B.1, 5A.1, 6A.2, 6B.1 and 7A.1 with PVEranged from 2.7-19.5%. Among the consistent QTL, five QTL had significant epistatic interactions (additive × additive) at least for one trait and none revealed significant additive × additive × environment interactions. Comparative analysis revealed that the region within the confidence interval of the QTL on 5B from 211.4-244.2 cM is also linked to genes for aspartate-semialdehyde dehydrogenase, splicing regulatory glutamine/lysine-rich protein 1 isoform X1, and UDP-glucose 6-dehydrogenase 1-like isoform X1. The stable QTL could be important for further validation, high throughput SNP development, and marker-assisted selection (MAS) in wheat.

Design of new genome- and gene-sourced primers and identification of QTL for seed oil content in a specially high-oil Brassica napus cultivar.

PubMed

Sun, Meiyu; Hua, Wei; Liu, Jing; Huang, Shunmou; Wang, Xinfa; Liu, Guihua; Wang, Hanzhong

2012-01-01

Rapeseed (Brassica napus L.) is one of most important oilseed crops in the world. There are now various rapeseed cultivars in nature that differ in their seed oil content because they vary in oil-content alleles and there are high-oil alleles among the high-oil rapeseed cultivars. For these experiments, we generated doubled haploid (DH) lines derived from the cross between the specially high-oil cultivar zy036 whose seed oil content is approximately 50% and the specially low-oil cultivar 51070 whose seed oil content is approximately 36%. First, to address the deficiency in polymorphic markers, we designed 5944 pairs of newly developed genome-sourced primers and 443 pairs of newly developed primers related to oil-content genes to complement the 2244 pairs of publicly available primers. Second, we constructed a new DH genetic linkage map using 527 molecular markers, consisting of 181 publicly available markers, 298 newly developed genome-sourced markers and 48 newly developed markers related to oil-content genes. The map contained 19 linkage groups, covering a total length of 2,265.54 cM with an average distance between markers of 4.30 cM. Third, we identified quantitative trait loci (QTL) for seed oil content using field data collected at three sites over 3 years, and found a total of 12 QTL. Of the 12 QTL associated with seed oil content identified, 9 were high-oil QTL which derived from the specially high-oil cultivar zy036. Two high-oil QTL on chromosomes A2 and C9 co-localized in two out of three trials. By QTL mapping for seed oil content, we found four candidate genes for seed oil content related to four gene markers: GSNP39, GSSR161, GIFLP106 and GIFLP046. This information will be useful for cloning functional genes correlated with seed oil content in the future.

Design of New Genome- and Gene-Sourced Primers and Identification of QTL for Seed Oil Content in a Specially High-Oil Brassica napus Cultivar

PubMed Central

Liu, Jing; Huang, Shunmou; Wang, Xinfa; Liu, Guihua; Wang, Hanzhong

2012-01-01

Rapeseed (Brassica napus L.) is one of most important oilseed crops in the world. There are now various rapeseed cultivars in nature that differ in their seed oil content because they vary in oil-content alleles and there are high-oil alleles among the high-oil rapeseed cultivars. For these experiments, we generated doubled haploid (DH) lines derived from the cross between the specially high-oil cultivar zy036 whose seed oil content is approximately 50% and the specially low-oil cultivar 51070 whose seed oil content is approximately 36%. First, to address the deficiency in polymorphic markers, we designed 5944 pairs of newly developed genome-sourced primers and 443 pairs of newly developed primers related to oil-content genes to complement the 2244 pairs of publicly available primers. Second, we constructed a new DH genetic linkage map using 527 molecular markers, consisting of 181 publicly available markers, 298 newly developed genome-sourced markers and 48 newly developed markers related to oil-content genes. The map contained 19 linkage groups, covering a total length of 2,265.54 cM with an average distance between markers of 4.30 cM. Third, we identified quantitative trait loci (QTL) for seed oil content using field data collected at three sites over 3 years, and found a total of 12 QTL. Of the 12 QTL associated with seed oil content identified, 9 were high-oil QTL which derived from the specially high-oil cultivar zy036. Two high-oil QTL on chromosomes A2 and C9 co-localized in two out of three trials. By QTL mapping for seed oil content, we found four candidate genes for seed oil content related to four gene markers: GSNP39, GSSR161, GIFLP106 and GIFLP046. This information will be useful for cloning functional genes correlated with seed oil content in the future. PMID:23077542

Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing

PubMed Central

Everett, Meredith V; Seeb, James E

2014-01-01

Understanding how organisms interact with their environments is increasingly important for conservation efforts in many species, especially in light of highly anticipated climate changes. One method for understanding this relationship is to use genetic maps and QTL mapping to detect genomic regions linked to phenotypic traits of importance for adaptation. We used high-throughput genotyping by sequencing (GBS) to both detect and map thousands of SNPs in haploid Chinook salmon (Oncorhynchus tshawytscha). We next applied this map to detect QTL related to temperature tolerance and body size in families of diploid Chinook salmon. Using these techniques, we mapped 3534 SNPs in 34 linkage groups which is consistent with the haploid chromosome number for Chinook salmon. We successfully detected three QTL for temperature tolerance and one QTL for body size at the experiment-wide level, as well as additional QTL significant at the chromosome-wide level. The use of haploids coupled with GBS provides a robust pathway to rapidly develop genomic resources in nonmodel organisms; these QTL represent preliminary progress toward linking traits of conservation interest to regions in the Chinook salmon genome. PMID:24822082

Genetic and environmental control of the Verticillium syndrome in Arabidopsis thaliana.

PubMed

Häffner, Eva; Karlovsky, Petr; Diederichsen, Elke

2010-11-02

Verticillium spp. are major pathogens of dicotyledonous plants such as cotton, tomato, olive or oilseed rape. Verticillium symptoms are often ambiguous and influenced by development and environment. The aim of the present study was to define disease and resistance traits of the complex Verticillium longisporum syndrome in Arabidopsis thaliana (L.) Heynh. A genetic approach was used to determine genetic, developmental and environmental factors controlling specific disease and resistance traits and to study their interrelations. A segregating F2/F3 population originating from ecotypes 'Burren' (Bur) and 'Landsberg erecta' (Ler) was established. Plants were root-dip inoculated and tested under greenhouse conditions. The Verticillium syndrome was dissected into components like systemic spread, stunting, development time and axillary branching. Systemic spread of V. longisporum via colonisation of the shoot was extensive in Ler; Bur showed a high degree of resistance against systemic spread. Fungal colonisation of the shoot apex was determined by (a) determining the percentage of plants from which the fungus could be re-isolated and (b) measuring fungal DNA content with quantitative real-time PCR (qPCR). Four quantitative trait loci (QTL) controlling systemic spread were identified for the percentage of plants showing fungal outgrowth, two of these QTL were confirmed with qPCR data. The degree of colonisation by V. longisporum was negatively correlated with development time. QTL controlling development time showed some overlap with QTL for resistance to systemic spread. Stunting depended on host genotype, development time and seasonal effects. Five QTL controlling this trait were identified which did not co-localize with QTL controlling systemic spread. V. longisporum induced increased axillary branching in Bur; two QTL controlling this reaction were found. Systemic spread of V. longisporum in the host as well as resistance to this major disease trait are described for the first time in natural A. thaliana accessions. This creates the possibility to study a major resistance mechanism against vascular pathogens in this model plant and to clone relevant genes of the involved pathways. Stunting resistance and resistance to systemic spread were controlled by different QTL and should be treated as separate traits. Developmental and environmental effects on pathogenesis and resistance need to be considered when designing and interpreting experiments in research and breeding.

Using probe genotypes to dissect QTL × environment interactions for grain yield components in winter wheat.

PubMed

Zheng, Bing Song; Le Gouis, Jacques; Leflon, Martine; Rong, Wen Ying; Laperche, Anne; Brancourt-Hulmel, Maryse

2010-11-01

Yield is known to be a complex trait, the expression of which interacts strongly with environmental conditions. Understanding the genetic basis of these genotype × environment interactions, particularly under limited input levels, is a key objective when selecting wheat genotypes adapted to specific environments. Our principal objectives were thus: (1) to identify genomic regions [quantitative trait loci (QTL)] involving QTL × environment interactions (QEI) and (2) to develop a strategy to understand the specificity of these regions to certain environments. The two main components of yield were studied: kernel number (KN) and thousand-kernel weight (TKW). The Arche × Récital doubled-haploid population of 222 lines was grown in replicated field trials during 2000 and 2001 at three locations in France, under two nitrogen levels. The 12 environments were characterized in terms of water deficit, radiation, temperature and nitrogen stress based on measurements conducted on the four-probe genotypes: Arche, Récital, Ritmo and Soissons. A four-step strategy was developed to explain QTL specificity to some environments: (1) the detection of QTL for KN and TKW in each environment; (2) the estimation of genotypic sensitivities as the factorial regression slope of KN and TKW to environmental covariates and the detection of QTL for these genotypic sensitivities; (3) study of the co-locations of QTL for KN and TKW and of the QTL for sensitivities; in the event of a co-location partitioning the QEI, appropriate covariates were employed; (4) a description of the environments where QTL were detected for KN and TKW using the environmental covariates. A total of 131 QTL were found to be associated with KN, TKW and their sensitivity to environmental covariates across the 12 environments. Four of these QTL, for both KN and TKW, were located on linkage groups 1B, 2D1, 4B and 5A1, and displayed pleiotropic effects. Factorial regression explained from 15.1 to 83.2% of the QEI for KN and involved three major environmental covariates: cumulative radiation-days ±3 days at meiosis, cumulative degree-days >25°C ±3 days at meiosis and nitrogen stress at flowering. For TKW, 13.5-81.8% of the effect of the QEI was partitioned and involved three major environmental covariates: water deficit from flowering to the milk stage, cumulative degree-days >0°C from the milk stage to maturity and soil water deficit at maturity. A comparative analysis was then performed on the QTL detected during this and previous studies published on QEI and some interacting QTL may be common to different genetic backgrounds. Focusing on these QTL common to different genetic backgrounds would give some guidance to understand genotype × environment interaction.

Success and failure in replication of genotype-phenotype associations: How does replication help in understanding the genetic basis of phenotypic variation in outbred populations?

PubMed

Schielzeth, Holger; Rios Villamil, Alejandro; Burri, Reto

2018-03-25

Recent developments in sequencing technologies have facilitated genomewide mapping of phenotypic variation in natural populations. Such mapping efforts face a number of challenges potentially leading to low reproducibility. However, reproducible research forms the basis of scientific progress. We here discuss the options for replication and the reasons for potential nonreproducibility. We then review the evidence for reproducible quantitative trait loci (QTL) with a focus on natural animal populations. Existing case studies of replication fall into three categories: (i) traits that have been mapped to major effect loci (including chromosomal inversion and supergenes) by independent research teams; (ii) QTL fine-mapped in discovery populations; and (iii) attempts to replicate QTL across multiple populations. Major effect loci, in particular those associated with inversions, have been successfully replicated in several cases within and across populations. Beyond such major effect variants, replication has been more successful within than across populations, suggesting that QTL discovered in natural populations may often be population-specific. This suggests that biological causes (differences in linkage patterns, allele frequencies or context-dependencies of QTL) contribute to nonreproducibility. Evidence from other fields, notably animal breeding and QTL mapping in humans, suggests that a significant fraction of QTL is indeed reproducible in direction and magnitude at least within populations. However, there is also a large number of QTL that cannot be easily reproduced. We put forward that more studies should explicitly address the causes and context-dependencies of QTL signals, in particular to disentangle linkage differences, allele frequency differences and gene-by-environment interactions as biological causes of nonreproducibility of QTL, especially between populations. © 2018 John Wiley & Sons Ltd.

Complex Genetic Effects on Early Vegetative Development Shape Resource Allocation Differences Between Arabidopsis lyrata Populations

PubMed Central

Remington, David L.; Leinonen, Päivi H.; Leppälä, Johanna; Savolainen, Outi

2013-01-01

Costs of reproduction due to resource allocation trade-offs have long been recognized as key forces in life history evolution, but little is known about their functional or genetic basis. Arabidopsis lyrata, a perennial relative of the annual model plant A. thaliana with a wide climatic distribution, has populations that are strongly diverged in resource allocation. In this study, we evaluated the genetic and functional basis for variation in resource allocation in a reciprocal transplant experiment, using four A. lyrata populations and F2 progeny from a cross between North Carolina (NC) and Norway parents, which had the most divergent resource allocation patterns. Local alleles at quantitative trait loci (QTL) at a North Carolina field site increased reproductive output while reducing vegetative growth. These QTL had little overlap with flowering date QTL. Structural equation models incorporating QTL genotypes and traits indicated that resource allocation differences result primarily from QTL effects on early vegetative growth patterns, with cascading effects on later vegetative and reproductive development. At a Norway field site, North Carolina alleles at some of the same QTL regions reduced survival and reproductive output components, but these effects were not associated with resource allocation trade-offs in the Norway environment. Our results indicate that resource allocation in perennial plants may involve important adaptive mechanisms largely independent of flowering time. Moreover, the contributions of resource allocation QTL to local adaptation appear to result from their effects on developmental timing and its interaction with environmental constraints, and not from simple models of reproductive costs. PMID:23979581

In the eye of the beholder: the effect of rater variability and different rating scales on QTL mapping.

PubMed

Poland, Jesse A; Nelson, Rebecca J

2011-02-01

The agronomic importance of developing durably resistant cultivars has led to substantial research in the field of quantitative disease resistance (QDR) and, in particular, mapping quantitative trait loci (QTL) for disease resistance. The assessment of QDR is typically conducted by visual estimation of disease severity, which raises concern over the accuracy and precision of visual estimates. Although previous studies have examined the factors affecting the accuracy and precision of visual disease assessment in relation to the true value of disease severity, the impact of this variability on the identification of disease resistance QTL has not been assessed. In this study, the effects of rater variability and rating scales on mapping QTL for northern leaf blight resistance in maize were evaluated in a recombinant inbred line population grown under field conditions. The population of 191 lines was evaluated by 22 different raters using a direct percentage estimate, a 0-to-9 ordinal rating scale, or both. It was found that more experienced raters had higher precision and that using a direct percentage estimation of diseased leaf area produced higher precision than using an ordinal scale. QTL mapping was then conducted using the disease estimates from each rater using stepwise general linear model selection (GLM) and inclusive composite interval mapping (ICIM). For GLM, the same QTL were largely found across raters, though some QTL were only identified by a subset of raters. The magnitudes of estimated allele effects at identified QTL varied drastically, sometimes by as much as threefold. ICIM produced highly consistent results across raters and for the different rating scales in identifying the location of QTL. We conclude that, despite variability between raters, the identification of QTL was largely consistent among raters, particularly when using ICIM. However, care should be taken in estimating QTL allele effects, because this was highly variable and rater dependent.

Exotic QTL improve grain quality in the tri-parental wheat population SW84

PubMed Central

Nedelkou, Ioanna-Pavlina; Maurer, Andreas; Schubert, Anne; Léon, Jens

2017-01-01

Developing the tri-parental exotic wheat population SW84 Genetic diversity of cultivated wheat was markedly reduced, first, during domestication and, second, since the onset of modern elite breeding. There is an increasing demand for utilizing genetic resources to increase genetic diversity and, simultaneously, to improve agronomic performance of cultivated wheat. To locate favorable effects of exotic wheat alleles, we developed the tri-parental wheat population SW84. The population was derived from crossing the hexaploid spring wheat cultivars Triso and Devon with one synthetic exotic donor accession, Syn084L, followed by two rounds of backcrossing and three rounds of selfing. SW84 consists of 359 BC2F4 lines, split into two families, D84 (Devon*Syn084L) and T84 (Triso*Syn084L). Studying the genetic control of grain quality in SW84 As a case study, grain quality of SW84 was studied in replicated field trials. Transgressive segregation was observed for all studied grain quality traits by evaluating SW84 for two years at two locations under low and high nitrogen supply. Subsequently, a genome-wide association study (GWAS) was carried out based on genomic data derived from a 90k Infinium iSELECT single nucleotide polymorphism (SNP) array. In total, GWAS yielded 37 marker-trait associations, summarized to 16 quantitative trait loci (QTL). These SNPs indicate genetic regulators of grain protein content, grain hardness, sedimentation value and sedimentation ratio. The majority of exotic QTL alleles (75%) exerted favorable effects, increasing grain protein content and sedimentation value in ten and two cases, respectively. For instance, two exotic QTL alleles were associated with a substantial increase of grain protein content and sedimentation value by 1.09% and 7.31 ml, respectively. This finding confirms the potential of exotic germplasm to improve grain quality in cultivated wheat. So far, the molecular nature of most of the detected QTL is unknown. However, two QTL correspond to known genes controlling grain quality: The major QTL on chromosome 6B, increasing grain protein content by 0.70%, on average, co-localizes with the NAM-B1 gene, known to control grain protein content as well as iron and zinc content. Likewise, the major QTL on chromosome 5D, reducing grain hardness by 8.98%, on average, co-localizes with the gene for puroindoline b (Pinb-D1) at the Ha locus. In total, 13 QTL were detected across families, whereas one and three QTL were exclusively detected in families D84 and T84, respectively. Likewise, ten QTL were detected across nitrogen treatments, whereas one and five QTL were exclusively detected under low and high N treatments, respectively. Our data indicate that most effects in SW84 act across families and N levels. Merging of data from two families or two N treatments may, thus, be considered in association studies to increase sample size and, as a result, QTL detection power. Utilizing favorable exotic QTL alleles in wheat breeding Our study serves as a model how favorable exotic QTL alleles can be located in exotic germplasm of wheat. In future, the localized favorable exotic QTL alleles will be utilized in wheat breeding programs to simultaneously improve grain quality and selectively expand genetic diversity of the elite wheat gene pool. PMID:28686676

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize

PubMed Central

2010-01-01

Background Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. Results In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. Conclusions CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu. PMID:20946609

Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize.

PubMed

Kelley, Rowena Y; Gresham, Cathy; Harper, Jonathan; Bridges, Susan M; Warburton, Marilyn L; Hawkins, Leigh K; Pechanova, Olga; Peethambaran, Bela; Pechan, Tibor; Luthe, Dawn S; Mylroie, J E; Ankala, Arunkanth; Ozkan, Seval; Henry, W B; Williams, W P

2010-10-07

Aspergillus flavus Link:Fr, an opportunistic fungus that produces aflatoxin, is pathogenic to maize and other oilseed crops. Aflatoxin is a potent carcinogen, and its presence markedly reduces the value of grain. Understanding and enhancing host resistance to A. flavus infection and/or subsequent aflatoxin accumulation is generally considered an efficient means of reducing grain losses to aflatoxin. Different proteomic, genomic and genetic studies of maize (Zea mays L.) have generated large data sets with the goal of identifying genes responsible for conferring resistance to A. flavus, or aflatoxin. In order to maximize the usage of different data sets in new studies, including association mapping, we have constructed a relational database with web interface integrating the results of gene expression, proteomic (both gel-based and shotgun), Quantitative Trait Loci (QTL) genetic mapping studies, and sequence data from the literature to facilitate selection of candidate genes for continued investigation. The Corn Fungal Resistance Associated Sequences Database (CFRAS-DB) (http://agbase.msstate.edu/) was created with the main goal of identifying genes important to aflatoxin resistance. CFRAS-DB is implemented using MySQL as the relational database management system running on a Linux server, using an Apache web server, and Perl CGI scripts as the web interface. The database and the associated web-based interface allow researchers to examine many lines of evidence (e.g. microarray, proteomics, QTL studies, SNP data) to assess the potential role of a gene or group of genes in the response of different maize lines to A. flavus infection and subsequent production of aflatoxin by the fungus. CFRAS-DB provides the first opportunity to integrate data pertaining to the problem of A. flavus and aflatoxin resistance in maize in one resource and to support queries across different datasets. The web-based interface gives researchers different query options for mining the database across different types of experiments. The database is publically available at http://agbase.msstate.edu.

Genetic dissection of quantitative trait locus for ethanol sensitivity in long- and short-sleep mice.

PubMed

Bennett, B; Carosone-Link, P; Beeson, M; Gordon, L; Phares-Zook, N; Johnson, T E

2008-08-01

Interval-specific congenic strains (ISCS) allow fine mapping of a quantitative trait locus (QTL), narrowing its confidence interval by an order of magnitude or more. In earlier work, we mapped four QTL specifying differential ethanol sensitivity, assessed by loss of righting reflex because of ethanol (LORE), in the inbred long-sleep (ILS) and inbred short-sleep (ISS) strains, accounting for approximately 50% of the genetic variance for this trait. Subsequently, we generated reciprocal congenic strains in which each full QTL interval from ILS was bred onto the ISS background and vice versa. An earlier paper reported construction and results of the ISCS on the ISS background; here, we describe this process and report results on the ILS background. We developed multiple ISCS for each Lore QTL in which the QTL interval was broken into a number of smaller intervals. For each of the four QTL regions (chromosomes 1, 2, 11 and 15), we were successful in reducing the intervals significantly. Multiple, positive strains were overlapped to generate a single, reduced interval. Subsequently, this reduced region was overlaid on previous reductions from the ISS background congenics, resulting in substantial reductions in all QTL regions by approximately 75% from the initial mapping study. Genes with sequence or expression polymorphisms in the reduced intervals are potential candidates; evidence for these is presented. Genetic background effects can be important in detection of single QTL; combining this information with the generation of congenics on both backgrounds, as described here, is a powerful approach for fine mapping QTL.

Genetic architecture and temporal patterns of biomass accumulation in spring barley revealed by image analysis.

PubMed

Neumann, Kerstin; Zhao, Yusheng; Chu, Jianting; Keilwagen, Jens; Reif, Jochen C; Kilian, Benjamin; Graner, Andreas

2017-08-10

Genetic mapping of phenotypic traits generally focuses on a single time point, but biomass accumulates continuously during plant development. Resolution of the temporal dynamics that affect biomass recently became feasible using non-destructive imaging. With the aim to identify key genetic factors for vegetative biomass formation from the seedling stage to flowering, we explored growth over time in a diverse collection of two-rowed spring barley accessions. High heritabilities facilitated the temporal analysis of trait relationships and identification of quantitative trait loci (QTL). Biomass QTL tended to persist only a short period during early growth. More persistent QTL were detected around the booting stage. We identified seven major biomass QTL, which together explain 55% of the genetic variance at the seedling stage, and 43% at the booting stage. Three biomass QTL co-located with genes or QTL involved in phenology. The most important locus for biomass was independent from phenology and is located on chromosome 7HL at 141 cM. This locus explained ~20% of the genetic variance, was significant over a long period of time and co-located with HvDIM, a gene involved in brassinosteroid synthesis. Biomass is a dynamic trait and is therefore orchestrated by different QTL during early and late growth stages. Marker-assisted selection for high biomass at booting stage is most effective by also including favorable alleles from seedling biomass QTL. Selection for dynamic QTL may enhance genetic gain for complex traits such as biomass or, in the future, even grain yield.

Combination of all-stage and high-temperature adult-plant resistance QTL confers high-level, durable resistance to stripe rust in winter wheat cultivar Madsen.

PubMed

Liu, L; Wang, M N; Feng, J Y; See, D R; Chao, S M; Chen, X M

2018-05-24

Wheat cultivar Madsen has a new gene on the short arm of chromosome 1A and two QTL for all-stage resistance and three QTL for high-temperature adult-plant resistance that in combination confer high-level, durable resistance to stripe rust. Wheat cultivar Madsen has maintained a high-level resistance to stripe rust over 30 years. To map quantitative trait loci (QTL) underlying the high-level, durable resistance, 156 recombinant inbred lines (RILs) developed from cross Avocet S × Madsen were phenotyped with selected races of Puccinia striiformis f. sp. tritici in the greenhouse seedling tests, and in naturally infected fields during 2015-2017. The RILs were genotyped by SSR and SNP markers from genotyping by sequencing and the 90 K wheat SNP chip. Three QTL for all-stage resistance were mapped on chromosomes 1AS, 1BS and 2AS, and two QTL for high-temperature adult-plant (HTAP) resistance were mapped on 3BS and 6BS. The most effective QTL on 2AS, explaining 8.97-23.10% of the phenotypic variation in seedling tests and 8.60-71.23% in field tests, contained Yr17 for all-stage resistance and an additional gene for HTAP resistance. The 6BS QTL, detected in all field tests, was identified as Yr78. The 1AS QTL, conferring all-stage resistance, was identified as a new gene, which explained 20.45 and 30.23% of variation in resistance to races PSTv-37 and PSTv-40, respectively, and contributed significantly to field resistance at Pullman in 2015-2017, but was not detected at Mount Vernon. The interactions among QTL were mostly additive, and RILs with all five QTL had the highest level of resistance in the field, similar to Madsen. Genotyping 148 US Pacific Northwest wheat cultivars with markers for the 1AS, 2AS and 6BS QTL validated the genes and markers, and indicated their usefulness for marker-assisted selection.

Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/resistant data

PubMed Central

Moen, Thomas; Sonesson, Anna K; Hayes, Ben; Lien, Sigbjørn; Munck, Hege; Meuwissen, Theo HE

2007-01-01

Background Infectious Salmon Anaemia (ISA) is a viral disease affecting farmed Atlantic salmon (Salmo salar) worldwide. The identification of Quantitative Trait Loci (QTL) affecting resistance to the disease could improve our understanding of the genetics underlying the trait and provide a means for Marker-Assisted Selection. We previously performed a genome scan on commercial Atlantic salmon families challenge tested for ISA resistance, identifying several putative QTL. In the present study, we set out to validate the strongest of these QTL in a larger family material coming from the same challenge test, and to determine the position of the QTL by interval mapping. We also wanted to explore different ways of performing QTL analysis within a survival analysis framework (i.e. using time-to-event data), and to compare results using survival analysis with results from analysis on the dichotomous trait 'affected/resistant'. Results The QTL, located on Atlantic salmon linkage group 8 (following SALMAP notation), was confirmed in the new data set. Its most likely position was at a marker cluster containing markers BHMS130, BHMS170 and BHMS553. Significant segregation distortion was observed in the same region, but was shown to be unrelated to the QTL. A maximum likelihood procedure for identifying QTL, based on the Cox proportional hazard model, was developed. QTL mapping was also done using the Haley-Knott method (affected/resistant data), and within a variance-component framework (affected/resistant data and time-to-event data). In all cases, analysis using affected/resistant data gave stronger evidence for a QTL than did analysis using time-to-event data. Conclusion A QTL for resistance to Infectious Salmon Anaemia in Atlantic salmon was validated in this study, and its more precise location on linkage group eight was determined. The QTL explained 6% of the phenotypic variation in resistance to the disease. The linkage group also displayed significant segregation distortion. Survival models proved in this case not to be more suitable than models based on the dichotomous trait 'affected/resistant' for analysing the data. PMID:17697344

Microsatellite mapping of QTL affecting growth, feed consumption, egg production, tonic immobility and body temperature of Japanese quail.

PubMed

Minvielle, Francis; Kayang, Boniface B; Inoue-Murayama, Miho; Miwa, Mitsuru; Vignal, Alain; Gourichon, David; Neau, André; Monvoisin, Jean-Louis; Ito, Shin'ichi

2005-06-08

The Japanese quail (Coturnix japonica) is both an animal model in biology and a commercial bird for egg and meat production. Modern research developments with this bird, however, have been slowed down by the limited information that is available on the genetics of the Japanese quail. Recently, quail genetic maps with microsatellites and AFLP have been produced which open the way to comparative works with the chicken (Gallus gallus), and to QTL detection for a variety of traits. The purpose of this work was to detect for the first time QTL for commercial traits and for more basic characters in an F2 experiment with 434 female quail, and to compare the nature and the position of the detected QTL with those from the first chicken genome scans carried out during the last few years. Genome-wide significant or suggestive QTL were found for clutch length, body weight and feed intake on CJA01, age at first egg and egg number on CJA06, and eggshell weight and residual feed intake on CJA20, with possible pleiotropy for the QTL affecting body weight and feed intake, and egg number and age at first egg. A suggestive QTL was found for tonic immobility on CJA01, and chromosome-wide significant QTL for body temperature were detected on CJA01 and CJA03. Other chromosome-wide significant QTL were found on CJA02, CJA05, CJA09 and CJA14. Parent-of-origin effects were found for QTL for body weight and feed intake on CJA01. Despite its limited length, the first quail microsatellite map was useful to detect new QTL for rarely reported traits, like residual feed intake, and to help establish some correspondence between the QTL for feed intake, body weight and tonic immobility detected in the present work and those reported on GGA01 in the chicken. Further comparative work is now possible in order to better estimate and understand the genetic similarities and differences of these two Phasianidae species.

Genetic basis of climatic adaptation in scots pine by bayesian quantitative trait locus analysis.

PubMed Central

Hurme, P; Sillanpää, M J; Arjas, E; Repo, T; Savolainen, O

2000-01-01

We examined the genetic basis of large adaptive differences in timing of bud set and frost hardiness between natural populations of Scots pine. As a mapping population, we considered an "open-pollinated backcross" progeny by collecting seeds of a single F(1) tree (cross between trees from southern and northern Finland) growing in southern Finland. Due to the special features of the design (no marker information available on grandparents or the father), we applied a Bayesian quantitative trait locus (QTL) mapping method developed previously for outcrossed offspring. We found four potential QTL for timing of bud set and seven for frost hardiness. Bayesian analyses detected more QTL than ANOVA for frost hardiness, but the opposite was true for bud set. These QTL included alleles with rather large effects, and additionally smaller QTL were supported. The largest QTL for bud set date accounted for about a fourth of the mean difference between populations. Thus, natural selection during adaptation has resulted in selection of at least some alleles of rather large effect. PMID:11063704

Box-Cox transformation for QTL mapping.

PubMed

Yang, Runqing; Yi, Nengjun; Xu, Shizhong

2006-01-01

The maximum likelihood method of QTL mapping assumes that the phenotypic values of a quantitative trait follow a normal distribution. If the assumption is violated, some forms of transformation should be taken to make the assumption approximately true. The Box-Cox transformation is a general transformation method which can be applied to many different types of data. The flexibility of the Box-Cox transformation is due to a variable, called transformation factor, appearing in the Box-Cox formula. We developed a maximum likelihood method that treats the transformation factor as an unknown parameter, which is estimated from the data simultaneously along with the QTL parameters. The method makes an objective choice of data transformation and thus can be applied to QTL analysis for many different types of data. Simulation studies show that (1) Box-Cox transformation can substantially increase the power of QTL detection; (2) Box-Cox transformation can replace some specialized transformation methods that are commonly used in QTL mapping; and (3) applying the Box-Cox transformation to data already normally distributed does not harm the result.

SZDB: A Database for Schizophrenia Genetic Research

PubMed Central

Wu, Yong; Yao, Yong-Gang

2017-01-01

Abstract Schizophrenia (SZ) is a debilitating brain disorder with a complex genetic architecture. Genetic studies, especially recent genome-wide association studies (GWAS), have identified multiple variants (loci) conferring risk to SZ. However, how to efficiently extract meaningful biological information from bulk genetic findings of SZ remains a major challenge. There is a pressing need to integrate multiple layers of data from various sources, eg, genetic findings from GWAS, copy number variations (CNVs), association and linkage studies, gene expression, protein–protein interaction (PPI), co-expression, expression quantitative trait loci (eQTL), and Encyclopedia of DNA Elements (ENCODE) data, to provide a comprehensive resource to facilitate the translation of genetic findings into SZ molecular diagnosis and mechanism study. Here we developed the SZDB database (http://www.szdb.org/), a comprehensive resource for SZ research. SZ genetic data, gene expression data, network-based data, brain eQTL data, and SNP function annotation information were systematically extracted, curated and deposited in SZDB. In-depth analyses and systematic integration were performed to identify top prioritized SZ genes and enriched pathways. Multiple types of data from various layers of SZ research were systematically integrated and deposited in SZDB. In-depth data analyses and integration identified top prioritized SZ genes and enriched pathways. We further showed that genes implicated in SZ are highly co-expressed in human brain and proteins encoded by the prioritized SZ risk genes are significantly interacted. The user-friendly SZDB provides high-confidence candidate variants and genes for further functional characterization. More important, SZDB provides convenient online tools for data search and browse, data integration, and customized data analyses. PMID:27451428

The genetic architecture of Drosophila sensory bristle number.

PubMed Central

Dilda, Christy L; Mackay, Trudy F C

2002-01-01

We have mapped quantitative trait loci (QTL) for Drosophila mechanosensory bristle number in six recombinant isogenic line (RIL) mapping populations, each of which was derived from an isogenic chromosome extracted from a line selected for high or low, sternopleural or abdominal bristle number and an isogenic wild-type chromosome. All RILs were evaluated as male and female F(1) progeny of crosses to both the selected and the wild-type parental chromosomes at three developmental temperatures (18 degrees, 25 degrees, and 28 degrees ). QTL for bristle number were mapped separately for each chromosome, trait, and environment by linkage to roo transposable element marker loci, using composite interval mapping. A total of 53 QTL were detected, of which 33 affected sternopleural bristle number, 31 affected abdominal bristle number, and 11 affected both traits. The effects of most QTL were conditional on sex (27%), temperature (14%), or both sex and temperature (30%). Epistatic interactions between QTL were also common. While many QTL mapped to the same location as candidate bristle development loci, several QTL regions did not encompass obvious candidate genes. These features are germane to evolutionary models for the maintenance of genetic variation for quantitative traits, but complicate efforts to understand the molecular genetic basis of variation for complex traits. PMID:12524340

QGene 4.0, an extensible Java QTL-analysis platform.

PubMed

Joehanes, Roby; Nelson, James C

2008-12-01

Of many statistical methods developed to date for quantitative trait locus (QTL) analysis, only a limited subset are available in public software allowing their exploration, comparison and practical application by researchers. We have developed QGene 4.0, a plug-in platform that allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Software and documentation are available at http://coding.plantpath.ksu.edu/qgene. Source code is available on request.

Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

PubMed Central

Rouse, Matthew N.; Tsilo, Toi J.; Macharia, Godwin K.; Bhavani, Sridhar; Jin, Yue; Anderson, James A.

2016-01-01

We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% – 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar marker-trait association studies in other plant species. PMID:27186883

A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.).

PubMed

Wang, Yijun; Xu, Jing; Deng, Dexiang; Ding, Haidong; Bian, Yunlong; Yin, Zhitong; Wu, Yarong; Zhou, Bo; Zhao, Ye

2016-02-01

The meta-QTL and candidate genes will facilitate the elucidation of molecular bases underlying agriculturally important traits and open new avenues for functional markers development and elite alleles introgression in maize breeding program. A large number of QTLs attributed to grain productivity and other agriculturally important traits have been identified and deposited in public repositories. The integration of fruitful QTL becomes a major issue in current plant genomics. To this end, we first collected QTL for six agriculturally important traits in maize, including yield, plant height, ear height, leaf angle, stay-green, and maize rough dwarf disease resistance. The meta-analysis method was then employed to retrieve 113 meta-QTL. Additionally, we also isolated candidate genes for target traits by the bioinformatic technique. Several candidates, including some well-characterized genes, GA3ox2 for plant height, lg1 and lg4 for leaf angle, zfl1 and zfl2 for flowering time, were co-localized with established meta-QTL intervals. Intriguingly, in a relatively narrow meta-QTL region, the maize ortholog of rice yield-related gene GW8/OsSPL16 was believed to be a candidate for yield. Leveraging results presented in this study will provide further insights into the genetic architecture of maize agronomic traits. Moreover, the meta-QTL and candidate genes reported here could be harnessed for the enhancement of stress tolerance and yield performance in maize and translation to other crops.

In-silico QTL mapping of postpubertal mammary ductal development in the mouse uncovers potential human breast cancer risk loci

USDA-ARS?s Scientific Manuscript database

Genetic background plays a dominant role in mammary gland development and breast cancer (BrCa). Despite this, the role of genetics is only partially understood. This study used strain-dependent variation in an inbred mouse mapping panel, to identify quantitative trait loci (QTL) underlying structura...

Mapping of new quantitative trait loci for sudden death syndrome and soybean cyst nematode resistance in two soybean populations.

PubMed

Swaminathan, Sivakumar; Abeysekara, Nilwala S; Knight, Joshua M; Liu, Min; Dong, Jia; Hudson, Matthew E; Bhattacharyya, Madan K; Cianzio, Silvia R

2018-05-01

Novel QTL conferring resistance to both the SDS and SCN was detected in two RIL populations. Dual resistant RILs could be used in breeding programs for developing resistant soybean cultivars. Soybean cultivars, susceptible to the fungus Fusarium virguliforme, which causes sudden death syndrome (SDS), and to the soybean cyst nematode (SCN) (Heterodera glycines), suffer yield losses valued over a billion dollars annually. Both pathogens may occur in the same production fields. Planting of cultivars genetically resistant to both pathogens is considered one of the most effective means to control the two pathogens. The objective of the study was to map quantitative trait loci (QTL) underlying SDS and SCN resistances. Two recombinant inbred line (RIL) populations were developed by crossing 'A95-684043', a high-yielding maturity group (MG) II line resistant to SCN, with 'LS94-3207' and 'LS98-0582' of MG IV, resistant to both F. virguliforme and SCN. Two hundred F 7 derived recombinant inbred lines from each population AX19286 (A95-684043 × LS94-3207) and AX19287 (A95-684043 × LS98-0582) were screened for resistance to each pathogen under greenhouse conditions. Five hundred and eighty and 371 SNP markers were used for mapping resistance QTL in each population. In AX19286, one novel SCN resistance QTL was mapped to chromosome 8. In AX19287, one novel SDS resistance QTL was mapped to chromosome 17 and one novel SCN resistance QTL was mapped to chromosome 11. Previously identified additional SDS and SCN resistance QTL were also detected in the study. Lines possessing superior resistance to both pathogens were also identified and could be used as germplasm sources for breeding SDS- and SCN-resistant soybean cultivars.

Fine mapping QTL for drought resistance traits in rice (Oryza sativa L.) using bulk segregant analysis.

PubMed

Salunkhe, Arvindkumar Shivaji; Poornima, R; Prince, K Silvas Jebakumar; Kanagaraj, P; Sheeba, J Annie; Amudha, K; Suji, K K; Senthil, A; Babu, R Chandra

2011-09-01

Drought stress is a major limitation to rice (Oryza sativa L.) yields and its stability, especially in rainfed conditions. Developing rice cultivars with inherent capacity to withstand drought stress would improve rainfed rice production. Mapping quantitative trait loci (QTLs) linked to drought resistance traits will help to develop rice cultivars suitable for water-limited environments through molecular marker-assisted selection (MAS) strategy. However, QTL mapping is usually carried out by genotyping large number of progenies, which is labour-intensive, time-consuming and cost-ineffective. Bulk segregant analysis (BSA) serves as an affordable strategy for mapping large effect QTLs by genotyping only the extreme phenotypes instead of the entire mapping population. We have previously mapped a QTL linked to leaf rolling and leaf drying in recombinant inbred (RI) lines derived from two locally adapted indica rice ecotypes viz., IR20/Nootripathu using BSA. Fine mapping the QTL will facilitate its application in MAS. BSA was done by bulking DNA of 10 drought-resistant and 12 drought-sensitive RI lines. Out of 343 rice microsatellites markers genotyped, RM8085 co-segregated among the RI lines constituting the respective bulks. RM8085 was mapped in the middle of the QTL region on chromosome 1 previously identified in these RI lines thus reducing the QTL interval from 7.9 to 3.8 cM. Further, the study showed that the region, RM212-RM302-RM8085-RM3825 on chromosome 1, harbours large effect QTLs for drought-resistance traits across several genetic backgrounds in rice. Thus, the QTL may be useful for drought resistance improvement in rice through MAS and map-based cloning.

Advanced backcross QTL mapping of resistance to Fusarium head blight and plant morphological traits in a Triticum macha × T. aestivum population.

PubMed

Buerstmayr, Maria; Lemmens, Marc; Steiner, Barbara; Buerstmayr, Hermann

2011-07-01

While many reports on genetic analysis of Fusarium head blight (FHB) resistance in bread wheat have been published during the past decade, only limited information is available on FHB resistance derived from wheat relatives. In this contribution, we report on the genetic analysis of FHB resistance derived from Triticum macha (Georgian spelt wheat). As the origin of T. macha is in the Caucasian region, it is supposed that its FHB resistance differs from other well-investigated resistance sources. To introduce valuable alleles from the landrace T. macha into a modern genetic background, we adopted an advanced backcross QTL mapping scheme. A backcross-derived recombinant-inbred line population of 321 BC(2)F(3) lines was developed from a cross of T. macha with the Austrian winter wheat cultivar Furore. The population was evaluated for Fusarium resistance in seven field experiments during four seasons using artificial inoculations. A total of 300 lines of the population were genetically fingerprinted using SSR and AFLP markers. The resulting linkage map covered 33 linkage groups with 560 markers. Five novel FHB-resistance QTL, all descending from T. macha, were found on four chromosomes (2A, 2B, 5A, 5B). Several QTL for morphological and developmental traits were mapped in the same population, which partly overlapped with FHB-resistance QTL. Only the 2BL FHB-resistance QTL co-located with a plant height QTL. The largest-effect FHB-resistance QTL in this population mapped at the spelt-type locus on chromosome 5A and was associated with the wild-type allele q, but it is unclear whether q has a pleiotropic effect on FHB resistance or is closely linked to a nearby resistance QTL.

Mapping quantitative trait loci for fear-like behaviors in mice.

PubMed

Gershenfeld, H K; Paul, S M

1997-11-15

Two mouse models developed for screening anxiolytic drugs were selected for genetic analysis, namely "wall-seeking" tendency in an open field ("thigmotaxis") and the light-to-dark transition (LD) paradigm, a conflict test. These tests measure differences in naturalistic tendencies of mice to explore a novel environment and to avoid a bright light or the center of an open field. In an F2 intercross of two strains of mice (A/J and C57BL/6J) that differ markedly in these behaviors, we estimated a broad sense heritability ranging from 0.3 to 0.59. With this intercross (n = 518), we have mapped several quantitative trait loci (QTL) for these behaviors by performing a genome-wide search. A significant QTL on chromosome 10 (near D10Mit237; LOD of 9.3) that affects LD behavior was identified, and suggestive QTL (LOD > 2.8) were mapped to chromosomes 6, 15, 19, and X. For center time behaviors, QTL were identified on chromosome 1 (LOD of 7.7 and 4.0 for the initial 5-min epoch and the first trial average of the next two 5-min epochs, respectively), and suggestive QTL (LOD > 2.8) were mapped to chromosomes 6 and 14. These QTL individually explain from 2.3 to 8.4% of the phenotypic variance. Collectively, the multiple independent QTL explain from 3.5 to 26.5% of the F2 population's phenotypic variance, depending on the trait. The complexity and heterogeneity of the genetic factors underlying these fear-like behaviors are illustrated by the lack of shared QTL between paradigms and by mapping different QTL for repeated trials of behavior. The identification of QTL affecting individual differences in fear-like behavior may lead to the identification of new gene products and pathways that modulate behavior, providing targets for rational drug design.

Bayesian QTL mapping using genome-wide SSR markers and segregating population derived from a cross of two commercial F1 hybrids of tomato.

PubMed

Ohyama, Akio; Shirasawa, Kenta; Matsunaga, Hiroshi; Negoro, Satomi; Miyatake, Koji; Yamaguchi, Hirotaka; Nunome, Tsukasa; Iwata, Hiroyoshi; Fukuoka, Hiroyuki; Hayashi, Takeshi

2017-08-01

Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato. So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F 2 population derived from a cross between two commercial F 1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F 1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F 2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance.

PubMed

Klein, Anthony; Houtin, Hervé; Rond, Céline; Marget, Pascal; Jacquin, Françoise; Boucherot, Karen; Huart, Myriam; Rivière, Nathalie; Boutet, Gilles; Lejeune-Hénaut, Isabelle; Burstin, Judith

2014-06-01

Avoidance mechanisms and intrinsic resistance are complementary strategies to improve winter frost tolerance and yield potential in field pea. The development of the winter pea crop represents a major challenge to expand plant protein production in temperate areas. Breeding winter cultivars requires the combination of freezing tolerance as well as high seed productivity and quality. In this context, we investigated the genetic determinism of winter frost tolerance and assessed its genetic relationship with yield and developmental traits. Using a newly identified source of frost resistance, we developed a population of recombinant inbred lines and evaluated it in six environments in Dijon and Clermont-Ferrand between 2005 and 2010. We developed a genetic map comprising 679 markers distributed over seven linkage groups and covering 947.1 cM. One hundred sixty-one quantitative trait loci (QTL) explaining 9-71 % of the phenotypic variation were detected across the six environments for all traits measured. Two clusters of QTL mapped on the linkage groups III and one cluster on LGVI reveal the genetic links between phenology, morphology, yield-related traits and frost tolerance in winter pea. QTL clusters on LGIII highlighted major developmental gene loci (Hr and Le) and the QTL cluster on LGVI explained up to 71 % of the winter frost damage variation. This suggests that a specific architecture and flowering ideotype defines frost tolerance in winter pea. However, two consistent frost tolerance QTL on LGV were independent of phenology and morphology traits, showing that different protective mechanisms are involved in frost tolerance. Finally, these results suggest that frost tolerance can be bred independently to seed productivity and quality.

Cell Wall Composition and Underlying QTL in an F1 Pseudo-Testcross Population of Switchgrass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serba, Desalegn D.; Sykes, Robert W.; Gjersing, Erica L.

Natural genetic variation for reduced recalcitrance can be used to improve switchgrass for biofuel production. A full-sib switchgrass mapping population developed by crossing a lowland genotype, AP13, and upland genotype, VS16, was evaluated at three locations (Ardmore and Burneyville, OK and Watkinsville, GA). Biomass harvested after senescence in 2009 and 2010 was evaluated at the National Renewable Energy Laboratory (NREL) for sugar release using enzymatic hydrolysis and for lignin content and syringyl/guaiacyl lignin monomer (S/G) ratio using pyrolysis molecular beam mass spectrometry (py-MBMS). Glucose and xylose release ranged from 120 to 313 and 123 to 263 mg g -1, respectively,more » while lignin content ranged from 19 to 27% of the dry biomass. Statistically significant differences were observed among the genotypes and the environments for the cell wall composition traits. Regression analysis showed that a unit increase in lignin content reduced total sugar release by an average of 10 mg g -1. Quantitative trait loci (QTL) analysis detected 9 genomic regions underlying sugar release and 14 for lignin content. The phenotypic variation explained by the individual QTL identified for sugar release ranged from 4.5 to 9.4 and for lignin content from 3.8 to 11.1%. Mapping of the QTL regions to the switchgrass genome sequence (v1.1) found that some of the QTL colocalized with genes involved in carbohydrate processing and metabolism, plant development, defense systems, and transcription factors. Finally, the markers associated with QTL can be implemented in breeding programs to efficiently develop improved switchgrass cultivars for biofuel production.« less

Cell Wall Composition and Underlying QTL in an F1 Pseudo-Testcross Population of Switchgrass

DOE PAGES

Serba, Desalegn D.; Sykes, Robert W.; Gjersing, Erica L.; ...

2016-04-23

Natural genetic variation for reduced recalcitrance can be used to improve switchgrass for biofuel production. A full-sib switchgrass mapping population developed by crossing a lowland genotype, AP13, and upland genotype, VS16, was evaluated at three locations (Ardmore and Burneyville, OK and Watkinsville, GA). Biomass harvested after senescence in 2009 and 2010 was evaluated at the National Renewable Energy Laboratory (NREL) for sugar release using enzymatic hydrolysis and for lignin content and syringyl/guaiacyl lignin monomer (S/G) ratio using pyrolysis molecular beam mass spectrometry (py-MBMS). Glucose and xylose release ranged from 120 to 313 and 123 to 263 mg g -1, respectively,more » while lignin content ranged from 19 to 27% of the dry biomass. Statistically significant differences were observed among the genotypes and the environments for the cell wall composition traits. Regression analysis showed that a unit increase in lignin content reduced total sugar release by an average of 10 mg g -1. Quantitative trait loci (QTL) analysis detected 9 genomic regions underlying sugar release and 14 for lignin content. The phenotypic variation explained by the individual QTL identified for sugar release ranged from 4.5 to 9.4 and for lignin content from 3.8 to 11.1%. Mapping of the QTL regions to the switchgrass genome sequence (v1.1) found that some of the QTL colocalized with genes involved in carbohydrate processing and metabolism, plant development, defense systems, and transcription factors. Finally, the markers associated with QTL can be implemented in breeding programs to efficiently develop improved switchgrass cultivars for biofuel production.« less

QTL mapping for benzoxazinoid content, preharvest sprouting, α-amylase activity, and leaf rust resistance in rye (Secale cereale L.)

PubMed Central

Masojć, Piotr; Krajewski, Paweł; Stochmal, Anna; Kowalczyk, Mariusz; Angelov, Mihail; Ivanova, Valentina; Schollenberger, Małgorzata; Wakuliński, Wojciech; Banaszak, Zofia; Banaszak, Katarzyna; Rakoczy-Trojanowska, Monika

2017-01-01

Mapping population of recombinant inbred lines (RILs) representing 541 × Ot1-3 cross exhibited wide variations of benzoxazinoid (BX) content in leaves and roots, brown rust resistance, α-amylase activity in the grain, and resistance to preharvest sprouting. QTL mapping of major BX species using a DArT-based map revealed a complex genetic architecture underlying the production of these main secondary metabolites engaged in stress and allelopathy responses. The synthesis of BX in leaves and roots was found to be regulated by different QTL. The QTL for the BX content, rust resistance, α-amylase activity, and preharvest sprouting partially overlapped; this points to their common genetic regulation by a definite subset of genes. Only one QTL for BX located on chromosome 7R coincided with the loci of the ScBx genes, which were mapped as two clusters on chromosomes 5RS (Bx3-Bx5) and 7R (Bx1-Bx2). The QTL common for several BX species, rust resistance, preharvest sprouting, and α-amylase activity are interesting objects for further exploration aimed at developing common markers for these important agronomic traits. PMID:29267335

Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules.

PubMed

Curtis, Ross E; Kim, Seyoung; Woolford, John L; Xu, Wenjie; Xing, Eric P

2013-03-21

Association analysis using genome-wide expression quantitative trait locus (eQTL) data investigates the effect that genetic variation has on cellular pathways and leads to the discovery of candidate regulators. Traditional analysis of eQTL data via pairwise statistical significance tests or linear regression does not leverage the availability of the structural information of the transcriptome, such as presence of gene networks that reveal correlation and potentially regulatory relationships among the study genes. We employ a new eQTL mapping algorithm, GFlasso, which we have previously developed for sparse structured regression, to reanalyze a genome-wide yeast dataset. GFlasso fully takes into account the dependencies among expression traits to suppress false positives and to enhance the signal/noise ratio. Thus, GFlasso leverages the gene-interaction network to discover the pleiotropic effects of genetic loci that perturb the expression level of multiple (rather than individual) genes, which enables us to gain more power in detecting previously neglected signals that are marginally weak but pleiotropically significant. While eQTL hotspots in yeast have been reported previously as genomic regions controlling multiple genes, our analysis reveals additional novel eQTL hotspots and, more interestingly, uncovers groups of multiple contributing eQTL hotspots that affect the expression level of functional gene modules. To our knowledge, our study is the first to report this type of gene regulation stemming from multiple eQTL hotspots. Additionally, we report the results from in-depth bioinformatics analysis for three groups of these eQTL hotspots: ribosome biogenesis, telomere silencing, and retrotransposon biology. We suggest candidate regulators for the functional gene modules that map to each group of hotspots. Not only do we find that many of these candidate regulators contain mutations in the promoter and coding regions of the genes, in the case of the Ribi group, we provide experimental evidence suggesting that the identified candidates do regulate the target genes predicted by GFlasso. Thus, this structured association analysis of a yeast eQTL dataset via GFlasso, coupled with extensive bioinformatics analysis, discovers a novel regulation pattern between multiple eQTL hotspots and functional gene modules. Furthermore, this analysis demonstrates the potential of GFlasso as a powerful computational tool for eQTL studies that exploit the rich structural information among expression traits due to correlation, regulation, or other forms of biological dependencies.

Characterizing the Pyrenophora teres f. maculata–Barley Interaction Using Pathogen Genetics

PubMed Central

Carlsen, Steven A.; Neupane, Anjan; Wyatt, Nathan A.; Richards, Jonathan K.; Faris, Justin D.; Xu, Steven S.; Brueggeman, Robert S.; Friesen, Timothy L.

2017-01-01

Pyrenophora teres f. maculata is the cause of the foliar disease spot form net blotch (SFNB) on barley. To evaluate pathogen genetics underlying the P. teres f. maculata–barley interaction, we developed a 105-progeny population by crossing two globally diverse isolates, one from North Dakota and the other from Western Australia. Progeny were phenotyped on a set of four barley genotypes showing a differential reaction to the parental isolates, then genotyped using a restriction site-associated-genotype-by-sequencing (RAD-GBS) approach. Genetic maps were developed for use in quantitative trait locus (QTL) analysis to identify virulence-associated QTL. Six QTL were identified on five different linkage groups and individually accounted for 20–37% of the disease variation, with the number of significant QTL ranging from two to four for the barley genotypes evaluated. The data presented demonstrate the complexity of virulence involved in the P. teres f. maculata–barley pathosystem and begins to lay the foundation for understanding this important interaction. PMID:28659291

QTL fine mapping with Bayes C(π): a simulation study.

PubMed

van den Berg, Irene; Fritz, Sébastien; Boichard, Didier

2013-06-19

Accurate QTL mapping is a prerequisite in the search for causative mutations. Bayesian genomic selection models that analyse many markers simultaneously should provide more accurate QTL detection results than single-marker models. Our objectives were to (a) evaluate by simulation the influence of heritability, number of QTL and number of records on the accuracy of QTL mapping with Bayes Cπ and Bayes C; (b) estimate the QTL status (homozygous vs. heterozygous) of the individuals analysed. This study focussed on the ten largest detected QTL, assuming they are candidates for further characterization. Our simulations were based on a true dairy cattle population genotyped for 38,277 phased markers. Some of these markers were considered biallelic QTL and used to generate corresponding phenotypes. Different numbers of records (4387 and 1500), heritability values (0.1, 0.4 and 0.7) and numbers of QTL (10, 100 and 1000) were studied. QTL detection was based on the posterior inclusion probability for individual markers, or on the sum of the posterior inclusion probabilities for consecutive markers, estimated using Bayes C or Bayes Cπ. The QTL status of the individuals was derived from the contrast between the sums of the SNP allelic effects of their chromosomal segments. The proportion of markers with null effect (π) frequently did not reach convergence, leading to poor results for Bayes Cπ in QTL detection. Fixing π led to better results. Detection of the largest QTL was most accurate for medium to high heritability, for low to moderate numbers of QTL, and with a large number of records. The QTL status was accurately inferred when the distribution of the contrast between chromosomal segment effects was bimodal. QTL detection is feasible with Bayes C. For QTL detection, it is recommended to use a large dataset and to focus on highly heritable traits and on the largest QTL. QTL statuses were inferred based on the distribution of the contrast between chromosomal segment effects.

Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences.

PubMed

Sabadin, P K; Malosetti, M; Boer, M P; Tardin, F D; Santos, F G; Guimarães, C T; Gomide, R L; Andrade, C L T; Albuquerque, P E P; Caniato, F F; Mollinari, M; Margarido, G R A; Oliveira, B F; Schaffert, R E; Garcia, A A F; van Eeuwijk, F A; Magalhaes, J V

2012-05-01

Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum.

Genetic analysis of genetic basis of a physiological disorder "straighthead’’ in rice (Oryza sativa L.)

USDA-ARS?s Scientific Manuscript database

Straighthead is a physiological disorder in rice that causes yield losses and is a serious threat to rice production worldwide. Identification of QTL conferring resistance will help develop resistant cultivars for straighthead control. We conducted linkage mapping to identify QTL involved with strai...

QTL and drought effects on leaf physiology in lowland Panicum virgatum

USDA-ARS?s Scientific Manuscript database

Switchgrass is a key component of plans to develop sustainable cellulosic ethanol production for bioenergy in the U.S. We sought quantitative trait loci (QTL) for leaf structure and function, and tested for genotype × environment interactions in response to drought using the Albany full-sib mapping...

Candidate Loci for Yield-Related Traits in Maize Revealed by a Combination of MetaQTL Analysis and Regional Association Mapping

PubMed Central

Chen, Lin; An, Yixin; Li, Yong-xiang; Li, Chunhui; Shi, Yunsu; Song, Yanchun; Zhang, Dengfeng; Wang, Tianyu; Li, Yu

2017-01-01

Maize grain yield and related traits are complex and are controlled by a large number of genes of small effect or quantitative trait loci (QTL). Over the years, a large number of yield-related QTLs have been identified in maize and deposited in public databases. However, integrating and re-analyzing these data and mining candidate loci for yield-related traits has become a major issue in maize. In this study, we collected information on QTLs conferring maize yield-related traits from 33 published studies. Then, 999 of these QTLs were iteratively projected and subjected to meta-analysis to obtain metaQTLs (MQTLs). A total of 76 MQTLs were found across the maize genome. Based on a comparative genomics strategy, several maize orthologs of rice yield-related genes were identified in these MQTL regions. Furthermore, three potential candidate genes (Gene ID: GRMZM2G359974, GRMZM2G301884, and GRMZM2G083894) associated with kernel size and weight within three MQTL regions were identified using regional association mapping, based on the results of the meta-analysis. This strategy, combining MQTL analysis and regional association mapping, is helpful for functional marker development and rapid identification of candidate genes or loci. PMID:29312420

Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.).

PubMed

Jiang, Congcong; Shi, Jiaqin; Li, Ruiyuan; Long, Yan; Wang, Hao; Li, Dianrong; Zhao, Jianyi; Meng, Jinling

2014-04-01

This report describes an integrative analysis of seed-oil-content quantitative trait loci (QTL) in Brassica napus , using a high-density genetic map to align QTL among different populations. Rapeseed (Brassica napus) is an important source of edible oil and sustainable energy. Given the challenge involved in using only a few genes to substantially increase the oil content of rapeseed without affecting the fatty acid composition, exploitation of a greater number of genetic loci that regulate the oil content variation among rapeseed germplasm is of fundamental importance. In this study, we investigated variation in the seed-oil content among two related genetic populations of Brassica napus, the TN double-haploid population and its derivative reconstructed-F2 population. Each population was grown in multiple experiments under different environmental conditions. Mapping of quantitative trait loci (QTL) identified 41 QTL in the TN populations. Furthermore, of the 20 pairs of epistatic interaction loci detected, approximately one-third were located within the QTL intervals. The use of common markers on different genetic maps and the TN genetic map as a reference enabled us to project QTL from an additional three genetic populations onto the TN genetic map. In summary, we used the TN genetic map of the B. napus genome to identify 46 distinct QTL regions that control seed-oil content on 16 of the 19 linkage groups of B. napus. Of these, 18 were each detected in multiple populations. The present results are of value for ongoing efforts to breed rapeseed with high oil content, and alignment of the QTL makes an important contribution to the development of an integrative system for genetic studies of rapeseed.

Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea.

PubMed

Desgroux, Aurore; L'Anthoëne, Virginie; Roux-Duparque, Martine; Rivière, Jean-Philippe; Aubert, Grégoire; Tayeh, Nadim; Moussart, Anne; Mangin, Pierre; Vetel, Pierrick; Piriou, Christophe; McGee, Rebecca J; Coyne, Clarice J; Burstin, Judith; Baranger, Alain; Manzanares-Dauleux, Maria; Bourion, Virginie; Pilet-Nayel, Marie-Laure

2016-02-20

Genome-wide association (GWA) mapping has recently emerged as a valuable approach for refining the genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil-borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. Linkage mapping studies reported quantitative trait loci (QTL) controlling resistance to A. euteiches in pea. However the confidence intervals (CIs) of these QTL remained large and were often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to use a GWA approach to validate and refine CIs of the previously reported Aphanomyces resistance QTL, as well as identify new resistance loci. A pea-Aphanomyces collection of 175 pea lines, enriched in germplasm derived from previously studied resistant sources, was evaluated for resistance to A. euteiches in field infested nurseries in nine environments and with two strains in climatic chambers. The collection was genotyped using 13,204 SNPs from the recently developed GenoPea Infinium® BeadChip. GWA analysis detected a total of 52 QTL of small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven previously reported main Aphanomyces resistance QTL and detected novel resistance loci. It also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of favourable haplotypes in the most resistant lines. Previous linkages between resistance alleles and undesired late-flowering alleles for dry pea breeding were mostly confirmed, but the linkage between loci controlling resistance and coloured flowers was broken due to the high resolution of the analysis. A high proportion of the putative candidate genes underlying resistance loci encoded stress-related proteins and others suggested that the QTL are involved in diverse functions. This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding.

Detection of eQTL modules mediated by activity levels of transcription factors.

PubMed

Sun, Wei; Yu, Tianwei; Li, Ker-Chau

2007-09-01

Studies of gene expression quantitative trait loci (eQTL) in different organisms have shown the existence of eQTL hot spots: each being a small segment of DNA sequence that harbors the eQTL of a large number of genes. Two questions of great interest about eQTL hot spots arise: (1) which gene within the hot spot is responsible for the linkages, i.e. which gene is the quantitative trait gene (QTG)? (2) How does a QTG affect the expression levels of many genes linked to it? Answers to the first question can be offered by available biological evidence or by statistical methods. The second question is harder to address. One simple situation is that the QTG encodes a transcription factor (TF), which regulates the expression of genes linked to it. However, previous results have shown that TFs are not overrepresented in the eQTL hot spots. In this article, we consider the scenario that the propagation of genetic perturbation from a QTG to other linked genes is mediated by the TF activity. We develop a procedure to detect the eQTL modules (eQTL hot spots together with linked genes) that are compatible with this scenario. We first detect 27 eQTL modules from a yeast eQTL data, and estimate TF activity profiles using the method of Yu and Li (2005). Then likelihood ratio tests (LRTs) are conducted to find 760 relationships supporting the scenario of TF activity mediation: (DNA polymorphism --> cis-linked gene --> TF activity --> downstream linked gene). They are organized into 4 eQTL modules: an amino acid synthesis module featuring a cis-linked gene LEU2 and the mediating TF Leu3; a pheromone response module featuring a cis-linked gene GPA1 and the mediating TF Ste12; an energy-source control module featuring two cis-linked genes, GSY2 and HAP1, and the mediating TF Hap1; a mitotic exit module featuring four cis-linked genes, AMN1, CSH1, DEM1 and TOS1, and the mediating TF complex Ace2/Swi5. Gene Ontology is utilized to reveal interesting functional groups of the downstream genes in each module. Our methods are implemented in an R package: eqtl.TF, which includes source codes and relevant data. It can be freely downloaded at http://www.stat.ucla.edu/~sunwei/software.htm. http://www.stat.ucla.edu/~sunwei/yeast_eQTL_TF/supplementary.pdf.

xQTL workbench: a scalable web environment for multi-level QTL analysis.

PubMed

Arends, Danny; van der Velde, K Joeri; Prins, Pjotr; Broman, Karl W; Möller, Steffen; Jansen, Ritsert C; Swertz, Morris A

2012-04-01

xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. m.a.swertz@rug.nl.

xQTL workbench: a scalable web environment for multi-level QTL analysis

PubMed Central

Arends, Danny; van der Velde, K. Joeri; Prins, Pjotr; Broman, Karl W.; Möller, Steffen; Jansen, Ritsert C.; Swertz, Morris A.

2012-01-01

Summary: xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. Availability: xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. Contact: m.a.swertz@rug.nl PMID:22308096

Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases

PubMed Central

Lee, Taein; Cheng, Chun-Huai; Ficklin, Stephen; Yu, Jing; Humann, Jodi; Main, Dorrie

2017-01-01

Abstract Tripal is an open-source database platform primarily used for development of genomic, genetic and breeding databases. We report here on the release of the Chado Loader, Chado Data Display and Chado Search modules to extend the functionality of the core Tripal modules. These new extension modules provide additional tools for (1) data loading, (2) customized visualization and (3) advanced search functions for supported data types such as organism, marker, QTL/Mendelian Trait Loci, germplasm, map, project, phenotype, genotype and their respective metadata. The Chado Loader module provides data collection templates in Excel with defined metadata and data loaders with front end forms. The Chado Data Display module contains tools to visualize each data type and the metadata which can be used as is or customized as desired. The Chado Search module provides search and download functionality for the supported data types. Also included are the tools to visualize map and species summary. The use of materialized views in the Chado Search module enables better performance as well as flexibility of data modeling in Chado, allowing existing Tripal databases with different metadata types to utilize the module. These Tripal Extension modules are implemented in the Genome Database for Rosaceae (rosaceae.org), CottonGen (cottongen.org), Citrus Genome Database (citrusgenomedb.org), Genome Database for Vaccinium (vaccinium.org) and the Cool Season Food Legume Database (coolseasonfoodlegume.org). Database URL: https://www.citrusgenomedb.org/, https://www.coolseasonfoodlegume.org/, https://www.cottongen.org/, https://www.rosaceae.org/, https://www.vaccinium.org/

Comparative mapping of quantitative trait loci sculpting the curd of Brassica oleracea.

PubMed

Lan, T H; Paterson, A H

2000-08-01

The enlarged inflorescence (curd) of cauliflower and broccoli provide not only a popular vegetable for human consumption, but also a unique opportunity for scientists who seek to understand the genetic basis of plant growth and development. By the comparison of quantitative trait loci (QTL) maps constructed from three different F(2) populations, we identified a total of 86 QTL that control eight curd-related traits in Brassica oleracea. The 86 QTL may reflect allelic variation in as few as 67 different genetic loci and 54 ancestral genes. Although the locations of QTL affecting a trait occasionally corresponded between different populations or between different homeologous Brassica chromosomes, our data supported other molecular and morphological data in suggesting that the Brassica genus is rapidly evolving. Comparative data enabled us to identify a number of candidate genes from Arabidopsis that warrant further investigation to determine if some of them might account for Brassica QTL. The Arabidopsis/Brassica system is an important example of both the challenges and opportunities associated with extrapolation of genomic information from facile models to large-genome taxa including major crops.

Genetics of Species Differences in the Wild Annual Sunflowers, Helianthus annuus and H. petiolaris

PubMed Central

Lexer, Christian; Rosenthal, David M.; Raymond, Olivier; Donovan, Lisa A.; Rieseberg, Loren H.

2005-01-01

Much of our knowledge of speciation genetics stems from quantitative trait locus (QTL) studies. However, interpretations of the size and distribution of QTL underlying species differences are complicated by differences in the way QTL magnitudes are estimated. Also, many studies fail to exploit information about QTL directions or to compare inter- and intraspecific QTL variation. Here, we comprehensively analyze an extensive QTL data set for an interspecific backcross between two wild annual sunflowers, Helianthus annuus and H. petiolaris, interpret different estimates of QTL magnitudes, identify trait groups that have diverged through selection, and compare inter- and intraspecific QTL magnitudes. Our results indicate that even minor QTL (in terms of backcross variance) may be surprisingly large compared to levels of standing variation in the parental species or phenotypic differences between them. Morphological traits, particularly flower morphology, were more strongly or consistently selected than life history or physiological traits. Also, intraspecific QTL were generally smaller than interspecific ones, consistent with the prediction that larger QTL are more likely to spread to fixation across a subdivided population. Our results inform the genetics of species differences in Helianthus and suggest an approach for the simultaneous mapping of inter- and intraspecific QTL. PMID:15545657

Identification of a QTL in Mus musculus for Alcohol Preference, Withdrawal, and Ap3m2 Expression Using Integrative Functional Genomics and Precision Genetics

PubMed Central

Bubier, Jason A.; Jay, Jeremy J.; Baker, Christopher L.; Bergeson, Susan E.; Ohno, Hiroshi; Metten, Pamela; Crabbe, John C.; Chesler, Elissa J.

2014-01-01

Extensive genetic and genomic studies of the relationship between alcohol drinking preference and withdrawal severity have been performed using animal models. Data from multiple such publications and public data resources have been incorporated in the GeneWeaver database with >60,000 gene sets including 285 alcohol withdrawal and preference-related gene sets. Among these are evidence for positional candidates regulating these behaviors in overlapping quantitative trait loci (QTL) mapped in distinct mouse populations. Combinatorial integration of functional genomics experimental results revealed a single QTL positional candidate gene in one of the loci common to both preference and withdrawal. Functional validation studies in Ap3m2 knockout mice confirmed these relationships. Genetic validation involves confirming the existence of segregating polymorphisms that could account for the phenotypic effect. By exploiting recent advances in mouse genotyping, sequence, epigenetics, and phylogeny resources, we confirmed that Ap3m2 resides in an appropriately segregating genomic region. We have demonstrated genetic and alcohol-induced regulation of Ap3m2 expression. Although sequence analysis revealed no polymorphisms in the Ap3m2-coding region that could account for all phenotypic differences, there are several upstream SNPs that could. We have identified one of these to be an H3K4me3 site that exhibits strain differences in methylation. Thus, by making cross-species functional genomics readily computable we identified a common QTL candidate for two related bio-behavioral processes via functional evidence and demonstrate sufficiency of the genetic locus as a source of variation underlying two traits. PMID:24923803

Identification of a QTL in Mus musculus for alcohol preference, withdrawal, and Ap3m2 expression using integrative functional genomics and precision genetics.

PubMed

Bubier, Jason A; Jay, Jeremy J; Baker, Christopher L; Bergeson, Susan E; Ohno, Hiroshi; Metten, Pamela; Crabbe, John C; Chesler, Elissa J

2014-08-01

Extensive genetic and genomic studies of the relationship between alcohol drinking preference and withdrawal severity have been performed using animal models. Data from multiple such publications and public data resources have been incorporated in the GeneWeaver database with >60,000 gene sets including 285 alcohol withdrawal and preference-related gene sets. Among these are evidence for positional candidates regulating these behaviors in overlapping quantitative trait loci (QTL) mapped in distinct mouse populations. Combinatorial integration of functional genomics experimental results revealed a single QTL positional candidate gene in one of the loci common to both preference and withdrawal. Functional validation studies in Ap3m2 knockout mice confirmed these relationships. Genetic validation involves confirming the existence of segregating polymorphisms that could account for the phenotypic effect. By exploiting recent advances in mouse genotyping, sequence, epigenetics, and phylogeny resources, we confirmed that Ap3m2 resides in an appropriately segregating genomic region. We have demonstrated genetic and alcohol-induced regulation of Ap3m2 expression. Although sequence analysis revealed no polymorphisms in the Ap3m2-coding region that could account for all phenotypic differences, there are several upstream SNPs that could. We have identified one of these to be an H3K4me3 site that exhibits strain differences in methylation. Thus, by making cross-species functional genomics readily computable we identified a common QTL candidate for two related bio-behavioral processes via functional evidence and demonstrate sufficiency of the genetic locus as a source of variation underlying two traits. Copyright © 2014 by the Genetics Society of America.

Exotic QTL improve grain quality in the tri-parental wheat population SW84.

PubMed

Nedelkou, Ioanna-Pavlina; Maurer, Andreas; Schubert, Anne; Léon, Jens; Pillen, Klaus

2017-01-01

Genetic diversity of cultivated wheat was markedly reduced, first, during domestication and, second, since the onset of modern elite breeding. There is an increasing demand for utilizing genetic resources to increase genetic diversity and, simultaneously, to improve agronomic performance of cultivated wheat. To locate favorable effects of exotic wheat alleles, we developed the tri-parental wheat population SW84. The population was derived from crossing the hexaploid spring wheat cultivars Triso and Devon with one synthetic exotic donor accession, Syn084L, followed by two rounds of backcrossing and three rounds of selfing. SW84 consists of 359 BC2F4 lines, split into two families, D84 (Devon*Syn084L) and T84 (Triso*Syn084L). As a case study, grain quality of SW84 was studied in replicated field trials. Transgressive segregation was observed for all studied grain quality traits by evaluating SW84 for two years at two locations under low and high nitrogen supply. Subsequently, a genome-wide association study (GWAS) was carried out based on genomic data derived from a 90k Infinium iSELECT single nucleotide polymorphism (SNP) array. In total, GWAS yielded 37 marker-trait associations, summarized to 16 quantitative trait loci (QTL). These SNPs indicate genetic regulators of grain protein content, grain hardness, sedimentation value and sedimentation ratio. The majority of exotic QTL alleles (75%) exerted favorable effects, increasing grain protein content and sedimentation value in ten and two cases, respectively. For instance, two exotic QTL alleles were associated with a substantial increase of grain protein content and sedimentation value by 1.09% and 7.31 ml, respectively. This finding confirms the potential of exotic germplasm to improve grain quality in cultivated wheat. So far, the molecular nature of most of the detected QTL is unknown. However, two QTL correspond to known genes controlling grain quality: The major QTL on chromosome 6B, increasing grain protein content by 0.70%, on average, co-localizes with the NAM-B1 gene, known to control grain protein content as well as iron and zinc content. Likewise, the major QTL on chromosome 5D, reducing grain hardness by 8.98%, on average, co-localizes with the gene for puroindoline b (Pinb-D1) at the Ha locus. In total, 13 QTL were detected across families, whereas one and three QTL were exclusively detected in families D84 and T84, respectively. Likewise, ten QTL were detected across nitrogen treatments, whereas one and five QTL were exclusively detected under low and high N treatments, respectively. Our data indicate that most effects in SW84 act across families and N levels. Merging of data from two families or two N treatments may, thus, be considered in association studies to increase sample size and, as a result, QTL detection power. Our study serves as a model how favorable exotic QTL alleles can be located in exotic germplasm of wheat. In future, the localized favorable exotic QTL alleles will be utilized in wheat breeding programs to simultaneously improve grain quality and selectively expand genetic diversity of the elite wheat gene pool.

Quantitative trait loci controlling leaf appearance and curd initiation of cauliflower in relation to temperature.

PubMed

Hasan, Yaser; Briggs, William; Matschegewski, Claudia; Ordon, Frank; Stützel, Hartmut; Zetzsche, Holger; Groen, Simon; Uptmoor, Ralf

2016-07-01

QTL regions on chromosomes C06 and C09 are involved in temperature dependent time to curd induction in cauliflower. Temperature is the main environmental factor influencing curding time of cauliflower (Brassica oleracea var. botrytis). Temperatures above 20-22 °C inhibit development towards curding even in many summer cultivars. To identify quantitative trait loci (QTL) controlling curding time and its related traits in a wide range of different temperature regimes from 12 to 27 °C, a doubled haploid (DH) mapping population segregating for curding time was developed and days to curd initiation (DCI), leaf appearance rate (LAR), and final leaf number (FLN) were measured. The population was genotyped with 176 single nucleotide polymorphism (SNP) markers. Composite interval mapping (CIM) revealed repeatedly detected QTL for DCI on C06 and C09. The estimated additive effect increased at high temperatures. Significant QTL × environment interactions (Q × E) for FLN and DCI on C06 and C09 suggest that these hotspot regions have major influences on temperature mediated curd induction. 25 % of the DH lines did not induce curds at temperatures higher than 22 °C. Applying a binary model revealed a QTL with LOD >15 on C06. Nearly all lines carrying the allele of the reliable early maturing parental line (PL) on that locus induced curds at high temperatures while only half of the DH lines carrying the allele of the unreliable PL reached the generative phase during the experiment. Large variation in LAR was observed. QTL for LAR were detected repeatedly in several environments on C01, C04 and C06. Negative correlations between LAR and DCI and QTL co-localizations on C04 and C06 suggest that LAR has also effects on development towards curd induction.

An empirical Bayes method for updating inferences in analysis of quantitative trait loci using information from related genome scans.

PubMed

Zhang, Kui; Wiener, Howard; Beasley, Mark; George, Varghese; Amos, Christopher I; Allison, David B

2006-08-01

Individual genome scans for quantitative trait loci (QTL) mapping often suffer from low statistical power and imprecise estimates of QTL location and effect. This lack of precision yields large confidence intervals for QTL location, which are problematic for subsequent fine mapping and positional cloning. In prioritizing areas for follow-up after an initial genome scan and in evaluating the credibility of apparent linkage signals, investigators typically examine the results of other genome scans of the same phenotype and informally update their beliefs about which linkage signals in their scan most merit confidence and follow-up via a subjective-intuitive integration approach. A method that acknowledges the wisdom of this general paradigm but formally borrows information from other scans to increase confidence in objectivity would be a benefit. We developed an empirical Bayes analytic method to integrate information from multiple genome scans. The linkage statistic obtained from a single genome scan study is updated by incorporating statistics from other genome scans as prior information. This technique does not require that all studies have an identical marker map or a common estimated QTL effect. The updated linkage statistic can then be used for the estimation of QTL location and effect. We evaluate the performance of our method by using extensive simulations based on actual marker spacing and allele frequencies from available data. Results indicate that the empirical Bayes method can account for between-study heterogeneity, estimate the QTL location and effect more precisely, and provide narrower confidence intervals than results from any single individual study. We also compared the empirical Bayes method with a method originally developed for meta-analysis (a closely related but distinct purpose). In the face of marked heterogeneity among studies, the empirical Bayes method outperforms the comparator.

Genetic control of soybean seed oil: II. QTL and genes that increase oil concentration without decreasing protein or with increased seed yield.

PubMed

Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

2013-06-01

Soybean [Glycine max (L.) Merrill] seed oil is the primary global source of edible oil and a major renewable and sustainable feedstock for biodiesel production. Therefore, increasing the relative oil concentration in soybean is desirable; however, that goal is complex due to the quantitative nature of the oil concentration trait and possible effects on major agronomic traits such as seed yield or protein concentration. The objectives of the present study were to study the relationship between seed oil concentration and important agronomic and seed quality traits, including seed yield, 100-seed weight, protein concentration, plant height, and days to maturity, and to identify oil quantitative trait loci (QTL) that are co-localized with the traits evaluated. A population of 203 F4:6 recombinant inbred lines, derived from a cross between moderately high oil soybean genotypes OAC Wallace and OAC Glencoe, was developed and grown across multiple environments in Ontario, Canada, in 2009 and 2010. Among the 11 QTL associated with seed oil concentration in the population, which were detected using either single-factor ANOVA or multiple QTL mapping methods, the number of QTL that were co-localized with other important traits QTL were six for protein concentration, four for seed yield, two for 100-seed weight, one for days to maturity, and one for plant height. The oil-beneficial allele of the QTL tagged by marker Sat_020 was positively associated with seed protein concentration. The oil favorable alleles of markers Satt001 and GmDGAT2B were positively correlated with seed yield. In addition, significant two-way epistatic interactions, where one of the interacting markers was solely associated with seed oil concentration, were identified for the selected traits in this study. The number of significant epistatic interactions was seven for yield, four for days to maturity, two for 100-seed weight, one for protein concentration, and one for plant height. The identified molecular markers associated with oil-related QTL in this study, which also have positive effects on other important traits such as seed yield and protein concentration, could be used in the soybean marker breeding programs aimed at developing either higher seed yield and oil concentration or higher seed protein and oil concentration per hectare. Alternatively, selecting complementary parents with greater breeding values due to positive epistatic interactions could lead to the development of higher oil soybean cultivars.

Deciphering mechanisms underlying the genetic variation of general production and liver quality traits in the overfed mule duck by pQTL analyses.

PubMed

François, Yoannah; Vignal, Alain; Molette, Caroline; Marty-Gasset, Nathalie; Davail, Stéphane; Liaubet, Laurence; Marie-Etancelin, Christel

2017-04-19

The aim of this study was to analyse the mechanisms that underlie phenotypic quantitative trait loci (QTL) in overfed mule ducks by identifying co-localized proteomic QTL (pQTL). The QTL design consisted of three families of common ducks that were progeny-tested by using 294 male mule ducks. This population of common ducks was genotyped using a genetic map that included 334 genetic markers located across 28 APL chromosomes (APL for Anas platyrhynchos). Mule ducks were phenotyped for 49 traits related to growth, metabolism, overfeeding ability and meat and fatty liver quality, and 326 soluble fatty liver proteins were quantified. One hundred and seventy-six pQTL and 80 phenotypic QTL were detected at the 5% chromosome-wide significance threshold. The great majority of the identified pQTL were trans-acting and localized on a chromosome other than that carrying the coding gene. The most significant pQTL (1% genome-wide significance) were found for alpha-enolase on APL18 and fatty acid synthase on APL24. Some proteins were associated with numerous pQTL (for example, 17 and 14 pQTL were detected for alpha-enolase and apolipoprotein A1, respectively) and pQTL hotspots were observed on some chromosomes (APL18, 24, 25 and 29). We detected 66 co-localized phenotypic QTL and pQTL for which the significance of the two-trait QTL (2t-QTL) analysis was higher than that of the strongest QTL using a single-trait approach. Among these, 16 2t-QTL were pleiotropic. For example, on APL15, melting rate and abundance of two alpha-enolase spots appeared to be impacted by a single locus that is involved in the glycolytic process. On APLZ, we identified a pleiotropic QTL that modified both the blood level of glucose at the beginning of the force-feeding period and the concentration of glutamate dehydrogenase, which, in humans, is involved in increased glucose absorption by the liver when the glutamate dehydrogenase 1 gene is mutated. We identified pleiotropic loci that affect metabolic pathways linked to glycolysis or lipogenesis, and in the end to fatty liver quality. Further investigation, via transcriptomics and metabolomics approaches, is required to confirm the biomarkers that were found to impact the genetic variability of these phenotypic traits.

Quantitative trait loci controlling cyanogenic glucoside and dry matter content in cassava (Manihot esculenta Crantz) roots.

PubMed

Balyejusa Kizito, Elizabeth; Rönnberg-Wästljung, Ann-Christin; Egwang, Thomas; Gullberg, Urban; Fregene, Martin; Westerbergh, Anna

2007-09-01

Cassava (Manihot esculenta Crantz) is a starchy root crop grown in the tropics mainly by small-scale farmers even though agro-industrial processing is rapidly increasing. For this processing market improved varieties with high dry matter root content (DMC) is required. Potentially toxic cyanogenic glucosides are synthesized in the leaves and translocated to the roots. Selection for varieties with low cyanogenic glucoside potential (CNP) and high DMC is among the principal objectives in cassava breeding programs. However, these traits are highly influenced by the environmental conditions and the genetic control of these traits is not well understood. An S(1) population derived from a cross between two bred cassava varieties (MCOL 1684 and Rayong 1) that differ in CNP and DMC was used to study the heritability and genetic basis of these traits. A broad-sense heritability of 0.43 and 0.42 was found for CNP and DMC, respectively. The moderate heritabilities for DMC and CNP indicate that the phenotypic variation of these traits is explained by a genetic component. We found two quantitative trait loci (QTL) on two different linkage groups controlling CNP and six QTL on four different linkage groups controlling DMC. One QTL for CNP and one QTL for DMC mapped near each other, suggesting pleiotrophy and/or linkage of QTL. The two QTL for CNP showed additive effects while the six QTL for DMC showed additive effect, dominance or overdominance. This study is a first step towards developing molecular marker tools for efficient breeding of CNP and DMC in cassava.

Genetic mapping of clubroot resistance genes in oilseed rape.

PubMed

Werner, S; Diederichsen, E; Frauen, M; Schondelmaier, J; Jung, C

2008-02-01

Clubroot caused by the obligate biotrophic protist Plasmodiophora brassicae is a major disease of Brassica species. Clubroot resistances introduced from B. oleracea var. 'Böhmerwaldkohl' and resistance from B. rapa ECD-04 were genetically mapped in oilseed rape (B. napus L.). A doubled haploid (DH) population of rape seed was developed by crossing a resistant DH-line derived from a resynthesized B. napus with the susceptible cultivar 'Express'. The DH population was tested in the greenhouse against seven P. brassicae isolates showing low and high virulence toward B. oleracea or/and B. rapa. DH-lines with highest or lowest disease scores were used in a bulked segregant analysis (BSA), and 43 polymorphic AFLPs were identified. A genetic map of the whole genome was constructed using 338 AFLP and 156 anchored SSR markers. Nineteen QTL were detected on chromosomes N02, N03, N08, N13, N15, N16 and N19 giving resistance to seven different isolates. Race-specific effects were observed for all QTL, none of the QTL conferred resistance to all isolates. The phenotypic variance explained by the respective QTL ranged between 10.3 and 67.5%. All QTL could be assigned to both ancestral genomes of B. napus. In contrast to previous reports, a clear differentiation into major QTL from B. rapa and minor QTL from B. oleracea could not be found. Composite interval mapping confirmed the linkage relationships determined by BSA, thus demonstrating that markers for oligogenic traits can be selected by merely testing the distributional extremes of a segregating population.

Genotyping of Endosperms to Determine Seed Dormancy Genes Regulating Germination Through Embryonic, Endospermic, or Maternal Tissues in Rice

PubMed Central

Gu, Xing-You; Zhang, Jinfeng; Ye, Heng; Zhang, Lihua; Feng, Jiuhuan

2014-01-01

Seed dormancy is imposed by one or more of the embryo, endosperm, and maternal tissues that belong to two generations and represent two ploidy levels. Many quantitative trait loci (QTL) have been identified for seed dormancy as measured by gross effects on reduced germination rate or delayed germination in crop or model plants. This research developed an endosperm genotype−based genetic approach to determine specific tissues through which a mapped QTL regulates germination using rice as a model. This approach involves testing germination velocity for partially after-ripened seeds harvested from single plants heterozygous for a tested QTL and genotyping endosperms from individual germinated and nongerminated seeds with a codominant DNA marker located on the QTL peak region. Information collected about the QTL includes genotypic frequencies in germinated and/or nongerminated subpopulations; allelic frequency distributions during a germination period; endosperm or embryo genotypic differences in germination velocity; and genotypic frequencies for gametes involved in the double fertilization to form the sampled seeds. Using this approach, the seed dormancy loci SD12, SD1-2, and SD7-1 were determined to regulate germination through the embryo, endosperm, and maternal tissues, respectively; SD12 and SD1-2 acted additively on germination velocity in the offspring tissues; and SD12 also was associated with the preferential fertilization of male gametes in rice. This new genetic approach can be used to characterize mapped genes/QTL for tissue-specific functions in endospermic seeds and for marker-assisted selection of QTL alleles before or immediately after germination in crop breeding. PMID:25480961

Expression quantitative trait loci: replication, tissue- and sex-specificity in mice.

PubMed

van Nas, Atila; Ingram-Drake, Leslie; Sinsheimer, Janet S; Wang, Susanna S; Schadt, Eric E; Drake, Thomas; Lusis, Aldons J

2010-07-01

By treating the transcript abundance as a quantitative trait, gene expression can be mapped to local or distant genomic regions relative to the gene encoding the transcript. Local expression quantitative trait loci (eQTL) generally act in cis (that is, control the expression of only the contiguous structural gene), whereas distal eQTL act in trans. Distal eQTL are more difficult to identify with certainty due to the fact that significant thresholds are very high since all regions of the genome must be tested, and confounding factors such as batch effects can produce false positives. Here, we compare findings from two large genetic crosses between mouse strains C3H/HeJ and C57BL/6J to evaluate the reliability of distal eQTL detection, including "hotspots" influencing the expression of multiple genes in trans. We found that >63% of local eQTL and >18% of distal eQTL were replicable at a threshold of LOD > 4.3 between crosses and 76% of local and >24% of distal eQTL at a threshold of LOD > 6. Additionally, at LOD > 4.3 four tissues studied (adipose, brain, liver, and muscle) exhibited >50% preservation of local eQTL and >17% preservation of distal eQTL. We observed replicated distal eQTL hotspots between the crosses on chromosomes 9 and 17. Finally, >69% of local eQTL and >10% of distal eQTL were preserved in most tissues between sexes. We conclude that most local eQTL are highly replicable between mouse crosses, tissues, and sex as compared to distal eQTL, which exhibited modest replicability.

Genetic dissection of the maize kernel development process via conditional QTL mapping for three developing kernel-related traits in an immortalized F2 population.

PubMed

Zhang, Zhanhui; Wu, Xiangyuan; Shi, Chaonan; Wang, Rongna; Li, Shengfei; Wang, Zhaohui; Liu, Zonghua; Xue, Yadong; Tang, Guiliang; Tang, Jihua

2016-02-01

Kernel development is an important dynamic trait that determines the final grain yield in maize. To dissect the genetic basis of maize kernel development process, a conditional quantitative trait locus (QTL) analysis was conducted using an immortalized F2 (IF2) population comprising 243 single crosses at two locations over 2 years. Volume (KV) and density (KD) of dried developing kernels, together with kernel weight (KW) at different developmental stages, were used to describe dynamic changes during kernel development. Phenotypic analysis revealed that final KW and KD were determined at DAP22 and KV at DAP29. Unconditional QTL mapping for KW, KV and KD uncovered 97 QTLs at different kernel development stages, of which qKW6b, qKW7a, qKW7b, qKW10b, qKW10c, qKV10a, qKV10b and qKV7 were identified under multiple kernel developmental stages and environments. Among the 26 QTLs detected by conditional QTL mapping, conqKW7a, conqKV7a, conqKV10a, conqKD2, conqKD7 and conqKD8a were conserved between the two mapping methodologies. Furthermore, most of these QTLs were consistent with QTLs and genes for kernel development/grain filling reported in previous studies. These QTLs probably contain major genes associated with the kernel development process, and can be used to improve grain yield and quality through marker-assisted selection.

Building phenotype networks to improve QTL detection: a comparative analysis of fatty acid and fat traits in pigs.

PubMed

Yang, B; Navarro, N; Noguera, J L; Muñoz, M; Guo, T F; Yang, K X; Ma, J W; Folch, J M; Huang, L S; Pérez-Enciso, M

2011-10-01

Models in QTL mapping can be improved by considering all potential variables, i.e. we can use remaining traits other than the trait under study as potential predictors. QTL mapping is often conducted by correcting for a few fixed effects or covariates (e.g. sex, age), although many traits with potential causal relationships between them are recorded. In this work, we evaluate by simulation several procedures to identify optimum models in QTL scans: forward selection, undirected dependency graph and QTL-directed dependency graph (QDG). The latter, QDG, performed better in terms of power and false discovery rate and was applied to fatty acid (FA) composition and fat deposition traits in two pig F2 crosses from China and Spain. Compared with the typical QTL mapping, QDG approach revealed several new QTL. To the contrary, several FA QTL on chromosome 4 (e.g. Palmitic, C16:0; Stearic, C18:0) detected by typical mapping vanished after adjusting for phenotypic covariates in QDG mapping. This suggests that the QTL detected in typical mapping could be indirect. When a QTL is supported by both approaches, there is an increased confidence that the QTL have a primary effect on the corresponding trait. An example is a QTL for C16:1 on chromosome 8. In conclusion, mapping QTL based on causal phenotypic networks can increase power and help to make more biologically sound hypothesis on the genetic architecture of complex traits. © 2011 Blackwell Verlag GmbH.

Genetic Architecture of Capitate Glandular Trichome Density in Florets of Domesticated Sunflower (Helianthus annuus L.)

PubMed Central

Gao, Qing-Ming; Kane, Nolan C.; Hulke, Brent S.; Reinert, Stephan; Pogoda, Cloe S.; Tittes, Silas; Prasifka, Jarrad R.

2018-01-01

Capitate glandular trichomes (CGT), one type of glandular trichomes, are most common in Asteraceae species. CGT can produce various secondary metabolites such as sesquiterpene lactones (STLs) and provide durable resistance to insect pests. In sunflower, CGT-based host resistance is effective to combat the specialist pest, sunflower moth. However, the genetic basis of CGT density is not well understood in sunflower. In this study, we identified two major QTL controlling CGT density in sunflower florets by using a F4 mapping population derived from the cross HA 300 × RHA 464 with a genetic linkage map constructed from genotyping-by-sequencing data and composed of 2121 SNP markers. One major QTL is located on chromosome 5, which explained 11.61% of the observed phenotypic variation, and the second QTL is located on chromosome 6, which explained 14.06% of the observed phenotypic variation. The QTL effects and the association between CGT density and QTL support interval were confirmed in a validation population which included 39 sunflower inbred lines with diverse genetic backgrounds. We also identified two strong candidate genes in the QTL support intervals, and the functions of their orthologs in other plant species suggested their potential roles in regulating capitate glandular trichome density in sunflower. Our results provide valuable information to sunflower breeding community for developing host resistance to sunflower insect pests. PMID:29375602

Gramene database in 2010: updates and extensions.

PubMed

Youens-Clark, Ken; Buckler, Ed; Casstevens, Terry; Chen, Charles; Declerck, Genevieve; Derwent, Paul; Dharmawardhana, Palitha; Jaiswal, Pankaj; Kersey, Paul; Karthikeyan, A S; Lu, Jerry; McCouch, Susan R; Ren, Liya; Spooner, William; Stein, Joshua C; Thomason, Jim; Wei, Sharon; Ware, Doreen

2011-01-01

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data.

A statistical framework for genetic association studies of power curves in bird flight

PubMed Central

Lin, Min; Zhao, Wei

2006-01-01

How the power required for bird flight varies as a function of forward speed can be used to predict the flight style and behavioral strategy of a bird for feeding and migration. A U-shaped curve was observed between the power and flight velocity in many birds, which is consistent to the theoretical prediction by aerodynamic models. In this article, we present a general genetic model for fine mapping of quantitative trait loci (QTL) responsible for power curves in a sample of birds drawn from a natural population. This model is developed within the maximum likelihood context, implemented with the EM algorithm for estimating the population genetic parameters of QTL and the simplex algorithm for estimating the QTL genotype-specific parameters of power curves. Using Monte Carlo simulation derived from empirical observations of power curves in the European starling (Sturnus vulgaris), we demonstrate how the underlying QTL for power curves can be detected from molecular markers and how the QTL detected affect the most appropriate flight speeds used to design an optimal migration strategy. The results from our model can be directly integrated into a conceptual framework for understanding flight origin and evolution. PMID:17066123

Using bioinformatics and systems genetics to dissect HDL-cholesterol genetics in an MRL/MpJ x SM/J intercross.

PubMed

Leduc, Magalie S; Blair, Rachael Hageman; Verdugo, Ricardo A; Tsaih, Shirng-Wern; Walsh, Kenneth; Churchill, Gary A; Paigen, Beverly

2012-06-01

A higher incidence of coronary artery disease is associated with a lower level of HDL-cholesterol. We searched for genetic loci influencing HDL-cholesterol in F2 mice from a cross between MRL/MpJ and SM/J mice. Quantitative trait loci (QTL) mapping revealed one significant HDL QTL (Apoa2 locus), four suggestive QTL on chromosomes 10, 11, 13, and 18 and four additional QTL on chromosomes 1 proximal, 3, 4, and 7 after adjusting HDL for the strong Apoa2 locus. A novel nonsynonymous polymorphism supports Lipg as the QTL gene for the chromosome 18 QTL, and a difference in Abca1 expression in liver tissue supports it as the QTL gene for the chromosome 4 QTL. Using weighted gene co-expression network analysis, we identified a module that after adjustment for Apoa2, correlated with HDL, was genetically determined by a QTL on chromosome 11, and overlapped with the HDL QTL. A combination of bioinformatics tools and systems genetics helped identify several candidate genes for both the chromosome 11 HDL and module QTL based on differential expression between the parental strains, cis regulation of expression, and causality modeling. We conclude that integrating systems genetics to a more-traditional genetics approach improves the power of complex trait gene identification.

An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci

PubMed Central

Ju, Jin Hyun; Crystal, Ronald G.

2017-01-01

Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis. CONFETI is designed to address two conflicting issues when searching for broad impact eQTL: the need to account for non-genetic confounding factors that can lower the power of the analysis or produce broad impact eQTL false positives, and the tendency of methods that account for confounding factors to model broad impact eQTL as non-genetic variation. The key advance of the CONFETI framework is the use of Independent Component Analysis (ICA) to identify variation likely caused by broad impact eQTL when constructing the sample covariance matrix used for the random effect in a mixed model. We show that CONFETI has better performance than other mixed model confounding factor methods when considering broad impact eQTL recovery from synthetic data. We also used the CONFETI framework and these same confounding factor methods to identify eQTL that replicate between matched twin pair datasets in the Multiple Tissue Human Expression Resource (MuTHER), the Depression Genes Networks study (DGN), the Netherlands Study of Depression and Anxiety (NESDA), and multiple tissue types in the Genotype-Tissue Expression (GTEx) consortium. These analyses identified both cis-eQTL and trans-eQTL impacting individual genes, and CONFETI had better or comparable performance to other mixed model confounding factor analysis methods when identifying such eQTL. In these analyses, we were able to identify and replicate a few broad impact eQTL although the overall number was small even when applying CONFETI. In light of these results, we discuss the broad impact eQTL that have been previously reported from the analysis of human data and suggest that considerable caution should be exercised when making biological inferences based on these reported eQTL. PMID:28505156

An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci.

PubMed

Ju, Jin Hyun; Shenoy, Sushila A; Crystal, Ronald G; Mezey, Jason G

2017-05-01

Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis. CONFETI is designed to address two conflicting issues when searching for broad impact eQTL: the need to account for non-genetic confounding factors that can lower the power of the analysis or produce broad impact eQTL false positives, and the tendency of methods that account for confounding factors to model broad impact eQTL as non-genetic variation. The key advance of the CONFETI framework is the use of Independent Component Analysis (ICA) to identify variation likely caused by broad impact eQTL when constructing the sample covariance matrix used for the random effect in a mixed model. We show that CONFETI has better performance than other mixed model confounding factor methods when considering broad impact eQTL recovery from synthetic data. We also used the CONFETI framework and these same confounding factor methods to identify eQTL that replicate between matched twin pair datasets in the Multiple Tissue Human Expression Resource (MuTHER), the Depression Genes Networks study (DGN), the Netherlands Study of Depression and Anxiety (NESDA), and multiple tissue types in the Genotype-Tissue Expression (GTEx) consortium. These analyses identified both cis-eQTL and trans-eQTL impacting individual genes, and CONFETI had better or comparable performance to other mixed model confounding factor analysis methods when identifying such eQTL. In these analyses, we were able to identify and replicate a few broad impact eQTL although the overall number was small even when applying CONFETI. In light of these results, we discuss the broad impact eQTL that have been previously reported from the analysis of human data and suggest that considerable caution should be exercised when making biological inferences based on these reported eQTL.

MeQTL analysis of childhood obesity links epigenetics with a risk SNP rs17782313 near MC4R from meta-analysis.

PubMed

Tang, Yuping; Jin, Bo; Zhou, Lingling; Lu, Weifeng

2017-01-10

Earlier GWAS has identified that rs17782313 near MC4R was associated with obesity. However, subsequent studies showed conflicting results, especially among childhood. Besides, the mechanisms underlying the association between rs17782313 and childhood obesity remain largely unexplored, and genetic and epigenetic may interact and together affect the development of childhood obesity. We conducted a comprehensive meta-analysis to assess the association between rs17782313 and childhood obesity. MeQTL and eQTL analysis was applied to explore the effect of rs17782313 on DNA methylation and MC4R expression. We found that rs17782313 near MC4R was associated with increased childhood obesity risk and BMI z-score in several inheritable models (P < 0.05). Additionally, the similar trend was observed among subgroups of Asians, Caucasian. Furthermore, meQTL and eQTL analysis indicated that individuals carrying rs17782313 TT genotype were significantly associated with increased methylation level of cg10097150 located in MC4R promoter and decreased expression of MC4R than those with CT/CC genotype (P = 1.7 × 10-4 and P = 1.9 × 10-3 respectively). Our results strongly confirmed that rs17782313 was associated with increased risk of childhood obesity. Furthermore, rs17782313 T allele was correlated with promoter hypermethylation and decreased expression of MC4R, thus involved in the development of childhood obesity.

The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci.

PubMed

Georgi, Laura; Johnson-Cicalese, Jennifer; Honig, Josh; Das, Sushma Parankush; Rajah, Veeran D; Bhattacharya, Debashish; Bassil, Nahla; Rowland, Lisa J; Polashock, James; Vorsa, Nicholi

2013-03-01

The first genetic map of cranberry (Vaccinium macrocarpon) has been constructed, comprising 14 linkage groups totaling 879.9 cM with an estimated coverage of 82.2 %. This map, based on four mapping populations segregating for field fruit-rot resistance, contains 136 distinct loci. Mapped markers include blueberry-derived simple sequence repeat (SSR) and cranberry-derived sequence-characterized amplified region markers previously used for fingerprinting cranberry cultivars. In addition, SSR markers were developed near cranberry sequences resembling genes involved in flavonoid biosynthesis or defense against necrotrophic pathogens, or conserved orthologous set (COS) sequences. The cranberry SSRs were developed from next-generation cranberry genomic sequence assemblies; thus, the positions of these SSRs on the genomic map provide information about the genomic location of the sequence scaffold from which they were derived. The use of SSR markers near COS and other functional sequences, plus 33 SSR markers from blueberry, facilitates comparisons of this map with maps of other plant species. Regions of the cranberry map were identified that showed conservation of synteny with Vitis vinifera and Arabidopsis thaliana. Positioned on this map are quantitative trait loci (QTL) for field fruit-rot resistance (FFRR), fruit weight, titratable acidity, and sound fruit yield (SFY). The SFY QTL is adjacent to one of the fruit weight QTL and may reflect pleiotropy. Two of the FFRR QTL are in regions of conserved synteny with grape and span defense gene markers, and the third FFRR QTL spans a flavonoid biosynthetic gene.

An 11-bp Insertion in Zea mays fatb Reduces the Palmitic Acid Content of Fatty Acids in Maize Grain

PubMed Central

Li, Qing; Yang, Xiaohong; Zheng, Debo; Warburton, Marilyn; Chai, Yuchao; Zhang, Pan; Guo, Yuqiu; Yan, Jianbing; Li, Jiansheng

2011-01-01

The ratio of saturated to unsaturated fatty acids in maize kernels strongly impacts human and livestock health, but is a complex trait that is difficult to select based on phenotype. Map-based cloning of quantitative trait loci (QTL) is a powerful but time-consuming method for the dissection of complex traits. Here, we combine linkage and association analyses to fine map QTL-Pal9, a QTL influencing levels of palmitic acid, an important class of saturated fatty acid. QTL-Pal9 was mapped to a 90-kb region, in which we identified a candidate gene, Zea mays fatb (Zmfatb), which encodes acyl-ACP thioesterase. An 11-bp insertion in the last exon of Zmfatb decreases palmitic acid content and concentration, leading to an optimization of the ratio of saturated to unsaturated fatty acids while having no effect on total oil content. We used three-dimensional structure analysis to explain the functional mechanism of the ZmFATB protein and confirmed the proposed model in vitro and in vivo. We measured the genetic effect of the functional site in 15 different genetic backgrounds and found a maximum change of 4.57 mg/g palmitic acid content, which accounts for ∼20–60% of the variation in the ratio of saturated to unsaturated fatty acids. A PCR-based marker for QTL-Pal9 was developed for marker-assisted selection of nutritionally healthier maize lines. The method presented here provides a new, efficient way to clone QTL, and the cloned palmitic acid QTL sheds lights on the genetic mechanism of oil biosynthesis and targeted maize molecular breeding. PMID:21931818

High-Throughput Phenotyping to Detect Drought Tolerance QTL in Wild Barley Introgression Lines

PubMed Central

Honsdorf, Nora; March, Timothy John; Berger, Bettina; Tester, Mark; Pillen, Klaus

2014-01-01

Drought is one of the most severe stresses, endangering crop yields worldwide. In order to select drought tolerant genotypes, access to exotic germplasm and efficient phenotyping protocols are needed. In this study the high-throughput phenotyping platform “The Plant Accelerator”, Adelaide, Australia, was used to screen a set of 47 juvenile (six week old) wild barley introgression lines (S42ILs) for drought stress responses. The kinetics of growth development was evaluated under early drought stress and well watered treatments. High correlation (r = 0.98) between image based biomass estimates and actual biomass was demonstrated, and the suitability of the system to accurately and non-destructively estimate biomass was validated. Subsequently, quantitative trait loci (QTL) were located, which contributed to the genetic control of growth under drought stress. In total, 44 QTL for eleven out of 14 investigated traits were mapped, which for example controlled growth rate and water use efficiency. The correspondence of those QTL with QTL previously identified in field trials is shown. For instance, six out of eight QTL controlling plant height were also found in previous field and glasshouse studies with the same introgression lines. This indicates that phenotyping juvenile plants may assist in predicting adult plant performance. In addition, favorable wild barley alleles for growth and biomass parameters were detected, for instance, a QTL that increased biomass by approximately 36%. In particular, introgression line S42IL-121 revealed improved growth under drought stress compared to the control Scarlett. The introgression line showed a similar behavior in previous field experiments, indicating that S42IL-121 may be an attractive donor for breeding of drought tolerant barley cultivars. PMID:24823485

A first linkage map and downy mildew resistance QTL discovery for sweet basil (Ocimum basilicum) facilitated by double digestion restriction site associated DNA sequencing (ddRADseq).

PubMed

Pyne, Robert; Honig, Josh; Vaiciunas, Jennifer; Koroch, Adolfina; Wyenandt, Christian; Bonos, Stacy; Simon, James

2017-01-01

Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed in both SNP and EST-SSR markers providing evidence of an O. basilicum allotetraploid genome structure and allowing for subsequent analysis of the mapping population as a diploid intercross. A dense linkage map was constructed using 42 EST-SSR and 1,847 SNP markers spanning 3,030.9 cM. Multiple quantitative trait loci (QTL) model (MQM) analysis identified three QTL that explained 37-55% of phenotypic variance associated with downy mildew response across three environments. A single major QTL, dm11.1 explained 21-28% of phenotypic variance and demonstrated dominant gene action. Two minor QTL dm9.1 and dm14.1 explained 5-16% and 4-18% of phenotypic variance, respectively. Evidence is provided for an additive effect between the two minor QTL and the major QTL dm11.1 increasing downy mildew susceptibility. Results indicate that ddRADseq-facilitated SNP and SSR marker genotyping is an effective approach for mapping the sweet basil genome.

A first linkage map and downy mildew resistance QTL discovery for sweet basil (Ocimum basilicum) facilitated by double digestion restriction site associated DNA sequencing (ddRADseq)

PubMed Central

Honig, Josh; Vaiciunas, Jennifer; Koroch, Adolfina; Wyenandt, Christian; Bonos, Stacy; Simon, James

2017-01-01

Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed in both SNP and EST-SSR markers providing evidence of an O. basilicum allotetraploid genome structure and allowing for subsequent analysis of the mapping population as a diploid intercross. A dense linkage map was constructed using 42 EST-SSR and 1,847 SNP markers spanning 3,030.9 cM. Multiple quantitative trait loci (QTL) model (MQM) analysis identified three QTL that explained 37–55% of phenotypic variance associated with downy mildew response across three environments. A single major QTL, dm11.1 explained 21–28% of phenotypic variance and demonstrated dominant gene action. Two minor QTL dm9.1 and dm14.1 explained 5–16% and 4–18% of phenotypic variance, respectively. Evidence is provided for an additive effect between the two minor QTL and the major QTL dm11.1 increasing downy mildew susceptibility. Results indicate that ddRADseq-facilitated SNP and SSR marker genotyping is an effective approach for mapping the sweet basil genome. PMID:28922359

The development of a dense SNP-based consensus map and QTL detection for black spot resistance in five diploid rose populations [abstract

USDA-ARS?s Scientific Manuscript database

Black spot (BS) disease (Diplocarpon rosae (Lib.) Wolf) of rose is the most important leaf disease of garden roses in warm humid areas. Although the partial (horizontal) resistance to black spot has been shown to be moderately heritable, the responsible quantitative trait loci (QTL) remain unidentif...

Mapping carcass and meat quality QTL on Sus Scrofa chromosome 2 in commercial finishing pigs

PubMed Central

Heuven, Henri CM; van Wijk, Rik HJ; Dibbits, Bert; van Kampen, Tony A; Knol, Egbert F; Bovenhuis, Henk

2009-01-01

Quantitative trait loci (QTL) affecting carcass and meat quality located on SSC2 were identified using variance component methods. A large number of traits involved in meat and carcass quality was detected in a commercial crossbred population: 1855 pigs sired by 17 boars from a synthetic line, which where homozygous (A/A) for IGF2. Using combined linkage and linkage disequilibrium mapping (LDLA), several QTL significantly affecting loin muscle mass, ham weight and ham muscles (outer ham and knuckle ham) and meat quality traits, such as Minolta-L* and -b*, ultimate pH and Japanese colour score were detected. These results agreed well with previous QTL-studies involving SSC2. Since our study is carried out on crossbreds, different QTL may be segregating in the parental lines. To address this question, we compared models with a single QTL-variance component with models allowing for separate sire and dam QTL-variance components. The same QTL were identified using a single QTL variance component model compared to a model allowing for separate variances with minor differences with respect to QTL location. However, the variance component method made it possible to detect QTL segregating in the paternal line (e.g. HAMB), the maternal lines (e.g. Ham) or in both (e.g. pHu). Combining association and linkage information among haplotypes improved slightly the significance of the QTL compared to an analysis using linkage information only. PMID:19284675

Identification of major and minor QTL for ecologically important morphological traits in three-spined sticklebacks (Gasterosteus aculeatus).

PubMed

Liu, Jun; Shikano, Takahito; Leinonen, Tuomas; Cano, José Manuel; Li, Meng-Hua; Merilä, Juha

2014-04-16

Quantitative trait locus (QTL) mapping studies of Pacific three-spined sticklebacks (Gasterosteus aculeatus) have uncovered several genomic regions controlling variability in different morphological traits, but QTL studies of Atlantic sticklebacks are lacking. We mapped QTL for 40 morphological traits, including body size, body shape, and body armor, in a F2 full-sib cross between northern European marine and freshwater three-spined sticklebacks. A total of 52 significant QTL were identified at the 5% genome-wide level. One major QTL explaining 74.4% of the total variance in lateral plate number was detected on LG4, whereas several major QTL for centroid size (a proxy for body size), and the lengths of two dorsal spines, pelvic spine, and pelvic girdle were mapped on LG21 with the explained variance ranging from 27.9% to 57.6%. Major QTL for landmark coordinates defining body shape variation also were identified on LG21, with each explaining ≥15% of variance in body shape. Multiple QTL for different traits mapped on LG21 overlapped each other, implying pleiotropy and/or tight linkage. Thus, apart from providing confirmatory data to support conclusions born out of earlier QTL studies of Pacific sticklebacks, this study also describes several novel QTL of both major and smaller effect for ecologically important traits. The finding that many major QTL mapped on LG21 suggests that this linkage group might be a hotspot for genetic determinants of ecologically important morphological traits in three-spined sticklebacks.

Loci on chromosomes 1A and 2A affect resistance to tan (yellow) spot in wheat populations not segregating for tsn1.

PubMed

Shankar, Manisha; Jorgensen, Dorthe; Taylor, Julian; Chalmers, Ken J; Fox, Rebecca; Hollaway, Grant J; Neate, Stephen M; McLean, Mark S; Vassos, Elysia; Golzar, Hossein; Loughman, Robert; Mather, Diane E

2017-12-01

QTL for tan spot resistance were mapped on wheat chromosomes 1A and 2A. Lines were developed with resistance alleles at these loci and at the tsn1 locus on chromosome 5B. These lines expressed significantly higher resistance than the parent with tsn1 only. Tan spot (syn. yellow spot and yellow leaf spot) caused by Pyrenophora tritici-repentis is an important foliar disease of wheat in Australia. Few resistance genes have been mapped in Australian germplasm and only one, known as tsn1 located on chromosome 5B, is known in Australian breeding programs. This gene confers insensitivity to the fungal effector ToxA. The main aim of this study was to map novel resistance loci in two populations: Calingiri/Wyalkatchem, which is fixed for the ToxA-insensitivity allele tsn1, and IGW2574/Annuello, which is fixed for the ToxA-sensitivity allele Tsn1. A second aim was to combine new loci with tsn1 to develop lines with improved resistance. Tan spot severity was evaluated at various growth stages and in multiple environments. Symptom severity traits exhibited quantitative variation. The most significant quantitative trait loci (QTL) were detected on chromosomes 2A and 1A. The QTL on 2A explained up to 29.2% of the genotypic variation in the Calingiri/Wyalkatchem population with the resistance allele contributed by Wyalkatchem. The QTL on 1A explained up to 28.1% of the genotypic variation in the IGW2574/Annuello population with the resistance allele contributed by Annuello. The resistance alleles at both QTL were successfully combined with tsn1 to develop lines that express significantly better resistance at both seedling and adult plant stages than Calingiri which has tsn1 only.

Genomic Correlates of Relationship QTL Involved in Fore- versus Hind Limb Divergence in Mice

PubMed Central

Pavlicev, Mihaela; Wagner, Günter P.; Noonan, James P.; Hallgrímsson, Benedikt; Cheverud, James M.

2013-01-01

Divergence of serially homologous elements of organisms is a common evolutionary pattern contributing to increased phenotypic complexity. Here, we study the genomic intervals affecting the variational independence of fore- and hind limb traits within an experimental mouse population. We use an advanced intercross of inbred mouse strains to map the loci associated with the degree of autonomy between fore- and hind limb long bone lengths (loci affecting the relationship between traits, relationship quantitative trait loci [rQTL]). These loci have been proposed to interact locally with the products of pleiotropic genes, thereby freeing the local trait from the variational constraint due to pleiotropic mutations. Using the known polymorphisms (single nucleotide polymorphisms [SNPs]) between the parental strains, we characterized and compared the genomic regions in which the rQTL, as well as their interaction partners (intQTL), reside. We find that these two classes of QTL intervals harbor different kinds of molecular variation. SNPs in rQTL intervals more frequently reside in limb-specific cis-regulatory regions than SNPs in intQTL intervals. The intQTL loci modified by the rQTL, in contrast, show the signature of protein-coding variation. This result is consistent with the widely accepted view that protein-coding mutations have broader pleiotropic effects than cis-regulatory polymorphisms. For both types of QTL intervals, the underlying candidate genes are enriched for genes involved in protein binding. This finding suggests that rQTL effects are caused by local interactions among the products of the causal genes harbored in rQTL and intQTL intervals. This is the first study to systematically document the population-level molecular variation underlying the evolution of character individuation. PMID:24065733

Genetic and Environmental Pathways in Type 1 Diabetes Complications

DTIC Science & Technology

2010-09-01

active duty members of the military, their families and retired military personnel will potentially allow focused preventative treatment of at- risk...association and assess potential heterogeneity of association signals, such as by ancestry. Query eQTL databases for relevant associations. Goals: 1a1...1, so that at most an average of 7 SNPs remain as potential risk SNPs at each of the 30 loci. In Stage 2 we will genotype another 2000 cases and

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS.

PubMed

Dobbyn, Amanda; Huckins, Laura M; Boocock, James; Sloofman, Laura G; Glicksberg, Benjamin S; Giambartolomei, Claudia; Hoffman, Gabriel E; Perumal, Thanneer M; Girdhar, Kiran; Jiang, Yan; Raj, Towfique; Ruderfer, Douglas M; Kramer, Robin S; Pinto, Dalila; Akbarian, Schahram; Roussos, Panos; Domenici, Enrico; Devlin, Bernie; Sklar, Pamela; Stahl, Eli A; Sieberts, Solveig K

2018-06-07

Causal genes and variants within genome-wide association study (GWAS) loci can be identified by integrating GWAS statistics with expression quantitative trait loci (eQTL) and determining which variants underlie both GWAS and eQTL signals. Most analyses, however, consider only the marginal eQTL signal, rather than dissect this signal into multiple conditionally independent signals for each gene. Here we show that analyzing conditional eQTL signatures, which could be important under specific cellular or temporal contexts, leads to improved fine mapping of GWAS associations. Using genotypes and gene expression levels from post-mortem human brain samples (n = 467) reported by the CommonMind Consortium (CMC), we find that conditional eQTL are widespread; 63% of genes with primary eQTL also have conditional eQTL. In addition, genomic features associated with conditional eQTL are consistent with context-specific (e.g., tissue-, cell type-, or developmental time point-specific) regulation of gene expression. Integrating the 2014 Psychiatric Genomics Consortium schizophrenia (SCZ) GWAS and CMC primary and conditional eQTL data reveals 40 loci with strong evidence for co-localization (posterior probability > 0.8), including six loci with co-localization of conditional eQTL. Our co-localization analyses support previously reported genes, identify novel genes associated with schizophrenia risk, and provide specific hypotheses for their functional follow-up. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Identification of Quantitative Trait Loci That Determine Plasma Total-Cholesterol and Triglyceride Concentrations in DDD/Sgn and C57BL/6J Inbred Mice.

PubMed

Suto, Jun-Ichi; Kojima, Misaki

2017-01-01

DDD/Sgn mice have significantly higher plasma lipid concentrations than C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for plasma total-cholesterol (CHO) and triglyceride (TG) concentrations in reciprocal F 2 male intercross populations between the two strains. By single-QTL scans, we identified four significant QTL on chromosomes (Chrs) 1, 5, 17, and 19 for CHO and two significant QTL on Chrs 1 and 12 for TG. By including cross direction as an interactive covariate, we identified separate significant QTL on Chr 17 for CHO but none for TG. When the large phenotypic effect of QTL on Chr 1 was controlled by composite interval mapping, we identified three additional significant QTL on Chrs 3, 4, and 9 for CHO but none for TG. QTL on Chr 19 was a novel QTL for CHO and the allelic effect of this QTL significantly differed between males and females. Whole-exome sequence analysis in DDD/Sgn mice suggested that Apoa2 and Acads were the plausible candidate genes underlying CHO QTL on Chrs 1 and 5, respectively. Thus, we identified a multifactorial basis for plasma lipid concentrations in male mice. These findings will provide insight into the genetic mechanisms of plasma lipid metabolism.

Identification of Quantitative Trait Loci That Determine Plasma Total-Cholesterol and Triglyceride Concentrations in DDD/Sgn and C57BL/6J Inbred Mice

PubMed Central

Kojima, Misaki

2017-01-01

DDD/Sgn mice have significantly higher plasma lipid concentrations than C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for plasma total-cholesterol (CHO) and triglyceride (TG) concentrations in reciprocal F2 male intercross populations between the two strains. By single-QTL scans, we identified four significant QTL on chromosomes (Chrs) 1, 5, 17, and 19 for CHO and two significant QTL on Chrs 1 and 12 for TG. By including cross direction as an interactive covariate, we identified separate significant QTL on Chr 17 for CHO but none for TG. When the large phenotypic effect of QTL on Chr 1 was controlled by composite interval mapping, we identified three additional significant QTL on Chrs 3, 4, and 9 for CHO but none for TG. QTL on Chr 19 was a novel QTL for CHO and the allelic effect of this QTL significantly differed between males and females. Whole-exome sequence analysis in DDD/Sgn mice suggested that Apoa2 and Acads were the plausible candidate genes underlying CHO QTL on Chrs 1 and 5, respectively. Thus, we identified a multifactorial basis for plasma lipid concentrations in male mice. These findings will provide insight into the genetic mechanisms of plasma lipid metabolism. PMID:28642824

Using bioinformatics and systems genetics to dissect HDL-cholesterol genetics in an MRL/MpJ × SM/J intercross[S

PubMed Central

Leduc, Magalie S.; Blair, Rachael Hageman; Verdugo, Ricardo A.; Tsaih, Shirng-Wern; Walsh, Kenneth; Churchill, Gary A.; Paigen, Beverly

2012-01-01

A higher incidence of coronary artery disease is associated with a lower level of HDL-cholesterol. We searched for genetic loci influencing HDL-cholesterol in F2 mice from a cross between MRL/MpJ and SM/J mice. Quantitative trait loci (QTL) mapping revealed one significant HDL QTL (Apoa2 locus), four suggestive QTL on chromosomes 10, 11, 13, and 18 and four additional QTL on chromosomes 1 proximal, 3, 4, and 7 after adjusting HDL for the strong Apoa2 locus. A novel nonsynonymous polymorphism supports Lipg as the QTL gene for the chromosome 18 QTL, and a difference in Abca1 expression in liver tissue supports it as the QTL gene for the chromosome 4 QTL. Using weighted gene co-expression network analysis, we identified a module that after adjustment for Apoa2, correlated with HDL, was genetically determined by a QTL on chromosome 11, and overlapped with the HDL QTL. A combination of bioinformatics tools and systems genetics helped identify several candidate genes for both the chromosome 11 HDL and module QTL based on differential expression between the parental strains, cis regulation of expression, and causality modeling. We conclude that integrating systems genetics to a more-traditional genetics approach improves the power of complex trait gene identification. PMID:22498810

Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts.

PubMed

Sumathi, Murugan; Bachpai, Vijaya Kumar Waman; Mayavel, A; Dasgupta, Modhumita Ghosh; Nagarajan, Binai; Rajasugunasekar, D; Sivakumar, Veerasamy; Yasodha, Ramasamy

2018-05-01

The eucalypt species, Eucalyptus tereticornis and Eucalyptus camaldulensis , show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross E. tereticornis  ×  E. camaldulensis using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against E. grandis sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.

Identification of Major and Minor QTL for Ecologically Important Morphological Traits in Three-Spined Sticklebacks (Gasterosteus aculeatus)

PubMed Central

Liu, Jun; Shikano, Takahito; Leinonen, Tuomas; Cano, José Manuel; Li, Meng-Hua; Merilä, Juha

2014-01-01

Quantitative trait locus (QTL) mapping studies of Pacific three-spined sticklebacks (Gasterosteus aculeatus) have uncovered several genomic regions controlling variability in different morphological traits, but QTL studies of Atlantic sticklebacks are lacking. We mapped QTL for 40 morphological traits, including body size, body shape, and body armor, in a F2 full-sib cross between northern European marine and freshwater three-spined sticklebacks. A total of 52 significant QTL were identified at the 5% genome-wide level. One major QTL explaining 74.4% of the total variance in lateral plate number was detected on LG4, whereas several major QTL for centroid size (a proxy for body size), and the lengths of two dorsal spines, pelvic spine, and pelvic girdle were mapped on LG21 with the explained variance ranging from 27.9% to 57.6%. Major QTL for landmark coordinates defining body shape variation also were identified on LG21, with each explaining ≥15% of variance in body shape. Multiple QTL for different traits mapped on LG21 overlapped each other, implying pleiotropy and/or tight linkage. Thus, apart from providing confirmatory data to support conclusions born out of earlier QTL studies of Pacific sticklebacks, this study also describes several novel QTL of both major and smaller effect for ecologically important traits. The finding that many major QTL mapped on LG21 suggests that this linkage group might be a hotspot for genetic determinants of ecologically important morphological traits in three-spined sticklebacks. PMID:24531726

Database of cattle candidate genes and genetic markers for milk production and mastitis

PubMed Central

Ogorevc, J; Kunej, T; Razpet, A; Dovc, P

2009-01-01

A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mammary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological functions in functional networks. A miRNA target search for mammary gland expressed miRNAs identified 359 putative binding sites in 3′UTRs of candidate genes. PMID:19508288

Cryptic Genetic Variation for Arabidopsis thaliana Seed Germination Speed in a Novel Salt Stress Environment

PubMed Central

Yuan, Wei; Flowers, Jonathan M.; Sahraie, Dustin J.; Purugganan, Michael D.

2016-01-01

The expansion of species ranges frequently necessitates responses to novel environments. In plants, the ability of seeds to disperse to marginal areas relies in part to its ability to germinate under stressful conditions. Here we examine the genetic architecture of Arabidopsis thaliana germination speed under a novel, saline environment, using an Extreme QTL (X-QTL) mapping platform we previously developed. We find that early germination in normal and salt conditions both rely on a QTL on the distal arm of chromosome 4, but we also find unique QTL on chromosomes 1, 2, 4, and 5 that are specific to salt stress environments. Moreover, different QTLs are responsible for early vs. late germination, suggesting a temporal component to the expression of life history under these stress conditions. Our results indicate that cryptic genetic variation exists for responses to a novel abiotic stress, which may suggest a role of such variation in adaptation to new climactic conditions or growth environments. PMID:27543295

Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice[S

PubMed Central

Leduc, Magalie S.; Hageman, Rachael S.; Verdugo, Ricardo A.; Tsaih, Shirng-Wern; Walsh, Kenneth; Churchill, Gary A.; Paigen, Beverly

2011-01-01

To identify genetic loci influencing lipid levels, we performed quantitative trait loci (QTL) analysis between inbred mouse strains MRL/MpJ and SM/J, measuring triglyceride levels at 8 weeks of age in F2 mice fed a chow diet. We identified one significant QTL on chromosome (Chr) 15 and three suggestive QTL on Chrs 2, 7, and 17. We also carried out microarray analysis on the livers of parental strains of 282 F2 mice and used these data to find cis-regulated expression QTL. We then narrowed the list of candidate genes under significant QTL using a “toolbox” of bioinformatic resources, including haplotype analysis; parental strain comparison for gene expression differences and nonsynonymous coding single nucleotide polymorphisms (SNP); cis-regulated eQTL in livers of F2 mice; correlation between gene expression and phenotype; and conditioning of expression on the phenotype. We suggest Slc25a7 as a candidate gene for the Chr 7 QTL and, based on expression differences, five genes (Polr3 h, Cyp2d22, Cyp2d26, Tspo, and Ttll12) as candidate genes for Chr 15 QTL. This study shows how bioinformatics can be used effectively to reduce candidate gene lists for QTL related to complex traits. PMID:21622629

Mapping Stripe Rust Resistance in a BrundageXCoda Winter Wheat Recombinant Inbred Line Population

PubMed Central

Case, Austin J.; Naruoka, Yukiko; Chen, Xianming; Garland-Campbell, Kimberly A.; Zemetra, Robert S.; Carter, Arron H.

2014-01-01

A recombinant inbred line (RIL) mapping population developed from a cross between winter wheat (Triticum aestivum L.) cultivars Coda and Brundage was evaluated for reaction to stripe rust (caused by Puccinia striiformis f. sp. tritici). Two hundred and sixty eight RIL from the population were evaluated in replicated field trials in a total of nine site-year locations in the U.S. Pacific Northwest. Seedling reaction to stripe rust races PST-100, PST-114 and PST-127 was also examined. A linkage map consisting of 2,391 polymorphic DNA markers was developed covering all chromosomes of wheat with the exception of 1D. Two QTL on chromosome 1B were associated with adult plant and seedling reaction and were the most significant QTL detected. Together these QTL reduced adult plant infection type from a score of seven to a score of two reduced disease severity by an average of 25% and provided protection against race PST-100, PST-114 and PST-127 in the seedling stage. The location of these QTL and the race specificity provided by them suggest that observed effects at this locus are due to a complementation of the previously known but defeated resistances of the cultivar Tres combining with that of Madsen (the two parent cultivars of Coda). Two additional QTL on chromosome 3B and one on 5B were associated with adult plant reaction only, and a single QTL on chromosome 5D was associated with seedling reaction to PST-114. Coda has been resistant to stripe rust since its release in 2000, indicating that combining multiple resistance genes for stripe rust provides durable resistance, especially when all-stage resistance genes are combined in a fashion to maximize the number of races they protect against. Identified molecular markers will allow for an efficient transfer of these genes into other cultivars, thereby continuing to provide excellent resistance to stripe rust. PMID:24642574

Meta-QTL for resistance to white mold in common bean

PubMed Central

Vasconcellos, Renato C. C.; Oraguzie, O. Blessing; Soler, Alvaro; Arkwazee, Haidar; Myers, James R.; Ferreira, Juan J.; Song, Qijian; McClean, Phil; Miklas, Phillip N.

2017-01-01

White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature). A meta-QTL analysis of the 37 QTL was conducted using the genetic linkage map of Stampede x Red Hawk population as the reference. The 37 QTL condensed into 17 named loci (12 previously named and five new) of which nine were defined as meta-QTL WM1.1, WM2.2, WM3.1, WM5.4, WM6.2, WM7.1, WM7.4, WM7.5, and WM8.3. The nine meta-QTL had confidence intervals ranging from 0.65 to 9.41 Mb. Candidate genes shown to express under S. sclerotiorum infection in other studies, including cell wall receptor kinase, COI1, ethylene responsive transcription factor, peroxidase, and MYB transcription factor, were found within the confidence interval for five of the meta-QTL. The nine meta-QTL are recommended as potential targets for MAS for partial resistance to white mold in common bean. PMID:28199342

Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL.

PubMed

Cavanagh, Colin R; Jonas, Elisabeth; Hobbs, Matthew; Thomson, Peter C; Tammen, Imke; Raadsma, Herman W

2010-09-16

An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

Germplasm-regression-combined (GRC) marker-trait association identification in plant breeding: a challenge for plant biotechnological breeding under soil water deficit conditions.

PubMed

Ruan, Cheng-Jiang; Xu, Xue-Xuan; Shao, Hong-Bo; Jaleel, Cheruth Abdul

2010-09-01

In the past 20 years, the major effort in plant breeding has changed from quantitative to molecular genetics with emphasis on quantitative trait loci (QTL) identification and marker assisted selection (MAS). However, results have been modest. This has been due to several factors including absence of tight linkage QTL, non-availability of mapping populations, and substantial time needed to develop such populations. To overcome these limitations, and as an alternative to planned populations, molecular marker-trait associations have been identified by the combination between germplasm and the regression technique. In the present preview, the authors (1) survey the successful applications of germplasm-regression-combined (GRC) molecular marker-trait association identification in plants; (2) describe how to do the GRC analysis and its differences from mapping QTL based on a linkage map reconstructed from the planned populations; (3) consider the factors that affect the GRC association identification, including selections of optimal germplasm and molecular markers and testing of identification efficiency of markers associated with traits; and (4) finally discuss the future prospects of GRC marker-trait association analysis used in plant MAS/QTL breeding programs, especially in long-juvenile woody plants when no other genetic information such as linkage maps and QTL are available.

Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes.

PubMed

Marone, Daniela; Russo, Maria A; Laidò, Giovanni; De Vita, Pasquale; Papa, Roberto; Blanco, Antonio; Gadaleta, Agata; Rubiales, Diego; Mastrangelo, Anna M

2013-08-19

Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat. The objective of this study was to identify the wheat genomic regions that are involved in the control of powdery mildew resistance through a quantitative trait loci (QTL) meta-analysis approach. This meta-analysis allows the use of collected QTL data from different published studies to obtain consensus QTL across different genetic backgrounds, thus providing a better definition of the regions responsible for the trait, and the possibility to obtain molecular markers that will be suitable for marker-assisted selection. Five QTL for resistance to powdery mildew were identified under field conditions in the durum-wheat segregating population Creso × Pedroso. An integrated map was developed for the projection of resistance genes/ alleles and the QTL from the present study and the literature, and to investigate their distribution in the wheat genome. Molecular markers that correspond to candidate genes for plant responses to pathogens were also projected onto the map, particularly considering NBS-LRR and receptor-like protein kinases. More than 80 independent QTL and 51 resistance genes from 62 different mapping populations were projected onto the consensus map using the Biomercator statistical software. Twenty-four MQTL that comprised 2-6 initial QTL that had widely varying confidence intervals were found on 15 chromosomes. The co-location of the resistance QTL and genes was investigated. Moreover, from analysis of the sequences of DArT markers, 28 DArT clones mapped on wheat chromosomes have been shown to be associated with the NBS-LRR genes and positioned in the same regions as the MQTL for powdery mildew resistance. The results from the present study provide a detailed analysis of the genetic basis of resistance to powdery mildew in wheat. The study of the Creso × Pedroso durum-wheat population has revealed some QTL that had not been previously identified. Furthermore, the analysis of the co-localization of resistance loci and functional markers provides a large list of candidate genes and opens up a new perspective for the fine mapping and isolation of resistance genes, and for the marker-assisted improvement of resistance in wheat.

Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes

PubMed Central

2013-01-01

Background Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat. The objective of this study was to identify the wheat genomic regions that are involved in the control of powdery mildew resistance through a quantitative trait loci (QTL) meta-analysis approach. This meta-analysis allows the use of collected QTL data from different published studies to obtain consensus QTL across different genetic backgrounds, thus providing a better definition of the regions responsible for the trait, and the possibility to obtain molecular markers that will be suitable for marker-assisted selection. Results Five QTL for resistance to powdery mildew were identified under field conditions in the durum-wheat segregating population Creso × Pedroso. An integrated map was developed for the projection of resistance genes/ alleles and the QTL from the present study and the literature, and to investigate their distribution in the wheat genome. Molecular markers that correspond to candidate genes for plant responses to pathogens were also projected onto the map, particularly considering NBS-LRR and receptor-like protein kinases. More than 80 independent QTL and 51 resistance genes from 62 different mapping populations were projected onto the consensus map using the Biomercator statistical software. Twenty-four MQTL that comprised 2–6 initial QTL that had widely varying confidence intervals were found on 15 chromosomes. The co-location of the resistance QTL and genes was investigated. Moreover, from analysis of the sequences of DArT markers, 28 DArT clones mapped on wheat chromosomes have been shown to be associated with the NBS-LRR genes and positioned in the same regions as the MQTL for powdery mildew resistance. Conclusions The results from the present study provide a detailed analysis of the genetic basis of resistance to powdery mildew in wheat. The study of the Creso × Pedroso durum-wheat population has revealed some QTL that had not been previously identified. Furthermore, the analysis of the co-localization of resistance loci and functional markers provides a large list of candidate genes and opens up a new perspective for the fine mapping and isolation of resistance genes, and for the marker-assisted improvement of resistance in wheat. PMID:23957646

Variation and inheritance of iron reductase activity in the roots of common bean (Phaseolus vulgaris L.) and association with seed iron accumulation QTL.

PubMed

Blair, Matthew W; Knewtson, Sharon Jb; Astudillo, Carolina; Li, Chee-Ming; Fernandez, Andrea C; Grusak, Michael A

2010-10-05

Iron deficiency anemia is a global problem which often affects women and children of developing countries. Strategy I plants, such as common bean (Phaseolus vulgaris L.) take up iron through a process that involves an iron reduction mechanism in their roots; this reduction is required to convert ferric iron to ferrous iron. Root absorbed iron is critical for the iron nutrition of the plant, and for the delivery of iron to the shoot and ultimately the seeds. The objectives of this study were to determine the variability and inheritance for iron reductase activity in a range of genotypes and in a low × high seed iron cross (DOR364 x G19833), to identify quantitative trait loci (QTL) for this trait, and to assess possible associations with seed iron levels. The experiments were carried out with hydroponically grown plants provided different amounts of iron varying between 0 and 20 μM Fe(III)-EDDHA. The parents, DOR364 and G19833, plus 13 other cultivated or wild beans, were found to differ in iron reductase activity. Based on these initial experiments, two growth conditions (iron limited and iron sufficient) were selected as treatments for evaluating the DOR364 × G19833 recombinant inbred lines. A single major QTL was found for iron reductase activity under iron-limited conditions (1 μM Fe) on linkage group b02 and another major QTL was found under iron sufficient conditions (15 μM Fe) on linkage group b11. Associations between the b11 QTL were found with several QTL for seed iron. Genes conditioning iron reductase activity in iron sufficient bean plants appear to be associated with genes contributing to seed iron accumulation. Markers for bean iron reductase (FRO) homologues were found with in silico mapping based on common bean synteny with soybean and Medicago truncatula on b06 and b07; however, neither locus aligned with the QTL for iron reductase activity. In summary, the QTL for iron reductase activity under iron limited conditions may be useful in environments where beans are grown in alkaline soils, while the QTL for iron reductase under sufficiency conditions may be useful for selecting for enhanced seed nutritional quality.

Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers.

PubMed

Li, Faji; Wen, Weie; He, Zhonghu; Liu, Jindong; Jin, Hui; Cao, Shuanghe; Geng, Hongwei; Yan, Jun; Zhang, Pingzhi; Wan, Yingxiu; Xia, Xianchun

2018-06-01

We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay. Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

QTL Mapping for Resistance to Iridovirus in Asian Seabass Using Genotyping-by-Sequencing.

PubMed

Wang, Le; Bai, Bin; Huang, Shuqing; Liu, Peng; Wan, Zi Yi; Ye, Baoqing; Wu, Jinlu; Yue, Gen Hua

2017-10-01

Identifying quantitative trait loci (QTL) for viral disease resistance is of particular importance in selective breeding programs of fish species. Genetic markers linked to QTL can be useful in marker-assisted selection (MAS) for elites resistant to specific pathogens. Here, we conducted a genome scan for QTL associated with Singapore grouper iridovirus (SGIV) resistance in an Asian seabass (Lates calcarifer) family, using a high-density linkage map generated with genotyping-by-sequencing. One genome-wide significant and three suggestive QTL were detected at LG21, LG6, LG13, and LG15, respectively. The phenotypic variation explained (PVE) by the four QTL ranged from 7.5 to 15.6%. The position of the most significant QTL at LG21 was located between 31.88 and 36.81 cM. The SNP marker (SNP130416) nearest to the peak of this QTL was significantly associated with SGIV resistance in an unrelated multifamily population. One candidate gene, MECOM, close to the peak of this QTL region, was predicted. Evidence of alternative splicing was observed for MECOM and one specific category of splicing variants was differentially expressed at 5 days post-SGIV infection. The QTL detected in this study are valuable resources and can be used in the selective breeding programs of Asian seabass with regard to resistance to SGIV.

Comparative quantitative trait loci for silique length and seed weight in Brassica napus.

PubMed

Fu, Ying; Wei, Dayong; Dong, Hongli; He, Yajun; Cui, Yixin; Mei, Jiaqin; Wan, Huafang; Li, Jiana; Snowdon, Rod; Friedt, Wolfgang; Li, Xiaorong; Qian, Wei

2015-09-23

Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus). Although many quantitative trait loci (QTL) for SL and SW have been identified in B. napus, comparative analysis for those QTL is seldom performed. In the present study, 20 and 21 QTL for SL and SW were identified in doubled haploid (DH) and DH-derived reconstructed F2 populations in rapeseed, explaining 55.1-74.3% and 24.4-62.9% of the phenotypic variation across three years, respectively. Of which, 17 QTL with partially or completely overlapped confidence interval on chromosome A09, were homologous with two overlapped QTL on chromosome C08 by aligning QTL confidence intervals with the reference genomes of Brassica crops. By high density selective genotyping of DH lines with extreme phenotypes, using a Brassica single-nucleotide polymorphism (SNP) array, the QTL on chromosome A09 was narrowed, and aligned into 1.14-Mb region from 30.84 to 31.98 Mb on chromosome R09 of B. rapa and 1.05-Mb region from 27.21 to 28.26 Mb on chromosome A09 of B. napus. The alignment of QTL with Brassica reference genomes revealed homologous QTL on A09 and C08 for SL. The narrowed QTL region provides clues for gene cloning and breeding cultivars by marker-assisted selection.

Mapping a Large Number of QTL for Durable Resistance to Stripe Rust in Winter Wheat Druchamp Using SSR and SNP Markers

PubMed Central

Hou, Lu; Chen, Xianming; Wang, Meinan; See, Deven R.; Chao, Shiaoman; Bulli, Peter; Jing, Jinxue

2015-01-01

Winter wheat Druchamp has both high-temperature adult-plant (HTAP) resistance and all-stage resistance to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). The HTAP resistance in Druchamp is durable as the variety has been resistant in adult-plant stage since it was introduced from France to the United States in late 1940s. To map the quantitative trait loci (QTL) for stripe rust resistance, an F8 recombinant inbred line (RIL) population from cross Druchamp × Michigan Amber was phenotyped for stripe rust response in multiple years in fields under natural infection and with selected Pst races under controlled greenhouse conditions, and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. Composite interval mapping (CIM) identified eight HTAP resistance QTL and three all-stage resistance QTL. Among the eight HTAP resistance QTL, QYrdr.wgp-1BL.2 (explaining 2.36-31.04% variation), QYrdr.wgp-2BL (2.81–15.65%), QYrdr.wgp-5AL (2.27–17.22%) and QYrdr.wgp-5BL.2 (2.42–15.13%) were significant in all tests; and QYrdr.wgp-1BL.1 (1.94–10.19%), QYrdr.wgp-1DS (2.04–27.24%), QYrdr.wgp-3AL (1.78–13.85%) and QYrdr.wgp-6BL.2 (1.69–33.71%) were significant in some of the tests. The three all-stage resistance QTL, QYrdr.wgp-5BL.1 (5.47–36.04%), QYrdr.wgp-5DL (9.27–11.94%) and QYrdr.wgp-6BL.1 (13.07-20.36%), were detected based on reactions in the seedlings tested with certain Pst races. Among the eleven QTL detected in Druchamp, at least three (QYrdr.wgp-5DL for race-specific all-stage resistance and QYrdr.wgp-3AL and QYrdr.wgp-6BL.2 for race non-specific HTAP resistance) are new. All these QTL, especially those for durable HTAP resistance, and their closely linked molecular markers could be useful for developing wheat cultivars with durable resistance to stripe rust. PMID:25970329

Further evidence that a terminal drought tolerance QTL of pearl millet is associated with reduced salt uptake

PubMed Central

Sharma, Parbodh C.; Singh, Dhananjay; Sehgal, Deepmala; Singh, Gurbachan; Hash, C.T.; Yadav, Rattan S.

2014-01-01

Earlier, we established that a major drought tolerance QTL on linkage group 2 of pearl millet is also associated with reduced salt uptake and enhanced growth under salt stress. Present study was undertaken to re-assess the performance of drought tolerant (PRLT 2/89-33) and drought sensitive (H 77/833-2) parents along with two QTL-NILs (ICMR 01029 and ICMR 01040), under salinity stress specifically imposed during post-flowering growth stages when plants had developed their ion sinks in full. Time course changes in ionic accumulation and their compartmentalization in different plant parts was studied, specifically to monitor and capture changes conferred by the two alleles at this QTL, at small intervals. Amongst different plant parts, higher accumulation of toxic ion Na+ was recorded in roots. Further, the Na+ concentration in roots of the testcross hybrid of the drought-sensitive parent (H 77/833-2) reached its maximum at ECiw 15 dS m−1 within 24 h after salinity imposition, whereas it continued to increase with time in the testcross hybrids of the drought tolerant parent PRLT 2/89-33 as well as those of its QTL-NILs (ICMR 01029 and ICMR 01004) and reached at its maximum at 120 h stage. Comparison of differential distribution of toxic ions in individual leaves revealed that Na+ ions were not uniformly distributed in the leaves of the drought-tolerant parent and drought-tolerant QTL-NILs; but accumulated preferentially in the older leaves, whereas the hybrid of the drought-sensitive parent showed significantly higher Na+ concentration in all main stem leaves irrespective of their age. Dynamics of chlorophyll and proline concentration variation studied under salt stress at late flowering stages revealed a greater reduction, almost twice, in both leaf chlorophyll and proline concentrations in younger leaves in the hybrids of the sensitive parent as compared to the tolerant parent and QTL NILs. Imposition of salinity stress even at flowering stage affected the yield performance in pearl millet, wherein higher yield was recorded in drought tolerant parent and the two QTL-NILs compared to drought sensitive parent. PMID:24895469

Mapping a Large Number of QTL for Durable Resistance to Stripe Rust in Winter Wheat Druchamp Using SSR and SNP Markers.

PubMed

Hou, Lu; Chen, Xianming; Wang, Meinan; See, Deven R; Chao, Shiaoman; Bulli, Peter; Jing, Jinxue

2015-01-01

Winter wheat Druchamp has both high-temperature adult-plant (HTAP) resistance and all-stage resistance to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). The HTAP resistance in Druchamp is durable as the variety has been resistant in adult-plant stage since it was introduced from France to the United States in late 1940s. To map the quantitative trait loci (QTL) for stripe rust resistance, an F8 recombinant inbred line (RIL) population from cross Druchamp × Michigan Amber was phenotyped for stripe rust response in multiple years in fields under natural infection and with selected Pst races under controlled greenhouse conditions, and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. Composite interval mapping (CIM) identified eight HTAP resistance QTL and three all-stage resistance QTL. Among the eight HTAP resistance QTL, QYrdr.wgp-1BL.2 (explaining 2.36-31.04% variation), QYrdr.wgp-2BL (2.81-15.65%), QYrdr.wgp-5AL (2.27-17.22%) and QYrdr.wgp-5BL.2 (2.42-15.13%) were significant in all tests; and QYrdr.wgp-1BL.1 (1.94-10.19%), QYrdr.wgp-1DS (2.04-27.24%), QYrdr.wgp-3AL (1.78-13.85%) and QYrdr.wgp-6BL.2 (1.69-33.71%) were significant in some of the tests. The three all-stage resistance QTL, QYrdr.wgp-5BL.1 (5.47-36.04%), QYrdr.wgp-5DL (9.27-11.94%) and QYrdr.wgp-6BL.1 (13.07-20.36%), were detected based on reactions in the seedlings tested with certain Pst races. Among the eleven QTL detected in Druchamp, at least three (QYrdr.wgp-5DL for race-specific all-stage resistance and QYrdr.wgp-3AL and QYrdr.wgp-6BL.2 for race non-specific HTAP resistance) are new. All these QTL, especially those for durable HTAP resistance, and their closely linked molecular markers could be useful for developing wheat cultivars with durable resistance to stripe rust.

Mapping of angular leaf spot resistance QTL in common bean (Phaseolus vulgaris L.) under different environments

PubMed Central

2012-01-01

Background Common bean (Phaseolus vulgaris L.) is the most important grain legume for human diet worldwide and the angular leaf spot (ALS) is one of the most devastating diseases of this crop, leading to yield losses as high as 80%. In an attempt to breed resistant cultivars, it is important to first understand the inheritance mode of resistance and to develop tools that could be used in assisted breeding. Therefore, the aim of this study was to identify quantitative trait loci (QTL) controlling resistance to ALS under natural infection conditions in the field and under inoculated conditions in the greenhouse. Results QTL analyses were made using phenotypic data from 346 recombinant inbreed lines from the IAC-UNA x CAL 143 cross, gathered in three experiments, two of which were conducted in the field in different seasons and one in the greenhouse. Joint composite interval mapping analysis of QTL x environment interaction was performed. In all, seven QTLs were mapped on five linkage groups. Most of them, with the exception of two, were significant in all experiments. Among these, ALS10.1DG,UC presented major effects (R2 between 16% - 22%). This QTL was found linked to the GATS11b marker of linkage group B10, which was consistently amplified across a set of common bean lines and was associated with the resistance. Four new QTLs were identified. Between them the ALS5.2 showed an important effect (9.4%) under inoculated conditions in the greenhouse. ALS4.2 was another major QTL, under natural infection in the field, explaining 10.8% of the variability for resistance reaction. The other QTLs showed minor effects on resistance. Conclusions The results indicated a quantitative inheritance pattern of ALS resistance in the common bean line CAL 143. QTL x environment interactions were observed. Moreover, the major QTL identified on linkage group B10 could be important for bean breeding, as it was stable in all the environments. Thereby, the GATS11b marker is a potential tool for marker assisted selection for ALS resistance. PMID:22738188

QTL Analysis of Kernel-Related Traits in Maize Using an Immortalized F2 Population

PubMed Central

Hu, Yanmin; Li, Weihua; Fu, Zhiyuan; Ding, Dong; Li, Haochuan; Qiao, Mengmeng; Tang, Jihua

2014-01-01

Kernel size and weight are important determinants of grain yield in maize. In this study, multivariate conditional and unconditional quantitative trait loci (QTL), and digenic epistatic analyses were utilized in order to elucidate the genetic basis for these kernel-related traits. Five kernel-related traits, including kernel weight (KW), volume (KV), length (KL), thickness (KT), and width (KWI), were collected from an immortalized F2 (IF2) maize population comprising of 243 crosses performed at two separate locations over a span of two years. A total of 54 unconditional main QTL for these five kernel-related traits were identified, many of which were clustered in chromosomal bins 6.04–6.06, 7.02–7.03, and 10.06–10.07. In addition, qKL3, qKWI6, qKV10a, qKV10b, qKW10a, and qKW7a were detected across multiple environments. Sixteen main QTL were identified for KW conditioned on the other four kernel traits (KL, KWI, KT, and KV). Thirteen main QTL were identified for KV conditioned on three kernel-shape traits. Conditional mapping analysis revealed that KWI and KV had the strongest influence on KW at the individual QTL level, followed by KT, and then KL; KV was mostly strongly influenced by KT, followed by KWI, and was least impacted by KL. Digenic epistatic analysis identified 18 digenic interactions involving 34 loci over the entire genome. However, only a small proportion of them were identical to the main QTL we detected. Additionally, conditional digenic epistatic analysis revealed that the digenic epistasis for KW and KV were entirely determined by their constituent traits. The main QTL identified in this study for determining kernel-related traits with high broad-sense heritability may play important roles during kernel development. Furthermore, digenic interactions were shown to exert relatively large effects on KL (the highest AA and DD effects were 4.6% and 6.7%, respectively) and KT (the highest AA effects were 4.3%). PMID:24586932

SNP discovery by high-throughput sequencing in soybean

PubMed Central

2010-01-01

Background With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits. Development of high-density genetic markers in the QTL regions of specific mapping populations is essential for fine-mapping and map-based cloning of economically important genes. Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation existing between any diverse genotypes that are usually used for QTL mapping studies. The massively parallel sequencing technologies (Roche GS/454, Illumina GA/Solexa, and ABI/SOLiD), have been widely applied to identify genome-wide sequence variations. However, it is still remains unclear whether sequence data at a low sequencing depth are enough to detect the variations existing in any QTL regions of interest in a crop genome, and how to prepare sequencing samples for a complex genome such as soybean. Therefore, with the aims of identifying SNP markers in a cost effective way for fine-mapping several QTL regions, and testing the validation rate of the putative SNPs predicted with Solexa short sequence reads at a low sequencing depth, we evaluated a pooled DNA fragment reduced representation library and SNP detection methods applied to short read sequences generated by Solexa high-throughput sequencing technology. Results A total of 39,022 putative SNPs were identified by the Illumina/Solexa sequencing system using a reduced representation DNA library of two parental lines of a mapping population. The validation rates of these putative SNPs predicted with low and high stringency were 72% and 85%, respectively. One hundred sixty four SNP markers resulted from the validation of putative SNPs and have been selectively chosen to target a known QTL, thereby increasing the marker density of the targeted region to one marker per 42 K bp. Conclusions We have demonstrated how to quickly identify large numbers of SNPs for fine mapping of QTL regions by applying massively parallel sequencing combined with genome complexity reduction techniques. This SNP discovery approach is more efficient for targeting multiple QTL regions in a same genetic population, which can be applied to other crops. PMID:20701770

Effect and mode of action of the Texel muscling QTL (TM-QTL) on carcass traits in purebred Texel lambs.

PubMed

Macfarlane, J M; Lambe, N R; Matika, O; Johnson, P L; Wolf, B T; Haresign, W; Bishop, S C; Bünger, L

2014-07-01

TM-QTL is a quantitative trait locus (QTL) on ovine chromosome 18 (OAR18) known to affect loin muscling in Texel sheep. Previous work suggested that its mode of inheritance is consistent with paternal polar overdominance, but this has yet to be formally demonstrated. This study used purebred Texel sheep segregating for TM-QTL to confirm its presence in the chromosomal region in which it was first reported and to determine its pattern of inheritance. To do so, this study used the first available data from a Texel flock, which included homozygote TM-QTL carriers (TM/TM; n=34) in addition to homozygote non-carriers (+/+; n=40 and, heterozygote TM-QTL-carriers inheriting TM-QTL from their sire (TM/+; n=53) or their dam (+/TM; n=17). Phenotypes included a wide range of loin muscling, carcass composition and tissue distribution traits. The presence of a QTL affecting ultrasound muscle depth on OAR18 was confirmed with a paternal QTL effect ranging from +0.54 to +2.82 mm UMD (s.e. 0.37 to 0.57 mm) across the sires segregating for TM-QTL. Loin muscle width, depth and area, loin muscle volume and dissected M. longissimus lumborum weight were significantly greater for TM/+ than +/+ lambs (+2.9% to +7.9%; P<0.05). There was significant evidence that the effect of TM-QTL on the various loin muscling traits measured was paternally polar overdominant (P<0.05). In contrast, there was an additive effect of TM-QTL on both live weight at 20 weeks and carcass weight; TM/TM animals were significantly (P<0.05) heavier than +/+ (+11.1% and +7.3%, respectively) and +/TM animals (+11.9% and +11.7%, respectively), with TM/+ intermediate. Weights of the leg, saddle and shoulder region (corrected for carcass weight) were similar in the genotypic groups. There was a tendency for lambs inheriting TM-QTL from their sire to be less fat with slightly more muscle than non-carriers. For example, carcass muscle weight measured by live animal CT-scanning was 2.8% higher in TM/TM than +/+ lambs (P<0.05), carcass muscle weight measured by carcass CT-scanning was 1.36% higher in TM/+ than +/+ lambs (P<0.05), and weight of fat trimmed from the carcass cuts was significantly lower for TM/+ than +/+ lambs (-11.2%; P<0.05). No negative effects of TM-QTL on carcass traits were found. Optimal commercial use of TM-QTL within the sheep industry would require some consideration, due to the apparently different mode of action of the two main effects of TM-QTL (on growth and muscling).

Two developmentally temporal quantitative trait loci underlie convergent evolution of increased branchial bone length in sticklebacks

PubMed Central

Erickson, Priscilla A.; Glazer, Andrew M.; Cleves, Phillip A.; Smith, Alyson S.; Miller, Craig T.

2014-01-01

In convergent evolution, similar phenotypes evolve repeatedly in independent populations, often reflecting adaptation to similar environments. Understanding whether convergent evolution proceeds via similar or different genetic and developmental mechanisms offers insight towards the repeatability and predictability of evolution. Oceanic populations of threespine stickleback fish, Gasterosteus aculeatus, have repeatedly colonized countless freshwater lakes and streams, where new diets lead to morphological adaptations related to feeding. Here, we show that heritable increases in branchial bone length have convergently evolved in two independently derived freshwater stickleback populations. In both populations, an increased bone growth rate in juveniles underlies the convergent adult phenotype, and one population also has a longer cartilage template. Using F2 crosses from these two freshwater populations, we show that two quantitative trait loci (QTL) control branchial bone length at distinct points in development. In both populations, a QTL on chromosome 21 controls bone length throughout juvenile development, and a QTL on chromosome 4 controls bone length only in adults. In addition to these similar developmental profiles, these QTL show similar chromosomal locations in both populations. Our results suggest that sticklebacks have convergently evolved longer branchial bones using similar genetic and developmental programmes in two independently derived populations. PMID:24966315

Genomic Dissection of Leaf Angle in Maize (Zea mays L.) Using a Four-Way Cross Mapping Population.

PubMed

Ding, Junqiang; Zhang, Luyan; Chen, Jiafa; Li, Xiantang; Li, Yongming; Cheng, Hongliang; Huang, Rongrong; Zhou, Bo; Li, Zhimin; Wang, Jiankang; Wu, Jianyu

2015-01-01

Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.

Genomic Dissection of Leaf Angle in Maize (Zea mays L.) Using a Four-Way Cross Mapping Population

PubMed Central

Li, Xiantang; Li, Yongming; Cheng, Hongliang; Huang, Rongrong; Zhou, Bo; Li, Zhimin; Wang, Jiankang; Wu, Jianyu

2015-01-01

Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize. PMID:26509792

Multiple Quantitative Trait Loci Influence the Shape of a Male-Specific Genital Structure in Drosophila melanogaster

PubMed Central

McNeil, Casey L.; Bain, Clint L.; Macdonald, Stuart J.

2011-01-01

The observation that male genitalia diverge more rapidly than other morphological traits during evolution is taxonomically widespread and likely due to some form of sexual selection. One way to elucidate the evolutionary forces acting on these traits is to detail the genetic architecture of variation both within and between species, a program of research that is considerably more tractable in a model system. Drosophila melanogaster and its sibling species, D. simulans, D. mauritiana, and D. sechellia, are morphologically distinguishable only by the shape of the posterior lobe, a male-specific elaboration of the genital arch. We extend earlier studies identifying quantitative trait loci (QTL) responsible for lobe divergence across species and report the first genetic dissection of lobe shape variation within a species. Using an advanced intercross mapping design, we identify three autosomal QTL contributing to the difference in lobe shape between a pair of D. melanogaster inbred lines. The QTL each contribute 4.6–10.7% to shape variation, and two show a significant epistatic interaction. Interestingly, these intraspecific QTL map to the same locations as interspecific lobe QTL, implying some shared genetic control of the trait within and between species. As a first step toward a mechanistic understanding of natural lobe shape variation, we find an association between our QTL data and a set of genes that show sex-biased expression in the developing genital imaginal disc (the precursor of the adult genitalia). These genes are good candidates to harbor naturally segregating polymorphisms contributing to posterior lobe shape. PMID:22384345

An Integrative Genetics Approach to Identify Candidate Genes Regulating BMD: Combining Linkage, Gene Expression, and Association

PubMed Central

Farber, Charles R; van Nas, Atila; Ghazalpour, Anatole; Aten, Jason E; Doss, Sudheer; Sos, Brandon; Schadt, Eric E; Ingram-Drake, Leslie; Davis, Richard C; Horvath, Steve; Smith, Desmond J; Drake, Thomas A; Lusis, Aldons J

2009-01-01

Numerous quantitative trait loci (QTLs) affecting bone traits have been identified in the mouse; however, few of the underlying genes have been discovered. To improve the process of transitioning from QTL to gene, we describe an integrative genetics approach, which combines linkage analysis, expression QTL (eQTL) mapping, causality modeling, and genetic association in outbred mice. In C57BL/6J × C3H/HeJ (BXH) F2 mice, nine QTLs regulating femoral BMD were identified. To select candidate genes from within each QTL region, microarray gene expression profiles from individual F2 mice were used to identify 148 genes whose expression was correlated with BMD and regulated by local eQTLs. Many of the genes that were the most highly correlated with BMD have been previously shown to modulate bone mass or skeletal development. Candidates were further prioritized by determining whether their expression was predicted to underlie variation in BMD. Using network edge orienting (NEO), a causality modeling algorithm, 18 of the 148 candidates were predicted to be causally related to differences in BMD. To fine-map QTLs, markers in outbred MF1 mice were tested for association with BMD. Three chromosome 11 SNPs were identified that were associated with BMD within the Bmd11 QTL. Finally, our approach provides strong support for Wnt9a, Rasd1, or both underlying Bmd11. Integration of multiple genetic and genomic data sets can substantially improve the efficiency of QTL fine-mapping and candidate gene identification. PMID:18767929

Fine-mapping of a marbling trait to a 2.9-cM region on bovine chromosome 7 in Japanese Black cattle.

PubMed

Hirano, T; Watanabe, T; Inoue, K; Sugimoto, Y

2008-02-01

To locate quantitative trait loci (QTL) for intramuscular fat deposition (marbling) in a local population of Japanese Black cattle, we performed a genome scan using a paternal half-sib family of Bull A. A marbling QTL was mapped in the region flanked by DIK0079 (20.7 cM) and TGLA303 (39.3 cM) on bovine chromosome (BTA) 7, affecting 5.0% of the total family variance. Haplotype analysis of the QTL region revealed that the marbling-increasing Q allele was transmitted from the dam. On the other hand, Bull B, a maternal half-sib of Bull A, did not receive the Q allele from its dam, based on the following findings: (i) a marbling QTL on BTA7 was not detected in the Bull B paternal half-sib family; (ii) recombination between DIK0079 (20.7 cM) and RM006 (25.4 cM) in the QTL region was observed in the maternal chromosome of Bull B; and (iii) the Q-harbouring steers from Bull A exhibited significantly higher marbling than the steers from Bull B and the remaining steers from Bull A. To precisely compare the maternal chromosomes of both bulls, we constructed a bacterial artificial chromosome contig covering the region between DIK0079 and RM006 and developed DNA markers. The recombination occurred between DIK8042 and DIK8044, indicating that the marbling QTL was in a 2.9-cM region flanked by DIK0079 and DIK8044.

Multi-environment QTL analysis of grain morphology traits and fine mapping of a kernel-width QTL in Zheng58 × SK maize population.

PubMed

Raihan, Mohammad Sharif; Liu, Jie; Huang, Juan; Guo, Huan; Pan, Qingchun; Yan, Jianbing

2016-08-01

Sixteen major QTLs regulating maize kernel traits were mapped in multiple environments and one of them, qKW - 9.2 , was restricted to 630 Kb, harboring 28 putative gene models. To elucidate the genetic basis of kernel traits, a quantitative trait locus (QTL) analysis was conducted in a maize recombinant inbred line population derived from a cross between two diverse parents Zheng58 and SK, evaluated across eight environments. Construction of a high-density linkage map was based on 13,703 single-nucleotide polymorphism markers, covering 1860.9 cM of the whole genome. In total, 18, 26, 23, and 19 QTLs for kernel length, width, thickness, and 100-kernel weight, respectively, were detected on the basis of a single-environment analysis, and each QTL explained 3.2-23.7 % of the phenotypic variance. Sixteen major QTLs, which could explain greater than 10 % of the phenotypic variation, were mapped in multiple environments, implying that kernel traits might be controlled by many minor and multiple major QTLs. The major QTL qKW-9.2 with physical confidence interval of 1.68 Mbp, affecting kernel width, was then selected for fine mapping using heterogeneous inbred families. At final, the location of the underlying gene was narrowed down to 630 Kb, harboring 28 putative candidate-gene models. This information will enhance molecular breeding for kernel traits and simultaneously assist the gene cloning underlying this QTL, helping to reveal the genetic basis of kernel development in maize.

Identification of Quantitative Trait Loci for Resistance to RSIVD in Red Sea Bream (Pagrus major).

PubMed

Sawayama, Eitaro; Tanizawa, Shiho; Kitamura, Shin-Ichi; Nakayama, Kei; Ohta, Kohei; Ozaki, Akiyuki; Takagi, Motohiro

2017-12-01

Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS). Two test families were developed using the candidate male in 2014 (Fam-2014) and 2015 (Fam-2015). These test families were challenged with RSIV, and phenotypes were evaluated. Then, de novo genome sequences of red sea bream were obtained through next-generation sequencing, and microsatellite markers were searched and selected for linkage map construction. One immune-related gene, MHC class IIβ, was also used for linkage map construction. Of the microsatellite markers searched, 148 and 197 were mapped on 23 and 27 linkage groups in the female and male linkage maps, respectively, covering approximately 65% of genomes in both sexes. One QTL linked to an RSIVD-resistant trait was found in linkage group 2 of the candidate male in Fam-2014, and the phenotypic variance of the QTL was 31.1%. The QTL was closely linked to MHC class IIβ. Moreover, the QTL observed in Fam-2014 was also significantly linked to an RSIVD-resistant trait in the candidate male of Fam-2015. Our results suggest that the RSIVD-resistant trait in the candidate male was controlled by one major QTL closely linked to the MHC class IIβ gene and could be useful for MAS of red sea bream.

A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv].

PubMed

Fang, Xiaomei; Dong, Kongjun; Wang, Xiaoqin; Liu, Tianpeng; He, Jihong; Ren, Ruiyu; Zhang, Lei; Liu, Rui; Liu, Xueying; Li, Man; Huang, Mengzhu; Zhang, Zhengsheng; Yang, Tianyu

2016-05-04

Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement. A total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar 'Yugu1'. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1. New SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.

Functional Multi-Locus QTL Mapping of Temporal Trends in Scots Pine Wood Traits

PubMed Central

Li, Zitong; Hallingbäck, Henrik R.; Abrahamsson, Sara; Fries, Anders; Gull, Bengt Andersson; Sillanpää, Mikko J.; García-Gil, M. Rosario

2014-01-01

Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals. PMID:25305041

Functional multi-locus QTL mapping of temporal trends in Scots pine wood traits.

PubMed

Li, Zitong; Hallingbäck, Henrik R; Abrahamsson, Sara; Fries, Anders; Gull, Bengt Andersson; Sillanpää, Mikko J; García-Gil, M Rosario

2014-10-09

Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals. Copyright © 2014 Li et al.

Small- and Large-Effect Quantitative Trait Locus Interactions Underlie Variation in Yeast Sporulation Efficiency

PubMed Central

Lorenz, Kim; Cohen, Barak A.

2012-01-01

Quantitative trait loci (QTL) with small effects on phenotypic variation can be difficult to detect and analyze. Because of this a large fraction of the genetic architecture of many complex traits is not well understood. Here we use sporulation efficiency in Saccharomyces cerevisiae as a model complex trait to identify and study small-effect QTL. In crosses where the large-effect quantitative trait nucleotides (QTN) have been genetically fixed we identify small-effect QTL that explain approximately half of the remaining variation not explained by the major effects. We find that small-effect QTL are often physically linked to large-effect QTL and that there are extensive genetic interactions between small- and large-effect QTL. A more complete understanding of quantitative traits will require a better understanding of the numbers, effect sizes, and genetic interactions of small-effect QTL. PMID:22942125

A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum interspecific populations and Gossypium hirsutum x Gossypium barbadense populations

USDA-ARS?s Scientific Manuscript database

Recent Meta-analysis of quantitative trait loci (QTL) in tetraploid cotton (Gossypium spp.) has identified regions of the genome with high concentrations of various trait QTL called clusters, and specific trait QTL called hotspots. The Meta-analysis included all population types of Gossypium mixing ...

Quantitative trait loci that control body weight in DDD/Sgn and C57BL/6J inbred mice.

PubMed

Suto, Jun-Ichi; Kojima, Misaki

2017-02-01

Inbred DDD/Sgn mice are heavier than inbred C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for body weight using R/qtl in reciprocal F 2 male populations between the two strains. We identified four significant QTL on Chrs 1, 2, 5, and 17 (proximal region). The DDD/Sgn allele was associated with increased body weight at QTL on Chrs 1 and 5, and the DDD/Sgn allele was associated with decreased body weight at QTL on Chrs 2 and 17. A multiple regression analysis indicated that the detected QTL explain 30.94 % of the body weight variation. Because DDD/Sgn male mice have extremely high levels of circulating testosterone relative to other inbred mouse strains, we performed QTL mapping for plasma testosterone level to examine the effect of testosterone levels on body weight. We identified one suggestive QTL on Chr 5, which overlapped with body weight QTL. The DDD/Sgn allele was associated with increased testosterone level. Thus, we confirmed that there was a genetic basis for the changes in body weight and testosterone levels in male mice. These findings provide insights into the genetic mechanism by which body weight is controlled in male mice.

Genetic control and comparative genomic analysis of flowering time in Setaria (Poaceae).

PubMed

Mauro-Herrera, Margarita; Wang, Xuewen; Barbier, Hugues; Brutnell, Thomas P; Devos, Katrien M; Doust, Andrew N

2013-02-01

We report the first study on the genetic control of flowering in Setaria, a panicoid grass closely related to switchgrass, and in the same subfamily as maize and sorghum. A recombinant inbred line mapping population derived from a cross between domesticated Setaria italica (foxtail millet) and its wild relative Setaria viridis (green millet), was grown in eight trials with varying environmental conditions to identify a small number of quantitative trait loci (QTL) that control differences in flowering time. Many of the QTL across trials colocalize, suggesting that the genetic control of flowering in Setaria is robust across a range of photoperiod and other environmental factors. A detailed comparison of QTL for flowering in Setaria, sorghum, and maize indicates that several of the major QTL regions identified in maize and sorghum are syntenic orthologs with Setaria QTL, although the maize large effect QTL on chromosome 10 is not. Several Setaria QTL intervals had multiple LOD peaks and were composed of multiple syntenic blocks, suggesting that observed QTL represent multiple tightly linked loci. Candidate genes from flowering time pathways identified in rice and Arabidopsis were identified in Setaria QTL intervals, including those involved in the CONSTANS photoperiod pathway. However, only three of the approximately seven genes cloned for flowering time in maize colocalized with Setaria QTL. This suggests that variation in flowering time in separate grass lineages is controlled by a combination of conserved and lineage specific genes.

Genetic Control and Comparative Genomic Analysis of Flowering Time in Setaria (Poaceae)

PubMed Central

Mauro-Herrera, Margarita; Wang, Xuewen; Barbier, Hugues; Brutnell, Thomas P.; Devos, Katrien M.; Doust, Andrew N.

2013-01-01

We report the first study on the genetic control of flowering in Setaria, a panicoid grass closely related to switchgrass, and in the same subfamily as maize and sorghum. A recombinant inbred line mapping population derived from a cross between domesticated Setaria italica (foxtail millet) and its wild relative Setaria viridis (green millet), was grown in eight trials with varying environmental conditions to identify a small number of quantitative trait loci (QTL) that control differences in flowering time. Many of the QTL across trials colocalize, suggesting that the genetic control of flowering in Setaria is robust across a range of photoperiod and other environmental factors. A detailed comparison of QTL for flowering in Setaria, sorghum, and maize indicates that several of the major QTL regions identified in maize and sorghum are syntenic orthologs with Setaria QTL, although the maize large effect QTL on chromosome 10 is not. Several Setaria QTL intervals had multiple LOD peaks and were composed of multiple syntenic blocks, suggesting that observed QTL represent multiple tightly linked loci. Candidate genes from flowering time pathways identified in rice and Arabidopsis were identified in Setaria QTL intervals, including those involved in the CONSTANS photoperiod pathway. However, only three of the approximately seven genes cloned for flowering time in maize colocalized with Setaria QTL. This suggests that variation in flowering time in separate grass lineages is controlled by a combination of conserved and lineage specific genes. PMID:23390604

Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.).

PubMed

Campbell, Raymond; Pont, Simon D A; Morris, Jenny A; McKenzie, Gaynor; Sharma, Sanjeev Kumar; Hedley, Pete E; Ramsay, Gavin; Bryan, Glenn J; Taylor, Mark A

2014-09-01

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient 'genetical genomics' analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.

Deficiency mapping of quantitative trait loci affecting longevity in Drosophila melanogaster.

PubMed Central

Pasyukova, E G; Vieira, C; Mackay, T F

2000-01-01

In a previous study, sex-specific quantitative trait loci (QTL) affecting adult longevity were mapped by linkage to polymorphic roo transposable element markers, in a population of recombinant inbred lines derived from the Oregon and 2b strains of Drosophila melanogaster. Two life span QTL were each located on chromosomes 2 and 3, within sections 33E-46C and 65D-85F on the cytological map, respectively. We used quantitative deficiency complementation mapping to further resolve the locations of life span QTL within these regions. The Oregon and 2b strains were each crossed to 47 deficiencies spanning cytological regions 32F-44E and 64C-76B, and quantitative failure of the QTL alleles to complement the deficiencies was assessed. We initially detected a minimum of five and four QTL in the chromosome 2 and 3 regions, respectively, illustrating that multiple linked factors contribute to each QTL detected by recombination mapping. The QTL locations inferred from deficiency mapping did not generally correspond to those of candidate genes affecting oxidative and thermal stress or glucose metabolism. The chromosome 2 QTL in the 35B-E region was further resolved to a minimum of three tightly linked QTL, containing six genetically defined loci, 24 genes, and predicted genes that are positional candidates corresponding to life span QTL. This region was also associated with quantitative variation in life span in a sample of 10 genotypes collected from nature. Quantitative deficiency complementation is an efficient method for fine-scale QTL mapping in Drosophila and can be further improved by controlling the background genotype of the strains to be tested. PMID:11063689

Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping

PubMed Central

Yi, Xin; Cheng, Jingye; Jiang, Zhengning; Hu, Wenjing; Bie, Tongde; Gao, Derong; Li, Dongsheng; Wu, Ronglin; Li, Yuling; Chen, Shulin; Cheng, Xiaoming; Liu, Jian; Zhang, Yong; Cheng, Shunhe

2018-01-01

Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL (QFhbs-jaas.2AL, QFhbp-jaas.2DS, and QFhbp-jaas.2DL) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding. PMID:29780395

Genetic Analysis of Fusarium Head Blight Resistance in CIMMYT Bread Wheat Line C615 Using Traditional and Conditional QTL Mapping.

PubMed

Yi, Xin; Cheng, Jingye; Jiang, Zhengning; Hu, Wenjing; Bie, Tongde; Gao, Derong; Li, Dongsheng; Wu, Ronglin; Li, Yuling; Chen, Shulin; Cheng, Xiaoming; Liu, Jian; Zhang, Yong; Cheng, Shunhe

2018-01-01

Fusarium head blight (FHB) is a destructive wheat disease present throughout the world, and host resistance is an effective and economical strategy used to control FHB. Lack of adequate resistance resource is still a main bottleneck for FHB genetics and wheat breeding research. The synthetic-derived bread wheat line C615, which does not carry the Fhb1 gene, is a promising source of FHB resistance for breeding. A population of 198 recombinant inbred lines (RILs) produced by crossing C615 with the susceptible cultivar Yangmai 13 was evaluated for FHB response using point and spray inoculations. As the disease phenotype is frequently complicated by other agronomic traits, we used both traditional and multivariate conditional QTL mapping approaches to investigate the genetic relationships (at the individual QTL level) between FHB resistance and plant height (PH), spike compactness (SC), and days to flowering (FD). A linkage map was constructed from 3,901 polymorphic SNP markers, which covered 2,549.2 cM. Traditional and conditional QTL mapping analyses found 13 and 22 QTL for FHB, respectively; 10 were identified by both methods. Among these 10, three QTL from C615 were detected in multiple years; these QTL were located on chromosomes 2AL, 2DS, and 2DL. Conditional QTL mapping analysis indicated that, at the QTL level, SC strongly influenced FHB in point inoculation; whereas PH and SC contributed more to FHB than did FD in spray inoculation. The three stable QTL ( QFhbs-jaas.2AL, QFhbp-jaas.2DS , and QFhbp-jaas.2DL ) for FHB were partly affected by or were independent of the three agronomic traits. The QTL detected in this study improve our understanding of the genetic relationships between FHB response and related traits at the QTL level and provide useful information for marker-assisted selection for the improvement of FHB resistance in breeding.

Comparative mapping of quantitative trait loci for Fusarium head blight resistance and anther retention in the winter wheat population Capo × Arina.

PubMed

Buerstmayr, Maria; Buerstmayr, Hermann

2015-08-01

Fusarium resistance in Arina is highly quantitative and governed by multiple small effect QTL. Anther retention has a high correlation with FHB susceptibility and appears a practicable indirect selection target for enhancing FHB resistance. The Swiss winter wheat cultivar Arina possesses a high resistance level constituted by a number of small to medium effect QTL reported from three independent mapping populations. Yet these overlap only for one resistance QTL on the long arm of chromosome 1B. The present study characterized Fusarium head blight (FHB) resistance in a population of 171 recombinant inbred lines from a cross between Arina (resistant) and Capo (moderately resistant). The population was evaluated for FHB resistance under field conditions for 3 years. Additionally, we phenotyped anther retention, plant height and flowering date to analyze their association with resistance. Lines with a low proportion of retained anthers after flowering and tall plants were significantly less diseased, while flowering date had no association with FHB severity. QTL analysis identified eight small to medium effect QTL for FHB severity, of which QTL on 1BS, 3B, 4AL and 6BL likely correspond to resistance alleles already detected in previously studied Arina populations. QTL for anther retention mapped to 4AL, 6BL and 5AS. Notably, QTL on 4AL and 6BL overlapped with QTL for FHB severity. A single small effect QTL for plant height was detected on 5AS and no QTL was identified for flowering date. Genotypes having three or four resistance alleles in combination showed a good resistance level, indicating pyramiding resistance QTL as a powerful approach for breeding resistant cultivars. Selection for rapid and complete anther extrusion appears promising as an indirect selection criterion for enhancing FHB resistance.

Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait

PubMed Central

Moen, Thomas; Baranski, Matthew; Sonesson, Anna K; Kjøglum, Sissel

2009-01-01

Background Infectious pancreatic necrosis (IPN) is one of the most prevalent and economically devastating diseases in Atlantic salmon (Salmo salar) farming worldwide. The disease causes large mortalities at both the fry- and post-smolt stages. Family selection for increased IPN resistance is performed through the use of controlled challenge tests, where survival rates of sib-groups are recorded. However, since challenge-tested animals cannot be used as breeding candidates, within-family selection is not performed and only half of the genetic variation for IPN resistance is being exploited. DNA markers linked to quantitative trait loci (QTL) affecting IPN resistance would therefore be a powerful selection tool. The aim of this study was to identify and fine-map QTL for IPN-resistance in Atlantic salmon, for use in marker-assisted selection to increase the rate of genetic improvement for this trait. Results A genome scan was carried out using 10 large full-sib families of challenge-tested Atlantic salmon post-smolts and microsatellite markers distributed across the genome. One major QTL for IPN-resistance was detected, explaining 29% and 83% of the phenotypic and genetic variances, respectively. This QTL mapped to the same location as a QTL recently detected in a Scottish Atlantic salmon population. The QTL was found to be segregating in 10 out of 20 mapping parents, and subsequent fine-mapping with additional markers narrowed the QTL peak to a 4 cM region on linkage group 21. Challenge-tested fry were used to show that the QTL had the same effect on fry as on post-smolt, with the confidence interval for QTL position in fry overlapping the confidence interval found in post-smolts. A total of 178 parents were tested for segregation of the QTL, identifying 72 QTL-heterozygous parents. Genotypes at QTL-heterozygous parents were used to determine linkage phases between alleles at the underlying DNA polymorphism and alleles at single markers or multi-marker haplotypes. One four-marker haplotype was found to be the best predictor of QTL alleles, and was successfully used to deduce genotypes of the underlying polymorphism in 72% of the parents of the next generation within a breeding nucleus. A highly significant population-level correlation was found between deduced alleles at the underlying polymorphism and survival of offspring groups in the fry challenge test, parents with the three deduced genotypes (QQ, Qq, qq) having mean offspring mortality rates of 0.13, 0.32, and 0.49, respectively. The frequency of the high-resistance allele (Q) in the population was estimated to be 0.30. Apart from this major QTL, one other experiment-wise significant QTL for IPN-resistance was detected, located on linkage group 4. Conclusion The QTL confirmed in this study represents a case of a major gene explaining the bulk of genetic variation for a presumed complex trait. QTL genotypes were deduced within most parents of the 2005 generation of a major breeding company, providing a solid framework for linkage-based MAS within the whole population in subsequent generations. Since haplotype-trait associations valid at the population level were found, there is also a potential for MAS based on linkage disequilibrium (LD). However, in order to use MAS across many generations without reassessment of linkage phases between markers and the underlying polymorphism, the QTL needs to be positioned with even greater accuracy. This will require higher marker densities than are currently available. PMID:19664221

Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass, Setaria

PubMed Central

Mauro-Herrera, Margarita; Doust, Andrew N.

2016-01-01

The architecture of a plant affects its ability to compete for light and to respond to environmental stresses, thus affecting overall fitness and productivity. Two components of architecture, branching and height, were studied in 182 F7 recombinant inbred lines (RILs) at the vegetative, flowering and mature developmental stages in the panicoid C4 model grass system, Setaria. The RIL population was derived from a cross between domesticated S. italica (foxtail millet) and its wild relative S. viridis (green foxtail). In both field and greenhouse trials the wild parent was taller initially, started branching earlier, and flowered earlier, while the domesticated parent was shorter initially, but flowered later, producing a robust tall plant architecture with more nodes and leaves on the main culm and few or no branches. Biomass was highly correlated with height of the plant and number of nodes on the main culm, and generally showed a negative relationship with branch number. However, several of the RILs with the highest biomass in both trials were significantly more branched than the domesticated parent of the cross. Quantitative trait loci (QTL) analyses indicate that both height and branching are controlled by multiple genetic regions, often with QTL for both traits colocalizing in the same genomic regions. Genomic positions of several QTL colocalize with QTL in syntenic regions in other species and contain genes known to control branching and height in sorghum, maize, and switchgrass. Included in these is the ortholog of the rice SD-1 semi-dwarfing gene, which underlies one of the major Setaria height QTL. Understanding the relationships between height and branching patterns in Setaria, and their genetic control, is an important step to gaining a comprehensive knowledge of the development and genetic regulation of panicoid grass architecture. PMID:26985990

Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass, Setaria.

PubMed

Mauro-Herrera, Margarita; Doust, Andrew N

2016-01-01

The architecture of a plant affects its ability to compete for light and to respond to environmental stresses, thus affecting overall fitness and productivity. Two components of architecture, branching and height, were studied in 182 F7 recombinant inbred lines (RILs) at the vegetative, flowering and mature developmental stages in the panicoid C4 model grass system, Setaria. The RIL population was derived from a cross between domesticated S. italica (foxtail millet) and its wild relative S. viridis (green foxtail). In both field and greenhouse trials the wild parent was taller initially, started branching earlier, and flowered earlier, while the domesticated parent was shorter initially, but flowered later, producing a robust tall plant architecture with more nodes and leaves on the main culm and few or no branches. Biomass was highly correlated with height of the plant and number of nodes on the main culm, and generally showed a negative relationship with branch number. However, several of the RILs with the highest biomass in both trials were significantly more branched than the domesticated parent of the cross. Quantitative trait loci (QTL) analyses indicate that both height and branching are controlled by multiple genetic regions, often with QTL for both traits colocalizing in the same genomic regions. Genomic positions of several QTL colocalize with QTL in syntenic regions in other species and contain genes known to control branching and height in sorghum, maize, and switchgrass. Included in these is the ortholog of the rice SD-1 semi-dwarfing gene, which underlies one of the major Setaria height QTL. Understanding the relationships between height and branching patterns in Setaria, and their genetic control, is an important step to gaining a comprehensive knowledge of the development and genetic regulation of panicoid grass architecture.

Fast and robust group-wise eQTL mapping using sparse graphical models.

PubMed

Cheng, Wei; Shi, Yu; Zhang, Xiang; Wang, Wei

2015-01-16

Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression traits. A major drawback of this approach is that it cannot model the joint effect of a set of SNPs on a set of genes, which may correspond to hidden biological pathways. We introduce a new approach to identify novel group-wise associations between sets of SNPs and sets of genes. Such associations are captured by hidden variables connecting SNPs and genes. Our model is a linear-Gaussian model and uses two types of hidden variables. One captures the set associations between SNPs and genes, and the other captures confounders. We develop an efficient optimization procedure which makes this approach suitable for large scale studies. Extensive experimental evaluations on both simulated and real datasets demonstrate that the proposed methods can effectively capture both individual and group-wise signals that cannot be identified by the state-of-the-art eQTL mapping methods. Considering group-wise associations significantly improves the accuracy of eQTL mapping, and the successful multi-layer regression model opens a new approach to understand how multiple SNPs interact with each other to jointly affect the expression level of a group of genes.

Early growth stages salinity stress tolerance in CM72 x Gairdner doubled haploid barley population

PubMed Central

Angessa, Tefera Tolera; Zhang, Xiao-Qi; Zhou, Gaofeng; Broughton, Sue; Zhang, Wenying

2017-01-01

A doubled haploid (DH) population of barley (Hordeum vulgare L.) generated from salinity tolerant genotype CM72 and salinity sensitive variety Gairdner was studied for salinity stress tolerance at germination, seedling emergence and first leaf full expansion growth stages. Germination study was conducted with deionized water, 150 mM and 300 mM NaCl treatments. Seedling stage salinity tolerance was conducted with three treatments: control, 150 mM NaCl added at seedling emergence and first leaf full expansion growth stages. Results from this study revealed transgressive phenotypic segregations for germination percentage and biomass at seedling stage. Twelve QTL were identified on chromosomes 2H–6H each explaining 10–25% of the phenotypic variations. A QTL located at 176.5 cM on chromosome 3H was linked with fresh weight per plant and dry weight per plant in salinity stress induced at first leaf full expansion growth stage, and dry weight per plant in salinity stress induced at seedling emergence. A stable QTL for germination at both 150 and 300 mM salinity stress was mapped on chromosome 2H but distantly located from a QTL linked with seedling stage salinity stress tolerance. QTL, associated markers and genotypes identified in this study play important roles in developing salinity stress tolerant barley varieties. PMID:28640858

Restriction fragment length polymorphism mapping of quantitative trait loci for malaria parasite susceptibility in the mosquito Aedes aegypti

DOE Office of Scientific and Technical Information (OSTI.GOV)

Severson, D.W.; Thathy, V.; Mori, A.

Susceptibility of the mosquito Aedes aegypti to the malarial parasite Plasmodium gallinaceum was investigated as a quantitative trait using restriction fragment length polymorphisms (RFLP). Two F{sub 2} populations of mosquitoes were independently prepared from pairwise matings between a highly susceptible and a refractory strain of A. aegypti. RFLP were tested for association with oocyst development on the mosquito midgut. Two putative quantitative trait loci (QTL) were identified that significantly affect susceptibility. One QTL, pgs [2,LF98], is located on chromosome 2 and accounted for 65 and 49% of the observed phenotypic variance in the two populations, respectively. A second QTL, pgs[3,MalI],more » is located on chromosome 3 and accounted for 14 and 10% of the observed phenotypic variance in the two populations, respectively. Both QTL exhibit a partial dominance effect on susceptibility, wherein the dominance effect is derived from the refractory parent. No indication of epistasis between these QTL was detected. Evidence suggests that either a tightly linked cluster of independent genes or a single locus affecting susceptibility to various mosquito-borne parasites and pathogens has evolved near the LF98 locus; in addition to P. gallinaceum susceptibility, this general genome region has previously been implicated in susceptibility to the filaria nematode Brugia malayi and the yellow fever virus. 35 refs., 2 figs., 3 tabs.« less

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors under Multiple Stresses in Brassica napus

PubMed Central

He, Yajun; Mao, Shaoshuai; Gao, Yulong; Zhu, Liying; Wu, Daoming; Cui, Yixin; Li, Jiana; Qian, Wei

2016-01-01

WRKY transcription factors play important roles in responses to environmental stress stimuli. Using a genome-wide domain analysis, we identified 287 WRKY genes with 343 WRKY domains in the sequenced genome of Brassica napus, 139 in the A sub-genome and 148 in the C sub-genome. These genes were classified into eight groups based on phylogenetic analysis. In the 343 WRKY domains, a total of 26 members showed divergence in the WRKY domain, and 21 belonged to group I. This finding suggested that WRKY genes in group I are more active and variable compared with genes in other groups. Using genome-wide identification and analysis of the WRKY gene family in Brassica napus, we observed genome duplication, chromosomal/segmental duplications and tandem duplication. All of these duplications contributed to the expansion of the WRKY gene family. The duplicate segments that were detected indicated that genome duplication events occurred in the two diploid progenitors B. rapa and B. olearecea before they combined to form B. napus. Analysis of the public microarray database and EST database for B. napus indicated that 74 WRKY genes were induced or preferentially expressed under stress conditions. According to the public QTL data, we identified 77 WRKY genes in 31 QTL regions related to various stress tolerance. We further evaluated the expression of 26 BnaWRKY genes under multiple stresses by qRT-PCR. Most of the genes were induced by low temperature, salinity and drought stress, indicating that the WRKYs play important roles in B. napus stress responses. Further, three BnaWRKY genes were strongly responsive to the three multiple stresses simultaneously, which suggests that these 3 WRKY may have multi-functional roles in stress tolerance and can potentially be used in breeding new rapeseed cultivars. We also found six tandem repeat pairs exhibiting similar expression profiles under the various stress conditions, and three pairs were mapped in the stress related QTL regions, indicating tandem duplicate WRKYs in the adaptive responses to environmental stimuli during the evolution process. Our results provide a framework for future studies regarding the function of WRKY genes in response to stress in B. napus. PMID:27322342

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors under Multiple Stresses in Brassica napus.

PubMed

He, Yajun; Mao, Shaoshuai; Gao, Yulong; Zhu, Liying; Wu, Daoming; Cui, Yixin; Li, Jiana; Qian, Wei

2016-01-01

WRKY transcription factors play important roles in responses to environmental stress stimuli. Using a genome-wide domain analysis, we identified 287 WRKY genes with 343 WRKY domains in the sequenced genome of Brassica napus, 139 in the A sub-genome and 148 in the C sub-genome. These genes were classified into eight groups based on phylogenetic analysis. In the 343 WRKY domains, a total of 26 members showed divergence in the WRKY domain, and 21 belonged to group I. This finding suggested that WRKY genes in group I are more active and variable compared with genes in other groups. Using genome-wide identification and analysis of the WRKY gene family in Brassica napus, we observed genome duplication, chromosomal/segmental duplications and tandem duplication. All of these duplications contributed to the expansion of the WRKY gene family. The duplicate segments that were detected indicated that genome duplication events occurred in the two diploid progenitors B. rapa and B. olearecea before they combined to form B. napus. Analysis of the public microarray database and EST database for B. napus indicated that 74 WRKY genes were induced or preferentially expressed under stress conditions. According to the public QTL data, we identified 77 WRKY genes in 31 QTL regions related to various stress tolerance. We further evaluated the expression of 26 BnaWRKY genes under multiple stresses by qRT-PCR. Most of the genes were induced by low temperature, salinity and drought stress, indicating that the WRKYs play important roles in B. napus stress responses. Further, three BnaWRKY genes were strongly responsive to the three multiple stresses simultaneously, which suggests that these 3 WRKY may have multi-functional roles in stress tolerance and can potentially be used in breeding new rapeseed cultivars. We also found six tandem repeat pairs exhibiting similar expression profiles under the various stress conditions, and three pairs were mapped in the stress related QTL regions, indicating tandem duplicate WRKYs in the adaptive responses to environmental stimuli during the evolution process. Our results provide a framework for future studies regarding the function of WRKY genes in response to stress in B. napus.

Genetic Mapping of the Leaf Number above the Primary Ear and Its Relationship with Plant Height and Flowering Time in Maize.

PubMed

Cui, Min; Jia, Bo; Liu, Huanhuan; Kan, Xin; Zhang, Yu; Zhou, Ronghua; Li, Zhipeng; Yang, Liang; Deng, Dexiang; Yin, Zhitong

2017-01-01

The leaf number above the primary ear (LA) is a major contributing factor to plant architecture in maize. The yield of leafy maize, which has extra LA compared to normal maize, is higher than normal maize in some regions. One major concern is that increasing LA may be accompanied by increased plant height and/or flowering time. Using an F 2:3 population comprising 192 families derived from a leafy maize line and a normal maize line, an association population comprising 437 inbred maize lines, and a pair of near-isogenic maize lines, we mapped the quantitative trait loci (QTL) associated with LA and assessed its genetic relationship with flowering time and plant height. Ten QTL with an additive and dominant effect, 18 pairs of interacting QTL in the F 2:3 population and seventeen significant SNPs in the association population were detected for LA. Two major QTL, qLA3-4 and qLA7-1 , were repeatedly detected and explained a large proportion of the phenotypic variation. The qLA3-4 was centered on lfy1 , which is a dominant gene underlying extra leaves above the ear in leafy maize. Four LA QTL were found to overlap with flowering time and/or plant height, which suggested that these QTL might have a pleiotropic effect. The pleiotropy of the lfy1 locus on LA, flowering time and plant height were validated by near-isogenic line analysis. These results enhance our understanding of the genetic architecture affecting maize LA and the development of maize hybrids with increased LA.

Dro1, a major QTL involved in deep rooting of rice under upland field conditions.

PubMed

Uga, Yusaku; Okuno, Kazutoshi; Yano, Masahiro

2011-05-01

Developing a deep root system is an important strategy for avoiding drought stress in rice. Using the 'basket' method, the ratio of deep rooting (RDR; the proportion of total roots that elongated through the basket bottom) was calculated to evaluate deep rooting. A new major quantitative trait locus (QTL) controlling RDR was detected on chromosome 9 by using 117 recombinant inbred lines (RILs) derived from a cross between the lowland cultivar IR64, with shallow rooting, and the upland cultivar Kinandang Patong (KP), with deep rooting. This QTL explained 66.6% of the total phenotypic variance in RDR in the RILs. A BC(2)F(3) line homozygous for the KP allele of the QTL had an RDR of 40.4%, compared with 2.6% for the homozygous IR64 allele. Fine mapping of this QTL was undertaken using eight BC(2)F(3) recombinant lines. The RDR QTL Dro1 (Deeper rooting 1) was mapped between the markers RM24393 and RM7424, which delimit a 608.4 kb interval in the reference cultivar Nipponbare. To clarify the influence of Dro1 in an upland field, the root distribution in different soil layers was quantified by means of core sampling. A line homozygous for the KP allele of Dro1 (Dro1-KP) and IR64 did not differ in root dry weight in the shallow soil layers (0-25 cm), but root dry weight of Dro1-KP in deep soil layers (25-50 cm) was significantly greater than that of IR64, suggesting that Dro1 plays a crucial role in increased deep rooting under upland field conditions.

Abiotic stress QTL in lettuce crop–wild hybrids: comparing greenhouse and field experiments

PubMed Central

Hartman, Yorike; Hooftman, Danny A P; Uwimana, Brigitte; Schranz, M Eric; van de Wiel, Clemens C M; Smulders, Marinus J M; Visser, Richard G F; Michelmore, Richard W; van Tienderen, Peter H

2014-01-01

The development of stress-tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans-)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives. PMID:25360276

Segregation of a QTL cluster for home-cage activity using a new mapping method based on regression analysis of congenic mouse strains

PubMed Central

Kato, S; Ishii, A; Nishi, A; Kuriki, S; Koide, T

2014-01-01

Recent genetic studies have shown that genetic loci with significant effects in whole-genome quantitative trait loci (QTL) analyses were lost or weakened in congenic strains. Characterisation of the genetic basis of this attenuated QTL effect is important to our understanding of the genetic mechanisms of complex traits. We previously found that a consomic strain, B6-Chr6CMSM, which carries chromosome 6 of a wild-derived strain MSM/Ms on the genetic background of C57BL/6J, exhibited lower home-cage activity than C57BL/6J. In the present study, we conducted a composite interval QTL analysis using the F2 mice derived from a cross between C57BL/6J and B6-Chr6CMSM. We found one QTL peak that spans 17.6 Mbp of chromosome 6. A subconsomic strain that covers the entire QTL region also showed lower home-cage activity at the same level as the consomic strain. We developed 15 congenic strains, each of which carries a shorter MSM/Ms-derived chromosomal segment from the subconsomic strain. Given that the results of home-cage activity tests on the congenic strains cannot be explained by a simple single-gene model, we applied regression analysis to segregate the multiple genetic loci. The results revealed three loci (loci 1–3) that have the effect of reducing home-cage activity and one locus (locus 4) that increases activity. We also found that the combination of loci 3 and 4 cancels out the effects of the congenic strains, which indicates the existence of a genetic mechanism related to the loss of QTLs. PMID:24781804

QTL mapping of genes controlling plasma insulin and leptin concentrations: metabolic effect of obesity QTLs identified in an F2 intercross between C57BL/6J and DDD.Cg-A(y) inbred mice.

PubMed

Suto, Jun-ichi

2013-07-31

DDD.Cg-A(y) female mice developed massive obesity as compared with B6.Cg-A(y) female mice. We previously identified quantitative trait loci (QTLs) for obesity on chromosomes 1, 6, 9 and 17 in F2 female mice, including F2A(y) (F2 mice with the A(y) allele) and F2 non- A(y) mice (F2 mice without the A(y) allele), produced by crossing C57BL/6J and DDD.Cg-A(y) strains. We here addressed the question whether the obesity QTLs share genetic bases with putative QTLs for plasma glucose, insulin and leptin concentrations. We performed QTL analyses for the first principal component (PC1) extracted from these metabolic measurements to identify the genes that contributed to the comprehensive evaluation of metabolic traits. By single QTL scans, we identified two significant QTLs for insulin concentration on chromosomes 6 and 12, three for leptin concentration on chromosomes 1, 6 and 17, and five for PC1 on chromosomes 1, 6, 12 (two loci) and 17. Although insulin and leptin concentrations and PC1 were not normally distributed in combined F2 mice, results of single QTL scans by parametric and non-parametric methods were very similar. Therefore, QTL scan by the parametric method was performed with the agouti locus genotype as a covariate. A significant QTL × covariate interaction was found for PC1 on chromosome 9. All obesity QTLs had significant metabolic effects. Thus, obesity- and diabetes-related traits in DDD.Cg-A(y) mice were largely controlled by QTLs on chromosomes 1, 6, 9, 12 and 17.

Identification and validation of QTL for grain yield and plant water status under contrasting water treatments in fall-sown spring wheats.

PubMed

Zhang, Junli; Gizaw, Shiferaw Abate; Bossolini, Eligio; Hegarty, Joshua; Howell, Tyson; Carter, Arron H; Akhunov, Eduard; Dubcovsky, Jorge

2018-05-16

Chromosome regions affecting grain yield, grain yield components and plant water status were identified and validated in fall-sown spring wheats grown under full and limited irrigation. Increases in wheat production are required to feed a growing human population. To understand the genetic basis of grain yield in fall-sown spring wheats, we performed a genome-wide association study (GWAS) including 262 photoperiod-insensitive spring wheat accessions grown under full and limited irrigation treatments. Analysis of molecular variance showed that 4.1% of the total variation in the panel was partitioned among accessions originally developed under fall-sowing or spring-sowing conditions, 11.7% among breeding programs within sowing times and 84.2% among accessions within breeding programs. We first identified QTL for grain yield, yield components and plant water status that were significant in at least three environments in the GWAS, and then selected those that were also significant in at least two environments in a panel of eight biparental mapping populations. We identified and validated 14 QTL for grain yield, 15 for number of spikelets per spike, one for kernel number per spike, 11 for kernel weight and 9 for water status, which were not associated with differences in plant height or heading date. We detected significant correlations among traits and colocated QTL that were consistent with those correlations. Among those, grain yield and plant water status were negatively correlated in all environments, and six QTL for these traits were colocated or tightly linked (< 1 cM). QTL identified and validated in this study provide useful information for the improvement of fall-sown spring wheats under full and limited irrigation.

QTL Mapping of Kernel Number-Related Traits and Validation of One Major QTL for Ear Length in Maize.

PubMed

Huo, Dongao; Ning, Qiang; Shen, Xiaomeng; Liu, Lei; Zhang, Zuxin

2016-01-01

The kernel number is a grain yield component and an important maize breeding goal. Ear length, kernel number per row and ear row number are highly correlated with the kernel number per ear, which eventually determines the ear weight and grain yield. In this study, two sets of F2:3 families developed from two bi-parental crosses sharing one inbred line were used to identify quantitative trait loci (QTL) for four kernel number-related traits: ear length, kernel number per row, ear row number and ear weight. A total of 39 QTLs for the four traits were identified in the two populations. The phenotypic variance explained by a single QTL ranged from 0.4% to 29.5%. Additionally, 14 overlapping QTLs formed 5 QTL clusters on chromosomes 1, 4, 5, 7, and 10. Intriguingly, six QTLs for ear length and kernel number per row overlapped in a region on chromosome 1. This region was designated qEL1.10 and was validated as being simultaneously responsible for ear length, kernel number per row and ear weight in a near isogenic line-derived population, suggesting that qEL1.10 was a pleiotropic QTL with large effects. Furthermore, the performance of hybrids generated by crossing 6 elite inbred lines with two near isogenic lines at qEL1.10 showed the breeding value of qEL1.10 for the improvement of the kernel number and grain yield of maize hybrids. This study provides a basis for further fine mapping, molecular marker-aided breeding and functional studies of kernel number-related traits in maize.

Reciprocal Genetics: Identifying QTL for General and Specific Combining Abilities in Hybrids Between Multiparental Populations from Two Maize (Zea mays L.) Heterotic Groups.

PubMed

Giraud, Héloïse; Bauland, Cyril; Falque, Matthieu; Madur, Delphine; Combes, Valérie; Jamin, Philippe; Monteil, Cécile; Laborde, Jacques; Palaffre, Carine; Gaillard, Antoine; Blanchard, Philippe; Charcosset, Alain; Moreau, Laurence

2017-11-01

Several plant and animal species of agricultural importance are commercialized as hybrids to take advantage of the heterosis phenomenon. Understanding the genetic architecture of hybrid performances is therefore of key importance. We developed two multiparental maize ( Zea mays L.) populations, each corresponding to an important heterotic group (dent or flint) and comprised of six connected biparental segregating populations of inbred lines (802 and 822 lines for each group, respectively) issued from four founder lines. Instead of using "testers" to evaluate their hybrid values, segregating lines were crossed according to an incomplete factorial design to produce 951 dent-flint hybrids, evaluated for four biomass production traits in eight environments. QTL detection was carried out for the general-combining-ability (GCA) and specific-combining-ability (SCA) components of hybrid value, considering allelic effects transmitted from each founder line. In total, 42 QTL were detected across traits. We detected mostly QTL affecting GCA, 31% (41% for dry matter yield) of which also had mild effects on SCA. The small impact of dominant effects is consistent with the known differentiation between the dent and flint heterotic groups and the small percentage of hybrid variance due to SCA observed in our design (∼20% for the different traits). Furthermore, most (80%) of GCA QTL were segregating in only one of the two heterotic groups. Relative to tester-based designs, use of hybrids between two multiparental populations appears highly cost efficient to detect QTL in two heterotic groups simultaneously. This presents new prospects for selecting superior hybrid combinations with markers. Copyright © 2017 by the Genetics Society of America.

Validation of mega-environment universal and specific QTL associated with seed yield and agronomic traits in soybeans.

PubMed

Palomeque, Laura; Liu, Li-Jun; Li, Wenbin; Hedges, Bradley R; Cober, Elroy R; Smid, Mathew P; Lukens, Lewis; Rajcan, Istvan

2010-03-01

The value of quantitative trait loci (QTL) is dependent on the strength of association with the traits of interest, allelic diversity at the QTL and the effect of the genetic background on the expression of the QTL. A number of recent studies have identified QTL associated with traits of interest that appear to be independent of the environment but dependent on the genetic background in which they are found. Therefore, the objective of this study was to validate universal and/or mega-environment-specific seed yield QTL that have been previously reported in an independent recombinant inbred line (RIL) population derived from the cross between an elite Chinese and Canadian parent. The population was evaluated at two field environments in China and in five environments in Canada in 2005 and 2006. Of the seven markers linked to seed yield QTL reported by our group in a previous study, four were polymorphic between the two parents. No association between seed yield and QTL was observed. The result could imply that seed yield QTL were either not stable in this particular genetic background or harboured different alleles than the ones in the original mapping population. QTL(U) Satt162 was associated with several agronomic traits of which lodging was validated. Both the non-adapted and adapted parent contributed favourable alleles to the progeny. Therefore, plant introductions have been validated as a source of favourable alleles that could increase the genetic variability of the soybean germplasm pool and lead to further improvements in seed yield and other agronomic traits.

Genome-scan analysis for genetic mapping of quantitative trait loci underlying birth weight and onset of puberty in doe kids (Capra hircus).

PubMed

Esmailizadeh, A K

2014-12-01

The objective of this study was to locate quantitative trait loci (QTL) causing variation in birth weight and age of puberty of doe kids in a population of Rayini cashmere goats. Four hundred and thirty kids from five half-sib families were genotyped for 116 microsatellite markers located on the caprine autosomes. The traits recorded were birth weight of the male and female kids, body weight at puberty, average daily gain from birth to age of puberty and age at puberty of the doe kids. QTL analysis was conducted using the least squares interval mapping approach. Linkage analysis indicated significant QTL for birth weight on Capra hircus chromosomes (CHI) 4, 5, 6, 18 and 21. Five QTL located on CHI 5, 14 and 29 were associated with age at puberty. Across-family analysis revealed evidence for overlapping QTL affecting birth weight (78 cM), body weight at puberty (72 cM), average daily gain from birth to age of puberty (72 cM) and age at puberty (76 cM) on CHI 5 and overlapping QTL controlling body weight at puberty and age at puberty on CHI 14 at 18-19 cM. The proportion of the phenotypic variance explained by the detected QTL ranged between 7.9% and 14.4%. Confirming some of the previously reported results for birth weight and growth QTL in goats, this study identified more QTL for these traits and is the first report of QTL for onset of puberty in doe kids. © 2014 Stichting International Foundation for Animal Genetics.

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement.

PubMed

Sandhu, Maninder; Sureshkumar, V; Prakash, Chandra; Dixit, Rekha; Solanke, Amolkumar U; Sharma, Tilak Raj; Mohapatra, Trilochan; S V, Amitha Mithra

2017-09-30

Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. 'Physical position search' is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the 'common genes across varieties' search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201.

Replication of long-bone length QTL in the F9-F10 LG,SM advanced intercross.

PubMed

Norgard, Elizabeth A; Jarvis, Joseph P; Roseman, Charles C; Maxwell, Taylor J; Kenney-Hunt, Jane P; Samocha, Kaitlin E; Pletscher, L Susan; Wang, Bing; Fawcett, Gloria L; Leatherwood, Christopher J; Wolf, Jason B; Cheverud, James M

2009-04-01

Quantitative trait locus (QTL) mapping techniques are frequently used to identify genomic regions associated with variation in phenotypes of interest. However, the F(2) intercross and congenic strain populations usually employed have limited genetic resolution resulting in relatively large confidence intervals that greatly inhibit functional confirmation of statistical results. Here we use the increased resolution of the combined F(9) and F(10) generations (n = 1455) of the LG,SM advanced intercross to fine-map previously identified QTL associated with the lengths of the humerus, ulna, femur, and tibia. We detected 81 QTL affecting long-bone lengths. Of these, 49 were previously identified in the combined F(2)-F(3) population of this intercross, while 32 represent novel contributors to trait variance. Pleiotropy analysis suggests that most QTL affect three to four long bones or serially homologous limb segments. We also identified 72 epistatic interactions involving 38 QTL and 88 novel regions. This analysis shows that using later generations of an advanced intercross greatly facilitates fine-mapping of confidence intervals, resolving three F(2)-F(3) QTL into multiple linked loci and narrowing confidence intervals of other loci, as well as allowing identification of additional QTL. Further characterization of the biological bases of these QTL will help provide a better understanding of the genetics of small variations in long-bone length.

Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine

Treesearch

A. Groover; M. Devey; T. Fiddler; J. Lee; R. Megraw; T. Mitchel-Olds; B. Sherman; S. Vujcic; C. Williams; D. Neale

1994-01-01

We report the identification of quantitative trait loci (QTL) influencing wood specific gravity (WSG) in an outbred pedigree of loblolly pine (Pinus taeda L.) . QTL mapping in an outcrossing species is complicated by the presence of multiple alleles (>2) at QTL and marker loci. Multiple alleles at QTL allow the examination of interaction among...

A high-density genetic map and growth related QTL mapping in bighead carp (Hypophthalmichthys nobilis)

PubMed Central

Fu, Beide; Liu, Haiyang; Yu, Xiaomu; Tong, Jingou

2016-01-01

Growth related traits in fish are controlled by quantitative trait loci (QTL), but no QTL for growth have been detected in bighead carp (Hypophthalmichthys nobilis) due to the lack of high-density genetic map. In this study, an ultra-high density genetic map was constructed with 3,121 SNP markers by sequencing 117 individuals in a F1 family using 2b-RAD technology. The total length of the map was 2341.27 cM, with an average marker interval of 0.75 cM. A high level of genomic synteny between our map and zebrafish was detected. Based on this genetic map, one genome-wide significant and 37 suggestive QTL for five growth-related traits were identified in 6 linkage groups (i.e. LG3, LG11, LG15, LG18, LG19, LG22). The phenotypic variance explained (PVE) by these QTL varied from 15.4% to 38.2%. Marker within the significant QTL region was surrounded by CRP1 and CRP2, which played an important role in muscle cell division. These high-density map and QTL information provided a solid base for QTL fine mapping and comparative genomics in bighead carp. PMID:27345016

Quantitative trait loci affecting lactose and total solids on chromosome 6 in Brazilian Gir dairy cattle.

PubMed

Silva, A A; Azevedo, A L S; Gasparini, K; Verneque, R S; Peixoto, M G C D; Panetto, B R; Guimarães, S E F; Machado, M A

2011-10-31

Fourteen Brazilian Gir sire families with 657 daughters were analyzed for quantitative trait loci (QTL) on chromosome 6 affecting lactose and total solids. Cows and sires were genotyped with 27 microsatellites with a mean spacing between markers of 4.9 cM. We used a 1% chromosome-wide threshold for QTL qualification. A QTL for lactose yield was found close to marker MNB66 in three families. A QTL for total solid yield was identified close to marker BMS2508 in three families. A QTL for lactose percentage, close to marker DIK1182, was identified in two families. A QTL for total solid percentage, close to marker MNB208, was identified in four families. These QTLs could be used for selection of animals in dairy production systems.

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

PubMed Central

Daware, Anurag; Das, Sweta; Srivastava, Rishi; Badoni, Saurabh; Singh, Ashok K.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

2016-01-01

Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16–74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7–8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice. PMID:27833617

Detection of QTL controlling metabolism, meat quality, and liver quality traits of the overfed interspecific hybrid mule duck.

PubMed

Kileh-Wais, M; Elsen, J M; Vignal, A; Feves, K; Vignoles, F; Fernandez, X; Manse, H; Davail, S; André, J M; Bastianelli, D; Bonnal, L; Filangi, O; Baéza, E; Guéméné, D; Genêt, C; Bernadet, M D; Dubos, F; Marie-Etancelin, C

2013-02-01

The mule duck, an interspecific hybrid obtained by crossing common duck (Anas platyrhynchos) females with Muscovy (Cairina moschata) drakes, is widely used for fatty liver production. The purpose of the present study was to detect and map single and pleiotropic QTL that segregate in the common duck species, and influence the expression of traits in their overfed mule duck offspring. To this end, we generated a common duck backcross (BC) population by crossing Kaiya and heavy Pekin experimental lines, which differ notably in regard to the BW and overfeeding ability of their mule progeny. The BC females were mated to Muscovy drakes and, on average, 4 male mule ducks hatched per BC female (1600 in total) and were measured for growth, metabolism during growth and the overfeeding period, overfeeding ability, and the quality of their breast meat and fatty liver. The phenotypic value of BC females was estimated for each trait by assigning to each female the mean value of the phenotypes of her offspring. Estimations allowed for variance, which depended on the number of male offspring per BC and the heritability of the trait considered. The genetic map used for QTL detection consisted of 91 microsatellite markers aggregated into 16 linkage groups (LG) covering a total of 778 cM. Twenty-two QTL were found to be significant at the 1% chromosome-wide threshold level using the single-trait detection option of the QTLMap software. Most of the QTL detected were related to the quality of breast meat and fatty liver: QTL for meat pH 20 min post mortem were mapped to LG4 (at the 1% genome-wide significance level), and QTL for meat lipid content and cooking losses were mapped to LG2a. The QTL related to fatty liver weight and liver protein and lipid content were for the most part detected on LG2c and LG9. Multitrait analysis highlighted the pleiotropic effects of QTL in these chromosome regions. Apart from the strong QTL for plasma triglyceride content at the end of the overfeeding period mapped to chromosome Z using single-trait analysis, all metabolic trait QTL were detected with the multitrait approach: the QTL mapped to LG14 and LG21 affected the plasma cholesterol and triglyceride contents, whereas the QTL mapped to LG2a seemed to impact glycemia and the basal plasma corticosterone content. A greater density genetic map will be needed to further fine map the QTL.

Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.).

PubMed

Ma, Yu; Coyne, Clarice J; Grusak, Michael A; Mazourek, Michael; Cheng, Peng; Main, Dorrie; McGee, Rebecca J

2017-02-13

Marker-assisted breeding is now routinely used in major crops to facilitate more efficient cultivar improvement. This has been significantly enabled by the use of next-generation sequencing technology to identify loci and markers associated with traits of interest. While rich in a range of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest domesticated crops in the world, remains behind many other crops in the availability of genomic and genetic resources. To further improve mineral nutrient levels in pea seeds requires the development of genome-wide tools. The objectives of this research were to develop these tools by: identifying genome-wide single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS); constructing a high-density linkage map and comparative maps with other legumes, and identifying quantitative trait loci (QTL) for levels of boron, calcium, iron, potassium, magnesium, manganese, molybdenum, phosphorous, sulfur, and zinc in the seed, as well as for seed weight. In this study, 1609 high quality SNPs were found to be polymorphic between 'Kiflica' and 'Aragorn', two parents of an F 6 -derived recombinant inbred line (RIL) population. Mapping 1683 markers including 75 previously published markers and 1608 SNPs developed from the present study generated a linkage map of size 1310.1 cM. Comparative mapping with other legumes demonstrated that the highest level of synteny was observed between pea and the genome of Medicago truncatula. QTL analysis of the RIL population across two locations revealed at least one QTL for each of the mineral nutrient traits. In total, 46 seed mineral concentration QTLs, 37 seed mineral content QTLs, and 6 seed weight QTLs were discovered. The QTLs explained from 2.4% to 43.3% of the phenotypic variance. The genome-wide SNPs and the genetic linkage map developed in this study permitted QTL identification for pea seed mineral nutrients that will serve as important resources to enable marker-assisted selection (MAS) for nutritional quality traits in pea breeding programs.

A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality

PubMed Central

2014-01-01

Background Numerous quantitative trait loci (QTL) have been detected in pigs over the past 20 years using microsatellite markers. However, due to the low density of these markers, the accuracy of QTL location has generally been poor. Since 2009, the dense genome coverage provided by the Illumina PorcineSNP60 BeadChip has made it possible to more accurately map QTL using genome-wide association studies (GWAS). Our objective was to perform high-density GWAS in order to identify genomic regions and corresponding haplotypes associated with production traits in a French Large White population of pigs. Methods Animals (385 Large White pigs from 106 sires) were genotyped using the PorcineSNP60 BeadChip and evaluated for 19 traits related to feed intake, growth, carcass composition and meat quality. Of the 64 432 SNPs on the chip, 44 412 were used for GWAS with an animal mixed model that included a regression coefficient for the tested SNPs and a genomic kinship matrix. SNP haplotype effects in QTL regions were then tested for association with phenotypes following phase reconstruction based on the Sscrofa10.2 pig genome assembly. Results Twenty-three QTL regions were identified on autosomes and their effects ranged from 0.25 to 0.75 phenotypic standard deviation units for feed intake and feed efficiency (four QTL), carcass (12 QTL) and meat quality traits (seven QTL). The 10 most significant QTL regions had effects on carcass (chromosomes 7, 10, 16, 17 and 18) and meat quality traits (two regions on chromosome 1 and one region on chromosomes 8, 9 and 13). Thirteen of the 23 QTL regions had not been previously described. A haplotype block of 183 kb on chromosome 1 (six SNPs) was identified and displayed three distinct haplotypes with significant (0.0001 < P < 0.03) associations with all evaluated meat quality traits. Conclusions GWAS analyses with the PorcineSNP60 BeadChip enabled the detection of 23 QTL regions that affect feed consumption, carcass and meat quality traits in a LW population, of which 13 were novel QTL. The proportionally larger number of QTL found for meat quality traits suggests a specific opportunity for improving these traits in the pig by genomic selection. PMID:24528607

Stripe rust and leaf rust resistance QTL mapping, epistatic interactions, and co-localization with stem rust resistance loci in spring wheat evaluated over three continents.

PubMed

Singh, A; Knox, R E; DePauw, R M; Singh, A K; Cuthbert, R D; Campbell, H L; Shorter, S; Bhavani, S

2014-11-01

In wheat, advantageous gene-rich or pleiotropic regions for stripe, leaf, and stem rust and epistatic interactions between rust resistance loci should be accounted for in plant breeding strategies. Leaf rust (Puccinia triticina Eriks.) and stripe rust (Puccinia striiformis f. tritici Eriks) contribute to major production losses in many regions worldwide. The objectives of this research were to identify and study epistatic interactions of quantitative trait loci (QTL) for stripe and leaf rust resistance in a doubled haploid (DH) population derived from the cross of Canadian wheat cultivars, AC Cadillac and Carberry. The relationship of leaf and stripe rust resistance QTL that co-located with stem rust resistance QTL previously mapped in this population was also investigated. The Carberry/AC Cadillac population was genotyped with DArT(®) and simple sequence repeat markers. The parents and population were phenotyped for stripe rust severity and infection response in field rust nurseries in Kenya (Njoro), Canada (Swift Current), and New Zealand (Lincoln); and for leaf rust severity and infection response in field nurseries in Canada (Swift Current) and New Zealand (Lincoln). AC Cadillac was a source of stripe rust resistance QTL on chromosomes 2A, 2B, 3A, 3B, 5B, and 7B; and Carberry was a source of resistance on chromosomes 2B, 4B, and 7A. AC Cadillac contributed QTL for resistance to leaf rust on chromosome 2A and Carberry contributed QTL on chromosomes 2B and 4B. Stripe rust resistance QTL co-localized with previously reported stem rust resistance QTL on 2B, 3B, and 7B, while leaf rust resistance QTL co-localized with 4B stem rust resistance QTL. Several epistatic interactions were identified both for stripe and leaf rust resistance QTL. We have identified useful combinations of genetic loci with main and epistatic effects. Multiple disease resistance regions identified on chromosomes 2A, 2B, 3B, 4B, 5B, and 7B are prime candidates for further investigation and validation of their broad resistance.

Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans.

PubMed

Snoek, Basten L; Sterken, Mark G; Bevers, Roel P J; Volkers, Rita J M; Van't Hof, Arjen; Brenchley, Rachel; Riksen, Joost A G; Cossins, Andrew; Kammenga, Jan E

2017-06-29

Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population. We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40-57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL. These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL.

Molecular mapping and improvement of leaf rust resistance in wheat breeding lines.

PubMed

Tsilo, Toi J; Kolmer, James A; Anderson, James A

2014-08-01

Leaf rust, caused by Puccinia triticina, is the most common and widespread disease of wheat (Triticum aestivum) worldwide. Deployment of host-plant resistance is one of the strategies to reduce losses due to leaf rust disease. The objective of this study was to map genes for adult-plant resistance to leaf rust in a recombinant inbred line (RIL) population originating from MN98550-5/MN99394-1. The mapping population of 139 RILs and five checks were evaluated in 2005, 2009, and 2010 in five environments. Natural infection occurred in the 2005 trials and trials in 2009 and 2010 were inoculated with leaf rust. Four quantitative trait loci (QTL) on chromosomes 2BS, 2DS, 7AL, and 7DS were detected. The QTL on 2BS explained up to 33.6% of the phenotypic variation in leaf rust response, whereas the QTL on 2DS, 7AL, and 7DS explained up to 15.7, 8.1, and 34.2%, respectively. Seedling infection type tests conducted with P. triticina races BBBD and SBDG confirmed that the QTL on 2BS and 2DS were Lr16 and Lr2a, respectively, and these genes were expressed in the seedling and field plot tests. The Lr2a gene mapped at the same location as Sr6. The QTL on 7DS was Lr34. The QTL on 7AL is a new QTL for leaf rust resistance. The joint effects of all four QTL explained 74% of the total phenotypic variation in leaf rust severity. Analysis of different combinations of QTL showed that the RILs containing all four or three of the QTL had the lowest average leaf rust severity in all five environments. Deployment of these QTL in combination or with other effective genes will lead to successful control of leaf rust.

Association mapping of seed quality traits using the Canadian flax (Linum usitatissimum L.) core collection.

PubMed

Soto-Cerda, Braulio J; Duguid, Scott; Booker, Helen; Rowland, Gordon; Diederichsen, Axel; Cloutier, Sylvie

2014-04-01

The identification of stable QTL for seed quality traits by association mapping of a diverse panel of linseed accessions establishes the foundation for assisted breeding and future fine mapping in linseed. Linseed oil is valued for its food and non-food applications. Modifying its oil content and fatty acid (FA) profiles to meet market needs in a timely manner requires clear understanding of their quantitative trait loci (QTL) architectures, which have received little attention to date. Association mapping is an efficient approach to identify QTL in germplasm collections. In this study, we explored the quantitative nature of seed quality traits including oil content (OIL), palmitic acid, stearic acid, oleic acid, linoleic acid (LIO) linolenic acid (LIN) and iodine value in a flax core collection of 390 accessions assayed with 460 microsatellite markers. The core collection was grown in a modified augmented design at two locations over 3 years and phenotypic data for all seven traits were obtained from all six environments. Significant phenotypic diversity and moderate to high heritability for each trait (0.73-0.99) were observed. Most of the candidate QTL were stable as revealed by multivariate analyses. Nine candidate QTL were identified, varying from one for OIL to three for LIO and LIN. Candidate QTL for LIO and LIN co-localized with QTL previously identified in bi-parental populations and some mapped nearby genes known to be involved in the FA biosynthesis pathway. Fifty-eight percent of the QTL alleles were absent (private) in the Canadian cultivars suggesting that the core collection possesses QTL alleles potentially useful to improve seed quality traits. The candidate QTL identified herein will establish the foundation for future marker-assisted breeding in linseed.

Boron toxicity in rice (Oryza sativa L.). I. Quantitative trait locus (QTL) analysis of tolerance to boron toxicity.

PubMed

Ochiai, K; Uemura, S; Shimizu, A; Okumoto, Y; Matoh, T

2008-06-01

Boron toxicity tolerance of rice plants was studied. Modern japonica subspecies such as Koshihikari, Nipponbare, and Sasanishiki were tolerant, whereas indica subspecies such as Kasalath and IR36 were intolerant to excessive application of boron (B), even though their shoot B contents under B toxicity were not significantly different. Recombinant inbred lines (RILs) of japonica Nekken-1 and indica IR36 were used for quantitative trait locus (QTL) analysis to identify the gene responsible for B toxicity tolerance. A major QTL that could explain 45% of the phenotypic variation was detected in chromosome 4. The QTL was confirmed using a population derived from a recombinant inbred line which is heterogenic at the QTL region. The QTL was also confirmed in other chromosome segment substitution lines (CSSLs).

A functional-structural model of rice linking quantitative genetic information with morphological development and physiological processes.

PubMed

Xu, Lifeng; Henke, Michael; Zhu, Jun; Kurth, Winfried; Buck-Sorlin, Gerhard

2011-04-01

Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype-phenotype model, we present here a three-dimensional functional-structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs. The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data. Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered. We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed.

A functional–structural model of rice linking quantitative genetic information with morphological development and physiological processes

PubMed Central

Xu, Lifeng; Henke, Michael; Zhu, Jun; Kurth, Winfried; Buck-Sorlin, Gerhard

2011-01-01

Background and Aims Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype–phenotype model, we present here a three-dimensional functional–structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs. Methods The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data. Key Results Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered. Conclusions We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed. PMID:21247905

Genetic Mapping of Quantitative Trait Loci Controlling Growth and Wood Quality Traits in Eucalyptus Grandis Using a Maternal Half-Sib Family and Rapd Markers

PubMed Central

Grattapaglia, D.; Bertolucci, FLG.; Penchel, R.; Sederoff, R. R.

1996-01-01

Quantitative trait loci (QTL) mapping of forest productivity traits was performed using an open pollinated half-sib family of Eucalyptus grandis. For volume growth, a sequential QTL mapping approach was applied using bulk segregant analysis (BSA), selective genotyping (SG) and cosegregation analysis (CSA). Despite the low heritability of this trait and the heterogeneous genetic background employed for mapping. BSA detected one putative QTL and SG two out of the three later found by CSA. The three putative QTL for volume growth were found to control 13.7% of the phenotypic variation, corresponding to an estimated 43.7% of the genetic variation. For wood specific gravity five QTL were identified controlling 24.7% of the phenotypic variation corresponding to 49% of the genetic variation. Overlapping QTL for CBH, WSG and percentage dry weight of bark were observed. A significant case of digenic epistasis was found, involving unlinked QTL for volume. Our results demonstrate the applicability of the within half-sib design for QTL mapping in forest trees and indicate the existence of major genes involved in the expression of economically important traits related to forest productivity in Eucalyptus grandis. These findings have important implications for marker-assisted tree breeding. PMID:8913761

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: IV. Growth performance.

PubMed

Nassar, M K; Goraga, Z S; Brockmann, G A

2015-08-01

Reciprocal crosses between the inbred lines New Hampshire (NHI) and White Leghorn (WL77) comprising 579 F2 individuals were used to map QTL for body weight and composition. Here, we examine the growth performance until 20 weeks of age. Linkage analysis provided evidence for highly significant QTL on GGA1, 2, 4, 10 and 27 which had specific effects on early or late growth. The highest QTL effects, accounting for 4.6-25.6% of the phenotypic F2 variance, were found on the distal region of GGA4 between 142 and 170 cM (F ≥ 13.68). The NHI QTL allele increased body mass by 141.86 g at 20 weeks. Using body weight as a covariate in the analysis of body composition traits provided evidence for genes in the GGA4 QTL region affecting fat mass independently of body mass. The QTL effect size differed between sexes and depended on the direction of cross. TBC1D1, CCKAR and PPARGC1A are functional candidate genes in the QTL peak region. Our study confirmed the importance of the distal GGA4 region for chicken growth performance. The strong effect of the GGA4 QTL makes fine mapping and gene discovery feasible. © 2015 Stichting International Foundation for Animal Genetics.

The genetic basis of postzygotic reproductive isolation between Drosophila santomea and D. yakuba due to hybrid male sterility.

PubMed

Moehring, Amanda J; Llopart, Ana; Elwyn, Susannah; Coyne, Jerry A; Mackay, Trudy F C

2006-05-01

A major unresolved challenge of evolutionary biology is to determine the nature of the allelic variants of "speciation genes": those alleles whose interaction produces inviable or infertile interspecific hybrids but does not reduce fitness in pure species. Here we map quantitative trait loci (QTL) affecting fertility of male hybrids between D. yakuba and its recently discovered sibling species, D. santomea. We mapped three to four X chromosome QTL and two autosomal QTL with large effects on the reduced fertility of D. yakuba and D. santomea backcross males. We observed epistasis between the X-linked QTL and also between the X and autosomal QTL. The X chromosome had a disproportionately large effect on hybrid sterility in both reciprocal backcross hybrids. However, the genetics of hybrid sterility differ between D. yakuba and D. santomea backcross males, both in terms of the magnitude of main effects and in the epistatic interactions. The QTL affecting hybrid fertility did not colocalize with QTL affecting sexual isolation in this species pair, but did colocalize with QTL affecting the marked difference in pigmentation between D. yakuba and D. santomea. These results provide the basis for future high-resolution mapping and ultimately, molecular cloning, of the interacting genes that contribute to hybrid sterility.

Genetic architecture of conspecific sperm precedence in Allonemobius fasciatus and A. socius.

PubMed

Britch, Seth C; Swartout, Emma J; Hampton, Daniel D; Draney, Michael L; Chu, Jiming; Marshall, Jeremy L; Howard, Daniel J

2007-06-01

The evolution of barriers to gene exchange is centrally important to speciation. We used the crickets Allonemobius fasciatus and A. socius to investigate the genetic architecture of conspecific sperm precedence (CSP), a postinsemination prezygotic reproductive barrier. With amplified fragment-length polymorphism (AFLP) markers and controlled crosses we constructed linkage maps and estimated positions of QTL associated with CSP. The majority of QTL have low to moderate effects, although a few QTL exist in A. socius with large effects, and the numbers of QTL are comparable to numbers of genes accounting for species differences in other studies. The QTL are spread across many unlinked markers, yet QTL placed with linked markers are on a small number of linkage groups that could reflect the role of the large Allonemobius sex chromosome in prezygotic isolation. Although many QTL had positive effects on conspecific sperm utilization several QTL also exerted negative effects, which could be explained by intraspecific sexual conflict, sperm competition, or epistasis of introgressed genes on novel backgrounds. One unexpected outcome was that A. socius CSP alleles have a stronger effect than those from A. fasciatus in hybrid females, causing hybrids to behave like A. socius with regard to sperm utilization. Implications of this asymmetry in the Allonemobius hybrid zone are discussed.

Linkage disequilibrium fine mapping of quantitative trait loci: A simulation study

PubMed Central

Abdallah, Jihad M; Goffinet, Bruno; Cierco-Ayrolles, Christine; Pérez-Enciso, Miguel

2003-01-01

Recently, the use of linkage disequilibrium (LD) to locate genes which affect quantitative traits (QTL) has received an increasing interest, but the plausibility of fine mapping using linkage disequilibrium techniques for QTL has not been well studied. The main objectives of this work were to (1) measure the extent and pattern of LD between a putative QTL and nearby markers in finite populations and (2) investigate the usefulness of LD in fine mapping QTL in simulated populations using a dense map of multiallelic or biallelic marker loci. The test of association between a marker and QTL and the power of the test were calculated based on single-marker regression analysis. The results show the presence of substantial linkage disequilibrium with closely linked marker loci after 100 to 200 generations of random mating. Although the power to test the association with a frequent QTL of large effect was satisfactory, the power was low for the QTL with a small effect and/or low frequency. More powerful, multi-locus methods may be required to map low frequent QTL with small genetic effects, as well as combining both linkage and linkage disequilibrium information. The results also showed that multiallelic markers are more useful than biallelic markers to detect linkage disequilibrium and association at an equal distance. PMID:12939203

Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers.

PubMed

Luo, Meijie; Zhao, Yanxin; Zhang, Ruyang; Xing, Jinfeng; Duan, Minxiao; Li, Jingna; Wang, Naishun; Wang, Wenguang; Zhang, Shasha; Chen, Zhihui; Zhang, Huasheng; Shi, Zi; Song, Wei; Zhao, Jiuran

2017-08-15

Salt stress significantly restricts plant growth and production. Maize is an important food and economic crop but is also a salt sensitive crop. Identification of the genetic architecture controlling salt tolerance facilitates breeders to select salt tolerant lines. However, the critical quantitative trait loci (QTLs) responsible for the salt tolerance of field-grown maize plants are still unknown. To map the main genetic factors contributing to salt tolerance in mature maize, a double haploid population (240 individuals) and 1317 single nucleotide polymorphism (SNP) markers were employed to produce a genetic linkage map covering 1462.05 cM. Plant height of mature maize cultivated in the saline field (SPH) and plant height-based salt tolerance index (ratio of plant height between saline and control fields, PHI) were used to evaluate salt tolerance of mature maize plants. A major QTL for SPH was detected on Chromosome 1 with the LOD score of 22.4, which explained 31.2% of the phenotypic variation. In addition, the major QTL conditioning PHI was also mapped at the same position on Chromosome 1, and two candidate genes involving in ion homeostasis were identified within the confidence interval of this QTL. The detection of the major QTL in adult maize plant establishes the basis for the map-based cloning of genes associated with salt tolerance and provides a potential target for marker assisted selection in developing maize varieties with salt tolerance.

A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues.

PubMed

Ying, Dingge; Li, Mulin Jun; Sham, Pak Chung; Li, Miaoxin

2018-04-26

Recently many studies showed single nucleotide polymorphisms (SNPs) affect gene expression and contribute to development of complex traits/diseases in a tissue context-dependent manner. However, little is known about haplotype's influence on gene expression and complex traits, which reflects the interaction effect between SNPs. In the present study, we firstly proposed a regulatory region guided eQTL haplotype association analysis approach, and then systematically investigate the expression quantitative trait loci (eQTL) haplotypes in 20 different tissues by the approach. The approach has a powerful design of reducing computational burden by the utilization of regulatory predictions for candidate SNP selection and multiple testing corrections on non-independent haplotypes. The application results in multiple tissues showed that haplotype-based eQTLs not only increased the number of eQTL genes in a tissue specific manner, but were also enriched in loci that associated with complex traits in a tissue-matched manner. In addition, we found that tag SNPs of eQTL haplotypes from whole blood were selectively enriched in certain combination of regulatory elements (e.g. promoters and enhancers) according to predicted chromatin states. In summary, this eQTL haplotype detection approach, together with the application results, shed insights into synergistic effect of sequence variants on gene expression and their susceptibility to complex diseases. The executable application "eHaplo" is implemented in Java and is publicly available at http://grass.cgs.hku.hk/limx/ehaplo/. jonsonfox@gmail.com, limiaoxin@mail.sysu.edu.cn. Supplementary data are available at Bioinformatics online.

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

PubMed Central

Kujur, Alice; Upadhyaya, Hari D.; Shree, Tanima; Bajaj, Deepak; Das, Shouvik; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement. PMID:25942004

A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis

PubMed Central

Qiu, Gao-Feng; Xiong, Liang-Wei; Han, Zhi-Ke; Liu, Zhi-Qiang; Feng, Jian-Bin; Wu, Xu-Gan; Yan, Yin-Long; Shen, Hong; Huang, Long; Chen, Li

2017-01-01

The Chinese mitten crab Eriocheir sinensis is the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9 cM with an average marker interval of 0.81 cM. QTL mapping localized three significant growth-related QTL to a 1.2 cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for the E. sinensis genome project and selective breeding programs. PMID:28045132

HpQTL: a geometric morphometric platform to compute the genetic architecture of heterophylly.

PubMed

Sun, Lidan; Wang, Jing; Zhu, Xuli; Jiang, Libo; Gosik, Kirk; Sang, Mengmeng; Sun, Fengsuo; Cheng, Tangren; Zhang, Qixiang; Wu, Rongling

2017-02-15

Heterophylly, i.e. morphological changes in leaves along the axis of an individual plant, is regarded as a strategy used by plants to cope with environmental change. However, little is known of the extent to which heterophylly is controlled by genes and how each underlying gene exerts its effect on heterophyllous variation. We described a geometric morphometric model that can quantify heterophylly in plants and further constructed an R-based computing platform by integrating this model into a genetic mapping and association setting. The platform, named HpQTL, allows specific quantitative trait loci mediating heterophyllous variation to be mapped throughout the genome. The statistical properties of HpQTL were examined and validated via computer simulation. Its biological relevance was demonstrated by results from a real data analysis of heterophylly in a wood plant, mei (Prunus mume). HpQTL provides a powerful tool to analyze heterophylly and its underlying genetic architecture in a quantitative manner. It also contributes a new approach for genome-wide association studies aimed to dissect the programmed regulation of plant development and evolution. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle

PubMed Central

Coppieters, Wouter; Mes, Ted HM; Druet, Tom; Farnir, Frédéric; Tamma, Nico; Schrooten, Chris; Cornelissen, Albert WCA; Georges, Michel; Ploeger, Harm W

2009-01-01

Background Parasitic gastroenteritis caused by nematodes is only second to mastitis in terms of health costs to dairy farmers in developed countries. Sustainable control strategies complementing anthelmintics are desired, including selective breeding for enhanced resistance. Results and Conclusion To quantify and characterize the genetic contribution to variation in resistance to gastro-intestinal parasites, we measured the heritability of faecal egg and larval counts in the Dutch Holstein-Friesian dairy cattle population. The heritability of faecal egg counts ranged from 7 to 21% and was generally higher than for larval counts. We performed a whole genome scan in 12 paternal half-daughter groups for a total of 768 cows, corresponding to the ~10% most and least infected daughters within each family (selective genotyping). Two genome-wide significant QTL were identified in an across-family analysis, respectively on chromosomes 9 and 19, coinciding with previous findings in orthologous chromosomal regions in sheep. We identified six more suggestive QTL by within-family analysis. An additional 73 informative SNPs were genotyped on chromosome 19 and the ensuing high density map used in a variance component approach to simultaneously exploit linkage and linkage disequilibrium in an initial inconclusive attempt to refine the QTL map position. PMID:19254385

Mapping QTL for Sex and Growth Traits in Salt-Tolerant Tilapia (Oreochromis spp. X O. mossambicus).

PubMed

Lin, Grace; Chua, Elaine; Orban, Laszlo; Yue, Gen Hua

2016-01-01

In aquaculture, growth and sex are economically important traits. To accelerate genetic improvement in increasing growth in salt-tolerant tilapia, we conducted QTL mapping for growth traits and sex with an F2 family, including 522 offspring and two parents. We used 144 polymorphic microsatellites evenly covering the genome of tilapia to genotype the family. QTL analyses were carried out using interval mapping for all individuals, males and females in the family, respectively. Using all individuals, three suggestive QTL for body weight, body length and body thickness respectively were detected in LG20, LG22 and LG12 and explained 2.4% to 3.1% of phenotypic variance (PV). When considering only males, five QTL for body weight were detected on five LGs, and explained 4.1 to 6.3% of PV. Using only females from the F2 family, three QTL for body weight were detected on LG1, LG6 and LG8, and explained 7.9-14.3% of PV. The QTL for body weight in males and females were located in different LGs, suggesting that in salt-tolerant tilapia, different set of genes 'switches' control the growth in males and females. QTL for sex were mapped on LG1 and LG22, indicating multigene sex determination in the salt-tolerant tilapia. This study provides new insights on the locations and effects of QTL for growth traits and sex, and sets the foundation for fine mapping for future marker-assisted selection for growth and sex in salt-tolerant tilapia aquaculture.

Mapping QTL for Sex and Growth Traits in Salt-Tolerant Tilapia (Oreochromis spp. X O. mossambicus)

PubMed Central

Lin, Grace; Chua, Elaine; Orban, Laszlo; Yue, Gen Hua

2016-01-01

In aquaculture, growth and sex are economically important traits. To accelerate genetic improvement in increasing growth in salt-tolerant tilapia, we conducted QTL mapping for growth traits and sex with an F2 family, including 522 offspring and two parents. We used 144 polymorphic microsatellites evenly covering the genome of tilapia to genotype the family. QTL analyses were carried out using interval mapping for all individuals, males and females in the family, respectively. Using all individuals, three suggestive QTL for body weight, body length and body thickness respectively were detected in LG20, LG22 and LG12 and explained 2.4% to 3.1% of phenotypic variance (PV). When considering only males, five QTL for body weight were detected on five LGs, and explained 4.1 to 6.3% of PV. Using only females from the F2 family, three QTL for body weight were detected on LG1, LG6 and LG8, and explained 7.9–14.3% of PV. The QTL for body weight in males and females were located in different LGs, suggesting that in salt-tolerant tilapia, different set of genes ‘switches’ control the growth in males and females. QTL for sex were mapped on LG1 and LG22, indicating multigene sex determination in the salt-tolerant tilapia. This study provides new insights on the locations and effects of QTL for growth traits and sex, and sets the foundation for fine mapping for future marker-assisted selection for growth and sex in salt-tolerant tilapia aquaculture. PMID:27870905

Genome-Wide Association Mapping Reveals Novel QTL for Seedling Leaf Rust Resistance in a Worldwide Collection of Winter Wheat.

PubMed

Li, Genqiao; Xu, Xiangyang; Bai, Guihua; Carver, Brett F; Hunger, Robert; Bonman, J Michael; Kolmer, James; Dong, Hongxu

2016-11-01

Leaf rust of wheat ( L.) is a major disease that causes significant yield losses worldwide. The short-lived nature of leaf rust resistance () genes necessitates a continuous search for novel sources of resistance. We performed a genome-wide association study (GWAS) on a panel of 1596 wheat accessions. The panel was evaluated for leaf rust reaction by testing with a bulk of Eriks. () isolates collected from multiple fields of Oklahoma in 2013 and two predominant races in the fields of Oklahoma in 2015. The panel was genotyped with a set of 5011 single-nucleotide polymorphism (SNP) markers. A total of 14 quantitative trait loci (QTL) for leaf rust resistance were identified at a false discovery rate (FDR) of 0.01 using the mixed linear model (MLM). Of these, eight QTL reside in the vicinity of known genes or QTL, and more studies are needed to determine their relationship with known loci. is a new QTL to bread wheat but is close to a locus previously identified in durum wheat [ L. subsp. (Desf.) Husn.]. The other five QTL, including , , , , and , are likely novel loci for leaf rust resistance. The uneven distribution of the 14 QTL in the six subpopulations of the panel suggests that wheat breeders can enhance leaf rust resistance by selectively introgressing some of these QTL into their breeding materials. In addition, another 31 QTL were significantly associated with leaf rust resistance at a FDR of 0.05. Copyright © 2016 Crop Science Society of America.

Genetic mapping of common bunt resistance and plant height QTL in wheat.

PubMed

Singh, Arti; Knox, Ron E; DePauw, R M; Singh, A K; Cuthbert, R D; Kumar, S; Campbell, H L

2016-02-01

Breeding for field resistance to common bunt in wheat will need to account for multiple genes and epistatic and QTL by environment interactions. Loci associated with quantitative resistance to common bunt are co-localized with other beneficial traits including plant height and rust resistance. Common bunt, also known as stinking smut, is caused by seed borne fungi Tilletia tritici (Bjerk.) Wint. [syn. Tilletia caries (DC.) Tul.] and Tilletia laevis Kühn [syn. Tilletia foetida (Wallr.) Liro.]. Common bunt is known to cause grain yield and quality losses in wheat due to bunt ball formation and infestation of the grain. The objectives of this research were to identify and map quantitative trait loci (QTL) for common bunt resistance, to study the epistatic interactions between the identified QTL, and investigate the co-localization of bunt resistance with plant height. A population of 261 doubled haploid lines from the cross Carberry/AC Cadillac and checks were genotyped with polymorphic genome wide microsatellite and DArT(®) markers. The lines were grown in 2011, 2012, and 2013 in separate nurseries for common bunt incidence and height evaluation. AC Cadillac contributed a QTL (QCbt.spa-6D) for common bunt resistance on chromosome 6D at markers XwPt-1695, XwPt-672044, and XwPt-5114. Carberry contributed QTL for bunt resistance on chromosomes 1B (QCbt.spa-1B at XwPt743523) 4B (QCbt.spa-4B at XwPt-744434-Xwmc617), 4D (QCbt.spa-4D at XwPt-9747), 5B (QCbt.spa-5B at XtPt-3719) and 7D (QCbt.spa-7D at Xwmc273). Significant epistatic interactions were identified for percent bunt incidence between QCbt.spa-1B × QCbt.spa-4B and QCbt.spa-1B × QCbt.spa-6D, and QTL by environment interaction between QCbt.spa-1B × QCbt.spa-6D. Plant height QTL were found on chromosomes 4B (QPh.spa-4B) and 6D (QPh.spa-6D) that co-located with bunt resistance QTL. The identification of previously unreported common bunt resistance QTL (on chromosomes 4B, 4D and 7D), and new understanding of QTL × QTL interactions will facilitate marker-assisted breeding for common bunt resistance.

eQTL Mapping Using RNA-seq Data

PubMed Central

Hu, Yijuan

2012-01-01

As RNA-seq is replacing gene expression microarrays to assess genome-wide transcription abundance, gene expression Quantitative Trait Locus (eQTL) studies using RNA-seq have emerged. RNA-seq delivers two novel features that are important for eQTL studies. First, it provides information on allele-specific expression (ASE), which is not available from gene expression microarrays. Second, it generates unprecedentedly rich data to study RNA-isoform expression. In this paper, we review current methods for eQTL mapping using ASE and discuss some future directions. We also review existing works that use RNA-seq data to study RNA-isoform expression and we discuss the gaps between these works and isoform-specific eQTL mapping. PMID:23667399

New quantitative trait loci in wheat for flag leaf resistance to Stagonospora nodorum blotch.

PubMed

Francki, M G; Shankar, M; Walker, E; Loughman, R; Golzar, H; Ohm, H

2011-11-01

Stagonospora nodorum blotch (SNB) is a significant disease in some wheat-growing regions of the world. Resistance in wheat to Stagonospora nodorum is complex, whereby genes for seedling, flag leaf, and glume resistance are independent. The aims of this study were to identify alternative genes for flag leaf resistance, to compare and contrast with known quantitative trait loci (QTL) for SNB resistance, and to determine the potential role of host-specific toxins for SNB QTL. Novel QTL for flag leaf resistance were identified on chromosome 2AS inherited from winter wheat parent 'P92201D5' and chromosome 1BS from spring wheat parent 'EGA Blanco'. The chromosomal map position of markers associated with QTL on 1BS and 2AS indicated that they were unlikely to be associated with known host-toxin insensitivity loci. A QTL on chromosome 5BL inherited from EGA Blanco had highly significant association with markers fcp001 and fcp620 based on disease evaluation in 2007 and, therefore, is likely to be associated with Tsn1-ToxA insensitivity for flag leaf resistance. However, fcp001 and fcp620 were not associated with a QTL detected based on disease evaluation in 2008, indicating two linked QTL for flag leaf resistance with multiple genes residing on 5BL. This study identified novel QTL and their effects in controlling flag leaf SNB resistance.

QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems

PubMed Central

Zhang, Ying; Thomas, Catherine L.; Xiang, Jinxia; Long, Yan; Wang, Xiaohua; Zou, Jun; Luo, Ziliang; Ding, Guangda; Cai, Hongmei; Graham, Neil S.; Hammond, John P.; King, Graham J.; White, Philip J.; Xu, Fangsen; Broadley, Martin R.; Shi, Lei; Meng, Jinling

2016-01-01

A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and ‘normal’ phosphate (Pi) supply using a ‘pouch and wick’ system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica. PMID:27624881

Two quantitative trait loci affect ACE activities in Mexican-Americans.

PubMed

Kammerer, Candace M; Gouin, Nicolas; Samollow, Paul B; VandeBerg, Jane F; Hixson, James E; Cole, Shelley A; MacCluer, Jean W; Atwood, Larry D

2004-02-01

Angiotensin-converting enzyme (ACE) activity is highly heritable and has been associated with cardiovascular disease. We are studying the effects of genes and environmental factors on hypertension and related phenotypes, such as ACE activity, in Mexican-American families. In the current study, we performed multipoint linkage analysis to search for quantitative trait loci (QTLs) that affect ACE activities on data from 793 individuals from 29 pedigrees from the San Antonio Family Heart Study. As expected, we obtained strong evidence (maximum log of the odds [LOD]=4.57, genomic P=0.003) that a QTL for ACE activity is located on chromosome 17 near the ACE structural locus. We subsequently performed linkage analyses conditional on the effect of this QTL and obtained strong evidence (LOD=3.34) for a second QTL on chromosome 4 near D4S1548. We next incorporated the ACEIns/Del genotypes in our analyses and removed the evidence for the chromosome 17 QTL (maximum LOD=0.60); however, we retained our evidence for the QTL on chromosome 4q. We conclude that the QTL on chromosome 17 is tightly linked to ACE and is in strong disequilibrium with the insertion/deletion polymorphism, which is consistent with other reports. We also have evidence that an additional QTL affects ACE activity. Identification of this additional QTL might lead to alternate means of prophylaxis.

BRISK--research-oriented storage kit for biology-related data.

PubMed

Tan, Alan; Tripp, Ben; Daley, Denise

2011-09-01

In genetic science, large-scale international research collaborations represent a growing trend. These collaborations have demanding and challenging database, storage, retrieval and communication needs. These studies typically involve demographic and clinical data, in addition to the results from numerous genomic studies (omics studies) such as gene expression, eQTL, genome-wide association and methylation studies, which present numerous challenges, thus the need for data integration platforms that can handle these complex data structures. Inefficient methods of data transfer and access control still plague research collaboration. As science becomes more and more collaborative in nature, the need for a system that adequately manages data sharing becomes paramount. Biology-Related Information Storage Kit (BRISK) is a package of several web-based data management tools that provide a cohesive data integration and management platform. It was specifically designed to provide the architecture necessary to promote collaboration and expedite data sharing between scientists. The software, documentation, Java source code and demo are available at http://genapha.icapture.ubc.ca/brisk/index.jsp. BRISK was developed in Java, and tested on an Apache Tomcat 6 server with a MySQL database. denise.daley@hli.ubc.ca.

QTLs for Seed Vigor-Related Traits Identified in Maize Seeds Germinated under Artificial Aging Conditions

PubMed Central

Han, Zanping; Ku, Lixia; Zhang, Zhenzhen; Zhang, Jun; Guo, ShuLei; Liu, Haiying; Zhao, Ruifang; Ren, Zhenzhen; Zhang, Liangkun; Su, Huihui; Dong, Lei; Chen, Yanhui

2014-01-01

High seed vigor is important for agricultural production due to the associated potential for increased growth and productivity. However, a better understanding of the underlying molecular mechanisms is required because the genetic basis for seed vigor remains unknown. We used single-nucleotide polymorphism (SNP) markers to map quantitative trait loci (QTLs) for four seed vigor traits in two connected recombinant inbred line (RIL) maize populations under four treatment conditions during seed germination. Sixty-five QTLs distributed between the two populations were identified and a meta-analysis was used to integrate genetic maps. Sixty-one initially identified QTLs were integrated into 18 meta-QTLs (mQTLs). Initial QTLs with contribution to phenotypic variation values of R2>10% were integrated into mQTLs. Twenty-three candidate genes for association with seed vigor traits coincided with 13 mQTLs. The candidate genes had functions in the glycolytic pathway and in protein metabolism. QTLs with major effects (R2>10%) were identified under at least one treatment condition for mQTL2, mQTL3-2, and mQTL3-4. Candidate genes included a calcium-dependent protein kinase gene (302810918) involved in signal transduction that mapped in the mQTL3-2 interval associated with germination energy (GE) and germination percentage (GP), and an hsp20/alpha crystallin family protein gene (At5g51440) that mapped in the mQTL3-4 interval associated with GE and GP. Two initial QTLs with a major effect under at least two treatment conditions were identified for mQTL5-2. A cucumisin-like Ser protease gene (At5g67360) mapped in the mQTL5-2 interval associated with GP. The chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 may be hot spots for QTLs related to seed vigor traits. The mQTLs and candidate genes identified in this study provide valuable information for the identification of additional quantitative trait genes. PMID:24651614

QTLs for seed vigor-related traits identified in maize seeds germinated under artificial aging conditions.

PubMed

Han, Zanping; Ku, Lixia; Zhang, Zhenzhen; Zhang, Jun; Guo, Shulei; Liu, Haiying; Zhao, Ruifang; Ren, Zhenzhen; Zhang, Liangkun; Su, Huihui; Dong, Lei; Chen, Yanhui

2014-01-01

High seed vigor is important for agricultural production due to the associated potential for increased growth and productivity. However, a better understanding of the underlying molecular mechanisms is required because the genetic basis for seed vigor remains unknown. We used single-nucleotide polymorphism (SNP) markers to map quantitative trait loci (QTLs) for four seed vigor traits in two connected recombinant inbred line (RIL) maize populations under four treatment conditions during seed germination. Sixty-five QTLs distributed between the two populations were identified and a meta-analysis was used to integrate genetic maps. Sixty-one initially identified QTLs were integrated into 18 meta-QTLs (mQTLs). Initial QTLs with contribution to phenotypic variation values of R(2)>10% were integrated into mQTLs. Twenty-three candidate genes for association with seed vigor traits coincided with 13 mQTLs. The candidate genes had functions in the glycolytic pathway and in protein metabolism. QTLs with major effects (R(2)>10%) were identified under at least one treatment condition for mQTL2, mQTL3-2, and mQTL3-4. Candidate genes included a calcium-dependent protein kinase gene (302810918) involved in signal transduction that mapped in the mQTL3-2 interval associated with germination energy (GE) and germination percentage (GP), and an hsp20/alpha crystallin family protein gene (At5g51440) that mapped in the mQTL3-4 interval associated with GE and GP. Two initial QTLs with a major effect under at least two treatment conditions were identified for mQTL5-2. A cucumisin-like Ser protease gene (At5g67360) mapped in the mQTL5-2 interval associated with GP. The chromosome regions for mQTL2, mQTL3-2, mQTL3-4, and mQTL5-2 may be hot spots for QTLs related to seed vigor traits. The mQTLs and candidate genes identified in this study provide valuable information for the identification of additional quantitative trait genes.

Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle.

PubMed

Uemoto, Yoshinobu; Sasaki, Shinji; Kojima, Takatoshi; Sugimoto, Yoshikazu; Watanabe, Toshio

2015-11-19

Genetic variance that is not captured by single nucleotide polymorphisms (SNPs) is due to imperfect linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTLs), and the extent of LD between SNPs and QTLs depends on different minor allele frequencies (MAF) between them. To evaluate the impact of MAF of QTLs on genomic evaluation, we performed a simulation study using real cattle genotype data. In total, 1368 Japanese Black cattle and 592,034 SNPs (Illumina BovineHD BeadChip) were used. We simulated phenotypes using real genotypes under different scenarios, varying the MAF categories, QTL heritability, number of QTLs, and distribution of QTL effect. After generating true breeding values and phenotypes, QTL heritability was estimated and the prediction accuracy of genomic estimated breeding value (GEBV) was assessed under different SNP densities, prediction models, and population size by a reference-test validation design. The extent of LD between SNPs and QTLs in this population was higher in the QTLs with high MAF than in those with low MAF. The effect of MAF of QTLs depended on the genetic architecture, evaluation strategy, and population size in genomic evaluation. In genetic architecture, genomic evaluation was affected by the MAF of QTLs combined with the QTL heritability and the distribution of QTL effect. The number of QTL was not affected on genomic evaluation if the number of QTL was more than 50. In the evaluation strategy, we showed that different SNP densities and prediction models affect the heritability estimation and genomic prediction and that this depends on the MAF of QTLs. In addition, accurate QTL heritability and GEBV were obtained using denser SNP information and the prediction model accounted for the SNPs with low and high MAFs. In population size, a large sample size is needed to increase the accuracy of GEBV. The MAF of QTL had an impact on heritability estimation and prediction accuracy. Most genetic variance can be captured using denser SNPs and the prediction model accounted for MAF, but a large sample size is needed to increase the accuracy of GEBV under all QTL MAF categories.

QTL Mapping of Genome Regions Controlling Manganese Uptake in Lentil Seed.

PubMed

Ates, Duygu; Aldemir, Secil; Yagmur, Bulent; Kahraman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Muhammed Bahattin

2018-05-04

This study evaluated Mn concentration in the seeds of 120 RILs of lentil developed from the cross "CDC Redberry" × "ILL7502". Micronutrient analysis using atomic absorption spectrometry indicated mean seed manganese (Mn) concentrations ranging from 8.5 to 26.8 mg/kg, based on replicated field trials grown at three locations in Turkey in 2012 and 2013. A linkage map of lentil was constructed and consisted of seven linkage groups with 5,385 DNA markers. The total map length was 973.1 cM, with an average distance between markers of 0.18 cM. A total of 6 QTL for Mn concentration were identified using composite interval mapping (CIM). All QTL were statistically significant and explained 15.3-24.1% of the phenotypic variation, with LOD scores ranging from 3.00 to 4.42. The high-density genetic map reported in this study will increase fundamental knowledge of the genome structure of lentil, and will be the basis for the development of micronutrient-enriched lentil genotypes to support biofortification efforts. Copyright © 2018 Ates et al.

Genome-Wide Association Study Reveals a New QTL for Salinity Tolerance in Barley (Hordeum vulgare L.)

PubMed Central

Fan, Yun; Zhou, Gaofeng; Shabala, Sergey; Chen, Zhong-Hua; Cai, Shengguan; Li, Chengdao; Zhou, Meixue

2016-01-01

Salinity stress is one of the most severe abiotic stresses that affect agricultural production. Genome wide association study (GWAS) has been widely used to detect genetic variations in extensive natural accessions with more recombination and higher resolution. In this study, 206 barley accessions collected worldwide were genotyped with 408 Diversity Arrays Technology (DArT) markers and evaluated for salinity stress tolerance using salinity tolerance score – a reliable trait developed in our previous work. GWAS for salinity tolerance had been conducted through a general linkage model and a mixed linkage model based on population structure and kinship. A total of 24 significant marker-trait associations were identified. A QTL on 4H with the nearest marker of bPb-9668 was consistently detected in all different methods. This QTL has not been reported before and is worth to be further confirmed with bi-parental populations. PMID:27446173

Genomic networks of hybrid sterility.

PubMed

Turner, Leslie M; White, Michael A; Tautz, Diethard; Payseur, Bret A

2014-02-01

Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci ("Dobzhansky-Muller incompatibilities"). The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus) provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven 'hotspots,' seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL-but not cis eQTL-were substantially lower when mapping was restricted to a 'fertile' subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is applicable in a broad range of organisms and we advocate for widespread adoption of a network-centered approach in speciation genetics.

Detecting the QTL-allele system of seed isoflavone content in Chinese soybean landrace population for optimal cross design and gene system exploration.

PubMed

Meng, Shan; He, Jianbo; Zhao, Tuanjie; Xing, Guangnan; Li, Yan; Yang, Shouping; Lu, Jiangjie; Wang, Yufeng; Gai, Junyi

2016-08-01

Utilizing an innovative GWAS in CSLRP, 44 QTL 199 alleles with 72.2 % contribution to SIFC variation were detected and organized into a QTL-allele matrix for cross design and gene annotation. The seed isoflavone content (SIFC) of soybeans is of great importance to health care. The Chinese soybean landrace population (CSLRP) as a genetic reservoir was studied for its whole-genome quantitative trait loci (QTL) system of the SIFC using an innovative restricted two-stage multi-locus genome-wide association study procedure (RTM-GWAS). A sample of 366 landraces was tested under four environments and sequenced using RAD-seq (restriction-site-associated DNA sequencing) technique to obtain 116,769 single nucleotide polymorphisms (SNPs) then organized into 29,119 SNP linkage disequilibrium blocks (SNPLDBs) for GWAS. The detected 44 QTL 199 alleles on 16 chromosomes (explaining 72.2 % of the total phenotypic variation) with the allele effects (92 positive and 107 negative) of the CSLRP were organized into a QTL-allele matrix showing the SIFC population genetic structure. Additional differentiation among eco-regions due to the SIFC in addition to that of genome-wide markers was found. All accessions comprised both positive and negative alleles, implying a great potential for recombination within the population. The optimal crosses were predicted from the matrices, showing transgressive potentials in the CSLRP. From the detected QTL system, 55 candidate genes related to 11 biological processes were χ (2)-tested as an SIFC candidate gene system. The present study explored the genome-wide SIFC QTL/gene system with the innovative RTM-GWAS and found the potentials of the QTL-allele matrix in optimal cross design and population genetic and genomic studies, which may have provided a solution to match the breeding by design strategy at both QTL and gene levels in breeding programs.

Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs.

PubMed

Jouffe, Vincent; Rowe, Suzanne; Liaubet, Laurence; Buitenhuis, Bart; Hornshøj, Henrik; SanCristobal, Magali; Mormède, Pierre; de Koning, D J

2009-07-16

Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH). Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming. This paper provides a case study for the integration of QTL data and microarray data for a species with limited genome sequence information and annotation. The results illustrate the challenges that must be addressed but also provide a roadmap for future work that is applicable to other non-model species.

QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods.

PubMed

Win, Khin Thanda; Vegas, Juan; Zhang, Chunying; Song, Kihwan; Lee, Sanghyeob

2017-01-01

QTL mapping using NGS-assisted BSA was successfully applied to an F 2 population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis. Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F 2 population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F 2 confirmed dm2.2 (R 2  = 10.8-24 %) and dm5.2 (R 2  = 14-27.2 %) as major QTLs and dm4.1 (R 2  = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R 2  = 28.2 %) was detected by the conventional QTL method using an F 3 population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.

Localization of QTLs for in vitro plant regeneration in tomato

PubMed Central

2011-01-01

Background Low regeneration ability limits biotechnological breeding approaches. The influence of genotype in the regeneration response is high in both tomato and other important crops. Despite the various studies that have been carried out on regeneration genetics, little is known about the key genes involved in this process. The aim of this study was to localize the genetic factors affecting regeneration in tomato. Results We developed two mapping populations (F2 and BC1) derived from a previously selected tomato cultivar (cv. Anl27) with low regeneration ability and a high regeneration accession of the wild species Solanum pennellii (PE-47). The phenotypic assay indicated dominance for bud induction and additive effects for both the percentage of explants with shoots and the number of regenerated shoots per explant. Two linkage maps were developed and six QTLs were identified on five chromosomes (1, 3, 4, 7 and 8) in the BC1 population by means of the Interval Mapping and restricted Multiple QTL Mapping methods. These QTLs came from S. pennellii, with the exception of the minor QTL located on chromosome 8, which was provided by cv. Anl27. The main QTLs correspond to those detected on chromosomes 1 and 7. In the F2 population, a QTL on chromosome 7 was identified on a similar region as that detected in the BC1 population. Marker segregation distortion was observed in this population in those areas where the QTLs of BC1 were detected. Furthermore, we located two tomato candidate genes using a marker linked to the high regeneration gene: Rg-2 (a putative allele of Rg-1) and LESK1, which encodes a serine/threonine kinase and was proposed as a marker for regeneration competence. As a result, we located a putative allele of Rg-2 in the QTL detected on chromosome 3 that we named Rg-3. LESK1, which is also situated on chromosome 3, is outside Rg-3. In a preliminary exploration of the detected QTL peaks, we found several genes that may be related to regeneration. Conclusions In this study we have identified new QTLs related to the complex process of regeneration from tissue culture. We have also located two candidate genes, discovering a putative allele of the high regeneration gene Rg-1 in the QTL on chromosome 3. The identified QTLs could represent a significant step toward the understanding of this process and the identification of other related candidate genes. It will also most likely facilitate the development of molecular markers for use in gene isolation. PMID:22014149

Localization of QTLs for in vitro plant regeneration in tomato.

PubMed

Trujillo-Moya, Carlos; Gisbert, Carmina; Vilanova, Santiago; Nuez, Fernando

2011-10-20

Low regeneration ability limits biotechnological breeding approaches. The influence of genotype in the regeneration response is high in both tomato and other important crops. Despite the various studies that have been carried out on regeneration genetics, little is known about the key genes involved in this process. The aim of this study was to localize the genetic factors affecting regeneration in tomato. We developed two mapping populations (F2 and BC1) derived from a previously selected tomato cultivar (cv. Anl27) with low regeneration ability and a high regeneration accession of the wild species Solanum pennellii (PE-47). The phenotypic assay indicated dominance for bud induction and additive effects for both the percentage of explants with shoots and the number of regenerated shoots per explant. Two linkage maps were developed and six QTLs were identified on five chromosomes (1, 3, 4, 7 and 8) in the BC1 population by means of the Interval Mapping and restricted Multiple QTL Mapping methods. These QTLs came from S. pennellii, with the exception of the minor QTL located on chromosome 8, which was provided by cv. Anl27. The main QTLs correspond to those detected on chromosomes 1 and 7. In the F2 population, a QTL on chromosome 7 was identified on a similar region as that detected in the BC1 population. Marker segregation distortion was observed in this population in those areas where the QTLs of BC1 were detected. Furthermore, we located two tomato candidate genes using a marker linked to the high regeneration gene: Rg-2 (a putative allele of Rg-1) and LESK1, which encodes a serine/threonine kinase and was proposed as a marker for regeneration competence. As a result, we located a putative allele of Rg-2 in the QTL detected on chromosome 3 that we named Rg-3. LESK1, which is also situated on chromosome 3, is outside Rg-3. In a preliminary exploration of the detected QTL peaks, we found several genes that may be related to regeneration. In this study we have identified new QTLs related to the complex process of regeneration from tissue culture. We have also located two candidate genes, discovering a putative allele of the high regeneration gene Rg-1 in the QTL on chromosome 3. The identified QTLs could represent a significant step toward the understanding of this process and the identification of other related candidate genes. It will also most likely facilitate the development of molecular markers for use in gene isolation.

An Integrated Genomic Approach for Rapid Delineation of Candidate Genes Regulating Agro-Morphological Traits in Chickpea

PubMed Central

Saxena, Maneesha S.; Bajaj, Deepak; Das, Shouvik; Kujur, Alice; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

2014-01-01

The identification and fine mapping of robust quantitative trait loci (QTLs)/genes governing important agro-morphological traits in chickpea still lacks systematic efforts at a genome-wide scale involving wild Cicer accessions. In this context, an 834 simple sequence repeat and single-nucleotide polymorphism marker-based high-density genetic linkage map between cultivated and wild parental accessions (Cicer arietinum desi cv. ICC 4958 and Cicer reticulatum wild cv. ICC 17160) was constructed. This inter-specific genetic map comprising eight linkage groups spanned a map length of 949.4 cM with an average inter-marker distance of 1.14 cM. Eleven novel major genomic regions harbouring 15 robust QTLs (15.6–39.8% R2 at 4.2–15.7 logarithm of odds) associated with four agro-morphological traits (100-seed weight, pod and branch number/plant and plant hairiness) were identified and mapped on chickpea chromosomes. Most of these QTLs showed positive additive gene effects with effective allelic contribution from ICC 4958, particularly for increasing seed weight (SW) and pod and branch number. One robust SW-influencing major QTL region (qSW4.2) has been narrowed down by combining QTL mapping with high-resolution QTL region-specific association analysis, differential expression profiling and gene haplotype-based association/LD mapping. This enabled to delineate a strong SW-regulating ABI3VP1 transcription factor (TF) gene at trait-specific QTL interval and consequently identified favourable natural allelic variants and superior high seed weight-specific haplotypes in the upstream regulatory region of this gene showing increased transcript expression during seed development. The genes (TFs) harbouring diverse trait-regulating QTLs, once validated and fine-mapped by our developed rapid integrated genomic approach and through gene/QTL map-based cloning, can be utilized as potential candidates for marker-assisted genetic enhancement of chickpea. PMID:25335477

Mapping quantitative trait loci with additive effects and additive x additive epistatic interactions for biomass yield, grain yield, and straw yield using a doubled haploid population of wheat (Triticum aestivum L.).

PubMed

Li, Z K; Jiang, X L; Peng, T; Shi, C L; Han, S X; Tian, B; Zhu, Z L; Tian, J C

2014-02-28

Biomass yield is one of the most important traits for wheat (Triticum aestivum L.)-breeding programs. Increasing the yield of the aerial parts of wheat varieties will be an integral component of future wheat improvement; however, little is known regarding the genetic control of aerial part yield. A doubled haploid population, comprising 168 lines derived from a cross between two winter wheat cultivars, 'Huapei 3' (HP3) and 'Yumai 57' (YM57), was investigated. Quantitative trait loci (QTL) for total biomass yield, grain yield, and straw yield were determined for additive effects and additive x additive epistatic interactions using the QTLNetwork 2.0 software based on the mixed-linear model. Thirteen QTL were determined to have significant additive effects for the three yield traits, of which six also exhibited epistatic effects. Eleven significant additive x additive interactions were detected, of which seven occurred between QTL showing epistatic effects only, two occurred between QTL showing epistatic effects and additive effects, and two occurred between QTL with additive effects. These QTL explained 1.20 to 10.87% of the total phenotypic variation. The QTL with an allele originating from YM57 on chromosome 4B and another QTL contributed by HP3 alleles on chromosome 4D were simultaneously detected on the same or adjacent chromosome intervals for the three traits in two environments. Most of the repeatedly detected QTL across environments were not significant (P > 0.05). These results have implications for selection strategies in wheat biomass yield and for increasing the yield of the aerial part of wheat.

Two distinct major QTL for resistance to fire blight co-localize on linkage group 12 in apple genotypes 'Evereste' and Malus floribunda clone 821.

PubMed

Durel, C-E; Denancé, C; Brisset, M-N

2009-02-01

Fire blight, caused by the bacterium Erwinia amylovora, is one of the most destructive diseases of apple (Malus xdomestica) worldwide. No major, qualitative gene for resistance to this disease has been identified so far in apple. A quantitative trait locus (QTL) analysis was performed in two F1 progenies derived from two controled crosses: one between the susceptible rootstock cultivar 'MM106' and the resistant ornamental cultivar 'Evereste' and the other one between the moderately susceptible cultivar 'Golden Delicious' and the wild apple Malus floribunda clone 821, with unknown level of fire blight resistance. Both progenies were inoculated in the greenhouse with the same reference strain of E. amylovora. The length of stem necrosis was scored 7 and 14 days after inoculation. A strong QTL effect was identified in both 'Evereste' and M. floribunda 821 at a similar position on the distal region of linkage group 12 of the apple genome. From 50% to 70% of the phenotypic variation was explained by the QTL in 'Evereste' progeny according to the scored trait. More than 40% of the phenotypic variation was explained by the M. floribunda QTL in the second progeny. It was shown that 'Evereste' and M. floribunda 821 carried distinct QTL alleles at that genomic position. A small additional QTL was identified in 'Evereste' on linkage group 15, which explained about 6% of the phenotypic variation. Although it was not possible to confirm whether or not 'Evereste' and M. floribunda QTL belonged to the same locus or two distinct closely related loci, these QTL can be valuable targets in marker-assisted selection to obtain fire blight resistant apple cultivars and form a starting point for discovering the function of the genes controlling apple fire blight resistance.

Relationship between QTL for grain shape, grain weight, test weight, milling yield, and plant height in the spring wheat cross RL4452/'AC Domain'.

PubMed

Cabral, Adrian L; Jordan, Mark C; Larson, Gary; Somers, Daryl J; Humphreys, D Gavin; McCartney, Curt A

2018-01-01

Kernel morphology characteristics of wheat are complex and quantitatively inherited. A doubled haploid (DH) population of the cross RL4452/'AC Domain' was used to study the genetic basis of seed shape. Quantitative trait loci (QTL) analyses were conducted on a total of 18 traits: 14 grain shape traits, flour yield (Fyd), and three agronomic traits (Plant height [Plht], 1000 Grain weight [Gwt], Test weight [Twt]), using data from trial locations at Glenlea, Brandon, and Morden in Manitoba, Canada, between 1999 and 2004. Kernel shape was studied through digital image analysis with an Acurum® grain analyzer. Plht, Gwt, Twt, Fyd, and grain shape QTL were correlated with each other and QTL analysis revealed that QTL for these traits often mapped to the same genetic locations. The most significant QTL for the grain shape traits were located on chromosomes 4B and 4D, each accounting for up to 24.4% and 53.3% of the total phenotypic variation, respectively. In addition, the most significant QTL for Plht, Gwt, and Twt were all detected on chromosome 4D at the Rht-D1 locus. Rht-D1b decreased Plht, Gwt, Twt, and kernel width relative to the Rht-D1a allele. A narrow genetic interval on chromosome 4B contained significant QTL for grain shape, Gwt, and Plht. The 'AC Domain' allele reduced Plht, Gwt, kernel length and width traits, but had no detectable effect on Twt. The data indicated that this variation was inconsistent with segregation at Rht-B1. Numerous QTL were identified that control these traits in this population.

Relationship between QTL for grain shape, grain weight, test weight, milling yield, and plant height in the spring wheat cross RL4452/‘AC Domain’

PubMed Central

Cabral, Adrian L.; Jordan, Mark C.; Larson, Gary; Somers, Daryl J.; Humphreys, D. Gavin

2018-01-01

Kernel morphology characteristics of wheat are complex and quantitatively inherited. A doubled haploid (DH) population of the cross RL4452/‘AC Domain’ was used to study the genetic basis of seed shape. Quantitative trait loci (QTL) analyses were conducted on a total of 18 traits: 14 grain shape traits, flour yield (Fyd), and three agronomic traits (Plant height [Plht], 1000 Grain weight [Gwt], Test weight [Twt]), using data from trial locations at Glenlea, Brandon, and Morden in Manitoba, Canada, between 1999 and 2004. Kernel shape was studied through digital image analysis with an Acurum® grain analyzer. Plht, Gwt, Twt, Fyd, and grain shape QTL were correlated with each other and QTL analysis revealed that QTL for these traits often mapped to the same genetic locations. The most significant QTL for the grain shape traits were located on chromosomes 4B and 4D, each accounting for up to 24.4% and 53.3% of the total phenotypic variation, respectively. In addition, the most significant QTL for Plht, Gwt, and Twt were all detected on chromosome 4D at the Rht-D1 locus. Rht-D1b decreased Plht, Gwt, Twt, and kernel width relative to the Rht-D1a allele. A narrow genetic interval on chromosome 4B contained significant QTL for grain shape, Gwt, and Plht. The ‘AC Domain’ allele reduced Plht, Gwt, kernel length and width traits, but had no detectable effect on Twt. The data indicated that this variation was inconsistent with segregation at Rht-B1. Numerous QTL were identified that control these traits in this population. PMID:29357369

Prioritizing quantitative trait loci for root system architecture in tetraploid wheat

PubMed Central

Maccaferri, Marco; El-Feki, Walid; Nazemi, Ghasemali; Salvi, Silvio; Canè, Maria Angela; Colalongo, Maria Chiara; Stefanelli, Sandra; Tuberosa, Roberto

2016-01-01

Optimization of root system architecture (RSA) traits is an important objective for modern wheat breeding. Linkage and association mapping for RSA in two recombinant inbred line populations and one association mapping panel of 183 elite durum wheat (Triticum turgidum L. var. durum Desf.) accessions evaluated as seedlings grown on filter paper/polycarbonate screening plates revealed 20 clusters of quantitative trait loci (QTLs) for root length and number, as well as 30 QTLs for root growth angle (RGA). Divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTLs were mapped on a high-density tetraploid consensus map based on transcript-associated Illumina 90K single nucleotide polymorphisms (SNPs) developed for bread and durum wheat, thus allowing for an accurate cross-referencing of RSA QTLs between durum and bread wheat. Among the main QTL clusters for root length and number highlighted in this study, 15 overlapped with QTLs for multiple RSA traits reported in bread wheat, while out of 30 QTLs for RGA, only six showed co-location with previously reported QTLs in wheat. Based on their relative additive effects/significance, allelic distribution in the association mapping panel, and co-location with QTLs for grain weight and grain yield, the RSA QTLs have been prioritized in terms of breeding value. Three major QTL clusters for root length and number (RSA_QTL_cluster_5#, RSA_QTL_cluster_6#, and RSA_QTL_cluster_12#) and nine RGA QTL clusters (QRGA.ubo-2A.1, QRGA.ubo-2A.3, QRGA.ubo-2B.2/2B.3, QRGA.ubo-4B.4, QRGA.ubo-6A.1, QRGA.ubo-6A.2, QRGA.ubo-7A.1, QRGA.ubo-7A.2, and QRGA.ubo-7B) appear particularly valuable for further characterization towards a possible implementation of breeding applications in marker-assisted selection and/or cloning of the causal genes underlying the QTLs. PMID:26880749

QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

PubMed Central

Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

2015-01-01

Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate rapid introgression of waterlogging tolerance in tropical maize breeding programs. PMID:25884393

QTL mapping of agronomic waterlogging tolerance using recombinant inbred lines derived from tropical maize (Zea mays L) germplasm.

PubMed

Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

2015-01-01

Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate rapid introgression of waterlogging tolerance in tropical maize breeding programs.

The genetic architecture of maize (Zea mays L.) kernel weight determination.

PubMed

Alvarez Prado, Santiago; López, César G; Senior, M Lynn; Borrás, Lucas

2014-09-18

Individual kernel weight is an important trait for maize yield determination. We have identified genomic regions controlling this trait by using the B73xMo17 population; however, the effect of genetic background on control of this complex trait and its physiological components is not yet known. The objective of this study was to understand how genetic background affected our previous results. Two nested stable recombinant inbred line populations (N209xMo17 and R18xMo17) were designed for this purpose. A total of 408 recombinant inbred lines were genotyped and phenotyped at two environments for kernel weight and five other traits related to kernel growth and development. All traits showed very high and significant (P < 0.001) phenotypic variability and medium-to-high heritability (0.60-0.90). When N209xMo17 and R18xMo17 were analyzed separately, a total of 23 environmentally stable quantitative trait loci (QTL) and five epistatic interactions were detected for N209xMo17. For R18xMo17, 59 environmentally stable QTL and 17 epistatic interactions were detected. A joint analysis detected 14 stable QTL regardless of the genetic background. Between 57 and 83% of detected QTL were population specific, denoting medium-to-high genetic background effects. This percentage was dependent on the trait. A meta-analysis including our previous B73xMo17 results identified five relevant genomic regions deserving further characterization. In summary, our grain filling traits were dominated by small additive QTL with several epistatic and few environmental interactions and medium-to-high genetic background effects. This study demonstrates that the number of detected QTL and additive effects for different physiologically related grain filling traits need to be understood relative to the specific germplasm. Copyright © 2014 Alvarez Prado et al.

Copy number variation of CBF-A14 at the Fr-A2 locus determines frost tolerance in winter durum wheat.

PubMed

Sieber, Alisa-Naomi; Longin, C Friedrich H; Leiser, Willmar L; Würschum, Tobias

2016-06-01

Frost tolerance in durum wheat is mainly controlled by copy number variation of CBF - A14 at the Fr - A2 locus. Frost tolerance is a key trait for successful breeding of winter durum wheat (Triticum durum) which can increase the yield performance in regions favoring autumn-sown winter cereals. The aim of this study was to investigate the genetic architecture of frost tolerance in order to provide molecular support for the breeding of winter durum wheat. To this end, a diverse panel of 170 winter and 14 spring durum wheat genotypes of worldwide origin was evaluated for frost tolerance in the field, as well as in a semi-controlled test. A total of 30,611 polymorphic genome-wide markers obtained by a genotyping-by-sequencing approach and markers for candidate loci were used to assess marker-trait associations. One major QTL was detected on chromosome 5A, likely corresponding to Frost Resistance-A2 (Fr-A2). Further analyses strongly support the conclusion that copy number variation of CBF-A14 at the Fr-A2 locus is the causal polymorphism underlying this major QTL. It explains 91.6 % of the genotypic variance and a haploblock of two strongly associated markers in the QTL region also allowed to capture the variance of this QTL. In addition to this major QTL, a much smaller contribution of 4.2 % was observed for Fr-B2. We further investigated this major QTL and found that the copy number of CBF-A14 and the frequency of the frost tolerant haplotype mirrored the climatic conditions in the genotypes' country of origin, suggesting selection through breeding. Two functional KASP markers were developed which facilitate a high-throughput screening of the haploblock and thus a marker-based breeding of frost tolerance in winter durum wheat.

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome.

PubMed

Ng, Bernard; White, Charles C; Klein, Hans-Ulrich; Sieberts, Solveig K; McCabe, Cristin; Patrick, Ellis; Xu, Jishu; Yu, Lei; Gaiteri, Chris; Bennett, David A; Mostafavi, Sara; De Jager, Philip L

2017-10-01

We report a multi-omic resource generated by applying quantitative trait locus (xQTL) analyses to RNA sequence, DNA methylation and histone acetylation data from the dorsolateral prefrontal cortex of 411 older adults who have all three data types. We identify SNPs significantly associated with gene expression, DNA methylation and histone modification levels. Many of these SNPs influence multiple molecular features, and we demonstrate that SNP effects on RNA expression are fully mediated by epigenetic features in 9% of these loci. Further, we illustrate the utility of our new resource, xQTL Serve, by using it to prioritize the cell type(s) most affected by an xQTL. We also reanalyze published genome wide association studies using an xQTL-weighted analysis approach and identify 18 new schizophrenia and 2 new bipolar susceptibility variants, which is more than double the number of loci that can be discovered with a larger blood-based expression eQTL resource.

Use of Genome Sequence Information for Meat Quality Trait QTL Mining for Causal Genes and Mutations on Pig Chromosome 17

PubMed Central

Hu, Zhi-Liang; Ramos, Antonio M.; Humphray, Sean J.; Rogers, Jane; Reecy, James M.; Rothschild, Max F.

2011-01-01

The newly available pig genome sequence has provided new information to fine map quantitative trait loci (QTL) in order to eventually identify causal variants. With targeted genomic sequencing efforts, we were able to obtain high quality BAC sequences that cover a region on pig chromosome 17 where a number of meat quality QTL have been previously discovered. Sequences from 70 BAC clones were assembled to form an 8-Mbp contig. Subsequently, we successfully mapped five previously identified QTL, three for meat color and two for lactate related traits, to the contig. With an additional 25 genetic markers that were identified by sequence comparison, we were able to carry out further linkage disequilibrium analysis to narrow down the genomic locations of these QTL, which allowed identification of the chromosomal regions that likely contain the causative variants. This research has provided one practical approach to combine genetic and molecular information for QTL mining. PMID:22303339

Biochemical and genetic analyses of N metabolism in maize testcross seedlings: 2. Roots.

PubMed

Silva, Ignacio Trucillo; Abbaraju, Hari Kishan R; Fallis, Lynne P; Liu, Hongjun; Lee, Michael; Dhugga, Kanwarpal S

2018-06-01

Intracellular factors differentially affected enzyme activities of N assimilation in the roots of maize testcrosses where alanine aminotransferase and glutamate synthase were the main enzymes regulating the levels of glutamate. N is a key macronutrient for plant growth and development. Breeding maize with improved efficiency in N use could help reduce environmental contamination as well as increase profitability for the farmers. Quantitative trait loci (QTL) mapping of traits related to N metabolism in the root tissue was undertaken in a maize testcross mapping population grown in hydroponic cultures. N concentration was negatively correlated with root and total dry mass. Neither the enzyme activities nor metabolites were appreciably correlated between the root and leaf tissues. Repeatability measures for most of the enzymes were lower than for dry mass. Weak negative correlations between most of the enzymes and dry mass resulted likely from dilution and suggested the presence of excess of enzyme activities for maximal biomass production. Glutamate synthase and alanine aminotransferase each explained more variation in glutamate concentration than either aspartate aminotransferase or asparagine synthetase whereas glutamine synthetase was inconsequential. Twenty-six QTL were identified across all traits. QTL models explained 7-43% of the variance with no significant epistasis between the QTL. Thirteen candidate genes were identified underlying QTL within 1-LOD confidence intervals. All the candidate genes were located in trans configuration, unlinked or even on different chromosomes, relative to the known genomic positions of the corresponding structural genes. Our results have implications in improving NUE in maize and other crop plants.

Quantitative Trait Loci for Cold Tolerance of Rice Recombinant Inbred Lines in Low Temperature Environments

PubMed Central

Jiang, Wenzhu; Jin, Yong-Mei; Lee, Joohyun; Lee, Kang-Ie; Piao, Rihua; Han, Longzhi; Shin, Jin-Chul; Jin, Rong-De; Cao, Tiehua; Pan, Hong-Yu; Du, Xinglin; Koh, Hee-Jong

2011-01-01

Low temperature is one of the major environmental stresses in rice cultivation in high-altitude and high-latitude regions. In this study, we cultivated a set of recombinant inbred lines (RIL) derived from Dasanbyeo (indica) / TR22183 (japonica) crosses in Yanji (high-latitude area), Kunming (high-altitude area), Chuncheon (cold water irrigation) and Suwon (normal) to evaluate the main effects of quantitative trait loci (QTL) and epistatic QTL (E-QTL) with regard to their interactions with environments for coldrelated traits. Six QTLs for spikelet fertility (SF) were identified in three cold treatment locations. Among them, four QTLs on chromosomes 2, 7, 8, and 10 were validated by several near isogenic lines (NILs) under cold treatment in Chuncheon. A total of 57 QTLs and 76 E-QTLs for nine cold-related traits were identified as distributing on all 12 chromosomes; among them, 19 QTLs and E-QTLs showed significant interactions of QTLs and environments (QEIs). The total phenotypic variation explained by each trait ranged from 13.2 to 29.1% in QTLs, 10.6 to 29.0% in EQTLs, 2.2 to 8.8% in QEIs and 1.0% to 7.7% in E-QTL × environment interactions (E-QEIs). These results demonstrate that epistatic effects and QEIs are important properties of QTL parameters for cold tolerance at the reproductive stage. In order to develop cold tolerant varieties adaptable to wide-ranges of cold stress, a strategy facilitating marker-assisted selection (MAS) is being adopted to accumulate QTLs identified from different environments. PMID:22080374

Genomic Regions Influencing Seminal Root Traits in Barley.

PubMed

Robinson, Hannah; Hickey, Lee; Richard, Cecile; Mace, Emma; Kelly, Alison; Borrell, Andrew; Franckowiak, Jerome; Fox, Glen

2016-03-01

Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley ( L.). Using a recently developed high-throughput phenotyping method, a panel of 30 barley genotypes and a doubled-haploid (DH) population (ND24260 × 'Flagship') comprising 330 lines genotyped with diversity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions. A high degree of phenotypic variation was observed in the panel of 30 genotypes: 13.5 to 82.2 and 3.6 to 6.9° for root angle and root number, respectively. A similar range was observed in the DH population: 16.4 to 70.5 and 3.6 to 6.5° for root angle and number, respectively. Seven quantitative trait loci (QTL) for seminal root traits (root angle, two QTL; root number, five QTL) were detected in the DH population. A major QTL influencing both root angle and root number (/) was positioned on chromosome 5HL. Across-species analysis identified 10 common genes underlying root trait QTL in barley, wheat ( L.), and sorghum [ (L.) Moench]. Here, we provide insight into seminal root phenotypes and provide a first look at the genetics controlling these traits in barley. Copyright © 2016 Crop Science Society of America.

Genome-wide association studies of growth traits in three dairy cattle breeds using whole-genome sequence data.

PubMed

Mao, X; Sahana, G; De Koning, D-J; Guldbrandtsen, B

2016-04-01

Male calves and culled cows of dairy cattle are used for beef production. However, unlike beef breeds, the genetics of growth performance traits in dairy breeds have not been extensively studied. Here, we performed a genome-wide association study (GWAS) on Holsteins ( = 5,519), Jerseys ( = 1,231), and Red Dairy Cattle ( = 4,410) to identify QTL for growth traits. First, a GWAS was performed within breeds using whole-genome sequence variants. Later, a meta-analysis was performed to combine information across the 3 breeds. We have identified several QTL that have large effects on growth traits in Holsteins and Red Dairy Cattle but with little overlap across breeds. Only 1 QTL located on chromosome 10 was shared between Holsteins and Red Dairy Cattle. The most significant variant (BTA10:59,164,533, rs43636323; -value = 2.8 × 10) in this QTL explained 2.4% of the total additive genetic variance in Red Dairy Cattle. The gene is a strong candidate for the underlying gene of this QTL. In Red Dairy Cattle, a QTL near 25 Mb on chromosome 14 was very significantly associated with growth traits, consistent with the previously reported gene , which affects growth in beef cattle and humans. No QTL for growth performance was statistically significant in Jerseys, possibly due to the low power of detection with the small sample size. The meta-analysis of the 3 breeds increased the power to detect QTL.

Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus × Bos indicus)

PubMed Central

2010-01-01

Background In tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus) microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos indicus to tick resistance and molecular biology tools might allow for the identification of molecular markers linked to resistance traits that could be used as an auxiliary tool in selection programs. The objective of this work was to identify QTL associated with tick resistance/susceptibility in a bovine F2 population derived from the Gyr (Bos indicus) × Holstein (Bos taurus) cross. Results Through a whole genome scan with microsatellite markers, we were able to map six genomic regions associated with bovine tick resistance. For most QTL, we have found that depending on the tick evaluation season (dry and rainy) different sets of genes could be involved in the resistance mechanism. We identified dry season specific QTL on BTA 2 and 10, rainy season specific QTL on BTA 5, 11 and 27. We also found a highly significant genome wide QTL for both dry and rainy seasons in the central region of BTA 23. Conclusions The experimental F2 population derived from Gyr × Holstein cross successfully allowed the identification of six highly significant QTL associated with tick resistance in cattle. QTL located on BTA 23 might be related with the bovine histocompatibility complex. Further investigation of these QTL will help to isolate candidate genes involved with tick resistance in cattle. PMID:20433753

Genetic Architecture of the Variation in Male-Specific Ossified Processes on the Anal Fins of Japanese Medaka.

PubMed

Kawajiri, Maiko; Fujimoto, Shingo; Yoshida, Kohta; Yamahira, Kazunori; Kitano, Jun

2015-10-28

Traits involved in reproduction evolve rapidly and show great diversity among closely related species. However, the genetic mechanisms that underlie the diversification of courtship traits are mostly unknown. Japanese medaka fishes (Oryzias latipes) use anal fins to attract females and to grasp females during courtship; the males have longer anal fins with male-specific ossified papillary processes on the fin rays. However, anal fin morphology varies between populations: the southern populations tend to have longer anal fins and more processes than the northern populations. In the present study, we conducted quantitative trait locus (QTL) mapping to investigate the genetic architecture underlying the variation in the number of papillary processes of Japanese medaka fish and compared the QTL with previously identified QTL controlling anal fin length. First, we found that only a few QTL were shared between anal fin length and papillary process number. Second, we found that the numbers of papillary processes on different fin rays often were controlled by different QTL. Finally, we produced another independent cross and found that some QTL were repeatable between the two crosses, whereas others were specific to only one cross. These results suggest that variation in the number of papillary processes is polygenic and controlled by QTL that are distinct from those controlling anal fin length. Thus, different courtship traits in Japanese medaka share a small number of QTL and have the potential for independent evolution. Copyright © 2015 Kawajiri et al.

QTL analysis of falling number and seed longevity in wheat (Triticum aestivum L.).

PubMed

Börner, Andreas; Nagel, Manuela; Agacka-Mołdoch, Monika; Gierke, Peter Ulrich; Oberforster, Michael; Albrecht, Theresa; Mohler, Volker

2018-02-01

Pre-harvest sprouting (PHS) and seed longevity (SL) are complex biological processes of major importance for agricultural production. In the present study, a recombinant inbred line (RIL) population derived from a cross between the German winter wheat (Triticum aestivum L.) cultivars History and Rubens was used to identify genetic factors controlling these two physiological seed traits. A falling number (FN) test was employed to evaluate PHS, while SL was measured using a germination test (and the speed of germination) after controlled deterioration. FN of the population was assessed in four environments; SL traits were measured in one environment. Four major quantitative trait loci (QTL) for FN were detected on chromosomes 4D, 5A, 5D, and 7B, whereas for SL traits, a major QTL was found on chromosome 1A. The FN QTL on chromosome 4D that coincided with the position of the dwarfing gene Rht-D1b only had effects in environments that were free of PHS. The remaining three QTL for FN were mostly pronounced under conditions conducive to PHS. The QTL on the long arm of chromosome 7B corresponded to the major gene locus controlling late maturity α-amylase (LMA) in wheat. The severity of the LMA phenotype became truly apparent under sprouting conditions. The position on the long arm of chromosome 1A of the QTL for SL points to a new QTL for this important regenerative seed trait.

Identification of QTL for reaction to three races of Colletotrichum trifolii and further analysis of inheritance of resistance in autotetraploid lucerne.

PubMed

Mackie, J M; Musial, J M; Armour, D J; Phan, H T T; Ellwood, S E; Aitken, K S; Irwin, J A G

2007-05-01

Anthracnose, caused by Colletotrichum trifolii, is one of the most serious diseases of lucerne worldwide. The disease is managed through deployment of resistant cultivars, but new pathotypes present a challenge to the successful implementation of this strategy. This paper reports the genetic map locations of quantitative trait loci (QTL) for reaction to races 1, 2 and 4 of C. trifolii in a single autotetraploid lucerne clone, designated W126 from the Australian cv. Trifecta. Resistance was mapped in a backcross population of 145 individuals, and reaction was assessed both by spray and injection inoculation of stems. Resistance to injection inoculation with races 1 and 4 was incompletely dominant and closely linked (phenotypic markers 2.2 cM apart); these resistances mapped to a linkage group homologous to Medicago truncatula linkage group 8. When the spray inoculation data were subjected to QTL analysis, the strongest QTL for resistance was located on linkage group 8; six QTL were identified for race 1 and four for race 4. Resistance to race 2 was incompletely recessive; four QTL were identified and these include one QTL on linkage group 4 that was also identified for race 1. Modelling of the interactions between individual QTL and marker effects allowed a total of 52-63% of the phenotypic variation to be described for each of the different races. These markers will have value in breeding lucerne, carrying multiple sources of resistance to the three known races of C. trifolii.

Genetic analysis of safflower domestication

PubMed Central

2014-01-01

Background Safflower (Carthamus tinctorius L.) is an oilseed crop in the Compositae (a.k.a. Asteraceae) that is valued for its oils rich in unsaturated fatty acids. Here, we present an analysis of the genetic architecture of safflower domestication and compare our findings to those from sunflower (Helianthus annuus L.), an independently domesticated oilseed crop within the same family. We mapped quantitative trait loci (QTL) underlying 24 domestication-related traits in progeny from a cross between safflower and its wild progenitor, Carthamus palaestinus Eig. Also, we compared QTL positions in safflower against those that have been previously identified in cultivated x wild sunflower crosses to identify instances of colocalization. Results We mapped 61 QTL, the vast majority of which (59) exhibited minor or moderate phenotypic effects. The two large-effect QTL corresponded to one each for flower color and leaf spininess. A total of 14 safflower QTL colocalized with previously reported sunflower QTL for the same traits. Of these, QTL for three traits (days to flower, achene length, and number of selfed seed) had cultivar alleles that conferred effects in the same direction in both species. Conclusions As has been observed in sunflower, and unlike many other crops, our results suggest that the genetics of safflower domestication is quite complex. Moreover, our comparative mapping results indicate that safflower and sunflower exhibit numerous instances of QTL colocalization, suggesting that parallel trait transitions during domestication may have been driven, at least in part, by parallel genotypic evolution at some of the same underlying genes. PMID:24502326

Fifteen years of quantitative trait loci studies in fish: challenges and future directions.

PubMed

Ashton, David T; Ritchie, Peter A; Wellenreuther, Maren

2017-03-01

Understanding the genetic basis of phenotypic variation is a major challenge in biology. Here, we systematically evaluate 146 quantitative trait loci (QTL) studies on teleost fish over the last 15 years to investigate (i) temporal trends and (ii) factors affecting QTL detection and fine-mapping. The number of fish QTL studies per year increased over the review period and identified a cumulative number of 3632 putative QTLs. Most studies used linkage-based mapping approaches and were conducted on nonmodel species with limited genomic resources. A gradual and moderate increase in the size of the mapping population and a sharp increase in marker density from 2011 onwards were observed; however, the number of QTLs and variance explained by QTLs changed only minimally over the review period. Based on these findings, we discuss the causative factors and outline how larger sample sizes, phenomics, comparative genomics, epigenetics and software development could improve both the quantity and quality of QTLs in future genotype-phenotype studies. Given that the technical limitations on DNA sequencing have mostly been overcome in recent years, a renewed focus on these and other study design factors will likely lead to significant improvements in QTL studies in the future. © 2016 John Wiley & Sons Ltd.

Identification of qSOR1, a major rice QTL involved in soil-surface rooting in paddy fields.

PubMed

Uga, Yusaku; Hanzawa, Eiko; Nagai, Shinsei; Sasaki, Kazuhiro; Yano, Masahiro; Sato, Tadashi

2012-01-01

Specific Indonesian lowland rice (Oryza sativa L.) cultivars elongate thick primary roots on the soil surface of paddy fields. To clarify the genetic factors controlling soil-surface rooting, we performed quantitative trait locus (QTL) analyses using 124 recombinant inbred lines (RILs) derived from a cross between Gemdjah Beton, an Indonesian lowland rice cultivar with soil-surface roots, and Sasanishiki, a Japanese lowland rice cultivar without soil-surface roots. These cultivars and the RILs were tested for soil-surface rooting in a paddy field. We identified four regions of chromosomes 3, 4, 6, and 7 that were associated with soil-surface rooting in the field. Among them, one major QTL was located on the long arm of chromosome 7. This QTL explained 32.5-53.6% of the total phenotypic variance across three field evaluations. To perform fine mapping of this QTL, we measured the basal root growth angle of crown roots at the seedling stage in seven BC(2)F(3) recombinant lines grown in small cups in a greenhouse. The QTL was mapped between markers RM21941 and RM21976, which delimit an 812-kb interval in the reference cultivar Nipponbare. We have designated this QTL qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1).

Power analysis of QTL detection in half-sib families using selective DNA pooling

PubMed Central

Baro, Jesús Á; Carleos, Carlos; Corral, Norberto; López, Teresa; Cañón, Javier

2001-01-01

Individual loci of economic importance (QTL) can be detected by comparing the inheritance of a trait and the inheritance of loci with alleles readily identifiable by laboratory methods (genetic markers). Data on allele segregation at the individual level are costly and alternatives have been proposed that make use of allele frequencies among progeny, rather than individual genotypes. Among the factors that may affect the power of the set up, the most important are those intrinsic to the QTL: the additive effect of the QTL, and its dominance, and distance between markers and QTL. Other factors are relative to the choice of animals and markers, such as the frequency of the QTL and marker alleles among dams and sires. Data collection may affect the detection power through the size of half-sib families, selection rate within families, and the technical error incurred when estimating genetic frequencies. We present results for a sensitivity analysis for QTL detection using pools of DNA from selected half-sibs. Simulations showed that conclusive detection may be achieved with families of at least 500 half-sibs if sires are chosen on the criteria that most of their marker alleles are either both missing, or one is fixed, among dams. PMID:11403746

Similar traits, different genes? Examining convergent evolution in related weedy rice populations.

PubMed

Thurber, Carrie S; Jia, Melissa H; Jia, Yulin; Caicedo, Ana L

2013-02-01

Convergent phenotypic evolution may or may not be associated with convergent genotypic evolution. Agricultural weeds have repeatedly been selected for weed-adaptive traits such as rapid growth, increased seed dispersal and dormancy, thus providing an ideal system for the study of convergent evolution. Here, we identify QTL underlying weedy traits and compare their genetic architecture to assess the potential for convergent genetic evolution in two distinct populations of weedy rice. F(2) offspring from crosses between an indica cultivar and two individuals from genetically differentiated U.S. weedy rice populations were used to map QTL for four quantitative (heading date, seed shattering, plant height and growth rate) and two qualitative traits. We identified QTL on nine of the twelve rice chromosomes, yet most QTL locations do not overlap between the two populations. Shared QTL among weed groups were only seen for heading date, a trait for which weedy groups have diverged from their cultivated ancestors and from each other. Sharing of some QTL with wild rice also suggests a possible role in weed evolution for genes under selection during domestication. The lack of overlapping QTL for the remaining traits suggests that, despite a close evolutionary relationship, weedy rice groups have adapted to the same agricultural environment through different genetic mechanisms. © 2012 Blackwell Publishing Ltd.

Genetic control of functional traits related to photosynthesis and water use efficiency in Pinus pinaster Ait. drought response: integration of genome annotation, allele association and QTL detection for candidate gene identification.

PubMed

de Miguel, Marina; Cabezas, José-Antonio; de María, Nuria; Sánchez-Gómez, David; Guevara, María-Ángeles; Vélez, María-Dolores; Sáez-Laguna, Enrique; Díaz, Luis-Manuel; Mancha, Jose-Antonio; Barbero, María-Carmen; Collada, Carmen; Díaz-Sala, Carmen; Aranda, Ismael; Cervera, María-Teresa

2014-06-12

Understanding molecular mechanisms that control photosynthesis and water use efficiency in response to drought is crucial for plant species from dry areas. This study aimed to identify QTL for these traits in a Mediterranean conifer and tested their stability under drought. High density linkage maps for Pinus pinaster were used in the detection of QTL for photosynthesis and water use efficiency at three water irrigation regimes. A total of 28 significant and 27 suggestive QTL were found. QTL detected for photochemical traits accounted for the higher percentage of phenotypic variance. Functional annotation of genes within the QTL suggested 58 candidate genes for the analyzed traits. Allele association analysis in selected candidate genes showed three SNPs located in a MYB transcription factor that were significantly associated with efficiency of energy capture by open PSII reaction centers and specific leaf area. The integration of QTL mapping of functional traits, genome annotation and allele association yielded several candidate genes involved with molecular control of photosynthesis and water use efficiency in response to drought in a conifer species. The results obtained highlight the importance of maintaining the integrity of the photochemical machinery in P. pinaster drought response.

Microsatellite mapping of QTLs affecting resistance to coccidiosis (Eimeria tenella) in a Fayoumi x White Leghorn cross.

PubMed

Pinard-van der Laan, Marie-Hélène; Bed'hom, Bertrand; Coville, Jean-Luc; Pitel, Frédérique; Feve, Katia; Leroux, Sophie; Legros, Hélène; Thomas, Aurélie; Gourichon, David; Repérant, Jean-Michel; Rault, Paul

2009-01-20

Avian coccidiosis is a major parasitic disease of poultry, causing severe economical loss to poultry production by affecting growth and feed efficiency of infected birds. Current control strategies using mainly drugs and more recently vaccination are showing drawbacks and alternative strategies are needed. Using genetic resistance that would limit the negative and very costly effects of the disease would be highly relevant. The purpose of this work was to detect for the first time QTL for disease resistance traits to Eimeria tenella in chicken by performing a genome scan in an F2 cross issued from a resistant Fayoumi line and a susceptible Leghorn line. The QTL analysis detected 21 chromosome-wide significant QTL for the different traits related to disease resistance (body weight growth, plasma coloration, hematocrit, rectal temperature and lesion) on 6 chromosomes. Out of these, a genome-wide very significant QTL for body weight growth was found on GGA1, five genome-wide significant QTL for body weight growth, plasma coloration and hematocrit and one for plasma coloration were found on GGA1 and GGA6, respectively. Two genome-wide suggestive QTL for plasma coloration and rectal temperature were found on GGA1 and GGA2, respectively. Other chromosme-wide significant QTL were identified on GGA2, GGA3, GGA6, GGA15 and GGA23. Parent-of-origin effects were found for QTL for body weight growth and plasma coloration on GGA1 and GGA3. Several QTL for different resistance phenotypes were identified as co-localized on the same location. Using an F2 cross from resistant and susceptible chicken lines proved to be a successful strategy to identify QTL for different resistance traits to Eimeria tenella, opening the way for further gene identification and underlying mechanisms and hopefully possibilities for new breeding strategies for resistance to coccidiosis in the chicken. From the QTL regions identified, several candidate genes and relevant pathways linked to innate immune and inflammatory responses were suggested. These results will be combined with functional genomics approaches on the same lines to provide positional candidate genes for resistance loci for coccidiosis. Results suggested also for further analysis, models tackling the complexity of the genetic architecture of these correlated disease resistance traits including potential epistatic effects.

OntoMate: a text-mining tool aiding curation at the Rat Genome Database

PubMed Central

Liu, Weisong; Laulederkind, Stanley J. F.; Hayman, G. Thomas; Wang, Shur-Jen; Nigam, Rajni; Smith, Jennifer R.; De Pons, Jeff; Dwinell, Melinda R.; Shimoyama, Mary

2015-01-01

The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu PMID:25619558

QTL Analyses in Multiple Populations Employed for the Fine Mapping and Identification of Candidate Genes at a Locus Affecting Sugar Accumulation in Melon (Cucumis melo L.)

PubMed Central

Argyris, Jason M.; Díaz, Aurora; Ruggieri, Valentino; Fernández, Marta; Jahrmann, Torben; Gibon, Yves; Picó, Belén; Martín-Hernández, Ana M.; Monforte, Antonio J.; Garcia-Mas, Jordi

2017-01-01

Sugar content is the major determinant of both fruit quality and consumer acceptance in melon (Cucumis melo L), and is a primary target for crop improvement. Near-isogenic lines (NILs) derived from the intraspecific cross between a “Piel de Sapo” (PS) type and the exotic cultivar “Songwhan Charmi” (SC), and several populations generated from the cross of PS × Ames 24294 (“Trigonus”), a wild melon, were used to identify QTL related to sugar and organic acid composition. Seventy-eight QTL were detected across several locations and different years, with three important clusters related to sugar content located on chromosomes 4, 5, and 7. Two PS × SC NILs (SC5-1 and SC5-2) sharing a common genomic interval of 1.7 Mb at the top of chromosome 5 contained QTL reducing soluble solids content (SSC) and sucrose content by an average of 29 and 68%, respectively. This cluster collocated with QTL affecting sugar content identified in other studies in lines developed from the PS × SC cross and supported the presence of a stable consensus locus involved in sugar accumulation that we named SUCQSC5.1. QTL reducing soluble solids and sucrose content identified in the “Trigonus” mapping populations, as well as QTL identified in previous studies from other ssp. agrestis sources, collocated with SUCQSC5.1, suggesting that they may be allelic and implying a role in domestication. In subNILs derived from the PS × SC5-1 cross, SUCQSC5.1 reduced SSC and sucrose content by an average of 18 and 34%, respectively, and was fine-mapped to a 56.1 kb interval containing four genes. Expression analysis of the candidate genes in mature fruit showed differences between the subNILs with PS alleles that were “high” sugar and SC alleles of “low” sugar phenotypes for MELO3C014519, encoding a putative BEL1-like homeodomain protein. Sequence differences in the gene predicted to affect protein function were restricted to SC and other ssp. agrestis cultivar groups. These results provide the basis for further investigation of genes affecting sugar accumulation in melon. PMID:29018473

Quantitative trait loci on chromosomes 2p, 4p, and 13q influence bone mineral density of the forearm and hip in Mexican Americans.

PubMed

Kammerer, Candace M; Schneider, Jennifer L; Cole, Shelley A; Hixson, James E; Samollow, Paul B; O'Connell, Jeffrey R; Perez, Reina; Dyer, Thomas D; Almasy, Laura; Blangero, John; Bauer, Richard L; Mitchell, Braxton D

2003-12-01

We performed a genome scan using BMD data of the forearm and hip on 664 individuals in 29 Mexican-American families. We obtained evidence for QTL on chromosome 4p, affecting forearm BMD overall, and on chromosomes 2p and 13q, affecting hip BMD in men. The San Antonio Family Osteoporosis Study (SAFOS) was designed to identify genes and environmental factors that influence bone mineral density (BMD) using data from large Mexican-American families. We performed a genome-wide linkage analysis using 416 highly polymorphic microsatellite markers spaced approximately 9.5 cM apart to locate and identify quantitative trait loci (QTL) that affect BMD of the forearm and hip. Multipoint variance components linkage analyses were done using data on all 664 subjects, as well as two subgroups of 259 men and 261 premenopausal women, from 29 families for which genotypic and phenotypic data were available. We obtained significant evidence for a QTL affecting forearm (radius midpoint) BMD in men and women combined on chromosome 4p near D4S2639 (maximum LOD = 4.33, genomic p = 0.006) and suggestive evidence for a QTL on chromosome 12q near locus D12S2070 (maximum conditional LOD = 2.35). We found suggestive evidence for a QTL influencing trochanter BMD on chromosome 6 (maximum LOD = 2.27), but no evidence for QTL affecting the femoral neck in men and women combined. In men, we obtained evidence for QTL affecting neck and trochanter BMD on chromosomes 2p near D2S1780 (maximum LOD = 3.98, genomic p = 0.013) and 13q near D13S788 (maximum LOD = 3.46, genomic p = 0.039), respectively. We found no evidence for QTL affecting forearm or hip BMD in premenopausal women. These results provide strong evidence that a QTL on chromosome 4p affects radius BMD in Mexican-American men and women, as well as evidence that QTL on chromosomes 2p and 13q affect hip BMD in men. Our results are consistent with some reports in humans and mice. J Bone Miner Res 2003;18:2245-2252

Transcriptome profiling of two maize inbreds with distinct responses to Gibberella ear rot disease to identify candidate resistance genes.

PubMed

Kebede, Aida Z; Johnston, Anne; Schneiderman, Danielle; Bosnich, Whynn; Harris, Linda J

2018-02-09

Gibberella ear rot (GER) is one of the most economically important fungal diseases of maize in the temperate zone due to moldy grain contaminated with health threatening mycotoxins. To develop resistant genotypes and control the disease, understanding the host-pathogen interaction is essential. RNA-Seq-derived transcriptome profiles of fungal- and mock-inoculated developing kernel tissues of two maize inbred lines were used to identify differentially expressed transcripts and propose candidate genes mapping within GER resistance quantitative trait loci (QTL). A total of 1255 transcripts were significantly (P ≤ 0.05) up regulated due to fungal infection in both susceptible and resistant inbreds. A greater number of transcripts were up regulated in the former (1174) than the latter (497) and increased as the infection progressed from 1 to 2 days after inoculation. Focusing on differentially expressed genes located within QTL regions for GER resistance, we identified 81 genes involved in membrane transport, hormone regulation, cell wall modification, cell detoxification, and biosynthesis of pathogenesis related proteins and phytoalexins as candidate genes contributing to resistance. Applying droplet digital PCR, we validated the expression profiles of a subset of these candidate genes from QTL regions contributed by the resistant inbred on chromosomes 1, 2 and 9. By screening global gene expression profiles for differentially expressed genes mapping within resistance QTL regions, we have identified candidate genes for gibberella ear rot resistance on several maize chromosomes which could potentially lead to a better understanding of Fusarium resistance mechanisms.

QTL detection for forage quality and stem histology in four connected mapping populations of the model legume Medicago truncatula.

PubMed

Lagunes Espinoza, Luz Del Carmen; Julier, Bernadette

2013-02-01

Forage quality combines traits related to protein content and energy value. High-quality forages contribute to increase farm autonomy by reducing the use of energy or protein-rich supplements. Genetic analyses in forage legume species are complex because of their tetraploidy and allogamy. Indeed, no genetic studies of quality have been published at the molecular level on these species. Nonetheless, mapping populations of the model species M. truncatula can be used to detect QTL for forage quality. Here, we studied a crossing design involving four connected populations of M. truncatula. Each population was composed of ca. 200 recombinant inbred lines (RIL). We sought population-specific QTL and QTL explaining the whole design variation. We grew parents and RIL in a greenhouse for 2 or 3 seasons and analysed plants for chemical composition of vegetative organs (protein content, digestibility, leaf-to-stem ratio) and stem histology (stem cross-section area, tissue proportions). Over the four populations and all the traits, QTL were found on all chromosomes. Among these QTL, only four genomic regions, on chromosomes 1, 3, 7 and 8, contributed to explaining the variations in the whole crossing design. Surprisingly, we found that quality QTL were located in the same genomic regions as morphological QTL. We thus confirmed the quantitative inheritance of quality traits and tight relationships between quality and morphology. Our findings could be explained by a co-location of genes involved in quality and morphology. This study will help to detect candidate genes involved in quantitative variation for quality in forage legume species.

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed.

PubMed

Martínez-Montes, Ángel M; Fernández, Almudena; Muñoz, María; Noguera, Jose Luis; Folch, Josep M; Fernández, Ana I

2018-01-01

One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0-3 Mb, for body weight, on SSC2, 3-9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed.

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. III

Treesearch

Kathleen D. Jermstad; Daniel L. Bassoni; Keith S. Jech; Gary A. Ritchie; Nicholas C. Wheeler; David B. Neale

2003-01-01

Quantitative trait loci (QTL) were mapped in the woody perennial Douglas fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) for complex traits controlling the timing of growth initiation and growth cessation. QTL were estimated under controlled environmental conditions to identify QTL interactions with photoperiod, moisture stress, winter chilling, and spring...

A quantitative trait locus mixture model that avoids spurious LOD score peaks.

PubMed Central

Feenstra, Bjarke; Skovgaard, Ib M

2004-01-01

In standard interval mapping of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. At any given location in the genome, the evidence of a putative QTL is measured by the likelihood ratio of the mixture model compared to a single normal distribution (the LOD score). This approach can occasionally produce spurious LOD score peaks in regions of low genotype information (e.g., widely spaced markers), especially if the phenotype distribution deviates markedly from a normal distribution. Such peaks are not indicative of a QTL effect; rather, they are caused by the fact that a mixture of normals always produces a better fit than a single normal distribution. In this study, a mixture model for QTL mapping that avoids the problems of such spurious LOD score peaks is presented. PMID:15238544

A quantitative trait locus mixture model that avoids spurious LOD score peaks.

PubMed

Feenstra, Bjarke; Skovgaard, Ib M

2004-06-01

In standard interval mapping of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. At any given location in the genome, the evidence of a putative QTL is measured by the likelihood ratio of the mixture model compared to a single normal distribution (the LOD score). This approach can occasionally produce spurious LOD score peaks in regions of low genotype information (e.g., widely spaced markers), especially if the phenotype distribution deviates markedly from a normal distribution. Such peaks are not indicative of a QTL effect; rather, they are caused by the fact that a mixture of normals always produces a better fit than a single normal distribution. In this study, a mixture model for QTL mapping that avoids the problems of such spurious LOD score peaks is presented.

A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle.

PubMed

Ma, Junwu; Yang, Jie; Zhou, Lisheng; Ren, Jun; Liu, Xianxian; Zhang, Hui; Yang, Bin; Zhang, Zhiyan; Ma, Huanban; Xie, Xianhua; Xing, Yuyun; Guo, Yuanmei; Huang, Lusheng

2014-10-01

Glycolytic potential (GP) in skeletal muscle is economically important in the pig industry because of its effect on pork processing yield. We have previously mapped a major quantitative trait loci (QTL) for GP on chromosome 3 in a White Duroc × Erhualian F2 intercross. We herein performed a systems genetic analysis to identify the causal variant underlying the phenotype QTL (pQTL). We first conducted genome-wide association analyses in the F2 intercross and an F19 Sutai pig population. The QTL was then refined to an 180-kb interval based on the 2-LOD drop method. We then performed expression QTL (eQTL) mapping using muscle transcriptome data from 497 F2 animals. Within the QTL interval, only one gene (PHKG1) has a cis-eQTL that was colocolizated with pQTL peaked at the same SNP. The PHKG1 gene encodes a catalytic subunit of the phosphorylase kinase (PhK), which functions in the cascade activation of glycogen breakdown. Deep sequencing of PHKG1 revealed a point mutation (C>A) in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon. The aberrant transcript induces nonsense-mediated decay, leading to lower protein level and weaker enzymatic activity in affected animals. The mutation causes an increase of 43% in GP and a decrease of>20% in water-holding capacity of pork. These effects were consistent across the F2 and Sutai populations, as well as Duroc × (Landrace × Yorkshire) hybrid pigs. The unfavorable allele exists predominantly in Duroc-derived pigs. The findings provide new insights into understanding risk factors affecting glucose metabolism, and would greatly contribute to the genetic improvement of meat quality in Duroc related pigs.

Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing.

PubMed

Branham, Sandra E; Stansell, Zachary J; Couillard, David M; Farnham, Mark W

2017-03-01

Five quantitative trait loci and one epistatic interaction were associated with heat tolerance in a doubled haploid population of broccoli evaluated in three summer field trials. Predicted rising global temperatures due to climate change have generated a demand for crops that are resistant to yield and quality losses from heat stress. Broccoli (Brassica oleracea var. italica) is a cool weather crop with high temperatures during production decreasing both head quality and yield. Breeding for heat tolerance in broccoli has potential to both expand viable production areas and extend the growing season but breeding efficiency is constrained by limited genetic information. A doubled haploid (DH) broccoli population segregating for heat tolerance was evaluated for head quality in three summer fields in Charleston, SC, USA. Multiple quantitative trait loci (QTL) mapping of 1,423 single nucleotide polymorphisms developed through genotyping-by-sequencing identified five QTL and one positive epistatic interaction that explained 62.1% of variation in heat tolerance. The QTL identified here can be used to develop markers for marker-assisted selection and to increase our understanding of the molecular mechanisms underlying plant response to heat stress.

High Diversity of Genes for Nonhost Resistance of Barley to Heterologous Rust Fungi

PubMed Central

Jafary, Hossein; Albertazzi, Giorgia; Marcel, Thierry C.; Niks, Rients E.

2008-01-01

Inheritance studies on the nonhost resistance of plants would normally require interspecific crosses that suffer from sterility and abnormal segregation. Therefore, we developed the barley–Puccinia rust model system to study, using forward genetics, the specificity, number, and diversity of genes involved in nonhost resistance. We developed two mapping populations by crossing the line SusPtrit, with exceptional susceptibility to heterologous rust species, with the immune barley cultivars Vada and Cebada Capa. These two mapping populations along with the Oregon Wolfe Barley population, which showed unexpected segregation for resistance to heterologous rusts, were phenotyped with four heterologous rust fungal species. Positions of QTL conferring nonhost resistance in the three mapping populations were compared using an integrated consensus map. The results confirmed that nonhost resistance in barley to heterologous rust species is controlled by QTL with different and overlapping specificities and by an occasional contribution of an R-gene for hypersensitivity. In each population, different sets of loci were implicated in resistance. Few genes were common between the populations, suggesting a high diversity of genes conferring nonhost resistance to heterologous pathogens. These loci were significantly associated with QTL for partial resistance to the pathogen Puccinia hordei and with defense-related genes. PMID:18430953

Genetic linkage of hyperglycemia and dyslipidemia in an intercross between BALB/cJ and SM/J Apoe-deficient mouse strains.

PubMed

Wang, Qian; Grainger, Andrew T; Manichaikul, Ani; Farber, Emily; Onengut-Gumuscu, Suna; Shi, Weibin

2015-11-10

Individuals with dyslipidemia often develop type 2 diabetes, and diabetic patients often have dyslipidemia. It remains to be determined whether there are genetic connections between the 2 disorders. A female F2 cohort, generated from BALB/cJ (BALB) and SM/J (SM) Apoe-deficient (Apoe(-/-)) strains, was started on a Western diet at 6 weeks of age and maintained on the diet for 12 weeks. Fasting plasma glucose and lipid levels were measured before and after 12 weeks of Western diet. 144 genetic markers across the entire genome were used for quantitative trait locus (QTL) analysis. One significant QTL on chromosome 9, named Bglu17 [26.4 cM, logarithm of odds ratio (LOD): 5.4], and 3 suggestive QTLs were identified for fasting glucose levels. The suggestive QTL near the proximal end of chromosome 9 (2.4 cM, LOD: 3.12) was replicated at both time points and named Bglu16. Bglu17 coincided with a significant QTL for HDL (high-density lipoprotein) and a suggestive QTL for non-HDL cholesterol levels. Plasma glucose levels were inversely correlated with HDL but positively correlated with non-HDL cholesterol levels in F2 mice on either chow or Western diet. A significant correlation between fasting glucose and triglyceride levels was also observed on the Western diet. Haplotype analysis revealed that "lipid genes" Sik3, Apoa1, and Apoc3 were probable candidates for Bglu17. We have identified multiple QTLs for fasting glucose and lipid levels. The colocalization of QTLs for both phenotypes and the sharing of potential candidate genes demonstrate genetic connections between dyslipidemia and type 2 diabetes.

Identification of quantitative trait loci affecting resistance to gastrointestinal parasites in a double backcross population of Red Maasai and Dorper sheep.

PubMed

Silva, M V B; Sonstegard, T S; Hanotte, O; Mugambi, J M; Garcia, J F; Nagda, S; Gibson, J P; Iraqi, F A; McClintock, A E; Kemp, S J; Boettcher, P J; Malek, M; Van Tassell, C P; Baker, R L

2012-02-01

A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal nematode resistance in sheep was completed using a double backcross population derived from Red Maasai and Dorper ewes bred to F(1) rams. This design provided an opportunity to map potentially unique genetic variation associated with a parasite-tolerant breed like Red Maasai, a breed developed to survive East African grazing conditions. Parasite indicator phenotypes (blood packed cell volume - PCV and faecal egg count - FEC) were collected on a weekly basis from 1064 lambs during a single 3-month post-weaning grazing challenge on infected pastures. The averages of last measurements for FEC (AVFEC) and PCV (AVPCV), along with decline in PCV from challenge start to end (PCVD), were used to select lambs (N = 371) for genotyping that represented the tails (10% threshold) of the phenotypic distributions. Marker genotypes for 172 microsatellite loci covering 25 of 26 autosomes (1560.7 cm) were scored and corrected by Genoprob prior to qxpak analysis that included Box-Cox transformed AVFEC and arcsine transformed PCV statistics. Significant QTL for AVFEC and AVPCV were detected on four chromosomes, and this included a novel AVFEC QTL on chromosome 6 that would have remained undetected without Box-Cox transformation methods. The most significant P-values for AVFEC, AVPCV and PCVD overlapped the same marker interval on chromosome 22, suggesting the potential for a single causative mutation, which remains unknown. In all cases, the favourable QTL allele was always contributed from Red Maasai, providing support for the idea that future marker-assisted selection for genetic improvement of production in East Africa will rely on markers in linkage disequilibrium with these QTL. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus.

PubMed

Lu, Xia; Luan, Sheng; Hu, Long Yang; Mao, Yong; Tao, Ye; Zhong, Sheng Ping; Kong, Jie

2016-06-01

The Kuruma prawn, Marsupenaeus japonicus, is one of the most promising marine invertebrates in the industry in Asia, Europe and Australia. However, the increasing global temperatures result in considerable economic losses in M. japonicus farming. In the present study, to select genetically improved animals for the sustainable development of the Kuruma prawn industry, a high-resolution genetic linkage map and quantitative trait locus (QTL) identification were performed using the RAD technology. The maternal map contained 5849 SNP markers and spanned 3127.23 cM, with an average marker interval of 0.535 cM. Instead, the paternal map contained 3927 SNP markers and spanned 3326.19 cM, with an average marker interval of 0.847 cM. The consensus map contained 9289 SNP markers and spanned 3610.90 cM, with an average marker interval of 0.388 cM and coverage of 99.06 % of the genome. The markers were grouped into 41 linkage groups in the maps. Significantly, negative correlation was detected between high-temperature tolerance (UTT) and body weight (BW). The QTL mapping revealed 129 significant QTL loci for UTT and four significant QTL loci for BW at the genome-wide significance threshold. Among these QTLs, 129 overlapped with linked SNPs, and the remaining four were located in regions between contiguous SNPs. They explained the total phenotypic variance ranging from 8.9 to 12.4 %. Because of a significantly negative correlation between growth and high-temperature tolerance, we demonstrate that this high-resolution linkage map and QTLs would be useful for further marker-assisted selection in the genetic improvement of M. japonicus.

GWAS analysis using interspecific backcross progenies reveals superior blue catfish alleles responsible for strong resistance against enteric septicemia of catfish.

PubMed

Tan, Suxu; Zhou, Tao; Wang, Wenwen; Jin, Yulin; Wang, Xiaozhu; Geng, Xin; Luo, Jian; Yuan, Zihao; Yang, Yujia; Shi, Huitong; Gao, Dongya; Dunham, Rex; Liu, Zhanjiang

2018-05-08

Infectious diseases pose significant threats to the catfish industry. Enteric septicemia of catfish (ESC) caused by Edwardsiella ictaluri is the most devastating disease for catfish aquaculture, causing huge economic losses annually. Channel catfish and blue catfish exhibit great contrast in resistance against ESC, with channel catfish being highly susceptible and blue catfish being highly resistant. As such, the interspecific backcross progenies provide an ideal system for the identification of quantitative trait locus (QTL). We previously reported one significant QTL on linkage group (LG) 1 using the third-generation backcrosses, but the number of founders used to make the second- and third-generation backcross progenies was very small. Although the third-generation backcross progenies provided a greater power for fine mapping than the first-generation backcrosses, some major QTL for disease resistance may have been missing due to the small numbers of founders used to produce the higher generation backcrosses. In this study, we performed a genome-wide association study using first-generation backcrosses with the catfish 690 K SNP arrays to identify additional ESC disease resistance QTL, especially those at the species level. Two genomic regions on LG1 and LG23 were determined to be significantly associated with ESC resistance as revealed by a mixed linear model and family-based association test. Examination of the resistance alleles indicated their origin from blue catfish, indicating that at least two major disease resistance loci exist among blue catfish populations. Upon further validation, markers linked with major ESC disease resistance QTL should be useful for marker-assisted introgression, allowing development of highly ESC resistant breeds of catfish.

QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits.

PubMed

Causse, M; Saliba-Colombani, V; Lecomte, L; Duffé, P; Rousselle, P; Buret, M

2002-10-01

The organoleptic quality of tomato fruit involves a set of attributes (flavour, aroma, texture) that can be evaluated either by sensory analyses or by instrumental measures. In order to study the genetic control of this characteristic, a recombinant inbred line (RIL) population was developed from an intraspecific cross between a cherry tomato line with a good overall aroma intensity and an inbred line with medium flavour but bigger fruits. A total of 38 traits involved in organoleptic quality were evaluated. Physical traits included fruit weight, diameter, colour, firmness, and elasticity. Chemical traits were dry matter weight, titratable acidity, pH, and the contents of soluble solids, sugars, lycopene, carotene, and 12 aroma volatiles. A panel of trained assessors quantified sensory attributes: flavour (sweetness and sourness), aroma (overall aroma intensity, together with candy, lemon, citrus fruit, and pharmaceutical aromas) and texture (firmness, meltiness, mealiness, juiciness, and skin difficult to swallow). RILs showed a large range of variation. Molecular markers were used to map a total of 130 quantitative trait loci (QTL) for the 38 traits. They were mainly distributed in a few chromosome regions. Major QTLs (R(2) >30%) were detected for fruit weight, diameter, colour, firmness, meltiness, and for six aroma volatiles. The relationships between instrumental measures and sensory traits were analysed with regard to the QTL map. A special insight was provided about the few regions where QTLs are related to multiple traits. A few examples are shown to illustrate how the simultaneous analysis of QTL segregation for related traits may aid in understanding the genetic control of quality traits and pave the way towards QTL characterization.

Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye.

PubMed

Yun, Lan; Larson, Steve R; Mott, Ivan W; Jensen, Kevin B; Staub, Jack E

2014-06-01

Rhizomes are prostrate subterranean stems that provide primitive mechanisms of vegetative dispersal, survival, and regrowth of perennial grasses and other monocots. The extent of rhizome proliferation varies greatly among grasses, being absent in cereals and other annuals, strictly confined in caespitose perennials, or highly invasive in some perennial weeds. However, genetic studies of rhizome proliferation are limited and genes controlling rhizomatous growth habit have not been elucidated. Quantitative trait loci (QTLs) controlling rhizome spreading were compared in reciprocal backcross populations derived from hybrids of rhizomatous creeping wildrye (Leymus triticoides) and caespitose basin wildrye (L. cinereus), which are perennial relatives of wheat. Two recessive QTLs were unique to the creeping wildrye backcross, one dominant QTL was unique to the basin wildrye backcross, and one additive QTL was detectable in reciprocal backcrosses with high log odds (LOD = 31.6) in the basin wildrye background. The dominant QTL located on linkage group (LG)-2a was aligned to a dominant rhizome orthogene (Rhz3) of perennial rice (Oryza longistamina) and perennial sorghum (Sorghum propinquum). Nonparametric 99 % confidence bounds of the 31.6-LOD QTL were localized to a distal 3.8-centiMorgan region of LG-6a, which corresponds to a 0.7-Mb region of Brachypodium Chromosome 3 containing 106 genes. An Aux/IAA auxin signal factor gene was located at the 31.6-LOD peak, which could explain the gravitropic and aphototropic behavior of rhizomes. Findings elucidate genetic mechanisms controlling rhizome development and architectural growth habit differences among plant species. Results have possible applications to improve perennial forage and turf grasses, extend the vegetative life cycle of annual cereals, such as wheat, or control the invasiveness of highly rhizomatous weeds such as quackgrass (Elymus repens).

Major quality trait analysis and QTL detection in hexaploid wheat in humid rain-fed agriculture.

PubMed

Li, H M; Tang, Z X; Zhang, H Q; Yan, B J; Ren, Z L

2013-05-21

Humid rain-fed agriculture is a special environment for wheat (Triticum aestivum) culture that tends to negatively affect wheat yield and quality. To identify quality characters of wheat in a humid environment, we conducted quality analysis and quantitative trait loci (QTL) detection in a recombinant inbred line whose parent had a high level of quality for several years. We found that high-quality wheat had less gluten content and lower protein content. Apparently, wheat quality and associated quantity traits were in a dynamic state of equilibrium. We detected 83 QTL for 10 wheat quality traits in this recombinant inbred line population. Nine QTL were detected in both evaluation years; Q.DT.scau-2A, linked to Xwmc522-2A, was detected at the same genetic location in both years. Other QTL for different traits were detected simultaneously in more than one location. Consequently, there appeared to be pleiotropic genes that control wheat quality. Based on previous studies and our research on QTL analysis of grain protein content, we conclude that there must be one or more genes for grain protein content on chromosome 6B, whose expression was little affected by environment. We constructed a consensus map and projected the QTL on it. It was useful for choosing optimal markers for marker-assisted breeding and map-based cloning.

QTL analysis of ergot resistance in sorghum.

PubMed

Parh, D K; Jordan, D R; Aitken, E A B; Mace, E S; Jun-ai, P; McIntyre, C L; Godwin, I D

2008-08-01

Sorghum ergot, caused predominantly by Claviceps africana Frederickson, Mantle, de Milliano, is a significant threat to the sorghum industry worldwide. The objectives of this study were firstly, to identify molecular markers linked to ergot resistance and to two pollen traits, pollen quantity (PQ) and pollen viability (PV), and secondly, to assess the relationship between the two pollen traits and ergot resistance in sorghum. A genetic linkage map of sorghum RIL population R931945-2-2 x IS 8525 (resistance source) was constructed using 303 markers including 36 SSR, 117 AFLP , 148 DArT and two morphological trait loci. Composite interval mapping identified nine, five, and four QTL linked to molecular markers for percentage ergot infection (PCERGOT), PQ and PV, respectively, at a LOD >2.0. Co-location/linkage of QTL were identified on four chromosomes while other QTL for the three traits mapped independently, indicating that both pollen and non pollen-based mechanisms of ergot resistance were operating in this sorghum population. Of the nine QTL identified for PCERGOT, five were identified using the overall data set while four were specific to the group data sets defined by temperature and humidity. QTL identified on SBI-02 and SBI-06 were further validated in additional populations. This is the first report of QTL associated with ergot resistance in sorghum. The markers reported herein could be used for marker-assisted selection for this important disease of sorghum.

A High Density Genetic Map Derived from RAD Sequencing and Its Application in QTL Analysis of Yield-Related Traits in Vigna unguiculata

PubMed Central

Pan, Lei; Wang, Nian; Wu, Zhihua; Guo, Rui; Yu, Xiaolu; Zheng, Yu; Xia, Qiuju; Gui, Songtao; Chen, Chanyou

2017-01-01

Cowpea [Vigna unguiculata (L.) Walp.] is an annual legume of economic importance and widely grown in the semi-arid tropics. However, high-density genetic maps of cowpea are still lacking. Here, we identified 34,868 SNPs (single nucleotide polymorphisms) that were distributed in the cowpea genome based on the RAD sequencing (restriction-site associated DNA sequencing) technique using a population of 170 individuals (two cowpea parents and 168 F2:3 progenies). Of these, 17,996 reliable SNPs were allotted to 11 consensus linkage groups (LGs). The length of the genetic map was 1,194.25 cM in total with a mean distance of 0.066 cM/SNP marker locus. Using this map and the F2:3 population, combined with the CIM (composite interval mapping) method, eleven quantitative trait loci (QTL) of yield-related trait were detected on seven LGs (LG4, 5, 6, 7, 9, 10, and 11) in cowpea. These QTL explained 0.05–17.32% of the total phenotypic variation. Among these, four QTL were for pod length, four QTL for thousand-grain weight (TGW), two QTL for grain number per pod, and one QTL for carpopodium length. Our results will provide a foundation for understanding genes related to grain yield in the cowpea and genus Vigna. PMID:28936219

Genetic and Quantitative Trait Locus Analysis of Cell Wall Components and Forage Digestibility in the Zheng58 × HD568 Maize RIL Population at Anthesis Stage

PubMed Central

Li, Kun; Wang, Hongwu; Hu, Xiaojiao; Ma, Feiqian; Wu, Yujin; Wang, Qi; Liu, Zhifang; Huang, Changling

2017-01-01

The plant cell wall plays vital roles in various aspects of the plant life cycle. It provides a basic structure for cells and gives mechanical rigidity to the whole plant. Some complex cell wall components are involved in signal transduction during pathogenic infection and pest infestations. Moreover, the lignification level of cell walls strongly influences the digestibility of forage plants. To determine the genetic bases of cell wall components and digestibility, quantitative trait locus (QTL) analyses for six related traits were performed using a recombinant inbred line (RIL) population from a cross between Zheng58 and HD568. Eight QTL for in vitro neutral detergent fiber (NDF) digestibility were observed, out of which only two increasing alleles came from HD568. Three QTL out of ten with alleles increasing in vitro dry matter digestibility also originated from HD568. Five–ten QTL were detected for lignin, cellulose content, acid detergent fiber, and NDF content. Among these results, 29.8% (14/47) of QTL explained >10% of the phenotypic variation in the RIL population, whereas 70.2% (33/47) explained ≤10%. These results revealed that in maize stalks, a few large-effect QTL and a number of minor-effect QTL contributed to most of the genetic components involved in cell wall biosynthesis and digestibility. PMID:28883827

Genetic and Quantitative Trait Locus Analysis of Cell Wall Components and Forage Digestibility in the Zheng58 × HD568 Maize RIL Population at Anthesis Stage.

PubMed

Li, Kun; Wang, Hongwu; Hu, Xiaojiao; Ma, Feiqian; Wu, Yujin; Wang, Qi; Liu, Zhifang; Huang, Changling

2017-01-01

The plant cell wall plays vital roles in various aspects of the plant life cycle. It provides a basic structure for cells and gives mechanical rigidity to the whole plant. Some complex cell wall components are involved in signal transduction during pathogenic infection and pest infestations. Moreover, the lignification level of cell walls strongly influences the digestibility of forage plants. To determine the genetic bases of cell wall components and digestibility, quantitative trait locus (QTL) analyses for six related traits were performed using a recombinant inbred line (RIL) population from a cross between Zheng58 and HD568. Eight QTL for in vitro neutral detergent fiber (NDF) digestibility were observed, out of which only two increasing alleles came from HD568. Three QTL out of ten with alleles increasing in vitro dry matter digestibility also originated from HD568. Five-ten QTL were detected for lignin, cellulose content, acid detergent fiber, and NDF content. Among these results, 29.8% (14/47) of QTL explained >10% of the phenotypic variation in the RIL population, whereas 70.2% (33/47) explained ≤10%. These results revealed that in maize stalks, a few large-effect QTL and a number of minor-effect QTL contributed to most of the genetic components involved in cell wall biosynthesis and digestibility.

Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine

USDA-ARS?s Scientific Manuscript database

Mapping quantitative trait loci (QTL) in swine at the US Meat Animal Research Center has relied heavily on linkage mapping in either F2 or Backcross families. QTL identified in the initial scans typically have very broad confidence intervals and further refinement of the QTL’s position is needed bef...

Validation of linked QTL for bacterial cold water disease resistance and spleen size on rainbow trout chromosome Omy19

USDA-ARS?s Scientific Manuscript database

Bacterial cold water disease (BCWD) is caused by infection with Flavobacterium psychrophilum, and results in significant economic losses in salmonid aquaculture. Previously, we identified a major QTL for BCWD resistance and a QTL for spleen size (SPLW = spleen weight and SPLI = spleen index) in naï...

Gene pyramiding enhances durable blast disease resistance in rice

PubMed Central

Fukuoka, Shuichi; Saka, Norikuni; Mizukami, Yuko; Koga, Hironori; Yamanouchi, Utako; Yoshioka, Yosuke; Hayashi, Nagao; Ebana, Kaworu; Mizobuchi, Ritsuko; Yano, Masahiro

2015-01-01

Effective control of blast, a devastating fungal disease of rice, would increase and stabilize worldwide food production. Resistance mediated by quantitative trait loci (QTLs), which usually have smaller individual effects than R-genes but confer broad-spectrum or non-race-specific resistance, is a promising alternative to less durable race-specific resistance for crop improvement, yet evidence that validates the impact of QTL combinations (pyramids) on the durability of plant disease resistance has been lacking. Here, we developed near-isogenic experimental lines representing all possible combinations of four QTL alleles from a durably resistant cultivar. These lines enabled us to evaluate the QTLs singly and in combination in a homogeneous genetic background. We present evidence that pyramiding QTL alleles, each controlling a different response to M. oryzae, confers strong, non-race-specific, environmentally stable resistance to blast disease. Our results suggest that this robust defence system provides durable resistance, thus avoiding an evolutionary “arms race” between a crop and its pathogen. PMID:25586962

Gene pyramiding enhances durable blast disease resistance in rice.

PubMed

Fukuoka, Shuichi; Saka, Norikuni; Mizukami, Yuko; Koga, Hironori; Yamanouchi, Utako; Yoshioka, Yosuke; Hayashi, Nagao; Ebana, Kaworu; Mizobuchi, Ritsuko; Yano, Masahiro

2015-01-14

Effective control of blast, a devastating fungal disease of rice, would increase and stabilize worldwide food production. Resistance mediated by quantitative trait loci (QTLs), which usually have smaller individual effects than R-genes but confer broad-spectrum or non-race-specific resistance, is a promising alternative to less durable race-specific resistance for crop improvement, yet evidence that validates the impact of QTL combinations (pyramids) on the durability of plant disease resistance has been lacking. Here, we developed near-isogenic experimental lines representing all possible combinations of four QTL alleles from a durably resistant cultivar. These lines enabled us to evaluate the QTLs singly and in combination in a homogeneous genetic background. We present evidence that pyramiding QTL alleles, each controlling a different response to M. oryzae, confers strong, non-race-specific, environmentally stable resistance to blast disease. Our results suggest that this robust defence system provides durable resistance, thus avoiding an evolutionary "arms race" between a crop and its pathogen.

Dahl (S × R) rat congenic strain analysis confirms and defines a chromosome 17 spatial navigation quantitative trait locus to <10 Mbp.

PubMed

Herrera, Victoria L; Pasion, Khristine A; Tan, Glaiza A; Ruiz-Opazo, Nelson

2013-01-01

A quantitative trait locus (QTL) linked with ability to find a platform in the Morris Water Maze (MWM) was located on chromosome 17 (Nav-5 QTL) using intercross between Dahl S and Dahl R rats. We developed two congenic strains, S.R17A and S.R17B introgressing Dahl R-chromosome 17 segments into Dahl S chromosome 17 region spanning putative Nav-5 QTL. Performance analysis of S.R17A, S.R17B and Dahl S rats in the Morris water maze (MWM) task showed a significantly decreased spatial navigation performance in S.R17B congenic rats when compared with Dahl S controls (P = 0.02). The S.R17A congenic segment did not affect MWM performance delimiting Nav-5 to the chromosome 17 65.02-74.66 Mbp region. Additional fine mapping is necessary to identify the specific gene variant accounting for Nav-5 effect on spatial learning and memory in Dahl rats.

Dynamic Quantitative Trait Locus Analysis of Plant Phenomic Data.

PubMed

Li, Zitong; Sillanpää, Mikko J

2015-12-01

Advanced platforms have recently become available for automatic and systematic quantification of plant growth and development. These new techniques can efficiently produce multiple measurements of phenotypes over time, and introduce time as an extra dimension to quantitative trait locus (QTL) studies. Functional mapping utilizes a class of statistical models for identifying QTLs associated with the growth characteristics of interest. A major benefit of functional mapping is that it integrates information over multiple timepoints, and therefore could increase the statistical power for QTL detection. We review the current development of computationally efficient functional mapping methods which provide invaluable tools for analyzing large-scale timecourse data that are readily available in our post-genome era. Copyright © 2015 Elsevier Ltd. All rights reserved.

The genetic architecture of UV floral patterning in sunflower.

PubMed

Moyers, Brook T; Owens, Gregory L; Baute, Gregory J; Rieseberg, Loren H

2017-07-01

The patterning of floral ultraviolet (UV) pigmentation varies both intra- and interspecifically in sunflowers and many other plant species, impacts pollinator attraction, and can be critical to reproductive success and crop yields. However, the genetic basis for variation in UV patterning is largely unknown. This study examines the genetic architecture for proportional and absolute size of the UV bullseye in Helianthus argophyllus , a close relative of the domesticated sunflower. A camera modified to capture UV light (320-380 nm) was used to phenotype floral UV patterning in an F 2 mapping population, then quantitative trait loci (QTL) were identified using genotyping-by-sequencing and linkage mapping. The ability of these QTL to predict the UV patterning of natural population individuals was also assessed. Proportional UV pigmentation is additively controlled by six moderate effect QTL that are predictive of this phenotype in natural populations. In contrast, UV bullseye size is controlled by a single large effect QTL that also controls flowerhead size and co-localizes with a major flowering time QTL in Helianthus . The co-localization of the UV bullseye size QTL, flowerhead size QTL and a previously known flowering time QTL may indicate a single highly pleiotropic locus or several closely linked loci, which could inhibit UV bullseye size from responding to selection without change in correlated characters. The genetic architecture of proportional UV pigmentation is relatively simple and different from that of UV bullseye size, and so should be able to respond to natural or artificial selection independently. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Two candidate genes for two quantitative trait loci epistatically attenuate hypertension in a novel pathway.

PubMed

Chauvet, Cristina; Ménard, Annie; Deng, Alan Y

2015-09-01

Multiple quantitative trait loci (QTLs) for blood pressure (BP) have been detected in rat models of human polygenic hypertension. They influence BP physiologically via epistatic modules. Little is known about the causal genes and virtually nothing is known on modularized mechanisms governing their regulatory connections. Two genes responsible for two individual BP QTLs on rat Chromosome 18 have been identified that belong to the same epistatic module. Treacher Collins-Franceschetti syndrome 1 (Tcof1) gene is the only function candidate for C18QTL3. Haloacid dehalogenase like hydrolase domain containing 2 (Hdhd2), although a gene of previously unknown function, is C18QTL4, and encodes a newly identified phosphatase. The current work has provided the premier evidence that Hdhd2/C18QTL4 and Tcof1/C18QTL3 may be involved in polygenic hypertension. Hdhd2/C18QTL4 can regulate the function of Tcof1/C18QTL3 via de-phosphorylation, and, for the first time, furbishes a molecular mechanism in support of a genetically epistatic hierarchy between two BP QTLs, and thus authenticates the epistasis-common pathway paradigm. The pathway initiated by Hdhd2/C18QTL4 upstream of Tcof1/C18QTL3 reveals novel mechanistic insights into BP modulations. Their discovery might yield innovative therapeutic targets and diagnostic tools predicated on a novel BP cause and mechanism that is determined by a regulatory hierarchy. Optimizing the de-phosphorylation capability and its downstream target could be antihypertensive. The conceptual paradigm of an order and regulatory hierarchy may help unravel genetic and molecular relationships among certain human BP QTLs.

Genetic Architecture of Ear Fasciation in Maize (Zea mays) under QTL Scrutiny

PubMed Central

Mendes-Moreira, Pedro; Alves, Mara L.; Satovic, Zlatko; dos Santos, João Pacheco; Santos, João Nina; Souza, João Cândido; Pêgo, Silas E.; Hallauer, Arnel R.; Vaz Patto, Maria Carlota

2015-01-01

Maize ear fasciation Knowledge of the genes affecting maize ear inflorescence may lead to better grain yield modeling. Maize ear fasciation, defined as abnormal flattened ears with high kernel row number, is a quantitative trait widely present in Portuguese maize landraces. Material and Methods Using a segregating population derived from an ear fasciation contrasting cross (consisting of 149 F2:3 families) we established a two location field trial using a complete randomized block design. Correlations and heritabilities for several ear fasciation-related traits and yield were determined. Quantitative Trait Loci (QTL) involved in the inheritance of those traits were identified and candidate genes for these QTL proposed. Results and Discussion Ear fasciation broad-sense heritability was 0.73. Highly significant correlations were found between ear fasciation and some ear and cob diameters and row number traits. For the 23 yield and ear fasciation-related traits, 65 QTL were identified, out of which 11 were detected in both environments, while for the three principal components, five to six QTL were detected per environment. Detected QTL were distributed across 17 genomic regions and explained individually, 8.7% to 22.4% of the individual traits or principal components phenotypic variance. Several candidate genes for these QTL regions were proposed, such as bearded-ear1, branched silkless1, compact plant1, ramosa2, ramosa3, tasselseed4 and terminal ear1. However, many QTL mapped to regions without known candidate genes, indicating potential chromosomal regions not yet targeted for maize ear traits selection. Conclusions Portuguese maize germplasm represents a valuable source of genes or allelic variants for yield improvement and elucidation of the genetic basis of ear fasciation traits. Future studies should focus on fine mapping of the identified genomic regions with the aim of map-based cloning. PMID:25923975

Genetic control of water use efficiency and leaf carbon isotope discrimination in sunflower (Helianthus annuus L.) subjected to two drought scenarios.

PubMed

Adiredjo, Afifuddin Latif; Navaud, Olivier; Muños, Stephane; Langlade, Nicolas B; Lamaze, Thierry; Grieu, Philippe

2014-01-01

High water use efficiency (WUE) can be achieved by coordination of biomass accumulation and water consumption. WUE is physiologically and genetically linked to carbon isotope discrimination (CID) in leaves of plants. A population of 148 recombinant inbred lines (RILs) of sunflower derived from a cross between XRQ and PSC8 lines was studied to identify quantitative trait loci (QTL) controlling WUE and CID, and to compare QTL associated with these traits in different drought scenarios. We conducted greenhouse experiments in 2011 and 2012 by using 100 balances which provided a daily measurement of water transpired, and we determined WUE, CID, biomass and cumulative water transpired by plants. Wide phenotypic variability, significant genotypic effects, and significant negative correlations between WUE and CID were observed in both experiments. A total of nine QTL controlling WUE and eight controlling CID were identified across the two experiments. A QTL for phenotypic response controlling WUE and CID was also significantly identified. The QTL for WUE were specific to the drought scenarios, whereas the QTL for CID were independent of the drought scenarios and could be found in all the experiments. Our results showed that the stable genomic regions controlling CID were located on the linkage groups 06 and 13 (LG06 and LG13). Three QTL for CID were co-localized with the QTL for WUE, biomass and cumulative water transpired. We found that CID and WUE are highly correlated and have common genetic control. Interestingly, the genetic control of these traits showed an interaction with the environment (between the two drought scenarios and control conditions). Our results open a way for breeding higher WUE by using CID and marker-assisted approaches and therefore help to maintain the stability of sunflower crop production.

Water Deficit and Salinity Stress Reveal Many Specific QTL for Plant Growth and Fruit Quality Traits in Tomato

PubMed Central

Diouf, Isidore A.; Derivot, Laurent; Bitton, Frédérique; Pascual, Laura; Causse, Mathilde

2018-01-01

Quality is a key trait in plant breeding, especially for fruit and vegetables. Quality involves several polygenic components, often influenced by environmental conditions with variable levels of genotype × environment interaction that must be considered in breeding strategies aiming to improve quality. In order to assess the impact of water deficit and salinity on tomato fruit quality, we evaluated a multi-parent advanced generation intercross (MAGIC) tomato population in contrasted environmental conditions over 2 years, one year in control vs. drought condition and the other in control vs. salt condition. Overall 250 individual lines from the MAGIC population—derived from eight parental lines covering a large diversity in cultivated tomato—were used to identify QTL in both experiments for fruit quality and yield component traits (fruit weight, number of fruit, Soluble Solid Content, firmness), phenology traits (time to flower and ripe) and a vegetative trait, leaf length. All the traits showed a large genotype variation (33–86% of total phenotypic variation) in both experiments and high heritability whatever the year or treatment. Significant genotype × treatment interactions were detected for five of the seven traits over the 2 years of experiments. QTL were mapped using 1,345 SNP markers. A total of 54 QTL were found among which 15 revealed genotype × environment interactions and 65% (35 QTL) were treatment specific. Confidence intervals of the QTL were projected on the genome physical map and allowed identifying regions carrying QTL co-localizations, suggesting pleiotropic regulation. We then applied a strategy for candidate gene detection based on the high resolution mapping offered by the MAGIC population, the allelic effect of each parental line at the QTL and the sequence information of the eight parental lines. PMID:29559986

Quantitative trait loci for magnitude of the plasma cortisol response to confinement in rainbow trout.

PubMed

Quillet, E; Krieg, F; Dechamp, N; Hervet, C; Bérard, A; Le Roy, P; Guyomard, R; Prunet, P; Pottinger, T G

2014-04-01

Better understanding of the mechanisms underlying interindividual variation in stress responses and their links with production traits is a key issue for sustainable animal breeding. In this study, we searched for quantitative trait loci (QTL) controlling the magnitude of the plasma cortisol stress response and compared them to body size traits in five F2 full-sib families issued from two rainbow trout lines divergently selected for high or low post-confinement plasma cortisol level. Approximately 1000 F2 individuals were individually tagged and exposed to two successive acute confinement challenges (1 month interval). Post-stress plasma cortisol concentrations were determined for each fish. A medium density genome scan was carried out (268 markers, overall marker spacing less than 10 cM). QTL detection was performed using qtlmap software, based on an interval mapping method (http://www.inra.fr/qtlmap). Overall, QTL of medium individual effects on cortisol responsiveness (<10% of phenotypic variance) were detected on 18 chromosomes, strongly supporting the hypothesis that control of the trait is polygenic. Although a core array of QTL controlled cortisol concentrations at both challenges, several QTL seemed challenge specific, suggesting that responses to the first and to a subsequent exposure to the confinement stressor are distinct traits sharing only part of their genetic control. Chromosomal location of the steroidogenic acute regulatory protein (STAR) makes it a good potential candidate gene for one of the QTL. Finally, comparison of body size traits QTL (weight, length and body conformation) with cortisol-associated QTL did not support evidence for negative genetic relationships between the two types of traits. © 2014 Stichting International Foundation for Animal Genetics.

Quantitative trait locus analysis of plasma cholesterol levels and body weight by controlling the effects of the Apoa2 allele in mice.

PubMed

Suto, Jun-ichi

2007-04-01

Colleagues and I previously performed quantitative trait locus (QTL) analysis on plasma total-cholesterol (T-CHO) levels in C57BL/6J (B6) x RR F2 mice. We identified only one significant QTL (Cq6) on chromosome 1 in a region containing the Apoa2 gene locus, a convincing candidate gene for Cq6. Because Cq6 was a highly significant QTL, we considered that the detection of other potential QTLs might be hindered. In the present study, QTL analysis was performed in B6.KK-Apoa2b N(8) x RR F2 mice [B6.KK-Apoa2b N(8) is a partial congenic strain carrying the Apoa2b allele from the KK strain, and RR also has the Apoa2b allele] by controlling of the effects of the Apoa2 allele, for identifying additional QTLs. Although no significant QTLs were identified, 2 suggestive QTLs were found on chromosomes 2 and 3 in place of the effects of the Apoa2 allele. A significant body weight QTL was identified on chromosome 3 (Bwq7, peak LOD score 5.2); its effect on body weight was not significant in previously analyzed B6 x RR F2 mice. Suggestive body weight QTL that had been identified in B6 x RR F2 mice on chromosome 4 (LOD score 3.8) was not identified in B6.KK-Apoa2b N(8) x RR F2 mice. Thus, contrary to expectation, the genetic control of body weight was also altered significantly by controlling of the effects of the Apoa2 allele. The QTL mapping strategy by controlling of the effects of a major QTL facilitated the identification of additional QTLs.

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

PubMed Central

Martínez-Montes, Ángel M.; Fernández, Almudena; Muñoz, María; Noguera, Jose Luis; Folch, Josep M.

2018-01-01

One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0–3 Mb, for body weight, on SSC2, 3–9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed. PMID:29522525

Genetic control of soybean seed oil: I. QTL and genes associated with seed oil concentration in RIL populations derived from crossing moderately high-oil parents.

PubMed

Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

2013-02-01

Soybean seed is a major source of oil for human consumption worldwide and the main renewable feedstock for biodiesel production in North America. Increasing seed oil concentration in soybean [Glycine max (L.) Merrill] with no or minimal impact on protein concentration could be accelerated by exploiting quantitative trait loci (QTL) or gene-specific markers. Oil concentration in soybean is a polygenic trait regulated by many genes with mostly small effects and which is negatively associated with protein concentration. The objectives of this study were to discover and validate oil QTL in two recombinant inbred line (RIL) populations derived from crosses between three moderately high-oil soybean cultivars, OAC Wallace, OAC Glencoe, and RCAT Angora. The RIL populations were grown across several environments over 2 years in Ontario, Canada. In a population of 203 F(3:6) RILs from a cross of OAC Wallace and OAC Glencoe, a total of 11 genomic regions on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping and single-factor ANOVA. The percentage of the phenotypic variation accounted for by each QTL ranged from 4 to 11 %. Of the five QTL that were tested in a population of 211 F(3:5) RILs from the cross RCAT Angora × OAC Wallace, a "trait-based" bidirectional selective genotyping analysis validated four QTL (80 %). In addition, a total of seven two-way epistatic interactions were identified for oil concentration in this study. The QTL and epistatic interactions identified in this study could be used in marker-assisted introgression aimed at pyramiding high-oil alleles in soybean cultivars to increase oil concentration for biodiesel as well as edible oil applications.

Genetic Architecture of Ear Fasciation in Maize (Zea mays) under QTL Scrutiny.

PubMed

Mendes-Moreira, Pedro; Alves, Mara L; Satovic, Zlatko; Dos Santos, João Pacheco; Santos, João Nina; Souza, João Cândido; Pêgo, Silas E; Hallauer, Arnel R; Vaz Patto, Maria Carlota

2015-01-01

Knowledge of the genes affecting maize ear inflorescence may lead to better grain yield modeling. Maize ear fasciation, defined as abnormal flattened ears with high kernel row number, is a quantitative trait widely present in Portuguese maize landraces. Using a segregating population derived from an ear fasciation contrasting cross (consisting of 149 F2:3 families) we established a two location field trial using a complete randomized block design. Correlations and heritabilities for several ear fasciation-related traits and yield were determined. Quantitative Trait Loci (QTL) involved in the inheritance of those traits were identified and candidate genes for these QTL proposed. Ear fasciation broad-sense heritability was 0.73. Highly significant correlations were found between ear fasciation and some ear and cob diameters and row number traits. For the 23 yield and ear fasciation-related traits, 65 QTL were identified, out of which 11 were detected in both environments, while for the three principal components, five to six QTL were detected per environment. Detected QTL were distributed across 17 genomic regions and explained individually, 8.7% to 22.4% of the individual traits or principal components phenotypic variance. Several candidate genes for these QTL regions were proposed, such as bearded-ear1, branched silkless1, compact plant1, ramosa2, ramosa3, tasselseed4 and terminal ear1. However, many QTL mapped to regions without known candidate genes, indicating potential chromosomal regions not yet targeted for maize ear traits selection. Portuguese maize germplasm represents a valuable source of genes or allelic variants for yield improvement and elucidation of the genetic basis of ear fasciation traits. Future studies should focus on fine mapping of the identified genomic regions with the aim of map-based cloning.

Genetic analysis of adult plant, quantitative resistance to stripe rust in wheat cultivar 'Stephens' in multi-environment trials.

PubMed

Dolores Vazquez, M; James Peterson, C; Riera-Lizarazu, Oscar; Chen, Xianming; Heesacker, Adam; Ammar, Karim; Crossa, Jose; Mundt, Christopher C

2012-01-01

The wheat (Triticum aestivum L.) cultivar 'Stephens' has been grown commercially in the USA Pacific Northwest for 30 years. The durable resistance of 'Stephens' to stripe rust (Puccinia striiformis f. sp. tritici) was believed to be due to a combination of seedling and adult plant resistance genes. Multilocation field trials, diversity array technology (DArT), and simple sequence repeat (SSR) markers were used to identify quantitative trait loci (QTL) for resistance. Recombinant inbred lines were assessed for stripe rust response in eight locations/years, five in 2008 and three in 2009. The data from Mt. Vernon, WA, differed from all other environments, and composite interval mapping (CIM) identified three QTL, QYrst.orr-1AL, QYrst.orr-4BS, and QYrpl.orr-6AL, which accounted for 12, 11, and 6% of the phenotypic variance, respectively. CIM across the remaining six environments identified four main QTL. Two QTL, QYrst.orr-2BS.2 and QYrst.orr-7AS, were detected in five of six environments and explained 11 and 15% of the phenotypic variance, respectively. Two other QTL, QYrst.orr-2AS and QYrpl.orr-4BL, were detected across four and three of six environments, and explained 19 and 9% of the phenotypic variance, respectively. The susceptible parent 'Platte' contributed QYrpl.orr-4BL and QYrpl.orr-6AL, with the remaining QTL originating from 'Stephens'. For each environment, additional minor QTL were detected, each accounting for 6-10% of the phenotypic variance. Different QTL with moderate effects were identified in both 'Stephens' and 'Platte'. Significant QTL × environment interactions were evident, suggesting that specificity to plant stage, pathogen genotype, and/or temperature was important.

A genome-wide association study reveals a QTL influencing caudal supernumerary teats in Holstein cattle.

PubMed

Joerg, H; Meili, C; Ruprecht, O; Bangerter, E; Burren, A; Bigler, A

2014-12-01

Supernumerary teats represent a common abnormality of the bovine udder. A genome-wide association study was performed based on the proportion of the occurrence of supernumerary teats in the daughters of 1097 Holstein bulls. The heritability of caudal supernumerary teats without mammary gland in this study was 0.604. The largest proportion of the heritability was attributable to BTA 20. The strongest evidence for association was with five SNPs on chromosome 20, referred to as a QTL. The mode of inheritance at this QTL was dominant. These findings reveal that the occurrence of caudal supernumerary teats without mammary gland in Holstein cattle is influenced by a QTL on chromosome 20 and a polygenic part. The data support the high potential of the SNPs in the QTL region as markers for breeding against caudal supernumerary teats. © 2014 Stichting International Foundation for Animal Genetics.

Prioritizing quantitative trait loci for root system architecture in tetraploid wheat.

PubMed

Maccaferri, Marco; El-Feki, Walid; Nazemi, Ghasemali; Salvi, Silvio; Canè, Maria Angela; Colalongo, Maria Chiara; Stefanelli, Sandra; Tuberosa, Roberto

2016-02-01

Optimization of root system architecture (RSA) traits is an important objective for modern wheat breeding. Linkage and association mapping for RSA in two recombinant inbred line populations and one association mapping panel of 183 elite durum wheat (Triticum turgidum L. var. durum Desf.) accessions evaluated as seedlings grown on filter paper/polycarbonate screening plates revealed 20 clusters of quantitative trait loci (QTLs) for root length and number, as well as 30 QTLs for root growth angle (RGA). Divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTLs were mapped on a high-density tetraploid consensus map based on transcript-associated Illumina 90K single nucleotide polymorphisms (SNPs) developed for bread and durum wheat, thus allowing for an accurate cross-referencing of RSA QTLs between durum and bread wheat. Among the main QTL clusters for root length and number highlighted in this study, 15 overlapped with QTLs for multiple RSA traits reported in bread wheat, while out of 30 QTLs for RGA, only six showed co-location with previously reported QTLs in wheat. Based on their relative additive effects/significance, allelic distribution in the association mapping panel, and co-location with QTLs for grain weight and grain yield, the RSA QTLs have been prioritized in terms of breeding value. Three major QTL clusters for root length and number (RSA_QTL_cluster_5#, RSA_QTL_cluster_6#, and RSA_QTL_cluster_12#) and nine RGA QTL clusters (QRGA.ubo-2A.1, QRGA.ubo-2A.3, QRGA.ubo-2B.2/2B.3, QRGA.ubo-4B.4, QRGA.ubo-6A.1, QRGA.ubo-6A.2, QRGA.ubo-7A.1, QRGA.ubo-7A.2, and QRGA.ubo-7B) appear particularly valuable for further characterization towards a possible implementation of breeding applications in marker-assisted selection and/or cloning of the causal genes underlying the QTLs. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

PubMed

Patil, Gunvant; Vuong, Tri D; Kale, Sandip; Valliyodan, Babu; Deshmukh, Rupesh; Zhu, Chengsong; Wu, Xiaolei; Bai, Yonghe; Yungbluth, Dennis; Lu, Fang; Kumpatla, Siva; Shannon, J Grover; Varshney, Rajeev K; Nguyen, Henry T

2018-04-04

The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil, and high sucrose. In this study, an interspecific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3× depth. Based on 91 342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4070 bins). In addition to bin mapping, quantitative trait loci (QTL) analysis for protein, oil, and sucrose was performed using 3343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared, and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next-generation sequencing technology enhanced mapping resolution (from 1325 to 50 Kb). A total of five, nine, and four QTLs were identified for protein, oil, and sucrose content, respectively, and some of the QTLs coincided with soybean domestication-related genomic loci. The major QTL for protein and oil were mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL were identified on Chr. 8 (qSuc_08) and harbours putative genes involved in sugar transport. In addition, genome-wide association using 91 342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL-based haplotype using whole-genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Mapping of a dominant rust resistance gene revealed two R genes around the major Rust_QTL in cultivated peanut (Arachis hypogaea L.).

PubMed

Mondal, Suvendu; Badigannavar, Anand M

2018-05-09

A consensus rust QTL was identified within a 1.25 cM map interval of A03 chromosome in cultivated peanut. This map interval contains a TIR-NB-LRR R gene and four pathogenesis-related genes. Disease resistance in plants is manifested due to the specific interaction between the R gene product and its cognate avirulence gene product (AVR) in the pathogen. Puccinia arachidis Speg. causes rust disease and inflicts economic damages to peanut. Till now, no experimental evidence is known for the action of R gene in peanut for rust resistance. A fine mapping approach towards the development of closely linked markers for rust resistance gene was undertaken in this study. Phenotyping of an RIL population at five environments for field rust score and subsequent QTL analysis has identified a 1.25 cM map interval that harbored a consensus major Rust_QTL in A03 chromosome. This Rust_QTL is flanked by two SSR markers: FRS72 and SSR_GO340445. Both the markers clearly identified strong association of the mapped region with rust reaction in both resistant and susceptible genotypes from a collection of 95 cultivated peanut germplasm. This 1.25 cM map interval contained 331.7 kb in the physical map of A. duranensis and had a TIR-NB-LRR category R gene (Aradu.Z87JB) and four glucan endo-1,3 β glucosidase genes (Aradu.RKA6 M, Aradu.T44NR, Aradu.IWV86 and Aradu.VG51Q). Another resistance gene analog was also found in the vicinity of mapped Rust_QTL. The sequence between SSR markers, FRS72 and FRS49, contains an LRR-PK (Aradu.JG217) which is equivalent to RHG4 in soybean. Probably, the protein kinase domain in AhRHG4 acts as an integrated decoy for the cognate AVR from Puccinia arachidis and helps the TIR-NB-LRR R-protein to initiate a controlled program cell death in resistant peanut plants.

Validation of linkage between BCWD resistance and spleen size QTL on Omy19 in rainbow trout: Pleiotropy versus linkage

USDA-ARS?s Scientific Manuscript database

Bacterial cold water disease (BCWD) is caused by infection with Flavobacterium psychrophilum, and results in significant economic losses in salmonid aquaculture. Previously, we identified a major QTL for BCWD resistance on Omy19 (h2q=0.57-0.67) as well as a QTL for surrogate measures of disease resi...

Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses

USDA-ARS?s Scientific Manuscript database

Our objective was to identify candidate QTL that had a large effect on seed weight using a selective population through GWAS and fixation index analysis. A selective population was previously used for the identification of QTL in linkage analysis of bi-parental RIL populations in plant species, but ...

Genomic Mapping of Direct and Correlated Responses to Long-Term Selection for Rapid Growth Rate in Mice

PubMed Central

Allan, Mark F.; Eisen, Eugene J.; Pomp, Daniel

2005-01-01

Understanding the genetic architecture of traits such as growth, body composition, and energy balance has become a primary focus for biomedical and agricultural research. The objective of this study was to map QTL in a large F2 (n = 1181) population resulting from an intercross between the M16 and ICR lines of mice. The M16 line, developed by long-term selection for 3- to 6-week weight gain, is larger, heavier, fatter, hyperphagic, and diabetic relative to its randomly selected control line of ICR origin. The F2 population was phenotyped for growth and energy intake at weekly intervals from 4 to 8 weeks of age and for body composition and plasma levels of insulin, leptin, TNFα, IL6, and glucose at 8 weeks and was genotyped for 80 microsatellite markers. Since the F2 was a cross between a selection line and its unselected control, the QTL identified likely represent genes that contributed to direct and correlated responses to long-term selection for rapid growth rate. Across all traits measured, 95 QTL were identified, likely representing 19 unique regions on 13 chromosomes. Four chromosomes (2, 6, 11, and 17) harbored loci contributing disproportionately to selection response. Several QTL demonstrating differential regulation of regional adipose deposition and age-dependent regulation of growth and energy consumption were identified. PMID:15944354

Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize.

PubMed

Chen, Lin; Li, Yong-xiang; Li, Chunhui; Wu, Xun; Qin, Weiwei; Li, Xin; Jiao, Fuchao; Zhang, Xiaojing; Zhang, Dengfeng; Shi, Yunsu; Song, Yanchun; Li, Yu; Wang, Tianyu

2016-04-12

Kernel weight and size are important components of grain yield in cereals. Although some information is available concerning the map positions of quantitative trait loci (QTL) for kernel weight and size in maize, little is known about the molecular mechanisms of these QTLs. qGW4.05 is a major QTL that is associated with kernel weight and size in maize. We combined linkage analysis and association mapping to fine-map and identify candidate gene(s) at qGW4.05. QTL qGW4.05 was fine-mapped to a 279.6-kb interval in a segregating population derived from a cross of Huangzaosi with LV28. By combining the results of regional association mapping and linkage analysis, we identified GRMZM2G039934 as a candidate gene responsible for qGW4.05. Candidate gene-based association mapping was conducted using a panel of 184 inbred lines with variable kernel weights and kernel sizes. Six polymorphic sites in the gene GRMZM2G039934 were significantly associated with kernel weight and kernel size. The results of linkage analysis and association mapping revealed that GRMZM2G039934 is the most likely candidate gene for qGW4.05. These results will improve our understanding of the genetic architecture and molecular mechanisms underlying kernel development in maize.

Adult Plant Leaf Rust Resistance Derived from Toropi Wheat is Conditioned by Lr78 and Three Minor QTL.

PubMed

Kolmer, J A; Bernardo, A; Bai, G; Hayden, M J; Chao, S

2018-02-01

Leaf rust caused by Puccinia triticina is an important disease of wheat in many regions worldwide. Durable or long-lasting leaf rust resistance has been difficult to achieve because populations of P. triticina are highly variable for virulence to race-specific resistance genes, and respond to selection by resistance genes in released wheat cultivars. The wheat cultivar Toropi, developed and grown in Brazil, was noted to have long-lasting leaf rust resistance that was effective only in adult plants. The objectives of this study were to determine the chromosome location of the leaf rust resistance genes derived from Toropi in two populations of recombinant inbred lines in a partial Thatcher wheat background. In the first population, a single gene with major effects on chromosome 5DS that mapped 2.2 centimorgans distal to IWA6289, strongly reduced leaf rust severity in all 3 years of field plot tests. This gene for adult plant leaf rust resistance was designated as Lr78. In the second population, quantitative trait loci (QTL) with small effects on chromosomes 1BL, 3BS, and 4BS were found. These QTL expressed inconsistently over 4 years of field plot tests. The adult plant leaf rust resistance derived from Toropi involved a complex combination of QTL with large and small effects.

Genetic architecture of fusarium head blight resistance in four winter triticale populations.

PubMed

Kalih, R; Maurer, H P; Miedaner, T

2015-03-01

Fusarium head blight (FHB) is a devastating disease that causes significant reductions in yield and quality in wheat, rye, and triticale. In triticale, knowledge of the genetic architecture of FHB resistance is missing but essential due to modern breeding requirements. In our study, four doubled-haploid triticale populations (N=120 to 200) were evaluated for resistance to FHB caused by artificial inoculation with Fusarium culmorum in four environments. DArT markers were used to genotype triticale populations. Seventeen quantitative trait loci (QTL) for FHB resistance were detected across all populations; six of them were derived from rye genome and located on chromosomes 4R, 5R, and 7R, which are here reported for the first time. The total cross-validated ratio of the explained phenotypic variance for all detected QTL in each population was 41 to 68%. In all, 17 QTL for plant height and 18 QTL for heading stage were also detected across all populations; 3 and 5 of them, respectively, were overlapping with QTL for FHB. In conclusion, FHB resistance in triticale is caused by a multitude of QTL, and pyramiding them contributes to higher resistance.

Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

PubMed Central

Dixit, Shalabh; Kumar Biswal, Akshaya; Min, Aye; Henry, Amelia; Oane, Rowena H.; Raorane, Manish L.; Longkumer, Toshisangba; Pabuayon, Isaiah M.; Mutte, Sumanth K.; Vardarajan, Adithi R.; Miro, Berta; Govindan, Ganesan; Albano-Enriquez, Blesilda; Pueffeld, Mandy; Sreenivasulu, Nese; Slamet-Loedin, Inez; Sundarvelpandian, Kalaipandian; Tsai, Yuan-Ching; Raghuvanshi, Saurabh; Hsing, Yue-Ie C.; Kumar, Arvind; Kohli, Ajay

2015-01-01

Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor ‘no apical meristem’ (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security. PMID:26507552

Mapping Late Leaf Spot Resistance in Peanut (Arachis hypogaea) Using QTL-seq Reveals Markers for Marker-Assisted Selection.

PubMed

Clevenger, Josh; Chu, Ye; Chavarro, Carolina; Botton, Stephanie; Culbreath, Albert; Isleib, Thomas G; Holbrook, C C; Ozias-Akins, Peggy

2018-01-01

Late leaf spot (LLS; Cercosporidium personatum ) is a major fungal disease of cultivated peanut ( Arachis hypogaea ). A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL) using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools. Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.

Mapping Late Leaf Spot Resistance in Peanut (Arachis hypogaea) Using QTL-seq Reveals Markers for Marker-Assisted Selection

PubMed Central

Clevenger, Josh; Chu, Ye; Chavarro, Carolina; Botton, Stephanie; Culbreath, Albert; Isleib, Thomas G.; Holbrook, C. C.; Ozias-Akins, Peggy

2018-01-01

Late leaf spot (LLS; Cercosporidium personatum) is a major fungal disease of cultivated peanut (Arachis hypogaea). A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL) using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools. Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping. PMID:29459876

QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies.

PubMed

Saatchi, Mahdi; Beever, Jonathan E; Decker, Jared E; Faulkner, Dan B; Freetly, Harvey C; Hansen, Stephanie L; Yampara-Iquise, Helen; Johnson, Kristen A; Kachman, Stephen D; Kerley, Monty S; Kim, JaeWoo; Loy, Daniel D; Marques, Elisa; Neibergs, Holly L; Pollak, E John; Schnabel, Robert D; Seabury, Christopher M; Shike, Daniel W; Snelling, Warren M; Spangler, Matthew L; Weaber, Robert L; Garrick, Dorian J; Taylor, Jeremy F

2014-11-20

The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental×Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake. A total of 5, 6, 11 and 10 significant QTL (defined as 1-Mb genome windows with Bonferroni-corrected P-value<0.05) were identified for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake, respectively. The identified QTL were population-specific and had little overlap across the 4 populations. The pleiotropic or closely linked QTL on BTA 7 at 23 Mb identified in the Angus population harbours a promising candidate gene ACSL6 (acyl-CoA synthetase long-chain family member 6), and was the largest effect QTL associated with dry matter intake and mid-test body weight explaining 10.39% and 14.25% of the additive genetic variance, respectively. Pleiotropic or closely linked QTL associated with average daily gain and mid-test body weight were detected on BTA 6 at 38 Mb and BTA 7 at 93 Mb confirming previous reports. No QTL for residual feed intake explained more than 2.5% of the additive genetic variance in any population. Marker-based estimates of heritability ranged from 0.21 to 0.49 for residual feed intake across the 4 populations. This GWAS study, which is the largest performed for feed efficiency and its component traits in beef cattle to date, identified several large-effect QTL that cumulatively explained a significant percentage of additive genetic variance within each population. Differences in the QTL identified among the different populations may be due to differences in power to detect QTL, environmental variation, or differences in the genetic architecture of trait variation among breeds. These results enhance our understanding of the biology of growth, feed intake and utilisation in beef cattle.

Pyramids of QTLs enhance host-plant resistance and Bt-mediated resistance to leaf-chewing insects in soybean.

PubMed

Ortega, María A; All, John N; Boerma, H Roger; Parrott, Wayne A

2016-04-01

QTL-M and QTL-E enhance soybean resistance to insects. Pyramiding these QTLs with cry1Ac increases protection against Bt-tolerant pests, presenting an opportunity to effectively deploy Bt with host-plant resistance genes. Plant resistance to leaf-chewing insects minimizes the need for insecticide applications, reducing crop production costs and pesticide concerns. In soybean [Glycine max (L.) Merr.], resistance to a broad range of leaf-chewing insects is found in PI 229358 and PI 227687. PI 229358's resistance is conferred by three quantitative trait loci (QTLs): M, G, and H. PI 227687's resistance is conferred by QTL-E. The letters indicate the soybean Linkage groups (LGs) on which the QTLs are located. This study aimed to determine if pyramiding PI 229358 and PI 227687 QTLs would enhance soybean resistance to leaf-chewing insects, and if pyramiding these QTLs with Bt (cry1Ac) enhances resistance against Bt-tolerant pests. The near-isogenic lines (NILs): Benning(ME), Benning(MGHE), and Benning(ME+cry1Ac) were developed. Benning(ME) and Benning(MGHE) were evaluated in detached-leaf and greenhouse assays with soybean looper [SBL, Chrysodeixis includens (Walker)], corn earworm [CEW, Helicoverpa zea (Boddie)], fall armyworm [FAW, Spodoptera frugiperda (J.E. Smith)], and velvetbean caterpillar [VBC, Anticarsia gemmatalis (Hübner)]; and in field-cage assays with SBL. Benning(ME+cry1Ac) was tested in detached-leaf assays against SBL, VBC, and Southern armyworm [SAW, Spodoptera eridania (Cramer)]. In the detached-leaf assay, Benning(ME) showed the strongest antibiosis against CEW, FAW, and VBC. In field-cage conditions, Benning(ME) and Benning(MGHE) suffered 61 % less defoliation than Benning. Benning(ME+cry1Ac) was more resistant than Benning(ME) and Benning (cry1Ac) against SBL and SAW. Agriculturally relevant levels of resistance in soybean can be achieved with just two loci, QTL-M and QTL-E. ME+cry1Ac could present an opportunity to protect the durability of Bt genes in elite soybean cultivars. These results should assist the development of effective pest management strategies, and sustainable deployment of Bt genes in soybean.

High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Siyao; Clark, Lindsay V.; Swaminathan, Kankshita

Miscanthus is a perennial C4 grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker-assisted selection. Thus, a high-density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F1 progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. High-density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms (SNPs) obtained from restriction site-associated DNA sequencing, and 138 previously mapped GoldenGate SNPs. The female parent (‘Strictus’) map spanned 1599 cM,more » with 1989 SNPs on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent (‘Kaskade’) map was 1612 cM, with 1821 SNPs, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci (QTL) for the zebra-striped trait, which was segregating in this population. Three QTL for zebra-striped presence/absence (zb1, zb2 on LG 7, and zb3 on LG 10) and three for zebra-striped intensity (zbi1, zbi2, zbi3 on LGs 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL, but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker–trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus.« less

High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

DOE PAGES

Liu, Siyao; Clark, Lindsay V.; Swaminathan, Kankshita; ...

2015-05-06

Miscanthus is a perennial C4 grass that has recently become an important bioenergy crop. The efficiency of breeding improved Miscanthus biomass cultivars could be greatly increased by marker-assisted selection. Thus, a high-density genetic map is critical to Miscanthus improvement. In this study, a mapping population of 261 F1 progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. High-density genetic maps for the two parents were produced with 3044 newly developed single nucleotide polymorphisms (SNPs) obtained from restriction site-associated DNA sequencing, and 138 previously mapped GoldenGate SNPs. The female parent (‘Strictus’) map spanned 1599 cM,more » with 1989 SNPs on 19 linkage groups, and an average intermarker spacing of 0.8 cM. The length of the male parent (‘Kaskade’) map was 1612 cM, with 1821 SNPs, and an average intermarker spacing of 0.9 cM. The utility of the map was confirmed by locating quantitative trait loci (QTL) for the zebra-striped trait, which was segregating in this population. Three QTL for zebra-striped presence/absence (zb1, zb2 on LG 7, and zb3 on LG 10) and three for zebra-striped intensity (zbi1, zbi2, zbi3 on LGs 7, 10, 3) were identified. Each allele that caused striping was recessive. Incomplete penetrance was observed for each zb QTL, but penetrance was greatest when two or more zb QTL were homozygous for the causative alleles. Similarly, the intensity of striping was greatest when two or more zbi QTL were homozygous for alleles that conferred the trait. Comparative mapping indicated putative correspondence between zb3 and/or zbi2 on LG 10 to previously sequenced genes conferring zebra stripe in maize and rice. These results demonstrate that the new map is useful for identifying marker–trait associations. The mapped markers will become a valuable community resource, facilitating comparisons among studies and the breeding of Miscanthus.« less

High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing.

PubMed

Tao, Aifen; Huang, Long; Wu, Guifen; Afshar, Reza Keshavarz; Qi, Jianmin; Xu, Jiantang; Fang, Pingping; Lin, Lihui; Zhang, Liwu; Lin, Peiqing

2017-05-08

Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups. An F 8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F 8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. 'SNP_only' markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F 8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14-15.63% of the phenotypic variance. To our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute.

A Semiparametric Approach for Composite Functional Mapping of Dynamic Quantitative Traits

PubMed Central

Yang, Runqing; Gao, Huijiang; Wang, Xin; Zhang, Ji; Zeng, Zhao-Bang; Wu, Rongling

2007-01-01

Functional mapping has emerged as a powerful tool for mapping quantitative trait loci (QTL) that control developmental patterns of complex dynamic traits. Original functional mapping has been constructed within the context of simple interval mapping, without consideration of separate multiple linked QTL for a dynamic trait. In this article, we present a statistical framework for mapping QTL that affect dynamic traits by capitalizing on the strengths of functional mapping and composite interval mapping. Within this so-called composite functional-mapping framework, functional mapping models the time-dependent genetic effects of a QTL tested within a marker interval using a biologically meaningful parametric function, whereas composite interval mapping models the time-dependent genetic effects of the markers outside the test interval to control the genome background using a flexible nonparametric approach based on Legendre polynomials. Such a semiparametric framework was formulated by a maximum-likelihood model and implemented with the EM algorithm, allowing for the estimation and the test of the mathematical parameters that define the QTL effects and the regression coefficients of the Legendre polynomials that describe the marker effects. Simulation studies were performed to investigate the statistical behavior of composite functional mapping and compare its advantage in separating multiple linked QTL as compared to functional mapping. We used the new mapping approach to analyze a genetic mapping example in rice, leading to the identification of multiple QTL, some of which are linked on the same chromosome, that control the developmental trajectory of leaf age. PMID:17947431

Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon

PubMed Central

Gharbi, Karim; Glover, Kevin A; Stone, Louise C; MacDonald, Elizabeth S; Matthews, Louise; Grimholt, Unni; Stear, Michael J

2009-01-01

Background Genetic variation has been shown to play a significant role in determining susceptibility to the salmon louse, Lepeophtheirus salmonis. However, the mechanisms involved in differential response to infection remain poorly understood. Recent findings in Atlantic salmon (Salmo salar) have provided evidence for a potential link between marker variation at the major histocompatibility complex (MHC) and differences in lice abundance among infected siblings, suggesting that MHC genes can modulate susceptibility to the parasite. In this study, we used quantitative trait locus (QTL) analysis to test the effect of genomic regions linked to MHC class I and II on linkage groups (LG) 15 and 6, respectively. Results Significant QTL effects were detected on both LG 6 and LG 15 in sire-based analysis but the QTL regions remained unresolved due to a lack of recombination between markers. In dam-based analysis, a significant QTL was identified on LG 6, which accounted for 12.9% of within-family variance in lice abundance. However, the QTL was located at the opposite end of DAA, with no significant overlap with the MHC class II region. Interestingly, QTL modelling also revealed evidence of sex-linked differences in lice abundance, indicating that males and females may have different susceptibility to infection. Conclusion Overall, QTL analysis provided relatively weak support for a proximal effect of classical MHC regions on lice abundance, which can partly be explained by linkage to other genes controlling susceptibility to L. salmonis on the same chromosome. PMID:19397823

Quantitative trait loci for response to ethanol in an intercontinental set of recombinant inbred lines of Drosophila melanogaster.

PubMed

Defays, Raquel; Bertoli, Carlos Ignacio

2012-12-01

Alcohol, a drug widely abused, impacts the central nervous system functioning of diverse organisms. The behavioral responses to acute alcohol exposure are remarkably similar among humans and fruit flies. In its natural environment, rich in fermentation products, the fruit fly Drosophila melanogaster encounters relatively high levels of ethanol. The effects of ethanol and its metabolites on Drosophila have been studied for decades, as a model for adaptive evolution. Although extensive work has been done for elucidating patterns of genetic variation, substantially less is known about the genomic regions or genes that underlie the genetic variation of this important trait. To identify regions containing genes involved in the responses to ethanol, we used a mapping population of recombinant inbred (RIL) lines to map quantitative trait loci (QTL) that affect variation in resistance and recovery from ethanol sedation in adults and ethanol resistance in larvae. We mapped fourteen QTL affecting the response to ethanol on the three chromosomes. Seven of the QTL influence the resistance to ethanol in adults, two QTL are related to ethanol-coma recovery in adults and five affect the survival to ethanol in larvae. Most of the QTL were trait specific, suggesting that overlapping but generally unique genetic architectures underlie each trait. Each QTL explained up to 16.8% of the genetic variance among lines. Potential candidate loci contained within our QTL regions were identified and analyzed. Copyright © 2012 Elsevier Inc. All rights reserved.

Genetic analysis and chromosome mapping of resistance to Fusarium oxysporum f. sp. niveum (FON) race 1 and race 2 in watermelon (Citrullus lanatus L.).

PubMed

Ren, Yi; Di Jiao; Gong, Guoyi; Zhang, Haiying; Guo, Shaogui; Zhang, Jie; Xu, Yong

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp . niveum (FON) is the major soilborne disease of watermelon ( Citrullus lanatus L.). The development and deployment of resistant cultivars is generally considered to be an effective approach to control FW. In this study, an F8 population consisting of 103 recombinant inbred lines derived from a cross between the cultivar 97103 and a wild accession PI 296341-FR was used for FON race 1 and race 2 fungal inoculations. One major QTL on chromosome 1 for FON race 1 resistance was detected with a logarithm of odds of 13.2 and explained phenotypic variation R 2  = 48.1 %; two QTLs of FON race 2 resistance on chromosomes 9 and 10 were discovered based on the high-density integrated genetic map we constructed. The nearest molecular marker should be useful for marker-assisted selection of FON race 1 and race 2 resistance. One receptor kinase, one glucan endo-1,3-β-glucosidase precursors and three acidic chitinase located in the FON-1 QTL genomic region. In Qfon2.1 QTL region, one lipoxygenase gene, five receptor-like kinases and four glutathione S-transferase genes are discovered. One arginine biosynthesis bifunctional protein, two receptor kinase proteins and one lipid-transfer protein located in Qfon2.2 QTL region. Based on SNP analysis by using 20 re-sequenced accessions of watermelon and 231-plant F 2 population generated from Black Diamond × Calhoun Grey, we developed a SNP marker Chr1SNP_502124 for FON-1 detection.

Dynamic QTLs for sugars and enzyme activities provide an overview of genetic control of sugar metabolism during peach fruit development.

PubMed

Desnoues, Elsa; Baldazzi, Valentina; Génard, Michel; Mauroux, Jehan-Baptiste; Lambert, Patrick; Confolent, Carole; Quilot-Turion, Bénédicte

2016-05-01

Knowledge of the genetic control of sugar metabolism is essential to enhance fruit quality and promote fruit consumption. The sugar content and composition of fruits varies with species, cultivar and stage of development, and is controlled by multiple enzymes. A QTL (quantitative trait locus) study was performed on peach fruit [Prunus persica (L.) Batsch], the model species for Prunus Progeny derived from an interspecific cross between P. persica cultivars and P. davidiana was used. Dynamic QTLs for fresh weight, sugars, acids, and enzyme activities related to sugar metabolism were detected at different stages during fruit development. Changing effects of alleles during fruit growth were observed, including inversions close to maturity. This QTL analysis was supplemented by the identification of genes annotated on the peach genome as enzymes linked to sugar metabolism or sugar transporters. Several cases of co-locations between annotated genes, QTLs for enzyme activities and QTLs controlling metabolite concentrations were observed and discussed. These co-locations raise hypotheses regarding the functional regulation of sugar metabolism and pave the way for further analyses to enable the identification of the underlying genes. In conclusion, we identified the potential impact on fruit breeding of the modification of QTL effect close to maturity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Interactions Between QTL SAP6 and SU91 on Resistance to Common Bacterial Blight in Red Kidney Bean and Pinto Bean Populations

USDA-ARS?s Scientific Manuscript database

Resistance to common bacterial blight in common bean is a complex trait that is quantitatively inherited. We examined the interaction between two independent QTL, SAP6 and SU91, which condition resistance to CBB.The QTL were studied in a pinto bean F2 population a cross between Othello (sap6 sap6 //...

Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle

PubMed Central

Ron, Micha; Israeli, Galit; Seroussi, Eyal; Weller, Joel I; Gregg, Jeffrey P; Shani, Moshe; Medrano, Juan F

2007-01-01

Background Many studies have found segregating quantitative trait loci (QTL) for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the confidence interval for QTL location by linkage analysis spans tens of map units, or hundreds of genes. Combining mapping and arraying has been suggested as an approach to identify candidate genes. Thus, gene expression analysis in the mammary gland of genes positioned in the confidence interval of the QTL can bridge the gap between fine mapping and quantitative trait nucleotide (QTN) determination. Results We hybridized Affymetrix microarray (MG-U74v2), containing 12,488 murine probes, with RNA derived from mammary gland of virgin, pregnant, lactating and involuting C57BL/6J mice in a total of nine biological replicates. We combined microarray data from two additional studies that used the same design in mice with a total of 75 biological replicates. The same filtering and normalization was applied to each microarray data using GeneSpring software. Analysis of variance identified 249 differentially expressed probe sets common to the three experiments along the four developmental stages of puberty, pregnancy, lactation and involution. 212 genes were assigned to their bovine map positions through comparative mapping, and thus form a list of candidate genes for previously identified QTLs for milk production traits. A total of 82 of the genes showed mammary gland-specific expression with at least 3-fold expression over the median representing all tissues tested in GeneAtlas. Conclusion This work presents a web tool for candidate genes for QTL (cgQTL) that allows navigation between the map of bovine milk production QTL, potential candidate genes and their level of expression in mammary gland arrays and in GeneAtlas. Three out of four confirmed genes that affect QTL in livestock (ABCG2, DGAT1, GDF8, IGF2) were over expressed in the target organ. Thus, cgQTL can be used to determine priority of candidate genes for QTN analysis based on differential expression in the target organ. PMID:17584498

The genetic architecture of growth and fillet traits in farmed Atlantic salmon (Salmo salar).

PubMed

Tsai, Hsin Yuan; Hamilton, Alastair; Guy, Derrick R; Tinch, Alan E; Bishop, Stephen C; Houston, Ross D

2015-05-19

Performance and quality traits such as harvest weight, fillet weight and flesh color are of economic importance to the Atlantic salmon aquaculture industry. The genetic factors underlying these traits are of scientific and commercial interest. However, such traits are typically polygenic in nature, with the number and size of QTL likely to vary between studies and populations. The aim of this study was to investigate the genetic basis of several growth and fillet traits measured at harvest in a large farmed salmon population by using SNP markers. Due to the marked heterochiasmy in salmonids, an efficient two-stage mapping approach was applied whereby QTL were detected using a sire-based linkage analysis, a sparse SNP marker map and exploiting low rates of recombination, while a subsequent dam-based analysis focused on the significant chromosomes with a denser map to confirm QTL and estimate their position. The harvest traits all showed significant heritability, ranging from 0.05 for fillet yield up to 0.53 for the weight traits. In the sire-based analysis, 1695 offspring with trait records and their 20 sires were successfully genotyped for the SNPs on the sparse map. Chromosomes 13, 18, 19 and 20 were shown to harbor genome-wide significant QTL affecting several growth-related traits. The QTL on chr. 13, 18 and 20 were detected in the dam-based analysis using 512 offspring from 10 dams and explained approximately 6-7 % of the within-family variation in these traits. We have detected several QTL affecting economically important complex traits in a commercial salmon population. Overall, the results suggest that the traits are relatively polygenic and that QTL tend to be pleiotropic (affecting the weight of several components of the harvested fish). Comparison of QTL regions across studies suggests that harvest trait QTL tend to be relatively population-specific. Therefore, the application of marker or genomic selection for improvement in these traits is likely to be most effective when the discovery population is closely related to the selection candidates (e.g. within-family genomic selection).

Mapping of quantitative adult plant field resistance to leaf rust and stripe rust in two European winter wheat populations reveals co-location of three QTL conferring resistance to both rust pathogens.

PubMed

Buerstmayr, Maria; Matiasch, Lydia; Mascher, Fabio; Vida, Gyula; Ittu, Marianna; Robert, Olivier; Holdgate, Sarah; Flath, Kerstin; Neumayer, Anton; Buerstmayr, Hermann

2014-09-01

We detected several, most likely novel QTL for adult plant resistance to rusts. Notably three QTL improved resistance to leaf rust and stripe rust simultaneously indicating broad spectrum resistance QTL. The rusts of wheat (Puccinia spp.) are destructive fungal wheat diseases. The deployment of resistant cultivars plays a central role in integrated rust disease management. Durability of resistance would be preferred, but is difficult to analyse. The Austrian winter wheat cultivar Capo was released in the 1989 and grown on a large acreage during more than two decades and maintained a good level of quantitative leaf rust and stripe rust resistance. Two bi-parental mapping populations: Capo × Arina and Capo × Furore were tested in multiple environments for severity of leaf rust and stripe rust at the adult plant stage in replicated field experiments. Quantitative trait loci associated with leaf rust and stripe rust severity were mapped using DArT and SSR markers. Five QTL were detected in multiple environments associated with resistance to leaf rust designated as QLr.ifa-2AL, QLr.ifa-2BL, QLr.ifa-2BS, QLr.ifa-3BS, and QLr.ifa-5BL, and five for resistance to stripe rust QYr.ifa-2AL, QYr.ifa-2BL, QYr.ifa-3AS, QYr.ifa-3BS, and QYr.ifa-5A. For all QTL apart from two (QYr.ifa-3AS, QLr.ifa-5BL) Capo contributed the resistance improving allele. The leaf rust and stripe rust resistance QTL on 2AL, 2BL and 3BS mapped to the same chromosome positions, indicating either closely linked genes or pleiotropic gene action. These three multiple disease resistance QTL (QLr.ifa-2AL/QYr.ifa-2AL, QLr.ifa.2BL/QYr.ifa-2BL, QLr.ifa-3BS/QYr.ifa.3BS) potentially contribute novel resistance sources for stripe rust and leaf rust. The long-lasting resistance of Capo apparently rests upon a combination of several genes. The described germplasm, QTL and markers are applicable for simultaneous resistance improvement against leaf rust and stripe rust.

Exercise Capacity and Response to Training Quantitative Trait Loci in a NZW X 129S1 Intercross and Combined Cross Analysis of Inbred Mouse Strains

PubMed Central

Massett, Michael P.; Avila, Joshua J.; Kim, Seung Kyum

2015-01-01

Genetic factors determining exercise capacity and the magnitude of the response to exercise training are poorly understood. The aim of this study was to identify quantitative trait loci (QTL) associated with exercise training in mice. Based on marked differences in training responses in inbred NZW (-0.65 ± 1.73 min) and 129S1 (6.18 ± 3.81 min) mice, a reciprocal intercross breeding scheme was used to generate 285 F2 mice. All F2 mice completed an exercise performance test before and after a 4-week treadmill running program, resulting in an increase in exercise capacity of 1.54 ± 3.69 min (range = -10 to +12 min). Genome-wide linkage scans were performed for pre-training, post-training, and change in run time. For pre-training exercise time, suggestive QTL were identified on Chromosomes 5 (57.4 cM, 2.5 LOD) and 6 (47.8 cM, 2.9 LOD). A significant QTL for post-training exercise capacity was identified on Chromosome 5 (43.4 cM, 4.1 LOD) and a suggestive QTL on Chromosomes 1 (55.7 cM, 2.3 LOD) and 8 (66.1 cM, 2.2 LOD). A suggestive QTL for the change in run time was identified on Chromosome 6 (37.8 cM, 2.7 LOD). To identify shared QTL, this data set was combined with data from a previous F2 cross between B6 and FVB strains. In the combined cross analysis, significant novel QTL for pre-training exercise time and change in exercise time were identified on Chromosome 12 (54.0 cM, 3.6 LOD) and Chromosome 6 (28.0 cM, 3.7 LOD), respectively. Collectively, these data suggest that combined cross analysis can be used to identify novel QTL and narrow the confidence interval of QTL for exercise capacity and responses to training. Furthermore, these data support the use of larger and more diverse mapping populations to identify the genetic basis for exercise capacity and responses to training. PMID:26710100

Screening of reproduction-related single-nucleotide variations from MeDIP-seq data in sheep.

PubMed

Cao, Jiaxue; Wei, Caihong; Zhang, Shuzhen; Capellini, Terence D; Zhang, Li; Zhao, Fuping; Li, Li; Zhong, Tao; Wang, Linjie; Du, Lixin; Zhang, Hongping

2016-11-01

Extensive variation in reproduction has arisen in Chinese Mongolian sheep during recent domestication. Hu and Small-tailed Han sheep, for example, have become non-seasonal breeders and exhibit higher fecundity than Tan and Ujumqin breeds. We therefore scanned reproduction-related single-nucleotide variations from methylated DNA-immunoprecipitation sequencing data generated from each of those four breeds to uncover potential mechanisms underlying this breed variation. We generated a high-quality map of single nucleotide variations (SNVs) in DNA methylation enriched regions, and found that the majority of variants are located within non-coding regions. We identified 359 SNVs within the Sheep Quantitative Trait Locus (QTL) database. Nineteen of these SNVs associated with the Aseasonal Reproduction QTL, and 10 out of the 19 reside close to genes with known reproduction functions. We also identified the well-known FecB mutation in high-fecundity sheep (Hu and Small-tailed Han sheep). When we applied these FecB finding to our breeding system, we improved lambing rate by 175%. In summary, this study provided strong candidate SNVs associated with sheep fecundity that can serve as targets for functional testing and to enhance selective breeding strategies. Mol. Reprod. Dev. 83: 958-967, 2016 © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Quantitative Trait Loci Differentiating the Outbreeding Mimulus Guttatus from the Inbreeding M. Platycalyx

PubMed Central

Lin, J. Z.; Ritland, K.

1997-01-01

Theoretical predictions about the evolution of selfing depend on the genetic architecture of loci controlling selfing (monogenic vs. polygenic determination, large vs. small effect of alleles, dominance vs. recessiveness), and studies of such architecture are lacking. We inferred the genetic basis of mating system differences between the outbreeding Mimulus guttatus and the inbreeding M. platycalyx by quantitative trait locus (QTL) mapping using random amplified polymorphic DNA and isozyme markers. One to three QTL were detected for each of five mating system characters, and each QTL explained 7.6-28.6% of the phenotypic variance. Taken together, QTL accounted for up to 38% of the variation in mating system characters, and a large proportion of variation was unaccounted for. Inferred QTL often affected more than one trait, contributing to the genetic correlation between those traits. These results are consistent with the hypothesis that quantitative variation in plant mating system characters is primarily controlled by loci with small effect. PMID:9215912

The genetic architecture of gene expression levels in wild baboons.

PubMed

Tung, Jenny; Zhou, Xiang; Alberts, Susan C; Stephens, Matthew; Gilad, Yoav

2015-02-25

Primate evolution has been argued to result, in part, from changes in how genes are regulated. However, we still know little about gene regulation in natural primate populations. We conducted an RNA sequencing (RNA-seq)-based study of baboons from an intensively studied wild population. We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substantial evidence for, and surprising power to detect, genetic effects on gene expression levels in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes; interestingly, genes with eQTL significantly overlapped between baboons and a comparable human eQTL data set. Our results suggest that genes vary in their tolerance of genetic perturbation, and that this property may be conserved across species. Further, they establish the feasibility of eQTL mapping using RNA-seq data alone, and represent an important step towards understanding the genetic architecture of gene expression in primates.

The genetic architecture of gene expression levels in wild baboons

PubMed Central

Tung, Jenny; Zhou, Xiang; Alberts, Susan C; Stephens, Matthew; Gilad, Yoav

2015-01-01

Primate evolution has been argued to result, in part, from changes in how genes are regulated. However, we still know little about gene regulation in natural primate populations. We conducted an RNA sequencing (RNA-seq)-based study of baboons from an intensively studied wild population. We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substantial evidence for, and surprising power to detect, genetic effects on gene expression levels in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes; interestingly, genes with eQTL significantly overlapped between baboons and a comparable human eQTL data set. Our results suggest that genes vary in their tolerance of genetic perturbation, and that this property may be conserved across species. Further, they establish the feasibility of eQTL mapping using RNA-seq data alone, and represent an important step towards understanding the genetic architecture of gene expression in primates. DOI: http://dx.doi.org/10.7554/eLife.04729.001 PMID:25714927

Replication of linkage to quantitative trait loci: variation in location and magnitude of the lod score.

PubMed

Hsueh, W C; Göring, H H; Blangero, J; Mitchell, B D

2001-01-01

Replication of linkage signals from independent samples is considered an important step toward verifying the significance of linkage signals in studies of complex traits. The purpose of this empirical investigation was to examine the variability in the precision of localizing a quantitative trait locus (QTL) by analyzing multiple replicates of a simulated data set with the use of variance components-based methods. Specifically, we evaluated across replicates the variation in both the magnitude and the location of the peak lod scores. We analyzed QTLs whose effects accounted for 10-37% of the phenotypic variance in the quantitative traits. Our analyses revealed that the precision of QTL localization was directly related to the magnitude of the QTL effect. For a QTL with effect accounting for > 20% of total phenotypic variation, > 90% of the linkage peaks fall within 10 cM from the true gene location. We found no evidence that, for a given magnitude of the lod score, the presence of interaction influenced the precision of QTL localization.

Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes

PubMed Central

Smith, H A; White, B J; Kundert, P; Cheng, C; Romero-Severson, J; Andolfatto, P; Besansky, N J

2015-01-01

Although freshwater (FW) is the ancestral habitat for larval mosquitoes, multiple species independently evolved the ability to survive in saltwater (SW). Here, we use quantitative trait locus (QTL) mapping to investigate the genetic architecture of osmoregulation in Anopheles mosquitoes, vectors of human malaria. We analyzed 1134 backcross progeny from a cross between the obligate FW species An. coluzzii, and its closely related euryhaline sibling species An. merus. Tests of 2387 markers with Bayesian interval mapping and machine learning (random forests) yielded six genomic regions associated with SW tolerance. Overlap in QTL regions from both approaches enhances confidence in QTL identification. Evidence exists for synergistic as well as disruptive epistasis among loci. Intriguingly, one QTL region containing ion transporters spans the 2Rop chromosomal inversion that distinguishes these species. Rather than a simple trait controlled by one or a few loci, our data are most consistent with a complex, polygenic mode of inheritance. PMID:25920668

[The study of tomato fruit weight quantitative trait locus and its application in genetics teaching].

PubMed

Wang, Hai-yan

2015-08-01

The classical research cases, which have greatly promoted the development of genetics in history, can be combined with the content of courses in genetics teaching to train students' ability of scientific thinking and genetic analysis. The localization and clone of gene controlling tomato fruit weight is a pioneer work in quantitative trait locus (QTL) studies and represents a complete process of QTL research in plants. Application of this integrated case in genetics teaching, which showed a wonderful process of scientific discovery and the fascination of genetic research, has inspired students' interest in genetics and achieved a good teaching effect.

Quantitative Trait Loci (QTL) that Underlie SCN Resistance in the Soybean [Glycine max (L.) Merr.] ‘PI438489B’ by ‘Hamilton’ Recombinant Inbred Line Population

USDA-ARS?s Scientific Manuscript database

Soybean cyst nematode caused by Heterodera glycines is the most devastating pest in soybean [Glycine max (L.) Merr.]. Resistance to SCN is complex, polygenic, race-cultivar specific, and controlled by several QTL. Our objective was to identify and map QTL for SCN resistance to races 3 and 5 using a ...

Extent of QTL Reuse During Repeated Phenotypic Divergence of Sympatric Threespine Stickleback.

PubMed

Conte, Gina L; Arnegard, Matthew E; Best, Jacob; Chan, Yingguang Frank; Jones, Felicity C; Kingsley, David M; Schluter, Dolph; Peichel, Catherine L

2015-11-01

How predictable is the genetic basis of phenotypic adaptation? Answering this question begins by estimating the repeatability of adaptation at the genetic level. Here, we provide a comprehensive estimate of the repeatability of the genetic basis of adaptive phenotypic evolution in a natural system. We used quantitative trait locus (QTL) mapping to discover genomic regions controlling a large number of morphological traits that have diverged in parallel between pairs of threespine stickleback (Gasterosteus aculeatus species complex) in Paxton and Priest lakes, British Columbia. We found that nearly half of QTL affected the same traits in the same direction in both species pairs. Another 40% influenced a parallel phenotypic trait in one lake but not the other. The remaining 10% of QTL had phenotypic effects in opposite directions in the two species pairs. Similarity in the proportional contributions of all QTL to parallel trait differences was about 0.4. Surprisingly, QTL reuse was unrelated to phenotypic effect size. Our results indicate that repeated use of the same genomic regions is a pervasive feature of parallel phenotypic adaptation, at least in sticklebacks. Identifying the causes of this pattern would aid prediction of the genetic basis of phenotypic evolution. Copyright © 2015 by the Genetics Society of America.

The Genetic Architecture of Response to Long-Term Artificial Selection for Oil Concentration in the Maize Kernel

PubMed Central

Laurie, Cathy C.; Chasalow, Scott D.; LeDeaux, John R.; McCarroll, Robert; Bush, David; Hauge, Brian; Lai, Chaoqiang; Clark, Darryl; Rocheford, Torbert R.; Dudley, John W.

2004-01-01

In one of the longest-running experiments in biology, researchers at the University of Illinois have selected for altered composition of the maize kernel since 1896. Here we use an association study to infer the genetic basis of dramatic changes that occurred in response to selection for changes in oil concentration. The study population was produced by a cross between the high- and low-selection lines at generation 70, followed by 10 generations of random mating and the derivation of 500 lines by selfing. These lines were genotyped for 488 genetic markers and the oil concentration was evaluated in replicated field trials. Three methods of analysis were tested in simulations for ability to detect quantitative trait loci (QTL). The most effective method was model selection in multiple regression. This method detected ∼50 QTL accounting for ∼50% of the genetic variance, suggesting that >50 QTL are involved. The QTL effect estimates are small and largely additive. About 20% of the QTL have negative effects (i.e., not predicted by the parental difference), which is consistent with hitchhiking and small population size during selection. The large number of QTL detected accounts for the smooth and sustained response to selection throughout the twentieth century. PMID:15611182

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: I. egg production traits.

PubMed

Goraga, Z S; Nassar, M K; Brockmann, G A

2012-04-01

A genome scan was performed to detect chromosomal regions that affect egg production traits in reciprocal crosses between two genetically and phenotypically extreme chicken lines: the partially inbred line New Hampshire (NHI) and the inbred line White Leghorn (WL77). The NHI line had been selected for high growth and WL77 for low egg weight before inbreeding. The result showed a highly significant region on chromosome 4 with multiple QTL for egg production traits between 19.2 and 82.1 Mb. This QTL region explained 4.3 and 16.1% of the phenotypic variance for number of eggs and egg weight in the F(2) population, respectively. The egg weight QTL effects are dependent on the direction of the cross. In addition, genome-wide suggestive QTL for egg weight were found on chromosomes 1, 5, and 9, and for number of eggs on chromosomes 5 and 7. A genome-wide significant QTL affecting age at first egg was mapped on chromosome 1. The difference between the parental lines and the highly significant QTL effects on chromosome 4 will further support fine mapping and candidate gene identification for egg production traits in chicken. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Induri, Brahma R; Ellis, Danielle R; Slavov, Goncho T.

2012-01-01

Understanding genetic variation for the response of Populus to heavy metals like cadmium (Cd) is an important step in elucidating the underlying mechanisms of tolerance. In this study, a pseudo-backcross pedigree of Populus trichocarpa Torr. & Gray and Populus deltoides Bart. was characterized for growth and performance traits after Cd exposure. A total of 16 quantitative trait loci (QTL) at logarithm of odds (LOD) ratio 2.5 were detected for total dry weight, its components and root volume. Major QTL for Cd responses were mapped to two different linkage groups and the relative allelic effects were in opposing directions on themore » two chromosomes, suggesting differential mechanisms at these two loci. The phenotypic variance explained by Cd QTL ranged from 5.9 to 11.6% and averaged 8.2% across all QTL. A whole-genome microarray study led to the identification of nine Cd-responsive genes from these QTL. Promising candidates for Cd tolerance include an NHL repeat membrane-spanning protein, a metal transporter and a putative transcription factor. Additional candidates in the QTL intervals include a putative homolog of a glutamate cysteine ligase, and a glutathione-S-transferase. Functional characterization of these candidate genes should enhance our understanding of Cd metabolism and transport and phytoremediation capabilities of Populus.« less

A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia

PubMed Central

Liu, Feng; Sun, Fei; Xia, Jun Hong; Li, Jian; Fu, Gui Hong; Lin, Grace; Tu, Rong Jian; Wan, Zi Yi; Quek, Delia; Yue, Gen Hua

2014-01-01

Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species. PMID:25435025

Meta-Analyses of QTLs Associated with Protein and Oil Contents and Compositions in Soybean [Glycine max (L.) Merr.] Seed.

PubMed

Van, Kyujung; McHale, Leah K

2017-06-01

Soybean [ Glycine max (L.) Merr.] is a valuable and nutritious crop in part due to the high protein meal and vegetable oil produced from its seed. Soybean producers desire cultivars with both elevated seed protein and oil concentrations as well as specific amino acid and fatty acid profiles. Numerous studies have identified quantitative trait loci (QTLs) associated with seed composition traits, but validation of these QTLs has rarely been carried out. In this study, we have collected information, including genetic location and additive effects, on each QTL for seed contents of protein and oil, as well as amino acid and fatty acid compositions from over 80 studies. Using BioMercator V. 4.2, a meta-QTL analysis was performed with genetic information comprised of 175 QTLs for protein, 205 QTLs for oil, 156 QTLs for amino acids, and 113 QTLs for fatty acids. A total of 55 meta-QTL for seed composition were detected on 6 out of 20 chromosomes. Meta-QTL possessed narrower confidence intervals than the original QTL and candidate genes were identified within each meta-QTL. These candidate genes elucidate potential natural genetic variation in genes contributing to protein and oil biosynthesis and accumulation, providing meaningful information to further soybean breeding programs.

Meta-Analyses of QTLs Associated with Protein and Oil Contents and Compositions in Soybean [Glycine max (L.) Merr.] Seed

PubMed Central

Van, Kyujung; McHale, Leah K.

2017-01-01

Soybean [Glycine max (L.) Merr.] is a valuable and nutritious crop in part due to the high protein meal and vegetable oil produced from its seed. Soybean producers desire cultivars with both elevated seed protein and oil concentrations as well as specific amino acid and fatty acid profiles. Numerous studies have identified quantitative trait loci (QTLs) associated with seed composition traits, but validation of these QTLs has rarely been carried out. In this study, we have collected information, including genetic location and additive effects, on each QTL for seed contents of protein and oil, as well as amino acid and fatty acid compositions from over 80 studies. Using BioMercator V. 4.2, a meta-QTL analysis was performed with genetic information comprised of 175 QTLs for protein, 205 QTLs for oil, 156 QTLs for amino acids, and 113 QTLs for fatty acids. A total of 55 meta-QTL for seed composition were detected on 6 out of 20 chromosomes. Meta-QTL possessed narrower confidence intervals than the original QTL and candidate genes were identified within each meta-QTL. These candidate genes elucidate potential natural genetic variation in genes contributing to protein and oil biosynthesis and accumulation, providing meaningful information to further soybean breeding programs. PMID:28587169

Quantitative trait loci for organ weights and adipose fat composition in Jersey and Limousin back-cross cattle finished on pasture or feedlot.

PubMed

Morris, C A; Bottema, C D K; Cullen, N G; Hickey, S M; Esmailizadeh, A K; Siebert, B D; Pitchford, W S

2010-12-01

A QTL study of live animal and carcass traits in beef cattle was carried out in New Zealand and Australia. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. This paper reports on weights of eight organs (heart, liver, lungs, kidneys, spleen, gastro-intestinal tract, fat, and rumen contents) and 12 fat composition traits (fatty acid (FA) percentages, saturated and monounsaturated FA subtotals, and fat melting point). The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. For organ weights and fat composition traits, 10 and 12 significant QTL locations (P<0.05), respectively, were detected on a genome-wide basis, in combined-sire or within-sire analyses. Seven QTL significant for organ weights were found at the proximal end of chromosome 2. This chromosome carries a variant myostatin allele (F94L), segregating from the Limousin ancestry, and this is a positional candidate for the QTL. Ten significant QTL for fat composition were found on chromosomes 19 and 26. Fatty acid synthase and stearoyl-CoA desaturase (SCD1), respectively, are positional candidate genes for these QTL. Two FA QTL found to be common to sire groups in both populations were for percentages of C14:0 and C14:1 (relative to all FAs) on chromosome 26, near the SCD1 candidate gene. © 2010 AgResearch Ltd, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

QTL mapping for Mediterranean corn borer resistance in European flint germplasm using recombinant inbred lines

PubMed Central

2010-01-01

Background Ostrinia nubilalis (ECB) and Sesamia nonagrioides (MCB) are two maize stem borers which cause important losses in temperate maize production, but QTL analyses for corn borer resistance were mostly restricted to ECB resistance and maize materials genetically related (mapping populations derived from B73). Therefore, the objective of this work was to identify and characterize QTLs for MCB resistance and agronomic traits in a RILs population derived from European flint inbreds. Results Three QTLs were detected for stalk tunnel length at bins 1.02, 3.05 and 8.05 which explained 7.5% of the RILs genotypic variance. The QTL at bin 3.05 was co-located to a QTL related to plant height and grain humidity and the QTL at bin 8.05 was located near a QTL related to yield. Conclusions Our results, when compared with results from other authors, suggest the presence of genes involved in cell wall biosynthesis or fortification with effects on resistance to different corn borer species and digestibility for dairy cattle. Particularly, we proposed five candidate genes related to cell wall characteristics which could explain the QTL for stalk tunnelling in the region 3.05. However, the small proportion of genotypic variance explained by the QTLs suggest that there are also many other genes of small effect regulating MCB resistance and we conclude that MAS seems not promising for this trait. Two QTLs detected for stalk tunnelling overlap with QTLs for agronomic traits, indicating the presence of pleitropism or linkage between genes affecting resistance and agronomic traits. PMID:20230603

Mapping QTL Associated with Photoperiod Sensitivity and Assessing the Importance of QTL×Environment Interaction for Flowering Time in Maize

PubMed Central

Wang, Cuiling; Chen, Yanhui; Ku, Lixia; Wang, Tiegu; Sun, Zhaohui; Cheng, Fangfang; Wu, Liancheng

2010-01-01

Background An understanding of the genetic determinism of photoperiod response of flowering is a prerequisite for the successful exchange of germplasm across different latitudes. In order to contribute to resolve the genetic basis of photoperiod sensitivity in maize, a set of 201 recombinant inbred lines (RIL), derived from a temperate and tropical inbred line cross were evaluated in 5 field trials spread in short- and long-day environments. Methodology/Principal Findings Firstly, QTL analyses for flowering time and photoperiod sensitivity in maize were conducted in individual photoperiod environments separately, and then, the total genetic effect was partitioned into additive effect (A) and additive-by-environment interaction effect (AE) by using a mixed-model-based composite interval mapping (MCIM) method. Conclusions/Significance Seven putative QTL were found associated with DPS thermal time based on the data estimated in individual environments. Nine putative QTL were found associated with DPS thermal time across environments and six of them showed significant QTL×enviroment (QE) interactions. Three QTL for photoperiod sensitivity were identified on chromosome 4, 9 and 10, which had the similar position to QTL for DPS thermal time in the two long-day environment. The major photoperiod sensitive loci qDPS10 responded to both short and long-day photoperiod environments and had opposite effects in different photoperiod environment. The QTL qDPS3, which had the greatest additive effect exclusively in the short-day environment, were photoperiod independent and should be classified in autonomous promotion pathway. PMID:21124912

Deciphering the genetic control of gene expression following Mycobacterium leprae antigen stimulation.

PubMed

Manry, Jérémy; Nédélec, Yohann; Fava, Vinicius M; Cobat, Aurélie; Orlova, Marianna; Thuc, Nguyen Van; Thai, Vu Hong; Laval, Guillaume; Barreiro, Luis B; Schurr, Erwin

2017-08-01

Leprosy is a human infectious disease caused by Mycobacterium leprae. A strong host genetic contribution to leprosy susceptibility is well established. However, the modulation of the transcriptional response to infection and the mechanism(s) of disease control are poorly understood. To address this gap in knowledge of leprosy pathogenicity, we conducted a genome-wide search for expression quantitative trait loci (eQTL) that are associated with transcript variation before and after stimulation with M. leprae sonicate in whole blood cells. We show that M. leprae antigen stimulation mainly triggered the upregulation of immune related genes and that a substantial proportion of the differential gene expression is genetically controlled. Indeed, using stringent criteria, we identified 318 genes displaying cis-eQTL at an FDR of 0.01, including 66 genes displaying response-eQTL (reQTL), i.e. cis-eQTL that showed significant evidence for interaction with the M. leprae stimulus. Such reQTL correspond to regulatory variations that affect the interaction between human whole blood cells and M. leprae sonicate and, thus, likely between the human host and M. leprae bacilli. We found that reQTL were significantly enriched among binding sites of transcription factors that are activated in response to infection, and that they were enriched among single nucleotide polymorphisms (SNPs) associated with susceptibility to leprosy per se and Type-I Reaction, and seven of them have been targeted by recent positive selection. Our study suggested that natural selection shaped our genomic diversity to face pathogen exposure including M. leprae infection.

Chromosomes 3B and 4D are associated with several milling and baking quality traits in a soft white spring wheat (Triticum aestivum L.) population.

PubMed

Carter, A H; Garland-Campbell, K; Morris, C F; Kidwell, K K

2012-04-01

Wheat is marketed based on end-use quality characteristics and better knowledge of the underlying genetics of specific quality parameters is essential to enhance the breeding process. A set of 188 recombinant inbred lines from a 'Louise' by 'Penawawa' mapping population was grown in two crop years at two locations in the Pacific Northwest region of the United States and data were collected on 17 end-use quality traits using established quality analysis protocols. Using an established genetic linkage map, composite interval mapping was used to identify QTL associated with 16 of the 17 quality traits. QTL were found on 13 of the 21 wheat chromosomes. A large number of QTL were located on chromosomes 3B and 4D and coincided with traits for milling quality and starch functionality. Chromosome 3B contained 10 QTL, which were localized to a 26.2 cM region. Chromosome 4D contained 7 QTL, all of which were located on an 18.8 cM region of this chromosome. The majority of the alleles for superior end-use quality were associated with the cultivar Louise. The identified QTL detected remained highly significant independent of grain yield and protein quantity. The identification of these QTL for end-use quality gives key insight into the relationship and complexity of end-use quality traits. It also improves our understanding of these relationships, thereby allowing plant breeders to make valuable gains from selection for these important traits.

QTL and association analysis for skin and fibre pigmentation in sheep provides evidence of a major causative mutation and epistatic effects.

PubMed

Raadsma, H W; Jonas, E; Fleet, M R; Fullard, K; Gongora, J; Cavanagh, C R; Tammen, I; Thomson, P C

2013-08-01

The pursuits of white features and white fleeces free of pigmented fibre have been important selection objectives for many sheep breeds. The cause and inheritance of non-white colour patterns in sheep has been studied since the early 19th century. Discovery of genetic causes, especially those which predispose pigmentation in white sheep, may lead to more accurate selection tools for improved apparel wool. This article describes an extended QTL study for 13 skin and fibre pigmentation traits in sheep. A total of 19 highly significant, 10 significant and seven suggestive QTL were identified in a QTL mapping experiment using an Awassi × Merino × Merino backcross sheep population. All QTL on chromosome 2 exceeded a LOD score of greater than 4 (range 4.4-30.1), giving very strong support for a major gene for pigmentation on this chromosome. Evidence of epistatic interactions was found for QTL for four traits on chromosomes 2 and 19. The ovine TYRP1 gene on OAR 2 was sequenced as a strong positional candidate gene. A highly significant association (P < 0.01) of grandparental haplotypes across nine segregating SNP/microsatellite markers including one non-synonymous SNP with pigmentation traits could be shown. Up to 47% of the observed variation in pigmentation was accounted for by models using TYRP1 haplotypes and 83% for models with interactions between two QTL probabilities, offering scope for marker-assisted selection for these traits. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.

QTL Mapping of Sex Determination Loci Supports an Ancient Pathway in Ants and Honey Bees.

PubMed

Miyakawa, Misato O; Mikheyev, Alexander S

2015-11-01

Sex determination mechanisms play a central role in life-history characteristics, affecting mating systems, sex ratios, inbreeding tolerance, etc. Downstream components of sex determination pathways are highly conserved, but upstream components evolve rapidly. Evolutionary dynamics of sex determination remain poorly understood, particularly because mechanisms appear so diverse. Here we investigate the origins and evolution of complementary sex determination (CSD) in ants and bees. The honey bee has a well-characterized CSD locus, containing tandemly arranged homologs of the transformer gene [complementary sex determiner (csd) and feminizer (fem)]. Such tandem paralogs appear frequently in aculeate hymenopteran genomes. However, only comparative genomic, but not functional, data support a broader role for csd/fem in sex determination, and whether species other than the honey bee use this pathway remains controversial. Here we used a backcross to test whether csd/fem acts as a CSD locus in an ant (Vollenhovia emeryi). After sequencing and assembling the genome, we computed a linkage map, and conducted a quantitative trait locus (QTL) analysis of diploid male production using 68 diploid males and 171 workers. We found two QTLs on separate linkage groups (CsdQTL1 and CsdQTL2) that jointly explained 98.0% of the phenotypic variance. CsdQTL1 included two tandem transformer homologs. These data support the prediction that the same CSD mechanism has indeed been conserved for over 100 million years. CsdQTL2 had no similarity to CsdQTL1 and included a 236-kb region with no obvious CSD gene candidates, making it impossible to conclusively characterize it using our data. The sequence of this locus was conserved in at least one other ant genome that diverged >75 million years ago. By applying QTL analysis to ants for the first time, we support the hypothesis that elements of hymenopteran CSD are ancient, but also show that more remains to be learned about the diversity of CSD mechanisms.

An eQTL Analysis of Partial Resistance to Puccinia hordei in Barley

PubMed Central

Chen, Xinwei; Hackett, Christine A.; Niks, Rients E.; Hedley, Peter E.; Booth, Clare; Druka, Arnis; Marcel, Thierry C.; Vels, Anton; Bayer, Micha; Milne, Iain; Morris, Jenny; Ramsay, Luke; Marshall, David; Cardle, Linda; Waugh, Robbie

2010-01-01

Background Genetic resistance to barley leaf rust caused by Puccinia hordei involves both R genes and quantitative trait loci. The R genes provide higher but less durable resistance than the quantitative trait loci. Consequently, exploring quantitative or partial resistance has become a favorable alternative for controlling disease. Four quantitative trait loci for partial resistance to leaf rust have been identified in the doubled haploid Steptoe (St)/Morex (Mx) mapping population. Further investigations are required to study the molecular mechanisms underpinning partial resistance and ultimately identify the causal genes. Methodology/Principal Findings We explored partial resistance to barley leaf rust using a genetical genomics approach. We recorded RNA transcript abundance corresponding to each probe on a 15K Agilent custom barley microarray in seedlings from St and Mx and 144 doubled haploid lines of the St/Mx population. A total of 1154 and 1037 genes were, respectively, identified as being P. hordei-responsive among the St and Mx and differentially expressed between P. hordei-infected St and Mx. Normalized ratios from 72 distant-pair hybridisations were used to map the genetic determinants of variation in transcript abundance by expression quantitative trait locus (eQTL) mapping generating 15685 eQTL from 9557 genes. Correlation analysis identified 128 genes that were correlated with resistance, of which 89 had eQTL co-locating with the phenotypic quantitative trait loci (pQTL). Transcript abundance in the parents and conservation of synteny with rice allowed us to prioritise six genes as candidates for Rphq11, the pQTL of largest effect, and highlight one, a phospholipid hydroperoxide glutathione peroxidase (HvPHGPx) for detailed analysis. Conclusions/Significance The eQTL approach yielded information that led to the identification of strong candidate genes underlying pQTL for resistance to leaf rust in barley and on the general pathogen response pathway. The dataset will facilitate a systems appraisal of this host-pathogen interaction and, potentially, for other traits measured in this population. PMID:20066049

Genetic dissection of main and epistatic effects of QTL based on augmented triple test cross design

PubMed Central

Zhang, Zheng; Dai, Zhijun; Chen, Yuan; Yuan, Xiong; Yuan, Zheming; Tang, Wenbang; Li, Lanzhi; Hu, Zhongli

2017-01-01

The use of heterosis has considerably increased the productivity of many crops; however, the biological mechanism underpinning the technique remains elusive. The North Carolina design III (NCIII) and the triple test cross (TTC) are powerful and popular genetic mating design that can be used to decipher the genetic basis of heterosis. However, when using the NCIII design with the present quantitative trait locus (QTL) mapping method, if epistasis exists, the estimated additive or dominant effects are confounded with epistatic effects. Here, we propose a two-step approach to dissect all genetic effects of QTL and digenic interactions on a whole genome without sacrificing statistical power based on an augmented TTC (aTTC) design. Because the aTTC design has more transformation combinations than do the NCIII and TTC designs, it greatly enriches the QTL mapping for studying heterosis. When the basic population comprises recombinant inbred lines (RIL), we can use the same materials in the NCIII design for aTTC-design QTL mapping with transformation combination Z1, Z2, and Z4 to obtain genetic effect of QTL and digenic interactions. Compared with RIL-based TTC design, RIL-based aTTC design saves time, money, and labor for basic population crossed with F1. Several Monte Carlo simulation studies were carried out to confirm the proposed approach; the present genetic parameters could be identified with high statistical power, precision, and calculation speed, even at small sample size or low heritability. Additionally, two elite rice hybrid datasets for nine agronomic traits were estimated for real data analysis. We dissected the genetic effects and calculated the dominance degree of each QTL and digenic interaction. Real mapping results suggested that the dominance degree in Z2 that mainly characterize heterosis showed overdominance and dominance for QTL and digenic interactions. Dominance and overdominance were the major genetic foundations of heterosis in rice. PMID:29240818

Genomic Networks of Hybrid Sterility

PubMed Central

Turner, Leslie M.; White, Michael A.; Tautz, Diethard; Payseur, Bret A.

2014-01-01

Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci (“Dobzhansky-Muller incompatibilities”). The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus) provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven ‘hotspots,’ seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL—but not cis eQTL—were substantially lower when mapping was restricted to a ‘fertile’ subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is applicable in a broad range of organisms and we advocate for widespread adoption of a network-centered approach in speciation genetics. PMID:24586194

Genome Wide Association Mapping of Seedling and Adult Plant Resistance to Barley Stripe Rust (Puccinia striiformis f. sp. hordei) in India.

PubMed

Visioni, Andrea; Gyawali, Sanjaya; Selvakumar, Rajan; Gangwar, Om P; Shekhawat, Pradeep S; Bhardwaj, Subhash C; Al-Abdallat, Ayed M; Kehel, Zakaria; Verma, Ramesh P S

2018-01-01

Barley stripe rust is caused by Puccinia striiformis f.sp. hordei , (Psh), occurs worldwide, and is a major disease in South Asia. The aim of this work was to identify and estimate effects of loci underlying quantitative resistance to rust at seedling and adult plant stages. HI-AM panel of 261 barley genotypes consisting of released cultivars from North and South America, Europe, Australia, advanced breeding lines, and local landraces from ICARDA barley program were screened at seedling and adult plant stages for resistance to Psh. Seedling resistance was evaluated with the five prevalent Psh races in India. Screening for the adult plant stage resistance was also performed in two different locations by inoculating with a mixture of the five races used for seedling screeing. The panel was genotyped using DaRT-Seq high-throughput genotyping platform. The genome-wide association mapping (GWAM) showed a total of 45 QTL located across the seven barley chromosomes for seedling resistance to the five races and 18 QTL for adult plant stage resistance. Common QTL for different races at seedling stage were found on all chromosomes except on chromosome 1H. Four common QTL associated with seedling and adult plant stage resistance were found on chromosomes 2, 5, and 6H. Moreover, one of the QTL located on the long arm of chromosome 5H showed stable effects across environments for adult plant stage resistance. Several QTL identified in this study were also reported before in bi-parental and association mapping populations studies validating current GWAM. However 15 new QTL were found at adult plant stage on all chromosomes except the 4H, explaining up to 36.79% of the variance. The promising QTL detected at both stages, once validated, can be used for MAS in Psh resistance breeding program globally.

Genomic Selection Outperforms Marker Assisted Selection for Grain Yield and Physiological Traits in a Maize Doubled Haploid Population Across Water Treatments.

PubMed

Cerrudo, Diego; Cao, Shiliang; Yuan, Yibing; Martinez, Carlos; Suarez, Edgar Antonio; Babu, Raman; Zhang, Xuecai; Trachsel, Samuel

2018-01-01

To increase genetic gain for tolerance to drought, we aimed to identify environmentally stable QTL in per se and testcross combination under well-watered (WW) and drought stressed (DS) conditions and evaluate the possible deployment of QTL using marker assisted and/or genomic selection (QTL/GS-MAS). A total of 169 doubled haploid lines derived from the cross between CML495 and LPSC7F64 and 190 testcrosses (tester CML494) were evaluated in a total of 11 treatment-by-population combinations under WW and DS conditions. In response to DS, grain yield (GY) and plant height (PHT) were reduced while time to anthesis and the anthesis silking interval (ASI) increased for both lines and hybrids. Forty-eight QTL were detected for a total of nine traits. The allele derived from CML495 generally increased trait values for anthesis, ASI, PHT, the normalized difference vegetative index (NDVI) and the green leaf area duration (GLAD; a composite trait of NDVI, PHT and senescence) while it reduced trait values for leaf rolling and senescence. The LOD scores for all detected QTL ranged from 2.0 to 7.2 explaining 4.4 to 19.4% of the observed phenotypic variance with R 2 ranging from 0 (GY, DS, lines) to 37.3% (PHT, WW, lines). Prediction accuracy of the model used for genomic selection was generally higher than phenotypic variance explained by the sum of QTL for individual traits indicative of the polygenic control of traits evaluated here. We therefore propose to use QTL-MAS in forward breeding to enrich the allelic frequency for a few desired traits with strong additive QTL in early selection cycles while GS-MAS could be used in more mature breeding programs to additionally capture alleles with smaller additive effects.

Genome Wide Association Mapping of Seedling and Adult Plant Resistance to Barley Stripe Rust (Puccinia striiformis f. sp. hordei) in India

PubMed Central

Visioni, Andrea; Gyawali, Sanjaya; Selvakumar, Rajan; Gangwar, Om P.; Shekhawat, Pradeep S.; Bhardwaj, Subhash C.; Al-Abdallat, Ayed M.; Kehel, Zakaria; Verma, Ramesh P. S.

2018-01-01

Barley stripe rust is caused by Puccinia striiformis f.sp. hordei, (Psh), occurs worldwide, and is a major disease in South Asia. The aim of this work was to identify and estimate effects of loci underlying quantitative resistance to rust at seedling and adult plant stages. HI-AM panel of 261 barley genotypes consisting of released cultivars from North and South America, Europe, Australia, advanced breeding lines, and local landraces from ICARDA barley program were screened at seedling and adult plant stages for resistance to Psh. Seedling resistance was evaluated with the five prevalent Psh races in India. Screening for the adult plant stage resistance was also performed in two different locations by inoculating with a mixture of the five races used for seedling screeing. The panel was genotyped using DaRT-Seq high-throughput genotyping platform. The genome-wide association mapping (GWAM) showed a total of 45 QTL located across the seven barley chromosomes for seedling resistance to the five races and 18 QTL for adult plant stage resistance. Common QTL for different races at seedling stage were found on all chromosomes except on chromosome 1H. Four common QTL associated with seedling and adult plant stage resistance were found on chromosomes 2, 5, and 6H. Moreover, one of the QTL located on the long arm of chromosome 5H showed stable effects across environments for adult plant stage resistance. Several QTL identified in this study were also reported before in bi-parental and association mapping populations studies validating current GWAM. However 15 new QTL were found at adult plant stage on all chromosomes except the 4H, explaining up to 36.79% of the variance. The promising QTL detected at both stages, once validated, can be used for MAS in Psh resistance breeding program globally. PMID:29740461

Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM)

PubMed Central

Vatter, Thomas; Maurer, Andreas; Perovic, Dragan; Kopahnke, Doris; Pillen, Klaus

2018-01-01

The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM) was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars. PMID:29370232

Considering causal genes in the genetic dissection of kernel traits in common wheat.

PubMed

Mohler, Volker; Albrecht, Theresa; Castell, Adelheid; Diethelm, Manuela; Schweizer, Günther; Hartl, Lorenz

2016-11-01

Genetic factors controlling thousand-kernel weight (TKW) were characterized for their association with other seed traits, including kernel width, kernel length, ratio of kernel width to kernel length (KW/KL), kernel area, and spike number per m 2 (SN). For this purpose, a genetic map was established utilizing a doubled haploid population derived from a cross between German winter wheat cultivars Pamier and Format. Association studies in a diversity panel of elite cultivars supplemented genetic analysis of kernel traits. In both populations, genomic signatures of 13 candidate genes for TKW and kernel size were analyzed. Major quantitative trait loci (QTL) for TKW were identified on chromosomes 1B, 2A, 2D, and 4D, and their locations coincided with major QTL for kernel size traits, supporting the common belief that TKW is a function of other kernel traits. The QTL on chromosome 2A was associated with TKW candidate gene TaCwi-A1 and the QTL on chromosome 4D was associated with dwarfing gene Rht-D1. A minor QTL for TKW on chromosome 6B coincided with TaGW2-6B. The QTL for kernel dimensions that did not affect TKW were detected on eight chromosomes. A major QTL for KW/KL located at the distal tip of chromosome arm 5AS is being reported for the first time. TaSus1-7A and TaSAP-A1, closely linked to each other on chromosome 7A, could be related to a minor QTL for KW/KL. Genetic analysis of SN confirmed its negative correlation with TKW in this cross. In the diversity panel, TaSus1-7A was associated with TKW. Compared to the Pamier/Format bi-parental population where TaCwi-A1a was associated with higher TKW, the same allele reduced grain yield in the diversity panel, suggesting opposite effects of TaCwi-A1 on these two traits.

Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM).

PubMed

Vatter, Thomas; Maurer, Andreas; Perovic, Dragan; Kopahnke, Doris; Pillen, Klaus; Ordon, Frank

2018-01-01

The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM) was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars.

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD.

PubMed

Sun, Wei; Kechris, Katerina; Jacobson, Sean; Drummond, M Bradley; Hawkins, Gregory A; Yang, Jenny; Chen, Ting-Huei; Quibrera, Pedro Miguel; Anderson, Wayne; Barr, R Graham; Basta, Patricia V; Bleecker, Eugene R; Beaty, Terri; Casaburi, Richard; Castaldi, Peter; Cho, Michael H; Comellas, Alejandro; Crapo, James D; Criner, Gerard; Demeo, Dawn; Christenson, Stephanie A; Couper, David J; Curtis, Jeffrey L; Doerschuk, Claire M; Freeman, Christine M; Gouskova, Natalia A; Han, MeiLan K; Hanania, Nicola A; Hansel, Nadia N; Hersh, Craig P; Hoffman, Eric A; Kaner, Robert J; Kanner, Richard E; Kleerup, Eric C; Lutz, Sharon; Martinez, Fernando J; Meyers, Deborah A; Peters, Stephen P; Regan, Elizabeth A; Rennard, Stephen I; Scholand, Mary Beth; Silverman, Edwin K; Woodruff, Prescott G; O'Neal, Wanda K; Bowler, Russell P

2016-08-01

Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p < 8 X 10-10) pQTLs in 38 (43%) of blood proteins tested. Most pQTL SNPs were novel with low overlap to eQTL SNPs. The pQTL SNPs explained >10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10-392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group.

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

PubMed Central

Drummond, M. Bradley; Hawkins, Gregory A.; Yang, Jenny; Chen, Ting-huei; Quibrera, Pedro Miguel; Anderson, Wayne; Barr, R. Graham; Bleecker, Eugene R.; Beaty, Terri; Casaburi, Richard; Castaldi, Peter; Cho, Michael H.; Comellas, Alejandro; Crapo, James D.; Criner, Gerard; Demeo, Dawn; Christenson, Stephanie A.; Couper, David J.; Doerschuk, Claire M.; Freeman, Christine M.; Gouskova, Natalia A.; Han, MeiLan K.; Hanania, Nicola A.; Hansel, Nadia N.; Hersh, Craig P.; Hoffman, Eric A.; Kaner, Robert J.; Kanner, Richard E.; Kleerup, Eric C.; Lutz, Sharon; Martinez, Fernando J.; Meyers, Deborah A.; Peters, Stephen P.; Regan, Elizabeth A.; Rennard, Stephen I.; Scholand, Mary Beth; Silverman, Edwin K.; Woodruff, Prescott G.; O’Neal, Wanda K.; Bowler, Russell P.

2016-01-01

Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p < 8 X 10−10) pQTLs in 38 (43%) of blood proteins tested. Most pQTL SNPs were novel with low overlap to eQTL SNPs. The pQTL SNPs explained >10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10−392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group. PMID:27532455

Dahl (S × R) Rat Congenic Strain Analysis Confirms and Defines a Chromosome 17 Spatial Navigation Quantitative Trait Locus to <10 Mbp

PubMed Central

Herrera, Victoria L.; Pasion, Khristine A.; Tan, Glaiza A.; Ruiz-Opazo, Nelson

2013-01-01

A quantitative trait locus (QTL) linked with ability to find a platform in the Morris Water Maze (MWM) was located on chromosome 17 (Nav-5 QTL) using intercross between Dahl S and Dahl R rats. We developed two congenic strains, S.R17A and S.R17B introgressing Dahl R-chromosome 17 segments into Dahl S chromosome 17 region spanning putative Nav-5 QTL. Performance analysis of S.R17A, S.R17B and Dahl S rats in the Morris water maze (MWM) task showed a significantly decreased spatial navigation performance in S.R17B congenic rats when compared with Dahl S controls (P = 0.02). The S.R17A congenic segment did not affect MWM performance delimiting Nav-5 to the chromosome 17 65.02–74.66 Mbp region. Additional fine mapping is necessary to identify the specific gene variant accounting for Nav-5 effect on spatial learning and memory in Dahl rats. PMID:23469157

Genome-Wide Association Mapping of Barley Yellow Dwarf Virus Tolerance in Spring Oat (Avena sativa L.)

PubMed Central

Foresman, Bradley J.; Oliver, Rebekah E.; Jackson, Eric W.; Chao, Shiaoman; Arruda, Marcio P.; Kolb, Frederic L.

2016-01-01

Barley yellow dwarf viruses (BYDVs) are responsible for the disease barley yellow dwarf (BYD) and affect many cereals including oat (Avena sativa L.). Until recently, the molecular marker technology in oat has not allowed for many marker-trait association studies to determine the genetic mechanisms for tolerance. A genome-wide association study (GWAS) was performed on 428 spring oat lines using a recently developed high-density oat single nucleotide polymorphism (SNP) array as well as a SNP-based consensus map. Marker-trait associations were performed using a Q-K mixed model approach to control for population structure and relatedness. Six significant SNP-trait associations representing two QTL were found on chromosomes 3C (Mrg17) and 18D (Mrg04). This is the first report of BYDV tolerance QTL on chromosome 3C (Mrg17) and 18D (Mrg04). Haplotypes using the two QTL were evaluated and distinct classes for tolerance were identified based on the number of favorable alleles. A large number of lines carrying both favorable alleles were observed in the panel. PMID:27175781

Novel Autism Subtype-Dependent Genetic Variants Are Revealed by Quantitative Trait and Subphenotype Association Analyses of Published GWAS Data

PubMed Central

Hu, Valerie W.; Addington, Anjene; Hyman, Alexander

2011-01-01

The heterogeneity of symptoms associated with autism spectrum disorders (ASDs) has presented a significant challenge to genetic analyses. Even when associations with genetic variants have been identified, it has been difficult to associate them with a specific trait or characteristic of autism. Here, we report that quantitative trait analyses of ASD symptoms combined with case-control association analyses using distinct ASD subphenotypes identified on the basis of symptomatic profiles result in the identification of highly significant associations with 18 novel single nucleotide polymorphisms (SNPs). The symptom categories included deficits in language usage, non-verbal communication, social development, and play skills, as well as insistence on sameness or ritualistic behaviors. Ten of the trait-associated SNPs, or quantitative trait loci (QTL), were associated with more than one subtype, providing partial replication of the identified QTL. Notably, none of the novel SNPs is located within an exonic region, suggesting that these hereditary components of ASDs are more likely related to gene regulatory processes (or gene expression) than to structural or functional changes in gene products. Seven of the QTL reside within intergenic chromosomal regions associated with rare copy number variants that have been previously reported in autistic samples. Pathway analyses of the genes associated with the QTL identified in this study implicate neurological functions and disorders associated with autism pathophysiology. This study underscores the advantage of incorporating both quantitative traits as well as subphenotypes into large-scale genome-wide analyses of complex disorders. PMID:21556359

Genetic dissection of ethanol tolerance in the budding yeast Saccharomyces cerevisiae.

PubMed

Hu, X H; Wang, M H; Tan, T; Li, J R; Yang, H; Leach, L; Zhang, R M; Luo, Z W

2007-03-01

Uncovering genetic control of variation in ethanol tolerance in natural populations of yeast Saccharomyces cerevisiae is essential for understanding the evolution of fermentation, the dominant lifestyle of the species, and for improving efficiency of selection for strains with high ethanol tolerance, a character of great economic value for the brewing and biofuel industries. To date, as many as 251 genes have been predicted to be involved in influencing this character. Candidacy of these genes was determined from a tested phenotypic effect following gene knockout, from an induced change in gene function under an ethanol stress condition, or by mutagenesis. This article represents the first genomics approach for dissecting genetic variation in ethanol tolerance between two yeast strains with a highly divergent trait phenotype. We developed a simple but reliable experimental protocol for scoring the phenotype and a set of STR/SNP markers evenly covering the whole genome. We created a mapping population comprising 319 segregants from crossing the parental strains. On the basis of the data sets, we find that the tolerance trait has a high heritability and that additive genetic variance dominates genetic variation of the trait. Segregation at five QTL detected has explained approximately 50% of phenotypic variation; in particular, the major QTL mapped on yeast chromosome 9 has accounted for a quarter of the phenotypic variation. We integrated the QTL analysis with the predicted candidacy of ethanol resistance genes and found that only a few of these candidates fall in the QTL regions.

Probability genotype imputation method and integrated weighted lasso for QTL identification.

PubMed

Demetrashvili, Nino; Van den Heuvel, Edwin R; Wit, Ernst C

2013-12-30

Many QTL studies have two common features: (1) often there is missing marker information, (2) among many markers involved in the biological process only a few are causal. In statistics, the second issue falls under the headings "sparsity" and "causal inference". The goal of this work is to develop a two-step statistical methodology for QTL mapping for markers with binary genotypes. The first step introduces a novel imputation method for missing genotypes. Outcomes of the proposed imputation method are probabilities which serve as weights to the second step, namely in weighted lasso. The sparse phenotype inference is employed to select a set of predictive markers for the trait of interest. Simulation studies validate the proposed methodology under a wide range of realistic settings. Furthermore, the methodology outperforms alternative imputation and variable selection methods in such studies. The methodology was applied to an Arabidopsis experiment, containing 69 markers for 165 recombinant inbred lines of a F8 generation. The results confirm previously identified regions, however several new markers are also found. On the basis of the inferred ROC behavior these markers show good potential for being real, especially for the germination trait Gmax. Our imputation method shows higher accuracy in terms of sensitivity and specificity compared to alternative imputation method. Also, the proposed weighted lasso outperforms commonly practiced multiple regression as well as the traditional lasso and adaptive lasso with three weighting schemes. This means that under realistic missing data settings this methodology can be used for QTL identification.

Regressive Evolution in the Mexican Cave Tetra, Astyanax mexicanus

PubMed Central

Protas, Meredith; Conrad, Melissa; Gross, Joshua B.; Tabin, Clifford; Borowsky, Richard

2007-01-01

Summary Cave adapted animals generally have reduced pigmentation and eyes, but the evolutionary forces driving the reductions are unknown; Darwin famously questioned the role of natural selection in eye loss in cave fishes; “As it is difficult to imagine that eyes, although useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse” [1]. We studied the genetic basis of this phenomenon in the Mexican cave tetra, Astyanax mexicanus, by mapping the quantitative trait loci (QTL) determining differences in eye/lens sizes and melanophore number between cave and surface fish. In addition, we mapped QTL for the putatively constructive traits of jaw size, tooth number, and numbers of taste buds. The data suggest that eyes and pigmentation regressed through different mechanisms. Cave alleles at each eye/lens QTL we detected caused size reductions. This uniform negative polarity is consistent with evolution by natural selection and inconsistent with evolution by drift. In contrast, QTL polarities for melanophore number were mixed, consistent with evolution by genetic drift or indirect selection through pleiotropy. Past arguments against a role for selection in regression of cave fish eyes cited the insignificant cost of their development [2, 3], but we argue that the energetic cost of their maintenance is sufficiently high for eyes to be detrimental in the cave environment. Regression, a ubiquitous aspect of all evolutionary change, can be caused either by selection or genetic drift/pleiotropy. PMID:17306543

Identification of QTLs for seed germination capability after various storage periods using two RIL populations in rice.

PubMed

Jiang, Wenzhu; Lee, Joohyun; Jin, Yong-Mei; Qiao, Yongli; Piao, Rihua; Jang, Sun Mi; Woo, Mi-Ok; Kwon, Soon-Wook; Liu, Xianhu; Pan, Hong-Yu; Du, Xinglin; Koh, Hee-Jong

2011-04-01

Seed germination capability of rice is one of the important traits in the production and storage of seeds. Quantitative trait loci (QTL) associated with seed germination capability in various storage periods was identified using two sets of recombinant inbred lines (RILs) which derived from crosses between Milyang 23 and Tong 88-7 (MT-RILs) and between Dasanbyeo and TR22183 (DT-RILs). A total of five and three main additive effects (QTLs) associated with seed germination capability were identified in MT-RILs and DT-RILs, respectively. Among them, six QTLs were identified repeatedly in various seed storage periods designated as qMT-SGC5.1, qMT-SGC7.2, and qMT-SGC9.1 on chromosomes 5, 7, and 9 in MT-RILs, and qDT-SGC2.1, qDT-SGC3.1, and qDT-SGC9.1 on chromosomes 2, 3, and 9 in DT-RILs, respectively. The QTL on chromosome 9 was identified in both RIL populations under all three storage periods, explaining up to 40% of the phenotypic variation. Eight and eighteen pairs additive × additive epistatic effect (epistatic QTL) were identified in MT-RILs and DT-RILs, respectively. In addition, several near isogenic lines (NILs) were developed to confirm six repeatable QTL effects using controlled deterioration test (CDT). The identified QTLs will be further studied to elucidate the mechanisms controlling seed germination capability, which have important implications for long-term seed storage.

Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association

PubMed Central

Di Guardo, Mario; Bink, Marco C.A.M.; Guerra, Walter; Letschka, Thomas; Lozano, Lidia; Busatto, Nicola; Poles, Lara; Tadiello, Alice; Bianco, Luca; Visser, Richard G.F.; van de Weg, Eric

2017-01-01

Abstract Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer’s appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions. Both plant materials were genotyped with a 20K single nucleotide polymorphism (SNP) array and phenotyped with a sophisticated high-resolution texture analyzer. The overall QTL results indicated the fundamental role of chromosome 10 in controlling the mechanical properties, while chromosomes 2 and 14 were more associated with the acoustic response. The latter QTL, moreover, showed a consistent relationship between the QTL-estimated genotypes and the acoustic performance assessed among seedlings. The in silico annotation of these intervals revealed interesting candidate genes potentially involved in fruit texture regulation, as suggested by the gene expression profile. The joint integration of these approaches sheds light on the specific control of fruit texture, enabling important genetic information to assist in the selection of valuable fruit quality apple varieties. PMID:28338805

Developmental loss of effect of a Chromosome 15 QTL on alcohol acceptance.

PubMed

McClearn, G E; Tarantino, L M; Hofer, S M; Jones, B; Plomin, R

1998-12-01

Human alcohol abuse and alcoholism have clear developmental features, suggesting the possibility of changes over time in heritability and in quantitative genetic architecture, and raising prospects of identifying individual genes or quantitative trait loci (QTLs) that display different influence on alcohol-related phenotypes at different ages. The identification of specific loci showing such age-related changes will open up opportunities of focused association studies and of genotype manipulation by various mating procedures. Most animal model research in alcohol assesses the phenotypes of the animals at an early age; developmental studies are rare. Here we report on a QTL on Chromosome (Chr) 15 of the mouse that has been shown in several populations, including BXD recombinant inbred strains, an F2, and genotypically selected lines, to affect a measure of alcohol consumption. In the present study, we measured alcohol acceptance in the genotypically selected animals and in an F4 sample at about 100 days and again at about 300 days of age. In both groups, and in both sexes, significant differences were observed at 100 days between animals that were homozygous for the "increasing" haplotype defining the QTL region and those homozygous for the "decreasing" haplotype. At 300 days of age, the effect is absent in females and has diminished or disappeared in males. The results provide a further confirmation of the Chr 15 QTL in young mice, offer a new perspective on the development of alcohol-related phenotypes, and have strong implications for research design.

Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage.

PubMed

Lee, Jonghoon; Izzah, Nur Kholilatul; Jayakodi, Murukarthick; Perumal, Sampath; Joh, Ho Jun; Lee, Hyeon Ju; Lee, Sang-Choon; Park, Jee Young; Yang, Ki-Woung; Nou, Il-Sup; Seo, Joodeok; Yoo, Jaeheung; Suh, Youngdeok; Ahn, Kyounggu; Lee, Ji Hyun; Choi, Gyung Ja; Yu, Yeisoo; Kim, Heebal; Yang, Tae-Jin

2015-02-03

Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F2:3 progenies and identified one major QTL and three minor QTLs. We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.

Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association.

PubMed

Di Guardo, Mario; Bink, Marco C A M; Guerra, Walter; Letschka, Thomas; Lozano, Lidia; Busatto, Nicola; Poles, Lara; Tadiello, Alice; Bianco, Luca; Visser, Richard G F; van de Weg, Eric; Costa, Fabrizio

2017-03-01

Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions. Both plant materials were genotyped with a 20K single nucleotide polymorphism (SNP) array and phenotyped with a sophisticated high-resolution texture analyzer. The overall QTL results indicated the fundamental role of chromosome 10 in controlling the mechanical properties, while chromosomes 2 and 14 were more associated with the acoustic response. The latter QTL, moreover, showed a consistent relationship between the QTL-estimated genotypes and the acoustic performance assessed among seedlings. The in silico annotation of these intervals revealed interesting candidate genes potentially involved in fruit texture regulation, as suggested by the gene expression profile. The joint integration of these approaches sheds light on the specific control of fruit texture, enabling important genetic information to assist in the selection of valuable fruit quality apple varieties. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

The Population Genomics of Repeated Evolution in the Blind Cavefish Astyanax mexicanus

PubMed Central

Bradic, Martina; Teotónio, Henrique; Borowsky, Richard L.

2013-01-01

Distinct populations of Astyanax mexicanus cavefish offer striking examples of repeatable convergence or parallelism in their independent evolutions from surface to cave phenotypes. However, the extent to which the repeatability of evolution occurred at the genetic level remains poorly understood. To address this, we first characterized the genetic diversity of 518 single-nucleotide polymorphisms (SNPs), obtained through RAD tag sequencing and distributed throughout the genome, in seven cave and three groups of surface populations. The cave populations represented two distinct lineages (old and new). Thirty-one SNPs were significantly differentiated between surface and old cave populations, two SNPs were differentiated between surface and new cave populations, and 44 SNPs were significantly differentiated in both old and new cave populations. In addition, we determined whether these SNPs map to the same locations of previously described quantitative trait loci (QTL) between surface and cave populations. A total of 25 differentiated SNPs co-map with several QTL, such as one containing a fibroblast growth factor gene (Fgf8) involved in eye development and lens size. Further, the identity of many SNPs that co-mapped with QTL was the same in independently derived cave populations. These conclusions were further confirmed by haplotype analyses of SNPs within QTL regions. Our findings indicate that the repeatability of evolution at the genetic level is substantial, suggesting that ancestral standing genetic variation significantly contributed to the population genetic variability used in adaptation to the cave environment. PMID:23927992

Molecular characterisation of resistance against potato wart races 1, 2, 6 and 18 in a tetraploid population of potato (Solanum tuberosum subsp. tuberosum).

PubMed

Groth, Jennifer; Song, Yesu; Kellermann, Adolf; Schwarzfischer, Andrea

2013-05-01

Potato wart is caused by the obligate biotrophic fungus Synchytrium endobioticum, which is subject to quarantine regulations due to the production of long persisting spores in the soil and the lack of effective fungicides. The objective of this study was to identify quantitative trait loci (QTL) for resistance against potato wart races (R) 1, 2, 6 and 18 in a tetraploid potato population developed by crossing cv. Saturna (resistant to R1) with cv. Panda (resistant to R1, R2, R6, R18). A total of 92 progenies were used for phenotyping and genotyping. Resistance tests were performed for races 1 and 18 in 2 years and for races 2 and 6 in 1 year on 10 to 20 eyepieces per genotype. Based on amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers, linkage maps were established for the female and male parent, respectively. Single marker analysis followed by a multiple regression analysis revealed initial marker-trait associations. The interval mapping routine of TetraploidMap was applied for QTL analysis. A major QTL for resistance against race 1 explaining between 46 % and 56 % of the phenotypic variation was identified near Sen1, a known resistance locus for potato wart race 1 on chromosome XI. Other resistance QTL were detected on chromosomes I (to R2), II (to R6, 18), VI (to R1, 2, 6, 18), VII (to R2, 6, 18), VIII (to R1, 2, 6, 18), X (to R2, 6, 18), XI (to R2, 6, 18) and on an unknown linkage group (to R18) explaining minor to moderate effects of the phenotypic variation. Resistance QTL against different potato wart races often overlapped, particularly concerning races 2, 6 and 18. Overall, this study gives a valuable insight into the complex inheritance of resistance against potato wart.

Ascertainment bias from imputation methods evaluation in wheat.

PubMed

Brandariz, Sofía P; González Reymúndez, Agustín; Lado, Bettina; Malosetti, Marcos; Garcia, Antonio Augusto Franco; Quincke, Martín; von Zitzewitz, Jarislav; Castro, Marina; Matus, Iván; Del Pozo, Alejandro; Castro, Ariel J; Gutiérrez, Lucía

2016-10-04

Whole-genome genotyping techniques like Genotyping-by-sequencing (GBS) are being used for genetic studies such as Genome-Wide Association (GWAS) and Genomewide Selection (GS), where different strategies for imputation have been developed. Nevertheless, imputation error may lead to poor performance (i.e. smaller power or higher false positive rate) when complete data is not required as it is for GWAS, and each marker is taken at a time. The aim of this study was to compare the performance of GWAS analysis for Quantitative Trait Loci (QTL) of major and minor effect using different imputation methods when no reference panel is available in a wheat GBS panel. In this study, we compared the power and false positive rate of dissecting quantitative traits for imputed and not-imputed marker score matrices in: (1) a complete molecular marker barley panel array, and (2) a GBS wheat panel with missing data. We found that there is an ascertainment bias in imputation method comparisons. Simulating over a complete matrix and creating missing data at random proved that imputation methods have a poorer performance. Furthermore, we found that when QTL were simulated with imputed data, the imputation methods performed better than the not-imputed ones. On the other hand, when QTL were simulated with not-imputed data, the not-imputed method and one of the imputation methods performed better for dissecting quantitative traits. Moreover, larger differences between imputation methods were detected for QTL of major effect than QTL of minor effect. We also compared the different marker score matrices for GWAS analysis in a real wheat phenotype dataset, and we found minimal differences indicating that imputation did not improve the GWAS performance when a reference panel was not available. Poorer performance was found in GWAS analysis when an imputed marker score matrix was used, no reference panel is available, in a wheat GBS panel.

Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle.

PubMed

Sahana, G; Guldbrandtsen, B; Thomsen, B; Holm, L-E; Panitz, F; Brøndum, R F; Bendixen, C; Lund, M S

2014-11-01

Mastitis is a mammary disease that frequently affects dairy cattle. Despite considerable research on the development of effective prevention and treatment strategies, mastitis continues to be a significant issue in bovine veterinary medicine. To identify major genes that affect mastitis in dairy cattle, 6 chromosomal regions on Bos taurus autosome (BTA) 6, 13, 16, 19, and 20 were selected from a genome scan for 9 mastitis phenotypes using imputed high-density single nucleotide polymorphism arrays. Association analyses using sequence-level variants for the 6 targeted regions were carried out to map causal variants using whole-genome sequence data from 3 breeds. The quantitative trait loci (QTL) discovery population comprised 4,992 progeny-tested Holstein bulls, and QTL were confirmed in 4,442 Nordic Red and 1,126 Jersey cattle. The targeted regions were imputed to the sequence level. The highest association signal for clinical mastitis was observed on BTA 6 at 88.97 Mb in Holstein cattle and was confirmed in Nordic Red cattle. The peak association region on BTA 6 contained 2 genes: vitamin D-binding protein precursor (GC) and neuropeptide FF receptor 2 (NPFFR2), which, based on known biological functions, are good candidates for affecting mastitis. However, strong linkage disequilibrium in this region prevented conclusive determination of the causal gene. A different QTL on BTA 6 located at 88.32 Mb in Holstein cattle affected mastitis. In addition, QTL on BTA 13 and 19 were confirmed to segregate in Nordic Red cattle and QTL on BTA 16 and 20 were confirmed in Jersey cattle. Although several candidate genes were identified in these targeted regions, it was not possible to identify a gene or polymorphism as the causal factor for any of these regions. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Identification of candidate genes involved in Witches' broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil.

PubMed

Royaert, Stefan; Jansen, Johannes; da Silva, Daniela Viana; de Jesus Branco, Samuel Martins; Livingstone, Donald S; Mustiga, Guiliana; Marelli, Jean-Philippe; Araújo, Ioná Santos; Corrêa, Ronan Xavier; Motamayor, Juan Carlos

2016-02-11

Witches' broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. We developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant 'TSH 1188' and the tolerant 'CCN 51' at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone 'SCAVINA 6'. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between 'CCN 51' and 'TSH 1188'. We combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the 'CCN 51' parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material.

Development of a QTL-environment-based predictive model for node addition rate in common bean.

PubMed

Zhang, Li; Gezan, Salvador A; Eduardo Vallejos, C; Jones, James W; Boote, Kenneth J; Clavijo-Michelangeli, Jose A; Bhakta, Mehul; Osorno, Juan M; Rao, Idupulapati; Beebe, Stephen; Roman-Paoli, Elvin; Gonzalez, Abiezer; Beaver, James; Ricaurte, Jaumer; Colbert, Raphael; Correll, Melanie J

2017-05-01

This work reports the effects of the genetic makeup, the environment and the genotype by environment interactions for node addition rate in an RIL population of common bean. This information was used to build a predictive model for node addition rate. To select a plant genotype that will thrive in targeted environments it is critical to understand the genotype by environment interaction (GEI). In this study, multi-environment QTL analysis was used to characterize node addition rate (NAR, node day - 1 ) on the main stem of the common bean (Phaseolus vulgaris L). This analysis was carried out with field data of 171 recombinant inbred lines that were grown at five sites (Florida, Puerto Rico, 2 sites in Colombia, and North Dakota). Four QTLs (Nar1, Nar2, Nar3 and Nar4) were identified, one of which had significant QTL by environment interactions (QEI), that is, Nar2 with temperature. Temperature was identified as the main environmental factor affecting NAR while day length and solar radiation played a minor role. Integration of sites as covariates into a QTL mixed site-effect model, and further replacing the site component with explanatory environmental covariates (i.e., temperature, day length and solar radiation) yielded a model that explained 73% of the phenotypic variation for NAR with root mean square error of 16.25% of the mean. The QTL consistency and stability was examined through a tenfold cross validation with different sets of genotypes and these four QTLs were always detected with 50-90% probability. The final model was evaluated using leave-one-site-out method to assess the influence of site on node addition rate. These analyses provided a quantitative measure of the effects on NAR of common beans exerted by the genetic makeup, the environment and their interactions.

Primary genome scan to identify putative quantitative trait loci for feedlot growth rate, feed intake, and feed efficiency of beef cattle.

PubMed

Nkrumah, J D; Sherman, E L; Li, C; Marques, E; Crews, D H; Bartusiak, R; Murdoch, B; Wang, Z; Basarab, J A; Moore, S S

2007-12-01

Feed intake and feed efficiency of beef cattle are economically relevant traits. The study was conducted to identify QTL for feed intake and feed efficiency of beef cattle by using genotype information from 100 microsatellite markers and 355 SNP genotyped across 400 progeny of 20 Angus, Charolais, or Alberta Hybrid bulls. Traits analyzed include feedlot ADG, daily DMI, feed-to-gain ratio [F:G, which is the reciprocal of the efficiency of gain (G:F)], and residual feed intake (RFI). A mixed model with sire as random and QTL effects as fixed was used to generate an F-statistic profile across and within families for each trait along each chromosome, followed by empirical permutation tests to determine significance thresholds for QTL detection. Putative QTL for ADG (chromosome-wise P < 0.05) were detected across families on chromosomes 5 (130 cM), 6 (42 cM), 7 (84 cM), 11 (20 cM), 14 (74 cM), 16 (22 cM), 17 (9 cM), 18 (46 cM), 19 (53 cM), and 28 (23 cM). For DMI, putative QTL that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 1 (93 cM), 3 (123 cM), 15 (31 cM), 17 (81 cM), 18 (49 cM), 20 (56 cM), and 26 (69 cM) in the across-family analyses. Putative across-family QTL influencing F:G that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 3 (62 cM), 5 (129 cM), 7 (27 cM), 11 (16 cM), 16 (30 cM), 17 (81 cM), 22 (72 cM), 24 (55 cM), and 28 (24 cM). Putative QTL influencing RFI that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 1 (90 cM), 5 (129 cM), 7 (22 cM), 8 (80 cM), 12 (89 cM), 16 (41 cM), 17 (19 cM), and 26 (48 cM) in the across-family analyses. In addition, a total of 4, 6, 1, and 8 chromosomes showed suggestive evidence (chromosome-wise, P < 0.10) for putative ADG, DMI, F:G, and RFI QTL, respectively. Most of the QTL detected across families were also detected within families, although the locations across families were not necessarily the locations within families, which is likely because of differences among families in marker informativeness for the different linkage groups. The locations and direction of some of the QTL effects reported in this study suggest potentially favorable pleiotropic effects for the underlying genes. Further studies will be required to confirm these QTL in other populations so that they can be fine-mapped for potential applications in marker-assisted selection and management of beef cattle.

Investigation of the Genetic Diversity and Quantitative Trait Loci Accounting for Important Agronomic and Seed Quality Traits in Brassica carinata

PubMed Central

Zhang, Wenshan; Hu, Dandan; Raman, Rosy; Guo, Shaomin; Wei, Zili; Shen, Xueqi; Meng, Jinling; Raman, Harsh; Zou, Jun

2017-01-01

Brassica carinata (BBCC) is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD) pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r2 = 0.1) in B subgenome (0.25 Mb) was shorter than that of C subgenome (0.40 Mb). Genome-wide association analysis (GWAS) identified a total of seven markers significantly associated with five seed quality traits in two experiments. To further identify the quantitative trait loci (QTL) for important agronomic and seed quality traits, we phenotyped a doubled haploid (DH) mapping population derived from the “YW” cross between two parents (Y-BcDH64 and W-BcDH76) representing from the two subpopulations. The YW DH population and its parents were grown in three contrasting environments; spring (Hezheng and Xining, China), semi-winter (Wuhan, China), and spring (Wagga Wagga, Australia) across 5 years for QTL mapping. Genetic bases of phenotypic variation in seed yield and its seven related traits, and six seed quality traits were determined. A total of 282 consensus QTL accounting for these traits were identified including nine major QTL for flowering time, oleic acid, linolenic acid, pod number of main inflorescence, and seed weight. Of these, 109 and 134 QTL were specific to spring and semi-winter environment, respectively, while 39 consensus QTL were identified in both contrasting environments. Two QTL identified for linolenic acid (B3) and erucic acid (C7) were validated in the diverse lines used for GWAS. A total of 25 QTL accounting for flowering time, erucic acid, and oleic acid were aligned to the homologous QTL or candidate gene regions in the C genome of B. napus. These results would not only provide insights for genetic improvement of this species, but will also identify useful genetic variation hidden in the Cc subgenome of B. carinata to improve canola cultivars. PMID:28484482

Genetic progress in multistage dairy cattle breeding schemes using genetic markers.

PubMed

Schrooten, C; Bovenhuis, H; van Arendonk, J A M; Bijma, P

2005-04-01

The aim of this paper was to explore general characteristics of multistage breeding schemes and to evaluate multistage dairy cattle breeding schemes that use information on quantitative trait loci (QTL). Evaluation was either for additional genetic response or for reduction in number of progeny-tested bulls while maintaining the same response. The reduction in response in multistage breeding schemes relative to comparable single-stage breeding schemes (i.e., with the same overall selection intensity and the same amount of information in the final stage of selection) depended on the overall selection intensity, the selection intensity in the various stages of the breeding scheme, and the ratio of the accuracies of selection in the various stages of the breeding scheme. When overall selection intensity was constant, reduction in response increased with increasing selection intensity in the first stage. The decrease in response was highest in schemes with lower overall selection intensity. Reduction in response was limited in schemes with low to average emphasis on first-stage selection, especially if the accuracy of selection in the first stage was relatively high compared with the accuracy in the final stage. Closed nucleus breeding schemes in dairy cattle that use information on QTL were evaluated by deterministic simulation. In the base scheme, the selection index consisted of pedigree information and own performance (dams), or pedigree information and performance of 100 daughters (sires). In alternative breeding schemes, information on a QTL was accounted for by simulating an additional index trait. The fraction of the variance explained by the QTL determined the correlation between the additional index trait and the breeding goal trait. Response in progeny test schemes relative to a base breeding scheme without QTL information ranged from +4.5% (QTL explaining 5% of the additive genetic variance) to +21.2% (QTL explaining 50% of the additive genetic variance). A QTL explaining 5% of the additive genetic variance allowed a 35% reduction in the number of progeny tested bulls, while maintaining genetic response at the level of the base scheme. Genetic progress was up to 31.3% higher for schemes with increased embryo production and selection of embryos based on QTL information. The challenge for breeding organizations is to find the optimum breeding program with regard to additional genetic progress and additional (or reduced) cost.

Copy number variation identification and analysis of the chicken genome using a 60K SNP BeadChip.

PubMed

Rao, Y S; Li, J; Zhang, R; Lin, X R; Xu, J G; Xie, L; Xu, Z Q; Wang, L; Gan, J K; Xie, X J; He, J; Zhang, X Q

2016-08-01

Copy number variation (CNV) is an important source of genetic variation in organisms and a main factor that affects phenotypic variation. A comprehensive study of chicken CNV can provide valuable information on genetic diversity and facilitate future analyses of associations between CNV and economically important traits in chickens. In the present study, an F2 full-sib chicken population (554 individuals), established from a cross between Xinghua and White Recessive Rock chickens, was used to explore CNV in the chicken genome. Genotyping was performed using a chicken 60K SNP BeadChip. A total of 1,875 CNV were detected with the PennCNV algorithm, and the average number of CNV was 3.42 per individual. The CNV were distributed across 383 independent CNV regions (CNVR) and covered 41 megabases (3.97%) of the chicken genome. Seven CNVR in 108 individuals were validated by quantitative real-time PCR, and 81 of these individuals (75%) also were detected with the PennCNV algorithm. In total, 274 CNVR (71.54%) identified in the current study were previously reported. Of these, 147 (38.38%) were reported in at least 2 studies. Additionally, 109 of the CNVR (28.46%) discovered here are novel. A total of 709 genes within or overlapping with the CNVR was retrieved. Out of the 2,742 quantitative trait loci (QTL) collected in the chicken QTL database, 43 QTL had confidence intervals overlapping with the CNVR, and 32 CNVR encompassed one or more functional genes. The functional genes located in the CNVR are likely to be the QTG that are associated with underlying economic traits. This study considerably expands our insight into the structural variation in the genome of chickens and provides an important resource for genomic variation, especially for genomic structural variation related to economic traits in chickens. © 2016 Poultry Science Association Inc.

Amplified fragment length polymorphism mapping of quantitative trait loci for malaria parasite susceptibility in the yellow fever mosquito Aedes aegypti.

PubMed

Zhong, Daibin; Menge, David M; Temu, Emmanuel A; Chen, Hong; Yan, Guiyun

2006-07-01

The yellow fever mosquito Aedes aegypti has been the subject of extensive genetic research due to its medical importance and the ease with which it can be manipulated in the laboratory. A molecular genetic linkage map was constructed using 148 amplified fragment length polymorphism (AFLP) and six single-strand conformation polymorphism (SSCP) markers. Eighteen AFLP primer combinations were used to genotype two reciprocal F2 segregating populations. Each primer combination generated an average of 8.2 AFLP markers eligible for linkage mapping. The length of the integrated map was 180.9 cM, giving an average marker resolution of 1.2 cM. Composite interval mapping revealed a total of six QTL significantly affecting Plasmodium susceptibility in the two reciprocal crosses of Ae. aegypti. Two common QTL on linkage group 2 were identified in both crosses that had similar effects on the phenotype, and four QTL were unique to each cross. In one cross, the four main QTL accounted for 64% of the total phenotypic variance, and digenic epistasis explained 11.8% of the variance. In the second cross, the four main QTL explained 66% of the variance, and digenic epistasis accounted for 16% of the variance. The actions of these QTL were either dominance or underdominance. Our results indicated that at least three new QTL were mapped on chromosomes 1 and 3. The polygenic nature of susceptibility to P. gallinaceum and epistasis are important factors for significant variation within or among mosquito strains. The new map provides additional information useful for further genetic investigation, such as identification of new genes and positional cloning.

Quantitative trait loci and candidate genes associated with starch pasting viscosity characteristics in cassava (Manihot esculenta Crantz).

PubMed

Thanyasiriwat, T; Sraphet, S; Whankaew, S; Boonseng, O; Bao, J; Lightfoot, D A; Tangphatsornruang, S; Triwitayakorn, K

2014-01-01

Starch pasting viscosity is an important quality trait in cassava (Manihot esculenta Crantz) cultivars. The aim here was to identify loci and candidate genes associated with the starch pasting viscosity. Quantitative trait loci (QTL) mapping for seven pasting viscosity parameters was carried out using 100 lines of an F1 mapping population from a cross between two cassava cultivars Huay Bong 60 and Hanatee. Starch samples were obtained from roots of cassava grown in 2008 and 2009 at Rayong, and in 2009 at Lop Buri province, Thailand. The traits showed continuous distribution among the F1 progeny with transgressive variation. Fifteen QTL were identified from mean trait data, with Logarithm of Odds (LOD) values from 2.77-13.01 and phenotype variations explained (PVE) from10.0-48.4%. In addition, 48 QTL were identified in separate environments. The LOD values ranged from 2.55-8.68 and explained 6.6-43.7% of phenotype variation. The loci were located on 19 linkage groups. The most important QTL for pasting temperature (PT) (qPT.1LG1) from mean trait values showed largest effect with highest LOD value (13.01) and PVE (48.4%). The QTL co-localised with PT and pasting time (PTi) loci that were identified in separate environments. Candidate genes were identified within the QTL peak regions. However, the major genes of interest, encoding the family of glycosyl or glucosyl transferases and hydrolases, were located at the periphery of QTL peaks. The loci identified could be effectively applied in breeding programmes to improve cassava starch quality. Alleles of candidate genes should be further studied in order to better understand their effects on starch quality traits. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

Linkage Screen for BMD Phenotypes in Male and Female COP and DA Rat Strains

PubMed Central

Koller, Daniel L; Liu, Lixiang; Alam, Imranul; Sun, Qiwei; Econs, Michael J; Foroud, Tatiana; Turner, Charles H

2008-01-01

Because particular inbred strains of experimental animals are informative for only a subset of the genes underlying variability in BMD, we undertook a genome screen to identify quantitative trait loci (QTLs) in 828 F2 progeny (405 males and 423 females) derived from the Copenhagen 2331 (COP) and dark agouti (DA) strains of rats. This screen was performed to complement our study in female Fischer 344 (F344) and Lewis (LEW) rats and to further delineate the factors underlying the complex genetic architecture of BMD in the rat model. Microsatellite genotyping was performed using markers at an average density of 20 cM. BMD was measured by pQCT and DXA. These data were analyzed in the R/qtl software to detect QTLs acting in both sexes as well as those having sex-specific effects. A QTL was detected in both sexes on chromosome 18 for midfemur volumetric BMD (vBMD; genome-wide, p < 0.01). On distal chromosome 1, a QTL was found for femur and vertebral aBMD as well as distal femur vBMD, and this QTL appears distinct from the proximal chromosome 1 QTL impacting BMD in our F344/LEW cross. Additional aBMD and vBMD QTLs and several sex-specific QTLs were also detected. These included a male-specific QTL (p < 0.01) on chromosome 8 and a female-specific QTL on chromosomes 7 and 14 (p < 0.01). Few of the QTLs identified showed overlap with the significant QTLs from the F344/LEW cross. These results confirm that the genetic influence on BMD in the rat model is quite complex and would seem to be influenced by a number of different genes, some of which have sex-specific effects. PMID:18707222

High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

PubMed

Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

2012-08-01

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

Quantitative Trait Loci Mapping of Genome Regions Controlling Permethrin Resistance in the Mosquito Aedes aegypti

PubMed Central

Saavedra-Rodriguez, Karla; Strode, Clare; Flores Suarez, Adriana; Fernandez Salas, Ildefonso; Ranson, Hilary; Hemingway, Janet; Black, William C.

2008-01-01

The mosquito Aedes aegypti is the principal vector of dengue and yellow fever flaviviruses. Permethrin is an insecticide used to suppress Ae. aegypti adult populations but metabolic and target site resistance to pyrethroids has evolved in many locations worldwide. Quantitative trait loci (QTL) controlling permethrin survival in Ae. aegypti were mapped in an F3 advanced intercross line. Parents came from a collection of mosquitoes from Isla Mujeres, México, that had been selected for permethrin resistance for two generations and a reference permethrin-susceptible strain originally from New Orleans. Following a 1-hr permethrin exposure, 439 F3 adult mosquitoes were phenotyped as knockdown resistant, knocked down/recovered, or dead. For QTL mapping, single nucleotide polymorphisms (SNPs) were identified at 22 loci with potential antixenobiotic activity including genes encoding cytochrome P450s (CYP), esterases (EST), or glutathione transferases (GST) and at 12 previously mapped loci. Seven antixenobiotic genes mapped to chromosome I, six to chromosome II, and nine to chromosome III. Two QTL of major effect were detected on chromosome III. One corresponds with a SNP previously associated with permethrin resistance in the para sodium channel gene and the second with the CCEunk7o esterase marker. Additional QTL but of relatively minor effect were also found. These included two sex-linked QTL on chromosome I affecting knockdown and recovery and a QTL affecting survival and recovery. On chromosome II, one QTL affecting survival and a second affecting recovery were detected. The patterns confirm that mutations in the para gene cause target-site insensitivity and are the major source of permethrin resistance but that other genes dispersed throughout the genome contribute to recovery and survival of mosquitoes following permethrin exposure. PMID:18723882

Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations.

PubMed

Melo, Thaise P; Takada, Luciana; Baldi, Fernando; Oliveira, Henrique N; Dias, Marina M; Neves, Haroldo H R; Schenkel, Flavio S; Albuquerque, Lucia G; Carvalheiro, Roberto

2016-06-21

QTL mapping through genome-wide association studies (GWAS) is challenging, especially in the case of low heritability complex traits and when few animals possess genotypic and phenotypic information. When most of the phenotypic information is from non-genotyped animals, GWAS can be performed using the weighted single-step GBLUP (WssGBLUP) method, which permits to combine all available information, even that of non-genotyped animals. However, it is not clear to what extent phenotypic information from non-genotyped animals increases the power of QTL detection, and whether factors such as the extent of linkage disequilibrium (LD) in the population and weighting SNPs in WssGBLUP affect the importance of using information from non-genotyped animals in GWAS. These questions were investigated in this study using real and simulated data. Analysis of real data showed that the use of phenotypes of non-genotyped animals affected SNP effect estimates and, consequently, QTL mapping. Despite some coincidence, the most important genomic regions identified by the analyses, either using or ignoring phenotypes of non-genotyped animals, were not the same. The simulation results indicated that the inclusion of all available phenotypic information, even that of non-genotyped animals, tends to improve QTL detection for low heritability complex traits. For populations with low levels of LD, this trend of improvement was less pronounced. Stronger shrinkage on SNPs explaining lower variance was not necessarily associated with better QTL mapping. The use of phenotypic information from non-genotyped animals in GWAS may improve the ability to detect QTL for low heritability complex traits, especially in populations in which the level of LD is high.

Complementary epistasis involving Sr12 explains adult plant resistance to stem rust in Thatcher wheat (Triticum aestivum L.).

PubMed

Rouse, Matthew N; Talbert, Luther E; Singh, Davinder; Sherman, Jamie D

2014-07-01

Quantitative trait loci conferring adult plant resistance to Ug99 stem rust in Thatcher wheat display complementary gene action suggesting multiple quantitative trait loci are needed for effective resistance. Adult plant resistance (APR) in wheat (Triticum aestivum L.) to stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is desirable because this resistance can be Pgt race non-specific. Resistance derived from cultivar Thatcher can confer high levels of APR to the virulent Pgt race TTKSK (Ug99) when combined with stem rust resistance gene Sr57 (Lr34). To identify the loci conferring APR in Thatcher, we evaluated 160 RILs derived from Thatcher crossed to susceptible cultivar McNeal for field stem rust reaction in Kenya for two seasons and in St. Paul for one season. All RILs and parents were susceptible as seedlings to race TTKSK. However, adult plant stem rust severities in Kenya varied from 5 to 80 %. Composite interval mapping identified four quantitative trait loci (QTL). Three QTL were inherited from Thatcher and one, Sr57, was inherited from McNeal. The markers closest to the QTL peaks were used in an ANOVA to determine the additive and epistatic effects. A QTL on 3BS was detected in all three environments and explained 27-35 % of the variation. The peak of this QTL was at the same location as the Sr12 seedling resistance gene effective to race SCCSC. Epistatic interactions were significant between Sr12 and QTL on chromosome arms 1AL and 2BS. Though Sr12 cosegregated with the largest effect QTL, lines with Sr12 were not always resistant. The data suggest that Sr12 or a linked gene, though not effective to race TTKSK alone, confers APR when combined with other resistance loci.

The Genetic Architecture of Seed Composition in Soybean Is Refined by Genome-Wide Association Scans Across Multiple Populations

PubMed Central

Vaughn, Justin N.; Nelson, Randall L.; Song, Qijian; Cregan, Perry B.; Li, Zenglu

2014-01-01

Soybean oil and meal are major contributors to world-wide food production. Consequently, the genetic basis for soybean seed composition has been intensely studied using family-based mapping. Population-based mapping approaches, in the form of genome-wide association (GWA) scans, have been able to resolve loci controlling moderately complex quantitative traits (QTL) in numerous crop species. Yet, it is still unclear how soybean’s unique population history will affect GWA scans. Using one of the populations in this study, we simulated phenotypes resulting from a range of genetic architectures. We found that with a heritability of 0.5, ∼100% and ∼33% of the 4 and 20 simulated QTL can be recovered, respectively, with a false-positive rate of less than ∼6×10−5 per marker tested. Additionally, we demonstrated that combining information from multi-locus mixed models and compressed linear-mixed models improves QTL identification and interpretation. We applied these insights to exploring seed composition in soybean, refining the linkage group I (chromosome 20) protein QTL and identifying additional oil QTL that may allow some decoupling of highly correlated oil and protein phenotypes. Because the value of protein meal is closely related to its essential amino acid profile, we attempted to identify QTL underlying methionine, threonine, cysteine, and lysine content. Multiple QTL were found that have not been observed in family-based mapping studies, and each trait exhibited associations across multiple populations. Chromosomes 1 and 8 contain strong candidate alleles for essential amino acid increases. Overall, we present these and additional data that will be useful in determining breeding strategies for the continued improvement of soybean’s nutrient portfolio. PMID:25246241

Genetic determinism of bone and mineral metabolism in meat-type chickens: A QTL mapping study.

PubMed

Mignon-Grasteau, Sandrine; Chantry-Darmon, Céline; Boscher, Marie-Yvonne; Sellier, Nadine; Chabault-Dhuit, Marie; Le Bihan-Duval, Elisabeth; Narcy, Agnès

2016-12-01

Skeletal integrity in meat-type chickens is affected by many factors including rapid growth rate, nutrition and genetics. To investigate the genetic basis of bone and mineral metabolism, a QTL detection study was conducted in an intercross between two lines of meat-type chickens divergently selected for their high (D +) or low (D -) digestive efficiency. Tibia size (length, diameter, volume) and ash content were determined at 3 weeks of age as well as phosphorus (P) retention and plasma concentration. Heritability of these traits and their genetic correlations with digestive efficiency were estimated. A QTL mapping study was performed using 3379 SNP markers. Tibia size, weight, ash content and breaking strength were highly heritable (0.42 to 0.61). Relative tibia diameter and volume as well as P retention were strongly and positively genetically correlated with digestive efficiency (0.57 to 0.80). A total of 35 QTL were identified (9 for tibia weight, 13 for tibia size, 5 for bone strength, 5 for bone mineralization, 2 for plasma P concentration and 1 for P retention). Six QTL were genome-wide significant, and 3 QTL for tibia relative volume, weight and ash weight on chromosome 6 were fixed, the positive allele coming from the D-line. For two QTL for ash content on chromosome 18 and relative tibia length on chromosome 26, the confidence intervals were small enough to identify potential candidate genes. These findings support the evidence of multiple genetic loci controlling bone and mineral metabolism. The identification of candidate genes may provide new perspectives in the understanding of bone regulation, even beyond avian species.

Robust Linear Models for Cis-eQTL Analysis.

PubMed

Rantalainen, Mattias; Lindgren, Cecilia M; Holmes, Christopher C

2015-01-01

Expression Quantitative Trait Loci (eQTL) analysis enables characterisation of functional genetic variation influencing expression levels of individual genes. In outbread populations, including humans, eQTLs are commonly analysed using the conventional linear model, adjusting for relevant covariates, assuming an allelic dosage model and a Gaussian error term. However, gene expression data generally have noise that induces heavy-tailed errors relative to the Gaussian distribution and often include atypical observations, or outliers. Such departures from modelling assumptions can lead to an increased rate of type II errors (false negatives), and to some extent also type I errors (false positives). Careful model checking can reduce the risk of type-I errors but often not type II errors, since it is generally too time-consuming to carefully check all models with a non-significant effect in large-scale and genome-wide studies. Here we propose the application of a robust linear model for eQTL analysis to reduce adverse effects of deviations from the assumption of Gaussian residuals. We present results from a simulation study as well as results from the analysis of real eQTL data sets. Our findings suggest that in many situations robust models have the potential to provide more reliable eQTL results compared to conventional linear models, particularly in respect to reducing type II errors due to non-Gaussian noise. Post-genomic data, such as that generated in genome-wide eQTL studies, are often noisy and frequently contain atypical observations. Robust statistical models have the potential to provide more reliable results and increased statistical power under non-Gaussian conditions. The results presented here suggest that robust models should be considered routinely alongside other commonly used methodologies for eQTL analysis.

Resistance to a Rhabdovirus (VHSV) in Rainbow Trout: Identification of a Major QTL Related to Innate Mechanisms

PubMed Central

Verrier, Eloi R.; Dorson, Michel; Mauger, Stéphane; Torhy, Corinne; Ciobotaru, Céline; Hervet, Caroline; Dechamp, Nicolas; Genet, Carine; Boudinot, Pierre; Quillet, Edwige

2013-01-01

Health control is a major issue in animal breeding and a better knowledge of the genetic bases of resistance to diseases is needed in farm animals including fish. The detection of quantitative trait loci (QTL) will help uncovering the genetic architecture of important traits and understanding the mechanisms involved in resistance to pathogens. We report here the detection of QTL for resistance to Viral Haemorrhagic Septicaemia Virus (VHSV), a major threat for European aquaculture industry. Two induced mitogynogenetic doubled haploid F2 rainbow trout (Oncorhynchus mykiss) families were used. These families combined the genome of susceptible and resistant F0 breeders and contained only fully homozygous individuals. For phenotyping, fish survival after an immersion challenge with the virus was recorded, as well as in vitro virus replication on fin explants. A bidirectional selective genotyping strategy identified seven QTL associated to survival. One of those QTL was significant at the genome-wide level and largely explained both survival and viral replication in fin explants in the different families of the design (up to 65% and 49% of phenotypic variance explained respectively). These results evidence the key role of innate defence in resistance to the virus and pave the way for the identification of the gene(s) responsible for resistance. The identification of a major QTL also opens appealing perspectives for selective breeding of fish with improved resistance. PMID:23390526

Ancestral QTL Alleles from Wild Emmer Wheat Improve Drought Resistance and Productivity in Modern Wheat Cultivars

PubMed Central

Merchuk-Ovnat, Lianne; Barak, Vered; Fahima, Tzion; Ordon, Frank; Lidzbarsky, Gabriel A.; Krugman, Tamar; Saranga, Yehoshua

2016-01-01

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs) from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum) and bread (T. aestivum) wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4) were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690–710 mm) and water-limited (290–320 mm) conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS), and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS). In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass—specifically under drought (7AS QTL in cv. Bar Nir background), under both treatments (2BS QTL), and a greater stability across treatments (1BL QTL). The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance. PMID:27148287

Discovery of genomic intervals that underlie nematode responses to benzimidazoles.

PubMed

Zamanian, Mostafa; Cook, Daniel E; Zdraljevic, Stefan; Brady, Shannon C; Lee, Daehan; Lee, Junho; Andersen, Erik C

2018-03-01

Parasitic nematodes impose a debilitating health and economic burden across much of the world. Nematode resistance to anthelmintic drugs threatens parasite control efforts in both human and veterinary medicine. Despite this threat, the genetic landscape of potential resistance mechanisms to these critical drugs remains largely unexplored. Here, we exploit natural variation in the model nematodes Caenorhabditis elegans and Caenorhabditis briggsae to discover quantitative trait loci (QTL) that control sensitivity to benzimidazoles widely used in human and animal medicine. High-throughput phenotyping of albendazole, fenbendazole, mebendazole, and thiabendazole responses in panels of recombinant lines led to the discovery of over 15 QTL in C. elegans and four QTL in C. briggsae associated with divergent responses to these anthelmintics. Many of these QTL are conserved across benzimidazole derivatives, but others show drug and dose specificity. We used near-isogenic lines to recapitulate and narrow the C. elegans albendazole QTL of largest effect and identified candidate variants correlated with the resistance phenotype. These QTL do not overlap with known benzimidazole target resistance genes from parasitic nematodes and present specific new leads for the discovery of novel mechanisms of nematode benzimidazole resistance. Analyses of orthologous genes reveal conservation of candidate benzimidazole resistance genes in medically important parasitic nematodes. These data provide a basis for extending these approaches to other anthelmintic drug classes and a pathway towards validating new markers for anthelmintic resistance that can be deployed to improve parasite disease control.

Identification and Correction of Sample Mix-Ups in Expression Genetic Data: A Case Study

PubMed Central

Broman, Karl W.; Keller, Mark P.; Broman, Aimee Teo; Kendziorski, Christina; Yandell, Brian S.; Sen, Śaunak; Attie, Alan D.

2015-01-01

In a mouse intercross with more than 500 animals and genome-wide gene expression data on six tissues, we identified a high proportion (18%) of sample mix-ups in the genotype data. Local expression quantitative trait loci (eQTL; genetic loci influencing gene expression) with extremely large effect were used to form a classifier to predict an individual’s eQTL genotype based on expression data alone. By considering multiple eQTL and their related transcripts, we identified numerous individuals whose predicted eQTL genotypes (based on their expression data) did not match their observed genotypes, and then went on to identify other individuals whose genotypes did match the predicted eQTL genotypes. The concordance of predictions across six tissues indicated that the problem was due to mix-ups in the genotypes (although we further identified a small number of sample mix-ups in each of the six panels of gene expression microarrays). Consideration of the plate positions of the DNA samples indicated a number of off-by-one and off-by-two errors, likely the result of pipetting errors. Such sample mix-ups can be a problem in any genetic study, but eQTL data allow us to identify, and even correct, such problems. Our methods have been implemented in an R package, R/lineup. PMID:26290572

A new QTL for resistance to Fusarium ear rot in maize.

PubMed

Li, Zhi-Min; Ding, Jun-Qiang; Wang, Rui-Xia; Chen, Jia-Fa; Sun, Xiao-Dong; Chen, Wei; Song, Wei-Bin; Dong, Hua-Fang; Dai, Xiao-Dong; Xia, Zong-Liang; Wu, Jian-Yu

2011-11-01

Understanding the inheritance of resistance to Fusarium ear rot is a basic prerequisite for an efficient resistance breeding in maize. In this study, 250 recombinant inbred lines (RILs) along with their resistant (BT-1) and susceptible (N6) parents were planted in Zhengzhou with three replications in 2007 and 2008. Each line was artificially inoculated using the nail-punch method. Significant genotypic variation in response to Fusarium ear rot was detected in both years. Based on a genetic map containing 207 polymorphic simple sequence repeat (SSR) markers with average genetic distances of 8.83 cM, the ear rot resistance quantitative trait loci (QTL) were analyzed by composite interval mapping with a mixed model (MCIM) across the environments. In total, four QTL were detected on chromosomes 3, 4, 5, and 6. The resistance allele at each of these four QTL was contributed by resistant parent BT-1, and accounted for 2.5-10.2% of the phenotypic variation. However, no significant epistasis interaction effect was detected after a two-dimensional genome scan. Among the four QTL, one QTL with the largest effect on chromosome 4 (bin 4.06) can be suggested to be a new locus for resistance to Fusarium ear rot, which broadens the genetic base for resistance to the disease and can be used for further genetic improvement in maize-breeding programs.

Factors affecting GEBV accuracy with single-step Bayesian models.

PubMed

Zhou, Lei; Mrode, Raphael; Zhang, Shengli; Zhang, Qin; Li, Bugao; Liu, Jian-Feng

2018-01-01

A single-step approach to obtain genomic prediction was first proposed in 2009. Many studies have investigated the components of GEBV accuracy in genomic selection. However, it is still unclear how the population structure and the relationships between training and validation populations influence GEBV accuracy in terms of single-step analysis. Here, we explored the components of GEBV accuracy in single-step Bayesian analysis with a simulation study. Three scenarios with various numbers of QTL (5, 50, and 500) were simulated. Three models were implemented to analyze the simulated data: single-step genomic best linear unbiased prediction (GBLUP; SSGBLUP), single-step BayesA (SS-BayesA), and single-step BayesB (SS-BayesB). According to our results, GEBV accuracy was influenced by the relationships between the training and validation populations more significantly for ungenotyped animals than for genotyped animals. SS-BayesA/BayesB showed an obvious advantage over SSGBLUP with the scenarios of 5 and 50 QTL. SS-BayesB model obtained the lowest accuracy with the 500 QTL in the simulation. SS-BayesA model was the most efficient and robust considering all QTL scenarios. Generally, both the relationships between training and validation populations and LD between markers and QTL contributed to GEBV accuracy in the single-step analysis, and the advantages of single-step Bayesian models were more apparent when the trait is controlled by fewer QTL.

A Flexible Computational Framework Using R and Map-Reduce for Permutation Tests of Massive Genetic Analysis of Complex Traits.

PubMed

Mahjani, Behrang; Toor, Salman; Nettelblad, Carl; Holmgren, Sverker

2017-01-01

In quantitative trait locus (QTL) mapping significance of putative QTL is often determined using permutation testing. The computational needs to calculate the significance level are immense, 10 4 up to 10 8 or even more permutations can be needed. We have previously introduced the PruneDIRECT algorithm for multiple QTL scan with epistatic interactions. This algorithm has specific strengths for permutation testing. Here, we present a flexible, parallel computing framework for identifying multiple interacting QTL using the PruneDIRECT algorithm which uses the map-reduce model as implemented in Hadoop. The framework is implemented in R, a widely used software tool among geneticists. This enables users to rearrange algorithmic steps to adapt genetic models, search algorithms, and parallelization steps to their needs in a flexible way. Our work underlines the maturity of accessing distributed parallel computing for computationally demanding bioinformatics applications through building workflows within existing scientific environments. We investigate the PruneDIRECT algorithm, comparing its performance to exhaustive search and DIRECT algorithm using our framework on a public cloud resource. We find that PruneDIRECT is vastly superior for permutation testing, and perform 2 ×10 5 permutations for a 2D QTL problem in 15 hours, using 100 cloud processes. We show that our framework scales out almost linearly for a 3D QTL search.

Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

PubMed Central

Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

2013-01-01

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

Identification and Correction of Sample Mix-Ups in Expression Genetic Data: A Case Study.

PubMed

Broman, Karl W; Keller, Mark P; Broman, Aimee Teo; Kendziorski, Christina; Yandell, Brian S; Sen, Śaunak; Attie, Alan D

2015-08-19

In a mouse intercross with more than 500 animals and genome-wide gene expression data on six tissues, we identified a high proportion (18%) of sample mix-ups in the genotype data. Local expression quantitative trait loci (eQTL; genetic loci influencing gene expression) with extremely large effect were used to form a classifier to predict an individual's eQTL genotype based on expression data alone. By considering multiple eQTL and their related transcripts, we identified numerous individuals whose predicted eQTL genotypes (based on their expression data) did not match their observed genotypes, and then went on to identify other individuals whose genotypes did match the predicted eQTL genotypes. The concordance of predictions across six tissues indicated that the problem was due to mix-ups in the genotypes (although we further identified a small number of sample mix-ups in each of the six panels of gene expression microarrays). Consideration of the plate positions of the DNA samples indicated a number of off-by-one and off-by-two errors, likely the result of pipetting errors. Such sample mix-ups can be a problem in any genetic study, but eQTL data allow us to identify, and even correct, such problems. Our methods have been implemented in an R package, R/lineup. Copyright © 2015 Broman et al.

Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs.

PubMed

Cherel, Pierre; Pires, José; Glénisson, Jérôme; Milan, Denis; Iannuccelli, Nathalie; Hérault, Frédéric; Damon, Marie; Le Roy, Pascale

2011-08-29

Detection of quantitative trait loci (QTLs) affecting meat quality traits in pigs is crucial for the design of efficient marker-assisted selection programs and to initiate efforts toward the identification of underlying polymorphisms. The RYR1 and PRKAG3 causative mutations, originally identified from major effects on meat characteristics, can be used both as controls for an overall QTL detection strategy for diversely affected traits and as a scale for detected QTL effects. We report on a microsatellite-based QTL detection scan including all autosomes for pig meat quality and carcass composition traits in an F2 population of 1,000 females and barrows resulting from an intercross between a Pietrain and a Large White-Hampshire-Duroc synthetic sire line. Our QTL detection design allowed side-by-side comparison of the RYR1 and PRKAG3 mutation effects seen as QTLs when segregating at low frequencies (0.03-0.08), with independent QTL effects detected from most of the same population, excluding any carrier of these mutations. Large QTL effects were detected in the absence of the RYR1 and PRKGA3 mutations, accounting for 12.7% of phenotypic variation in loin colour redness CIE-a* on SSC6 and 15% of phenotypic variation in glycolytic potential on SSC1. We detected 8 significant QTLs with effects on meat quality traits and 20 significant QTLs for carcass composition and growth traits under these conditions. In control analyses including mutation carriers, RYR1 and PRKAG3 mutations were detected as QTLs, from highly significant to suggestive, and explained 53% to 5% of the phenotypic variance according to the trait. Our results suggest that part of muscle development and backfat thickness effects commonly attributed to the RYR1 mutation may be a consequence of linkage with independent QTLs affecting those traits. The proportion of variation explained by the most significant QTLs detected in this work is close to the influence of major-effect mutations on the least affected traits, but is one order of magnitude lower than effect on variance of traits primarily affected by these causative mutations. This suggests that uncovering physiological traits directly affected by genetic polymorphisms would be an appropriate approach for further characterization of QTLs.

Joint analysis of quantitative trait loci and major-effect causative mutations affecting meat quality and carcass composition traits in pigs

PubMed Central

2011-01-01

Background Detection of quantitative trait loci (QTLs) affecting meat quality traits in pigs is crucial for the design of efficient marker-assisted selection programs and to initiate efforts toward the identification of underlying polymorphisms. The RYR1 and PRKAG3 causative mutations, originally identified from major effects on meat characteristics, can be used both as controls for an overall QTL detection strategy for diversely affected traits and as a scale for detected QTL effects. We report on a microsatellite-based QTL detection scan including all autosomes for pig meat quality and carcass composition traits in an F2 population of 1,000 females and barrows resulting from an intercross between a Pietrain and a Large White-Hampshire-Duroc synthetic sire line. Our QTL detection design allowed side-by-side comparison of the RYR1 and PRKAG3 mutation effects seen as QTLs when segregating at low frequencies (0.03-0.08), with independent QTL effects detected from most of the same population, excluding any carrier of these mutations. Results Large QTL effects were detected in the absence of the RYR1 and PRKGA3 mutations, accounting for 12.7% of phenotypic variation in loin colour redness CIE-a* on SSC6 and 15% of phenotypic variation in glycolytic potential on SSC1. We detected 8 significant QTLs with effects on meat quality traits and 20 significant QTLs for carcass composition and growth traits under these conditions. In control analyses including mutation carriers, RYR1 and PRKAG3 mutations were detected as QTLs, from highly significant to suggestive, and explained 53% to 5% of the phenotypic variance according to the trait. Conclusions Our results suggest that part of muscle development and backfat thickness effects commonly attributed to the RYR1 mutation may be a consequence of linkage with independent QTLs affecting those traits. The proportion of variation explained by the most significant QTLs detected in this work is close to the influence of major-effect mutations on the least affected traits, but is one order of magnitude lower than effect on variance of traits primarily affected by these causative mutations. This suggests that uncovering physiological traits directly affected by genetic polymorphisms would be an appropriate approach for further characterization of QTLs. PMID:21875434

The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize (Zea mays L.).

PubMed

Zhang, J; Ku, L X; Han, Z P; Guo, S L; Liu, H J; Zhang, Z Z; Cao, L R; Cui, X J; Chen, Y H

2014-09-01

Maize architecture is a major contributing factor to their high level of productivity. Maize varieties with an erect-leaf-angle (LA) phenotype, which increases light harvesting for photosynthesis and grain-filling, have elevated grain yields. Although a large body of information is available on the map positions of quantitative trait loci (QTL) for LA, little is known about the molecular mechanism of these QTL. In this study, the ZmCLA4 gene, which is responsible for the qLA4-1 QTL associated with LA, was identified and isolated by fine mapping and positional cloning. The ZmCLA4 gene is an orthologue of LAZY1 in rice and Arabidopsis. Sequence analysis revealed two SNPs and two indel sites in ZmCLA4 between the D132 and D132-NIL inbred maize lines. Association analysis showed that C/T/mutation667 and CA/indel965 were strongly associated with LA. Subcellular localization verified the functions of a predicted transmembrane domain and a nuclear localization signal in ZmCLA4. Transgenic maize plants with a down-regulated ZmCLA4 RNAi construct and transgenic rice plants over-expressing ZmCLA4 confirmed that the ZmCLA4 gene located in the qLA4 QTL regulated LA. The allelic variants of ZmCLA4 in the D132 and D132-NIL lines exhibited significant differences in leaf angle. ZmCLA4 transcript accumulation was higher in D132-NIL than in D132 during all the developmental stages and was negatively correlated with LA. The gravitropic response was increased and cell shape and number at the leaf and stem junctions were altered in D132-NIL relative to D132. These findings suggest that ZmCLA4 plays a negative role in the control of maize LA through the alteration of mRNA accumulation, leading to altered shoot gravitropism and cell development. The cloning of the gene responsible for the qLA4-1 QTL provides information on the molecular mechanisms of LA in maize and an opportunity for the improvement of plant architecture with regard to LA through maize breeding. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Separate loci underlie resistance to root infection and leaf scorch during soybean sudden death syndrome.

PubMed

Kazi, S; Shultz, J; Afzal, J; Johnson, J; Njiti, V N; Lightfoot, D A

2008-05-01

Soybean [Glycine max (L.) Merr.] cultivars show differences in their resistance to both the leaf scorch and root rot of sudden death syndrome (SDS). The syndrome is caused by root colonization by Fusarium virguliforme (ex. F. solani f. sp. glycines). Root susceptibility combined with reduced leaf scorch resistance has been associated with resistance to Heterodera glycines HG Type 1.3.6.7 (race 14) of the soybean cyst nematode (SCN). In contrast, the rhg1 locus underlying resistance to Hg Type 0 was found clustered with three loci for resistance to SDS leaf scorch and one for root infection. The aims of this study were to compare the inheritance of resistance to leaf scorch and root infection in a population that segregated for resistance to SCN and to identify the underlying quantitative trait loci (QTL). "Hartwig", a cultivar partially resistant to SDS leaf scorch, F. virguliforme root infection and SCN HG Type 1.3.6.7 was crossed with the partially susceptible cultivar "Flyer". Ninety-two F5-derived recombinant inbred lines and 144 markers were used for map development. Four QTL found in earlier studies were confirmed. One contributed resistance to leaf scorch on linkage group (LG) C2 (Satt277; P = 0.004, R2 = 15%). Two on LG G underlay root infection at R8 (Satt038; P = 0.0001 R2 = 28.1%; Satt115; P = 0.003, R2 = 12.9%). The marker Satt038 was linked to rhg1 underlying resistance to SCN Hg Type 0. The fourth QTL was on LG D2 underlying resistance to root infection at R6 (Satt574; P = 0.001, R2 = 10%). That QTL was in an interval previously associated with resistance to both SDS leaf scorch and SCN Hg Type 1.3.6.7. The QTL showed repulsion linkage with resistance to SCN that may explain the relative susceptibility to SDS of some SCN resistant cultivars. One additional QTL was discovered on LG G underlying resistance to SDS leaf scorch measured by disease index (Satt130; P = 0.003, R2 = 13%). The loci and markers will provide tagged alleles with which to improve the breeding of cultivars combining resistances to SDS leaf scorch, root infection and SCN HG Type 1.3.6.7.

A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis.

PubMed

Ishikawa, Akira

2017-11-27

Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

Putative Microsatellite DNA Marker-Based Wheat Genomic Resource for Varietal Improvement and Management.

PubMed

Jaiswal, Sarika; Sheoran, Sonia; Arora, Vasu; Angadi, Ulavappa B; Iquebal, Mir A; Raghav, Nishu; Aneja, Bharti; Kumar, Deepender; Singh, Rajender; Sharma, Pradeep; Singh, G P; Rai, Anil; Tiwari, Ratan; Kumar, Dinesh

2017-01-01

Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. Triticum aestivum SSR database ( TaSSRDb ) is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at http://webtom.cabgrid.res.in/wheatssr/. For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476,169) from complex, hexaploid wheat genome (~17 GB) along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb) and lowest (74.57 SSRs/Mb) SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT) lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL (Quantitative trait locus) discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness, Uniformity, and Stability) testing, EDV (Essentially Derived Variety)/IV (Initial Variety) disputes, seed purity and hybrid wheat testing. All these are required in germplasm management as well as also in the endeavor of wheat productivity.

Putative Microsatellite DNA Marker-Based Wheat Genomic Resource for Varietal Improvement and Management

PubMed Central

Jaiswal, Sarika; Sheoran, Sonia; Arora, Vasu; Angadi, Ulavappa B.; Iquebal, Mir A.; Raghav, Nishu; Aneja, Bharti; Kumar, Deepender; Singh, Rajender; Sharma, Pradeep; Singh, G. P.; Rai, Anil; Tiwari, Ratan; Kumar, Dinesh

2017-01-01

Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. Triticum aestivum SSR database (TaSSRDb) is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at http://webtom.cabgrid.res.in/wheatssr/. For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476,169) from complex, hexaploid wheat genome (~17 GB) along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb) and lowest (74.57 SSRs/Mb) SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT) lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL (Quantitative trait locus) discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness, Uniformity, and Stability) testing, EDV (Essentially Derived Variety)/IV (Initial Variety) disputes, seed purity and hybrid wheat testing. All these are required in germplasm management as well as also in the endeavor of wheat productivity. PMID:29234333

Selection for low erucic acid and genetic mapping of loci affecting the accumulation of very long-chain fatty acids in meadowfoam seed storage lipids.

PubMed

Gandhi, S D; Kishore, V K; Crane, J M; Slabaugh, M B; Knapp, S J

2009-06-01

Erucic acid (22:1(13)) has been identified as an anti-nutritional compound in meadowfoam (Limnanthes alba) and other oilseeds in the Brassicales, a classification which has necessitated the development of low erucic acid cultivars for human consumption. The erucic acid concentrations of meadowfoam wild types (8%-24%) surpass industry standards for human consumption (

Comparative Genome-Wide-Association Mapping Identifies Common Loci Controlling Root System Architecture and Resistance to Aphanomyces euteiches in Pea.

PubMed

Desgroux, Aurore; Baudais, Valentin N; Aubert, Véronique; Le Roy, Gwenola; de Larambergue, Henri; Miteul, Henri; Aubert, Grégoire; Boutet, Gilles; Duc, Gérard; Baranger, Alain; Burstin, Judith; Manzanares-Dauleux, Maria; Pilet-Nayel, Marie-Laure; Bourion, Virginie

2017-01-01

Combining plant genetic resistance with architectural traits that are unfavorable to disease development is a promising strategy for reducing epidemics. However, few studies have identified root system architecture (RSA) traits with the potential to limit root disease development. Pea is a major cultivated legume worldwide and has a wide level of natural genetic variability for plant architecture. The root pathogen Aphanomyces euteiches is a major limiting factor of pea crop yield. This study aimed to increase the knowledge on the diversity of loci and candidate genes controlling RSA traits in pea and identify RSA genetic loci associated with resistance to A. euteiches which could be combined with resistance QTL in breeding. A comparative genome wide association (GWA) study of plant architecture and resistance to A. euteiches was conducted at the young plant stage in a collection of 266 pea lines contrasted for both traits. The collection was genotyped using 14,157 SNP markers from recent pea genomic resources. It was phenotyped for ten root, shoot and overall plant architecture traits, as well as three disease resistance traits in controlled conditions, using image analysis. We identified a total of 75 short-size genomic intervals significantly associated with plant architecture and overlapping with 46 previously detected QTL. The major consistent intervals included plant shoot architecture or flowering genes ( PsLE, PsTFL1 ) with putative pleiotropic effects on root architecture. A total of 11 genomic intervals were significantly associated with resistance to A. euteiches confirming several consistent previously identified major QTL. One significant SNP, mapped to the major QTL Ae-Ps7.6 , was associated with both resistance and RSA traits. At this marker, the resistance-enhancing allele was associated with an increased total root projected area, in accordance with the correlation observed between resistance and larger root systems in the collection. Seven additional intervals associated with plant architecture overlapped with GWA intervals previously identified for resistance to A. euteiches . This study provides innovative results about genetic interdependency of root disease resistance and RSA inheritance. It identifies pea lines, QTL, closely-linked markers and candidate genes for marker-assisted-selection of RSA loci to reduce Aphanomyces root rot severity in future pea varieties.

Comparative Genome-Wide-Association Mapping Identifies Common Loci Controlling Root System Architecture and Resistance to Aphanomyces euteiches in Pea

PubMed Central

Desgroux, Aurore; Baudais, Valentin N.; Aubert, Véronique; Le Roy, Gwenola; de Larambergue, Henri; Miteul, Henri; Aubert, Grégoire; Boutet, Gilles; Duc, Gérard; Baranger, Alain; Burstin, Judith; Manzanares-Dauleux, Maria; Pilet-Nayel, Marie-Laure; Bourion, Virginie

2018-01-01

Combining plant genetic resistance with architectural traits that are unfavorable to disease development is a promising strategy for reducing epidemics. However, few studies have identified root system architecture (RSA) traits with the potential to limit root disease development. Pea is a major cultivated legume worldwide and has a wide level of natural genetic variability for plant architecture. The root pathogen Aphanomyces euteiches is a major limiting factor of pea crop yield. This study aimed to increase the knowledge on the diversity of loci and candidate genes controlling RSA traits in pea and identify RSA genetic loci associated with resistance to A. euteiches which could be combined with resistance QTL in breeding. A comparative genome wide association (GWA) study of plant architecture and resistance to A. euteiches was conducted at the young plant stage in a collection of 266 pea lines contrasted for both traits. The collection was genotyped using 14,157 SNP markers from recent pea genomic resources. It was phenotyped for ten root, shoot and overall plant architecture traits, as well as three disease resistance traits in controlled conditions, using image analysis. We identified a total of 75 short-size genomic intervals significantly associated with plant architecture and overlapping with 46 previously detected QTL. The major consistent intervals included plant shoot architecture or flowering genes (PsLE, PsTFL1) with putative pleiotropic effects on root architecture. A total of 11 genomic intervals were significantly associated with resistance to A. euteiches confirming several consistent previously identified major QTL. One significant SNP, mapped to the major QTL Ae-Ps7.6, was associated with both resistance and RSA traits. At this marker, the resistance-enhancing allele was associated with an increased total root projected area, in accordance with the correlation observed between resistance and larger root systems in the collection. Seven additional intervals associated with plant architecture overlapped with GWA intervals previously identified for resistance to A. euteiches. This study provides innovative results about genetic interdependency of root disease resistance and RSA inheritance. It identifies pea lines, QTL, closely-linked markers and candidate genes for marker-assisted-selection of RSA loci to reduce Aphanomyces root rot severity in future pea varieties. PMID:29354146

Identification of QTL for Early Vigor and Stay-Green Conferring Tolerance to Drought in Two Connected Advanced Backcross Populations in Tropical Maize (Zea mays L.)

PubMed Central

Trachsel, Samuel; Sun, Dapeng; SanVicente, Felix M.; Zheng, Hongjian; Atlin, Gary N.; Suarez, Edgar Antonio; Babu, Raman; Zhang, Xuecai

2016-01-01

We aimed to identify quantitative trait loci (QTL) for secondary traits related to grain yield (GY) in two BC1F2:3 backcross populations (LPSpop and DTPpop) under well-watered (4 environments; WW) and drought stressed (6; DS) conditions to facilitate breeding efforts towards drought tolerant maize. GY reached 5.6 and 5.8 t/ha under WW in the LPSpop and the DTPpop, respectively. Under DS, grain yield was reduced by 65% (LPSpop) to 59% (DTPpop) relative to WW. GY was strongly associated with the normalized vegetative index (NDVI; r ranging from 0.61 to 0.96) across environmental conditions and with an early flowering under drought stressed conditions (r ranging from -0.18 to -0.25) indicative of the importance of early vigor and drought escape for GY. Out of the 105 detected QTL, 53 were overdominant indicative of strong heterosis. For 14 out of 18 detected vigor QTL, as well as for eight flowering time QTL the trait increasing allele was derived from CML491. Collocations of early vigor QTL with QTL for stay green (bin 2.02, WW, LPSpop; 2.07, DS, DTPpop), the number of ears per plant (bins 2.02, 2.05, WW, LPSpop; 5.02, DS, LPSpop) and GY (bin 2.07, WW, DTPpop; 5.04, WW, LPSpop), reinforce the importance of the observed correlations. LOD scores for early vigor QTL in these bins ranged from 2.2 to 11.25 explaining 4.6 (additivity: +0.28) to 19.9% (additivity: +0.49) of the observed phenotypic variance. A strong flowering QTL was detected in bin 2.06 across populations and environmental conditions explaining 26–31.3% of the observed phenotypic variation (LOD: 13–17; additivity: 0.1–0.6d). Improving drought tolerance while at the same time maintaining yield potential could be achieved by combining alleles conferring early vigor from the recurrent parent with alleles advancing flowering from the donor. Additionally bin 8.06 (DTPpop) harbored a QTL for GY under WW (additivity: 0.27 t/ha) and DS (additivity: 0.58 t/ha). R2 ranged from 0 (DTPpop, WW) to 26.54% (LPSpop, DS) for NDVI, 18.6 (LPSpop, WW) to 42.45% (LPSpop, DS) for anthesis and from 0 (DTPpop, DS) to 24.83% (LPSpop, WW) for GY. Lines out-yielding the best check by 32.5% (DTPpop, WW) to 60% (DTPpop, DS) for all population-by-irrigation treatment combination (except LPSpop, WW) identified are immediately available for the use by breeders. PMID:26999525

Genetic Architecture of Palm Oil Fatty Acid Composition in Cultivated Oil Palm (Elaeis guineensis Jacq.) Compared to Its Wild Relative E. oleifera (H.B.K) Cortés

PubMed Central

Montoya, Carmenza; Cochard, Benoit; Flori, Albert; Cros, David; Lopes, Ricardo; Cuellar, Teresa; Espeout, Sandra; Syaputra, Indra; Villeneuve, Pierre; Pina, Michel; Ritter, Enrique; Leroy, Thierry; Billotte, Norbert

2014-01-01

We searched for quantitative trait loci (QTL) associated with the palm oil fatty acid composition of mature fruits of the oil palm E. guineensis Jacq. in comparison with its wild relative E. oleifera (H.B.K) Cortés. The oil palm cross LM2T x DA10D between two heterozygous parents was considered in our experiment as an intraspecific representative of E. guineensis. Its QTLs were compared to QTLs published for the same traits in an interspecific Elaeis pseudo-backcross used as an indirect representative of E. oleifera. Few correlations were found in E. guineensis between pulp fatty acid proportions and yield traits, allowing for the rather independent selection of both types of traits. Sixteen QTLs affecting palm oil fatty acid proportions and iodine value were identified in oil palm. The phenotypic variation explained by the detected QTLs was low to medium in E. guineensis, ranging between 10% and 36%. The explained cumulative variation was 29% for palmitic acid C16:0 (one QTL), 68% for stearic acid C18:0 (two QTLs), 50% for oleic acid C18:1 (three QTLs), 25% for linoleic acid C18:2 (one QTL), and 40% (two QTLs) for the iodine value. Good marker co-linearity was observed between the intraspecific and interspecific Simple Sequence Repeat (SSR) linkage maps. Specific QTL regions for several traits were found in each mapping population. Our comparative QTL results in both E. guineensis and interspecific materials strongly suggest that, apart from two common QTL zones, there are two specific QTL regions with major effects, which might be one in E. guineensis, the other in E. oleifera, which are independent of each other and harbor QTLs for several traits, indicating either pleiotropic effects or linkage. Using QTL maps connected by highly transferable SSR markers, our study established a good basis to decipher in the future such hypothesis at the Elaeis genus level. PMID:24816555

Comparing power and precision of within-breed and multibreed genome-wide association studies of production traits using whole-genome sequence data for 5 French and Danish dairy cattle breeds.

PubMed

van den Berg, Irene; Boichard, Didier; Lund, Mogens Sandø

2016-11-01

The objective of this study was to compare mapping precision and power of within-breed and multibreed genome-wide association studies (GWAS) and to compare the results obtained by the multibreed GWAS with 3 meta-analysis methods. The multibreed GWAS was expected to improve mapping precision compared with a within-breed GWAS because linkage disequilibrium is conserved over shorter distances across breeds than within breeds. The multibreed GWAS was also expected to increase detection power for quantitative trait loci (QTL) segregating across breeds. GWAS were performed for production traits in dairy cattle, using imputed full genome sequences of 16,031 bulls, originating from 6 French and Danish dairy cattle populations. Our results show that a multibreed GWAS can be a valuable tool for the detection and fine mapping of quantitative trait loci. The number of QTL detected with the multibreed GWAS was larger than the number detected by the within-breed GWAS, indicating an increase in power, especially when the 2 Holstein populations were combined. The largest number of QTL was detected when all populations were combined. The analysis combining all breeds was, however, dominated by Holstein, and QTL segregating in other breeds but not in Holstein were sometimes overshadowed by larger QTL segregating in Holstein. Therefore, the GWAS combining all breeds except Holstein was useful to detect such peaks. Combining all breeds except Holstein resulted in smaller QTL intervals on average, but this outcome was not the case when the Holstein populations were included in the analysis. Although no decrease in the average QTL size was observed, mapping precision did improve for several QTL. Out of 3 different multibreed meta-analysis methods, the weighted z-scores model resulted in the most similar results to the full multibreed GWAS and can be useful as an alternative to a full multibreed GWAS. Differences between the multibreed GWAS and the meta-analyses were larger when different breeds were combined than when the 2 Holstein populations were combined. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle

PubMed Central

2014-01-01

Background Genome wide association studies (GWAS) in most cattle breeds result in large genomic intervals of significant associations making it difficult to identify causal mutations. This is due to the extensive, low-level linkage disequilibrium within a cattle breed. As there is less linkage disequilibrium across breeds, multibreed GWAS may improve precision of causal variant mapping. Here we test this hypothesis in a Holstein and Jersey cattle data set with 17,925 individuals with records for production and functional traits and 632,003 SNP markers. Results By using a cross validation strategy within the Holstein and Jersey data sets, we were able to identify and confirm a large number of QTL. As expected, the precision of mapping these QTL within the breeds was limited. In the multibreed analysis, we found that many loci were not segregating in both breeds. This was partly an artefact of power of the experiments, with the number of QTL shared between the breeds generally increasing with trait heritability. False discovery rates suggest that the multibreed analysis was less powerful than between breed analyses, in terms of how much genetic variance was explained by the detected QTL. However, the multibreed analysis could more accurately pinpoint the location of the well-described mutations affecting milk production such as DGAT1. Further, the significant SNP in the multibreed analysis were significantly enriched in genes regions, to a considerably greater extent than was observed in the single breed analyses. In addition, we have refined QTL on BTA5 and BTA19 to very small intervals and identified a small number of potential candidate genes in these, as well as in a number of other regions. Conclusion Where QTL are segregating across breed, multibreed GWAS can refine these to reasonably small genomic intervals. However, such QTL appear to represent only a fraction of the genetic variation. Our results suggest a significant proportion of QTL affecting milk production segregate within rather than across breeds, at least for Holstein and Jersey cattle. PMID:24456127

Detection of a Cis eQTL Controlling BMCO1 Gene Expression Leads to the Identification of a QTG for Chicken Breast Meat Color

PubMed Central

Le Bihan-Duval, Elisabeth; Nadaf, Javad; Berri, Cécile; Pitel, Frédérique; Graulet, Benoît; Godet, Estelle; Leroux, Sophie Y.; Demeure, Olivier; Lagarrigue, Sandrine; Duby, Cécile; Cogburn, Larry A.; Beaumont, Catherine M.; Duclos, Michel J.

2011-01-01

Classical quantitative trait loci (QTL) analysis and gene expression QTL (eQTL) were combined to identify the causal gene (or QTG) underlying a highly significant QTL controlling the variation of breast meat color in a F2 cross between divergent high-growth (HG) and low-growth (LG) chicken lines. Within this meat quality QTL, BCMO1 (Accession number GenBank: AJ271386), encoding the β-carotene 15, 15′-monooxygenase, a key enzyme in the conversion of β-carotene into colorless retinal, was a good functional candidate. Analysis of the abundance of BCMO1 mRNA in breast muscle of the HG x LG F2 population allowed for the identification of a strong cis eQTL. Moreover, reevaluation of the color QTL taking BCMO1 mRNA levels as a covariate indicated that BCMO1 mRNA levels entirely explained the variations in meat color. Two fully-linked single nucleotide polymorphisms (SNP) located within the proximal promoter of BCMO1 gene were identified. Haplotype substitution resulted in a marked difference in BCMO1 promoter activity in vitro. The association study in the F2 population revealed a three-fold difference in BCMO1 expression leading to a difference of 1 standard deviation in yellow color between the homozygous birds at this haplotype. This difference in meat yellow color was fully consistent with the difference in carotenoid content (i.e. lutein and zeaxanthin) evidenced between the two alternative haplotypes. A significant association between the haplotype, the level of BCMO1 expression and the yellow color of the meat was also recovered in an unrelated commercial broiler population. The mutation could be of economic importance for poultry production by making possible a gene-assisted selection for color, a determining aspect of meat quality. Moreover, this natural genetic diversity constitutes a new model for the study of β-carotene metabolism which may act upon diverse biological processes as precursor of the vitamin A. PMID:21750696

Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation: A Genome-Wide Analysis among 1,800 South Asians

PubMed Central

Pierce, Brandon L.; Tong, Lin; Chen, Lin S.; Rahaman, Ronald; Argos, Maria; Jasmine, Farzana; Roy, Shantanu; Paul-Brutus, Rachelle; Westra, Harm-Jan; Franke, Lude; Esko, Tonu; Zaman, Rakibuz; Islam, Tariqul; Rahman, Mahfuzar; Baron, John A.; Kibriya, Muhammad G.; Ahsan, Habibul

2014-01-01

A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis- and trans-eQTLs and determine if observed trans-eQTL associations are mediated by expression of transcripts in cis with the SNPs showing trans-association, using Sobel tests of mediation. We observed 434 independent trans-eQTL associations at a false-discovery rate of 0.05, and 189 of these trans-eQTLs were also cis-eQTLs (enrichment P<0.0001). Among these 189 trans-eQTL associations, 39 were significantly attenuated after adjusting for a cis-mediator based on Sobel P<10-5. We attempted to replicate 21 of these mediation signals in two European cohorts, and while only 7 trans-eQTL associations were present in one or both cohorts, 6 showed evidence of cis-mediation. Analyses of simulated data show that complete mediation will be observed as partial mediation in the presence of mediator measurement error or imperfect LD between measured and causal variants. Our data demonstrates that trans-associations can become significantly stronger or switch directions after adjusting for a potential mediator. Using simulated data, we demonstrate that this phenomenon is expected in the presence of strong cis-trans confounding and when the measured cis-transcript is correlated with the true (unmeasured) mediator. In conclusion, by applying mediation analysis to eQTL data, we show that a substantial fraction of observed trans-eQTL associations can be explained by cis-mediation. Future studies should focus on understanding the mechanisms underlying widespread cis-mediation and their relevance to disease biology, as well as using mediation analysis to improve eQTL discovery. PMID:25474530

Genetic architecture of palm oil fatty acid composition in cultivated oil palm (Elaeis guineensis Jacq.) compared to its wild relative E. oleifera (H.B.K) Cortés.

PubMed

Montoya, Carmenza; Cochard, Benoit; Flori, Albert; Cros, David; Lopes, Ricardo; Cuellar, Teresa; Espeout, Sandra; Syaputra, Indra; Villeneuve, Pierre; Pina, Michel; Ritter, Enrique; Leroy, Thierry; Billotte, Norbert

2014-01-01

We searched for quantitative trait loci (QTL) associated with the palm oil fatty acid composition of mature fruits of the oil palm E. guineensis Jacq. in comparison with its wild relative E. oleifera (H.B.K) Cortés. The oil palm cross LM2T x DA10D between two heterozygous parents was considered in our experiment as an intraspecific representative of E. guineensis. Its QTLs were compared to QTLs published for the same traits in an interspecific Elaeis pseudo-backcross used as an indirect representative of E. oleifera. Few correlations were found in E. guineensis between pulp fatty acid proportions and yield traits, allowing for the rather independent selection of both types of traits. Sixteen QTLs affecting palm oil fatty acid proportions and iodine value were identified in oil palm. The phenotypic variation explained by the detected QTLs was low to medium in E. guineensis, ranging between 10% and 36%. The explained cumulative variation was 29% for palmitic acid C16:0 (one QTL), 68% for stearic acid C18:0 (two QTLs), 50% for oleic acid C18:1 (three QTLs), 25% for linoleic acid C18:2 (one QTL), and 40% (two QTLs) for the iodine value. Good marker co-linearity was observed between the intraspecific and interspecific Simple Sequence Repeat (SSR) linkage maps. Specific QTL regions for several traits were found in each mapping population. Our comparative QTL results in both E. guineensis and interspecific materials strongly suggest that, apart from two common QTL zones, there are two specific QTL regions with major effects, which might be one in E. guineensis, the other in E. oleifera, which are independent of each other and harbor QTLs for several traits, indicating either pleiotropic effects or linkage. Using QTL maps connected by highly transferable SSR markers, our study established a good basis to decipher in the future such hypothesis at the Elaeis genus level.

Mapping and expression of candidate genes for development rate in rainbow trout (Oncorhynchus mykiss)

USDA-ARS?s Scientific Manuscript database

Development rate has important implications for many aspects of an individual's biology. In rainbow trout (Oncorhynchus mykiss), a major QTL for embryonic development rate has been detected on chromosome 5, but at present, few candidate genes have been mapped to this region. This paucity of known ge...

Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance

PubMed Central

Hawkins, Leigh K.; Mylroie, J. Erik; Oliveira, Dafne A.; Smith, J. Spencer; Ozkan, Seval; Windham, Gary L.; Williams, W. Paul; Warburton, Marilyn L.

2015-01-01

Maize (Zea mays L.) is a crop of global importance, but prone to contamination by aflatoxins produced by fungi in the genus Aspergillus. The development of resistant germplasm and the identification of genes contributing to resistance would aid in the reduction of the problem with a minimal need for intervention by farmers. Chitinolytic enzymes respond to attack by potential pathogens and have been demonstrated to increase insect and fungal resistance in plants. Here, all chitinase genes in the maize genome were characterized via sequence diversity and expression patterns. Recent evolution within this gene family was noted. Markers from within each gene were developed and used to map the phenotypic effect on resistance of each gene in up to four QTL mapping populations and one association panel. Seven chitinase genes were identified that had alleles associated with increased resistance to aflatoxin accumulation and A. flavus infection in field grown maize. The chitinase in bin 1.05 identified a new and highly significant QTL, while chitinase genes in bins 2.04 and 5.03 fell directly beneath the peaks of previously published QTL. The expression patterns of these genes corroborate possible grain resistance mechanisms. Markers from within the gene sequences or very closely linked to them are presented to aid in the use of marker assisted selection to improve this trait. PMID:26090679

Mapping Loci That Control Tuber and Foliar Symptoms Caused by PVY in Autotetraploid Potato (Solanum tuberosum L.).

PubMed

da Silva, Washington L; Ingram, Jason; Hackett, Christine A; Coombs, Joseph J; Douches, David; Bryan, Glenn J; De Jong, Walter; Gray, Stewart

2017-11-06

Potato tuber necrotic ringspot disease (PTNRD) is a tuber deformity associated with infection by the tuber necrotic strain of Potato virus Y (PVY NTN ). PTNRD negatively impacts tuber quality and marketability, and poses a serious threat to seed and commercial potato production worldwide. PVY NTN symptoms differ in the cultivars Waneta and Pike: Waneta expresses severe PTNRD and foliar mosaic with vein and leaf necrosis, whereas Pike does not express PTNRD and mosaic is the only foliar symptom. To map loci that influence tuber and foliar symptoms, 236 F 1 progeny of a cross between Waneta and Pike were inoculated with PVY NTN isolate NY090029 and genotyped using 12,808 potato SNPs. Foliar symptom type and severity were monitored for 10 wk, while tubers were evaluated for PTNRD expression at harvest and again after 60 d in storage. Pairwise correlation analyses indicate a strong association between PTNRD and vein necrosis (τ = 0.4195). QTL analyses revealed major-effect QTL on chromosomes 4 and 5 for mosaic, 4 for PTNRD, and 5 for foliar necrosis symptoms. Locating QTL associated with PVY-related symptoms provides a foundation for breeders to develop markers that can be used to eliminate potato clones with undesirable phenotypes, e.g. , those likely to develop PTNRD or to be symptomless carriers of PVY. Copyright © 2017 Silva et al.

Characterization of the Maize Chitinase Genes and Their Effect on Aspergillus flavus and Aflatoxin Accumulation Resistance.

PubMed

Hawkins, Leigh K; Mylroie, J Erik; Oliveira, Dafne A; Smith, J Spencer; Ozkan, Seval; Windham, Gary L; Williams, W Paul; Warburton, Marilyn L

2015-01-01

Maize (Zea mays L.) is a crop of global importance, but prone to contamination by aflatoxins produced by fungi in the genus Aspergillus. The development of resistant germplasm and the identification of genes contributing to resistance would aid in the reduction of the problem with a minimal need for intervention by farmers. Chitinolytic enzymes respond to attack by potential pathogens and have been demonstrated to increase insect and fungal resistance in plants. Here, all chitinase genes in the maize genome were characterized via sequence diversity and expression patterns. Recent evolution within this gene family was noted. Markers from within each gene were developed and used to map the phenotypic effect on resistance of each gene in up to four QTL mapping populations and one association panel. Seven chitinase genes were identified that had alleles associated with increased resistance to aflatoxin accumulation and A. flavus infection in field grown maize. The chitinase in bin 1.05 identified a new and highly significant QTL, while chitinase genes in bins 2.04 and 5.03 fell directly beneath the peaks of previously published QTL. The expression patterns of these genes corroborate possible grain resistance mechanisms. Markers from within the gene sequences or very closely linked to them are presented to aid in the use of marker assisted selection to improve this trait.

A sampling algorithm for segregation analysis

PubMed Central

Tier, Bruce; Henshall, John

2001-01-01

Methods for detecting Quantitative Trait Loci (QTL) without markers have generally used iterative peeling algorithms for determining genotype probabilities. These algorithms have considerable shortcomings in complex pedigrees. A Monte Carlo Markov chain (MCMC) method which samples the pedigree of the whole population jointly is described. Simultaneous sampling of the pedigree was achieved by sampling descent graphs using the Metropolis-Hastings algorithm. A descent graph describes the inheritance state of each allele and provides pedigrees guaranteed to be consistent with Mendelian sampling. Sampling descent graphs overcomes most, if not all, of the limitations incurred by iterative peeling algorithms. The algorithm was able to find the QTL in most of the simulated populations. However, when the QTL was not modeled or found then its effect was ascribed to the polygenic component. No QTL were detected when they were not simulated. PMID:11742631

The Genetics of Resistance to Morinda Fruit Toxin During the Postembryonic Stages in Drosophila sechellia

PubMed Central

Huang, Yan; Erezyilmaz, Deniz

2015-01-01

Although a great deal has been learned regarding the genetic changes that give rise to adaptation in bacteria and yeast, an understanding of how new complex traits arise in multicellular organisms is far less complete. Many phytophagous insect species are ecological specialists that have adapted to utilize a single host plant. Drosophila sechellia is a specialist that utilizes the ripe fruit of Morinda citrifolia, which is toxic to its sibling species, D. simulans. Here we apply multiplexed shotgun genotyping and QTL analysis to examine the genetic basis of resistance to M. citrifolia fruit toxin in interspecific hybrids. We identify a locus of large effect on the third chromosome (QTL-IIIsima) in the D. simulans backcross that was not detected in previous analyses. We also identify a highly significant QTL of large effect on the X chromosome, QTL-Xsim. Additional smaller-effect loci were also identified in the D. simulans and D. sechellia backcrosses. We did not detect significant epistasis between loci. Instead, our analysis reveals large and smaller-effect loci that contribute to M. citrifolia resistance additively. The additive effect of each locus suggests that partial resistance to lower levels of M. citrifolia toxin could be passed through introgression from D. sechellia to D. simulans in nature. The identification of the major effect loci, QTL-IIIsima and QTL-Xsim, is an important step toward identifying the molecular basis of adaptation in a multicellular organism. PMID:26224784

Genomic linkage of male song and female acoustic preference QTL underlying a rapid species radiation

PubMed Central

Shaw, Kerry L.; Lesnick, Sky C.

2009-01-01

The genetic coupling hypothesis of signal-preference evolution, whereby the same genes control male signal and female preference for that signal, was first inspired by the evolution of cricket acoustic communication nearly 50 years ago. To examine this hypothesis, we compared the genomic location of quantitative trait loci (QTL) underlying male song and female acoustic preference variation in the Hawaiian cricket genus Laupala. We document a QTL underlying female acoustic preference variation between 2 closely related species (Laupala kohalensis and Laupala paranigra). This preference QTL colocalizes with a song QTL identified previously, providing compelling evidence for a genomic linkage of the genes underlying these traits. We show that both song and preference QTL make small to moderate contributions to the behavioral difference between species, suggesting that divergence in mating behavior among Laupala species is due to the fixation of many genes of minor effect. The diversity of acoustic signaling systems in crickets exemplifies the evolution of elaborate male displays by sexual selection through female choice. Our data reveal genetic conditions that would enable functional coordination between song and acoustic preference divergence during speciation, resulting in a behaviorally coupled mode of signal-preference evolution. Interestingly, Laupala exhibits one of the fastest rates of speciation in animals, concomitant with equally rapid evolution in sexual signaling behaviors. Genomic linkage may facilitate rapid speciation by contributing to genetic correlations between sexual signaling behaviors that eventually cause sexual isolation between diverging populations. PMID:19487670

Integrated Genome-wide association and hypothalamus eQTL studies indicate a link between the circadian rhythm-related gene PER1 and coping behavior

PubMed Central

Ponsuksili, Siriluck; Zebunke, Manuela; Murani, Eduard; Trakooljul, Nares; Krieter, Joachim; Puppe, Birger; Schwerin, Manfred; Wimmers, Klaus

2015-01-01

Animal personality and coping styles are basic concepts for evaluating animal welfare. Struggling response of piglets in so-called backtests early in life reflects their coping strategy. Behavioral reactions of piglets in backtests have a moderate heritability, but their genetic basis largely remains unknown. Here, latency, duration and frequency of struggling attempts during one-minute backtests were repeatedly recorded of piglets at days 5, 12, 19, and 26. A genome-wide association study for backtest traits revealed 465 significant SNPs (FDR ≤ 0.05) mostly located in QTL (quantitative trait locus) regions on chromosome 3, 5, 12 and 16. In order to capture genes in these regions, 37 transcripts with significant SNPs were selected for expressionQTL analysis in the hypothalamus. Eight genes (ASGR1, CPAMD8, CTC1, FBXO39, IL19, LOC100511790, RAD51B, UBOX5) had cis- and five (RANGRF, PER1, PDZRN3, SH2D4B, LONP2) had trans-expressionQTL. In particular, for PER1, with known physiological implications for maintenance of circadian rhythms, a role in coping behavior was evidenced by confirmed association in an independent population. For CTC1 a cis-expression QTL and the consistent relationship of gene polymorphism, mRNA expression level and backtest traits promoted its link to coping style. GWAS and eQTL analyses uncovered positional and functional gene candidates for coping behavior. PMID:26537429

Integrated Genome-wide association and hypothalamus eQTL studies indicate a link between the circadian rhythm-related gene PER1 and coping behavior.

PubMed

Ponsuksili, Siriluck; Zebunke, Manuela; Murani, Eduard; Trakooljul, Nares; Krieter, Joachim; Puppe, Birger; Schwerin, Manfred; Wimmers, Klaus

2015-11-05

Animal personality and coping styles are basic concepts for evaluating animal welfare. Struggling response of piglets in so-called backtests early in life reflects their coping strategy. Behavioral reactions of piglets in backtests have a moderate heritability, but their genetic basis largely remains unknown. Here, latency, duration and frequency of struggling attempts during one-minute backtests were repeatedly recorded of piglets at days 5, 12, 19, and 26. A genome-wide association study for backtest traits revealed 465 significant SNPs (FDR ≤ 0.05) mostly located in QTL (quantitative trait locus) regions on chromosome 3, 5, 12 and 16. In order to capture genes in these regions, 37 transcripts with significant SNPs were selected for expressionQTL analysis in the hypothalamus. Eight genes (ASGR1, CPAMD8, CTC1, FBXO39, IL19, LOC100511790, RAD51B, UBOX5) had cis- and five (RANGRF, PER1, PDZRN3, SH2D4B, LONP2) had trans-expressionQTL. In particular, for PER1, with known physiological implications for maintenance of circadian rhythms, a role in coping behavior was evidenced by confirmed association in an independent population. For CTC1 a cis-expression QTL and the consistent relationship of gene polymorphism, mRNA expression level and backtest traits promoted its link to coping style. GWAS and eQTL analyses uncovered positional and functional gene candidates for coping behavior.

Whole-genome scan identifies quantitative trait loci for chronic pastern dermatitis in German draft horses.

PubMed

Mittmann, E Henrike; Mömke, Stefanie; Distl, Ottmar

2010-02-01

Chronic pastern dermatitis (CPD), also known as chronic progressive lymphedema (CPL), is a skin disease that affects draft horses. This disease causes painful lower-leg swelling, nodule formation, and skin ulceration, interfering with movement. The aim of this whole-genome scan was to identify quantitative trait loci (QTL) for CPD in German draft horses. We recorded clinical data for CPD in 917 German draft horses and collected blood samples from these horses. Of these 917 horses, 31 paternal half-sib families comprising 378 horses from the breeds Rhenish German, Schleswig, Saxon-Thuringian, and South German were chosen for genotyping. Each half-sib family was constituted by only one draft horse breed. Genotyping was done for 318 polymorphic microsatellites evenly distributed on all equine autosomes and the X chromosome with a mean distance of 7.5 Mb. An across-breed multipoint linkage analysis revealed chromosome-wide significant QTL on horse chromosomes (ECA) 1, 9, 16, and 17. Analyses by breed confirmed the QTL on ECA1 in South German and the QTL on ECA9, 16, and 17 in Saxon-Thuringian draft horses. For the Rhenish German and Schleswig draft horses, additional QTL on ECA4 and 10 and for the South German draft horses an additional QTL on ECA7 were found. This is the first whole-genome scan for CPD in draft horses and it is an important step toward the identification of candidate genes.

High-resolution mapping of a major effect QTL from wild tomato Solanum habrochaites that influences water relations under root chilling.

PubMed

Arms, Erin M; Bloom, Arnold J; St Clair, Dina A

2015-09-01

QTL stm9 controlling rapid-onset water stress tolerance in S. habrochaites was high-resolution mapped to a chromosome 9 region that contains genes associated with abiotic stress tolerances. Wild tomato (Solanum habrochaites) exhibits tolerance to abiotic stresses, including drought and chilling. Root chilling (6 °C) induces rapid-onset water stress by impeding water movement from roots to shoots. S. habrochaites responds to such changes by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) fails to close stomata and wilts. This response (shoot turgor maintenance under root chilling) is controlled by a major QTL (designated stm9) on chromosome 9, which was previously fine-mapped to a 2.7-cM region. Recombinant sub-near-isogenic lines for chromosome 9 were marker-selected, phenotyped for shoot turgor maintenance under root chilling in two sets of replicated experiments (Fall and Spring), and the data were used to high-resolution map QTL stm9 to a 0.32-cM region. QTL mapping revealed a single QTL that was coincident for both the Spring and Fall datasets, suggesting that the gene or genes contributing to shoot turgor maintenance under root chilling reside within the marker interval H9-T1673. In the S. lycopersicum reference genome sequence, this chromosome 9 region is gene-rich and contains representatives of gene families that have been associated with abiotic stress tolerance.

Quantitative Trait Locus Analysis for Deep-Sowing Germination Ability in the Maize IBM Syn10 DH Population

PubMed Central

Liu, Hongjun; Zhang, Lin; Wang, Jiechen; Li, Changsheng; Zeng, Xing; Xie, Shupeng; Zhang, Yongzhong; Liu, Sisi; Hu, Songlin; Wang, Jianhua; Lee, Michael; Lübberstedt, Thomas; Zhao, Guangwu

2017-01-01

Deep-sowing is an effective measure to ensure seeds absorbing water from deep soil layer and emerging normally in arid and semiarid regions. However, existing varieties demonstrate poor germination ability in deep soil layer and some key quantitative trait loci (QTL) or genes related to deep-sowing germination ability remain to be identified and analyzed. In this study, a high-resolution genetic map based on 280 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population which comprised 6618 bin markers was used for the QTL analysis of deep-sowing germination related traits. The results showed significant differences in germination related traits under deep-sowing condition (12.5 cm) and standard-germination condition (2 cm) between two parental lines. In total, 8, 11, 13, 15, and 18 QTL for germination rate, seedling length, mesocotyl length, plumule length, and coleoptile length were detected for the two sowing conditions, respectively. These QTL explained 2.51–7.8% of the phenotypic variance with LOD scores ranging from 2.52 to 7.13. Additionally, 32 overlapping QTL formed 11 QTL clusters on all chromosomes except for chromosome 8, indicating the minor effect genes have a pleiotropic role in regulating various traits. Furthermore, we identified six candidate genes related to deep-sowing germination ability, which were co-located in the cluster regions. The results provide a basis for molecular marker assisted breeding and functional study in deep-sowing germination ability of maize. PMID:28588594

Genetic Analysis of Seed-Soluble Oligosaccharides in Relation to Seed Storability of Arabidopsis1

PubMed Central

Bentsink, Leónie; Alonso-Blanco, Carlos; Vreugdenhil, Dick; Tesnier, Karine; Groot, Steven P.C.; Koornneef, Maarten

2000-01-01

Seed oligosaccharides (OSs) and especially raffinose series OSs (RSOs) are hypothesized to play an important role in the acquisition of desiccation tolerance and consequently in seed storability. In the present work we analyzed the seed-soluble OS (sucrose, raffinose, and stachyose) content of several Arabidopsis accessions and thus identified the genotype Cape Verde Islands having a very low RSO content. By performing quantitative trait loci (QTL) mapping in a recombinant inbred line population, we found one major QTL responsible for the practically monogenic segregation of seed stachyose content. This locus also affected the content of the two other OSs, sucrose, and raffinose. Two candidate genes encoding respectively for galactinol synthase and raffinose synthase were located within the genomic region around this major QTL. In addition, three smaller-effect QTL were identified, each one specifically affecting the content of an individual OS. Seed storability was analyzed in the same recombinant inbred line population by measuring viability (germination) under two different seed aging assays: after natural aging during 4 years of dry storage at room temperature and after artificial aging induced by a controlled deterioration test. Thus, four QTL responsible for the variation of this trait were mapped. Comparison of the QTL genetic positions showed that the genomic region containing the major OS locus did not significantly affect the seed storability. We concluded that in the studied material neither RSOs nor sucrose content had a specific effect on seed storability. PMID:11115877

QTL mapping of fruit mineral contents provides new chances for molecular breeding of tomato nutritional traits.

PubMed

Capel, Carmen; Yuste-Lisbona, Fernando J; López-Casado, Gloria; Angosto, Trinidad; Heredia, Antonio; Cuartero, Jesús; Fernández-Muñoz, Rafael; Lozano, Rafael; Capel, Juan

2017-05-01

Agronomical characterization of a RIL population for fruit mineral contents allowed for the identification of QTL controlling these fruit quality traits, flanked by co-dominant markers useful for marker-assisted breeding. Tomato quality is a multi-variant attribute directly depending on fruit chemical composition, which in turn determines the benefits of tomato consumption for human health. Commercially available tomato varieties possess limited variability in fruit quality traits. Wild species, such as Solanum pimpinellifolium, could provide different nutritional advantages and can be used for tomato breeding to improve overall fruit quality. Determining the genetic basis of the inheritance of all the traits that contribute to tomato fruit quality will increase the efficiency of the breeding program necessary to take advantage of the wild species variability. A high-density linkage map has been constructed from a recombinant inbred line (RIL) population derived from a cross between tomato Solanum lycopersicum and the wild-relative species S. pimpinellifolium. The RIL population was evaluated for fruit mineral contents during three consecutive growing seasons. The data obtained allowed for the identification of main QTL and novel epistatic interaction among QTL controlling fruit mineral contents on the basis of a multiple-environment analysis. Most of the QTL were flanked by candidate genes providing valuable information for both tomato breeding for new varieties with novel nutritional properties and the starting point to identify the genes underlying these QTL, which will help to reveal the genetic basis of tomato fruit nutritional properties.

Quantitative Trait Locus Analysis for Deep-Sowing Germination Ability in the Maize IBM Syn10 DH Population.

PubMed

Liu, Hongjun; Zhang, Lin; Wang, Jiechen; Li, Changsheng; Zeng, Xing; Xie, Shupeng; Zhang, Yongzhong; Liu, Sisi; Hu, Songlin; Wang, Jianhua; Lee, Michael; Lübberstedt, Thomas; Zhao, Guangwu

2017-01-01

Deep-sowing is an effective measure to ensure seeds absorbing water from deep soil layer and emerging normally in arid and semiarid regions. However, existing varieties demonstrate poor germination ability in deep soil layer and some key quantitative trait loci (QTL) or genes related to deep-sowing germination ability remain to be identified and analyzed. In this study, a high-resolution genetic map based on 280 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population which comprised 6618 bin markers was used for the QTL analysis of deep-sowing germination related traits. The results showed significant differences in germination related traits under deep-sowing condition (12.5 cm) and standard-germination condition (2 cm) between two parental lines. In total, 8, 11, 13, 15, and 18 QTL for germination rate, seedling length, mesocotyl length, plumule length, and coleoptile length were detected for the two sowing conditions, respectively. These QTL explained 2.51-7.8% of the phenotypic variance with LOD scores ranging from 2.52 to 7.13. Additionally, 32 overlapping QTL formed 11 QTL clusters on all chromosomes except for chromosome 8, indicating the minor effect genes have a pleiotropic role in regulating various traits. Furthermore, we identified six candidate genes related to deep-sowing germination ability, which were co-located in the cluster regions. The results provide a basis for molecular marker assisted breeding and functional study in deep-sowing germination ability of maize.

The Diversity Outbred Mouse Population

PubMed Central

Churchill, Gary A.; Gatti, Daniel M.; Munger, Steven C.; Svenson, Karen L.

2012-01-01

The Diversity Outbred (DO) population is a heterogeneous stock derived from the same eight founder strains as the Collaborative Cross (CC) inbred strains. Genetically heterogeneous DO mice display a broad range of phenotypes. Natural levels of heterozygosity provide genetic buffering and, as a result, DO mice are robust and breed well. Genetic mapping analysis in the DO presents new challenges and opportunities. Specialized algorithms are required to reconstruct haplotypes from high-density SNP array data. The eight founder haplotypes can be combined into 36 possible diplotypes, which must be accommodated in QTL mapping analysis. Population structure of the DO must be taken into account here. Estimated allele effects of 8 founder haplotypes provide information that is not available in two-parent crosses and can dramatically reduce the number of candidate loci. Allele effects can also distinguish chance co-location of QTL from pleiotropy – which provides a basis for establishing causality in expression QTL studies. We recommended sample sizes of 200 to 800 mice for QTL mapping studies, larger than for traditional crosses. The CC inbred strains provide a resource for independent validation of DO mapping results. Genetic heterogeneity of the DO can provide a powerful advantage in our ability to generalize conclusions to other genetically diverse populations. Genetic diversity can also help to avoid the pitfall of identifying an idiosyncratic reaction that occurs only in a limited genetic context. Informatics tools and data resources associated with the CC, the DO, and their founder strains are developing rapidly. We anticipate a flood of new results to follow as our community begins to adopt and utilize these new genetic resource populations. PMID:22892839

Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance.

PubMed

Geffroy, V; Sévignac, M; De Oliveira, J C; Fouilloux, G; Skroch, P; Thoquet, P; Gepts, P; Langin, T; Dron, M

2000-03-01

Anthracnose, one of the most important diseases of common bean (Phaseolus vulgaris), is caused by the fungus Colletotrichum lindemuthianum. A "candidate gene" approach was used to map anthracnose resistance quantitative trait loci (QTL). Candidate genes included genes for both pathogen recognition (resistance genes and resistance gene analogs [RGAs]) and general plant defense (defense response genes). Two strains of C. lindemuthianum, identified in a world collection of 177 strains, displayed a reproducible and differential aggressiveness toward BAT93 and JaloEEP558, two parental lines of P. vulgaris representing the two major gene pools of this crop. A reliable test was developed to score partial resistance in aerial organs of the plant (stem, leaf, petiole) under controlled growth chamber conditions. BAT93 was more resistant than JaloEEP558 regardless of the organ or strain tested. With a recombinant inbred line (RIL) population derived from a cross between these two parental lines, 10 QTL were located on a genetic map harboring 143 markers, including known defense response genes, anthracnose-specific resistance genes, and RGAs. Eight of the QTL displayed isolate specificity. Two were co-localized with known defense genes (phenylalanine ammonia-lyase and hydroxyproline-rich glycoprotein) and three with anthracnose-specific resistance genes and/or RGAs. Interestingly, two QTL, with different allelic contribution, mapped on linkage group B4 in a 5.0 cM interval containing Andean and Mesoamerican specific resistance genes against C. lindemuthianum and 11 polymorphic fragments revealed with a RGA probe. The possible relationship between genes underlying specific and partial resistance is discussed.

pc8.1, a major QTL for pigment content in pepper fruit, is associated with variation in plastid compartment size.

PubMed

Brand, Arnon; Borovsky, Yelena; Meir, Sagit; Rogachev, Ilana; Aharoni, Asaph; Paran, Ilan

2012-03-01

Studies on the genetic control of pigment content in pepper fruit have focused mainly on monogenic mutations leading to changes in fruit color. In addition to the qualitative variation in fruit color, quantitative variation in pigment content and color intensity exists in pepper giving rise to a range of color intensities. However, the genetic basis for this variation is poorly understood, hindering the development of peppers that are rich in these beneficial compounds. In this paper, quantitative variation in pigment content was studied in a cross between a dark-green Capsicum annuum pepper and a light-green C. chinense pepper. Two major pigment content QTLs that control chlorophyll content were identified, pc8.1 and pc10.1. The major QTL pc8.1, also affected carotenoid content in the ripe fruit. However, additional analyses in subsequent generations did not reveal a consistent effect of this QTL on carotenoid content in ripe fruit. Confocal microscopy analyses of green immature fruits of the parents and of near-isogenic lines for pc8.1 indicated that the QTL exerts its effect via increasing chloroplast compartment size in the dark-green genotypes, predominantly in a fruit-specific manner. Metabolic analyses indicated that in addition to chlorophyll, chloroplast-associated tocopherols and carotenoids are also elevated. Future identification of the genes controlling pigment content QTLs in pepper will provide a better understanding of this important trait and new opportunities for breeding peppers and other Solanaceae species with enhanced nutritional value.

A Novel and Major Quantitative Trait Locus for Fusarium Crown Rot Resistance in a Genotype of Wild Barley (Hordeum spontaneum L.)

PubMed Central

Chen, Guangdeng; Liu, Yaxi; Ma, Jun; Zheng, Zhi; Wei, Yuming; McIntyre, C. Lynne; Zheng, You-Liang; Liu, Chunji

2013-01-01

Fusarium crown rot (FCR), caused by various Fusarium species, is a destructive disease of cereal crops in semiarid regions worldwide. As part of our contribution to the development of Fusarium resistant cultivars, we identified several novel sources of resistance by systematically assessing barley genotypes representing different geographical origins and plant types. One of these sources of resistance was investigated in this study by generating and analysing two populations of recombinant inbred lines. A major locus conferring FCR resistance, designated as Qcrs.cpi-4H, was detected in one of the populations (mapping population) and the effects of the QTL was confirmed in the other population. The QTL was mapped to the distal end of chromosome arm 4HL and it is effective against both of the Fusarium isolates tested, one F. pseudograminearum and the other F. graminearum. The QTL explains up to 45.3% of the phenotypic variance. As distinct from an earlier report which demonstrated co-locations of loci conferring FCR resistance and plant height in barley, a correlation between these two traits was not detected in the mapping population. However, as observed in a screen of random genotypes, an association between FCR resistance and plant growth rate was detected and a QTL controlling the latter was detected near the Qcrs.cpi-4H locus in the mapping population. Existing data indicate that, although growth rate may affect FCR resistance, different genes at this locus are likely involved in controlling these two traits. PMID:23536780

Behavioral genomics of honeybee foraging and nest defense

NASA Astrophysics Data System (ADS)

Hunt, Greg J.; Amdam, Gro V.; Schlipalius, David; Emore, Christine; Sardesai, Nagesh; Williams, Christie E.; Rueppell, Olav; Guzmán-Novoa, Ernesto; Arechavaleta-Velasco, Miguel; Chandra, Sathees; Fondrk, M. Kim; Beye, Martin; Page, Robert E.

2007-04-01

The honeybee has been the most important insect species for study of social behavior. The recently released draft genomic sequence for the bee will accelerate honeybee behavioral genetics. Although we lack sufficient tools to manipulate this genome easily, quantitative trait loci (QTLs) that influence natural variation in behavior have been identified and tested for their effects on correlated behavioral traits. We review what is known about the genetics and physiology of two behavioral traits in honeybees, foraging specialization (pollen versus nectar), and defensive behavior, and present evidence that map-based cloning of genes is more feasible in the bee than in other metazoans. We also present bioinformatic analyses of candidate genes within QTL confidence intervals (CIs). The high recombination rate of the bee made it possible to narrow the search to regions containing only 17-61 predicted peptides for each QTL, although CIs covered large genetic distances. Knowledge of correlated behavioral traits, comparative bioinformatics, and expression assays facilitated evaluation of candidate genes. An overrepresentation of genes involved in ovarian development and insulin-like signaling components within pollen foraging QTL regions suggests that an ancestral reproductive gene network was co-opted during the evolution of foraging specialization. The major QTL influencing defensive/aggressive behavior contains orthologs of genes involved in central nervous system activity and neurogenesis. Candidates at the other two defensive-behavior QTLs include modulators of sensory signaling ( Am5HT 7 serotonin receptor, AmArr4 arrestin, and GABA-B-R1 receptor). These studies are the first step in linking natural variation in honeybee social behavior to the identification of underlying genes.

Ecological genomics of Boechera stricta: identification of a QTL controlling the allocation of methionine- vs branched-chain amino acid-derived glucosinolates and levels of insect herbivory.

PubMed

Schranz, M E; Manzaneda, A J; Windsor, A J; Clauss, M J; Mitchell-Olds, T

2009-05-01

In the Brassicaceae, glucosinolates influence the feeding, reproduction and development of many insect herbivores. Glucosinolate production and effects on herbivore feeding have been extensively studied in the model species, Arabidopsis thaliana and Brassica crops, both of which constitutively produce leaf glucosinolates mostly derived from the amino acid, methionine. Much less is known about the regulation or role in defense of glucosinolates derived from other aliphatic amino acids, such as the branched-chain amino acids (BCAA), valine and isoleucine. We have identified a glucosinolate polymorphism in Boechera stricta controlling the allocation to BCAA- vs methionine-derived glucosinolates in both leaves and seeds. B. stricta is a perennial species that grows in mostly undisturbed habitats of western North America. We have measured glucosinolate profiles and concentrations in 192 F(2) lines that have earlier been used for genetic map construction. We also performed herbivory assays on six F(3) replicates per F(2) line using the generalist lepidopteran, Trichoplusia ni. Quantitative trait locus (QTL) analysis identified a single locus controlling both glucosinolate profile and levels of herbivory, the branched chain-methionine allocation or BCMA QTL. We have delimited this QTL to a small genomic region with a 1.0 LOD confidence interval just 1.9 cm wide, which, in A. thaliana, contains approximately 100 genes. We also found that methionine-derived glucosinolates provided significantly greater defense than the BCAA-derived glucosinolates against feeding by this generalist insect herbivore. The future positional cloning of this locus will allow for testing various adaptive explanations.

QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheep

PubMed Central

Poissant, J; Davis, C S; Malenfant, R M; Hogg, J T; Coltman, D W

2012-01-01

Dissecting the genetic architecture of fitness-related traits in wild populations is key to understanding evolution and the mechanisms maintaining adaptive genetic variation. We took advantage of a recently developed genetic linkage map and phenotypic information from wild pedigreed individuals from Ram Mountain, Alberta, Canada, to study the genetic architecture of ecologically important traits (horn volume, length, base circumference and body mass) in bighorn sheep. In addition to estimating sex-specific and cross-sex quantitative genetic parameters, we tested for the presence of quantitative trait loci (QTLs), colocalization of QTLs between bighorn sheep and domestic sheep, and sex × QTL interactions. All traits showed significant additive genetic variance and genetic correlations tended to be positive. Linkage analysis based on 241 microsatellite loci typed in 310 pedigreed animals resulted in no significant and five suggestive QTLs (four for horn dimension on chromosomes 1, 18 and 23, and one for body mass on chromosome 26) using genome-wide significance thresholds (Logarithm of odds (LOD) >3.31 and >1.88, respectively). We also confirmed the presence of a horn dimension QTL in bighorn sheep at the only position known to contain a similar QTL in domestic sheep (on chromosome 10 near the horns locus; nominal P<0.01) and highlighted a number of regions potentially containing weight-related QTLs in both species. As expected for sexually dimorphic traits involved in male–male combat, loci with sex-specific effects were detected. This study lays the foundation for future work on adaptive genetic variation and the evolutionary dynamics of sexually dimorphic traits in bighorn sheep. PMID:21847139

Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes.

PubMed

Xu, Xuewen; Yu, Ting; Xu, Ruixue; Shi, Yang; Lin, Xiaojian; Xu, Qiang; Qi, Xiaohua; Weng, Yiqun; Chen, Xuehao

2016-03-01

A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.

Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot.

PubMed

Morris, C A; Pitchford, W S; Cullen, N G; Esmailizadeh, A K; Hickey, S M; Hyndman, D; Dodds, K G; Afolayan, R A; Crawford, A M; Bottema, C D K

2009-10-01

A quantitative trait locus (QTL) study was carried out in two countries, recording live animal and carcass composition traits. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin breed backgrounds. The New Zealand cattle were reared on pasture to carcass weights averaging 229 kg, whilst the Australian cattle were reared on grass and finished on grain (for at least 180 days) to carcass weights averaging 335 kg. From 11 live animal traits and 31 carcass composition traits respectively, 5 and 22 QTL were detected in combined-sire analyses, which were significant (P < 0.05) on a genome-wise basis. Fourteen significant traits for carcass composition QTL were on chromosome 2 and these were traits associated with muscling and fatness. This chromosome carried a variant myostatin allele (F94L), segregating from the Limousin ancestry. Despite very different cattle management systems between the two countries, the two populations had a large number of QTL in common. Of the 18 traits which were common to both countries, and which had significant QTL at the genome-wise level, eight were significant in both countries.

Practical applications of the bioinformatics toolbox for narrowing quantitative trait loci.

PubMed

Burgess-Herbert, Sarah L; Cox, Allison; Tsaih, Shirng-Wern; Paigen, Beverly

2008-12-01

Dissecting the genes involved in complex traits can be confounded by multiple factors, including extensive epistatic interactions among genes, the involvement of epigenetic regulators, and the variable expressivity of traits. Although quantitative trait locus (QTL) analysis has been a powerful tool for localizing the chromosomal regions underlying complex traits, systematically identifying the causal genes remains challenging. Here, through its application to plasma levels of high-density lipoprotein cholesterol (HDL) in mice, we demonstrate a strategy for narrowing QTL that utilizes comparative genomics and bioinformatics techniques. We show how QTL detected in multiple crosses are subjected to both combined cross analysis and haplotype block analysis; how QTL from one species are mapped to the concordant regions in another species; and how genomewide scans associating haplotype groups with their phenotypes can be used to prioritize the narrowed regions. Then we illustrate how these individual methods for narrowing QTL can be systematically integrated for mouse chromosomes 12 and 15, resulting in a significantly reduced number of candidate genes, often from hundreds to <10. Finally, we give an example of how additional bioinformatics resources can be combined with experiments to determine the most likely quantitative trait genes.

Identification of quantitative trait Loci for resistance to southern leaf blight and days to anthesis in a maize recombinant inbred line population.

PubMed

Balint-Kurti, P J; Krakowsky, M D; Jines, M P; Robertson, L A; Molnár, T L; Goodman, M M; Holl, J B

2006-10-01

ABSTRACT A recombinant inbred line population derived from a cross between the maize lines NC300 (resistant) and B104 (susceptible) was evaluated for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O and for days to anthesis in four environments (Clayton, NC, and Tifton, GA, in both 2004 and 2005). Entry mean and average genetic correlations between disease ratings in different environments were high (0.78 to 0.89 and 0.9, respectively) and the overall entry mean heritability for SLB resistance was 0.89. When weighted mean disease ratings were fitted to a model using multiple interval mapping, seven potential quantitative trait loci (QTL) were identified, the two strongest being on chromosomes 3 (bin 3.04) and 9 (bin 9.03-9.04). These QTL explained a combined 80% of the phenotypic variation for SLB resistance. Some time-point-specific SLB resistance QTL were also identified. There was no significant correlation between disease resistance and days to anthesis. Six putative QTL for time to anthesis were identified, none of which coincided with any SLB resistance QTL.

Gramene 2013: comparative plant genomics resources.

PubMed

Monaco, Marcela K; Stein, Joshua; Naithani, Sushma; Wei, Sharon; Dharmawardhana, Palitha; Kumari, Sunita; Amarasinghe, Vindhya; Youens-Clark, Ken; Thomason, James; Preece, Justin; Pasternak, Shiran; Olson, Andrew; Jiao, Yinping; Lu, Zhenyuan; Bolser, Dan; Kerhornou, Arnaud; Staines, Dan; Walts, Brandon; Wu, Guanming; D'Eustachio, Peter; Haw, Robin; Croft, David; Kersey, Paul J; Stein, Lincoln; Jaiswal, Pankaj; Ware, Doreen

2014-01-01

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.

A Genetic Map Between Gossypium hirsutum and the Brazilian Endemic G. mustelinum and Its Application to QTL Mapping

PubMed Central

Wang, Baohua; Liu, Limei; Zhang, Dong; Zhuang, Zhimin; Guo, Hui; Qiao, Xin; Wei, Lijuan; Rong, Junkang; May, O. Lloyd; Paterson, Andrew H.; Chee, Peng W.

2016-01-01

Among the seven tetraploid cotton species, little is known about transmission genetics and genome organization in Gossypium mustelinum, the species most distant from the source of most cultivated cotton, G. hirsutum. In this research, an F2 population was developed from an interspecific cross between G. hirsutum and G. mustelinum (HM). A genetic linkage map was constructed mainly using simple sequence repeat (SSRs) and restriction fragment length polymorphism (RFLP) DNA markers. The arrangements of most genetic loci along the HM chromosomes were identical to those of other tetraploid cotton species. However, both major and minor structural rearrangements were also observed, for which we propose a parsimony-based model for structural divergence of tetraploid cottons from common ancestors. Sequences of mapped markers were used for alignment with the 26 scaffolds of the G. hirsutum draft genome, and showed high consistency. Quantitative trait locus (QTL) mapping of fiber elongation in advanced backcross populations derived from the same parents demonstrated the value of the HM map. The HM map will serve as a valuable resource for QTL mapping and introgression of G. mustelinum alleles into G. hirsutum, and help clarify evolutionary relationships between the tetraploid cotton genomes. PMID:27172208

Quantitative Resistance to Plant Pathogens in Pyramiding Strategies for Durable Crop Protection.

PubMed

Pilet-Nayel, Marie-Laure; Moury, Benoît; Caffier, Valérie; Montarry, Josselin; Kerlan, Marie-Claire; Fournet, Sylvain; Durel, Charles-Eric; Delourme, Régine

2017-01-01

Quantitative resistance has gained interest in plant breeding for pathogen control in low-input cropping systems. Although quantitative resistance frequently has only a partial effect and is difficult to select, it is considered more durable than major resistance (R) genes. With the exponential development of molecular markers over the past 20 years, resistance QTL have been more accurately detected and better integrated into breeding strategies for resistant varieties with increased potential for durability. This review summarizes current knowledge on the genetic inheritance, molecular basis, and durability of quantitative resistance. Based on this knowledge, we discuss how strategies that combine major R genes and QTL in crops can maintain the effectiveness of plant resistance to pathogens. Combining resistance QTL with complementary modes of action appears to be an interesting strategy for breeding effective and potentially durable resistance. Combining quantitative resistance with major R genes has proven to be a valuable approach for extending the effectiveness of major genes. In the plant genomics era, improved tools and methods are becoming available to better integrate quantitative resistance into breeding strategies. Nevertheless, optimal combinations of resistance loci will still have to be identified to preserve resistance effectiveness over time for durable crop protection.

Genetic control of plant height in European winter wheat cultivars.

PubMed

Würschum, Tobias; Langer, Simon M; Longin, C Friedrich H

2015-05-01

Plant height variation in European winter wheat cultivars is mainly controlled by the Rht - D1 and Rht - B1 semi-dwarfing genes, but also by other medium- or small-effect QTL and potentially epistatic QTL enabling fine adjustments of plant height. Plant height is an important goal in wheat (Triticum aestivum L.) breeding as it affects crop performance and thus yield and quality. The aim of this study was to investigate the genetic control of plant height in European winter wheat cultivars. To this end, a panel of 410 winter wheat varieties from across Europe was evaluated for plant height in multi-location field trials and genotyped for the candidate loci Rht-B1, Rht-D1, Rht8, Ppd-B1 copy number variation and Ppd-D1 as well as by a genotyping-by-sequencing approach yielding 23,371 markers with known map position. We found that Rht-D1 and Rht-B1 had the largest effects on plant height in this cultivar collection explaining 40.9 and 15.5% of the genotypic variance, respectively, while Ppd-D1 and Rht8 accounted for 3.0 and 2.0% of the variance, respectively. A genome-wide scan for marker-trait associations yielded two additional medium-effect QTL located on chromosomes 6A and 5B explaining 11.0 and 5.7% of the genotypic variance after the effects of the candidate loci were accounted for. In addition, we identified several small-effect QTL as well as epistatic QTL contributing to the genetic architecture of plant height. Taken together, our results show that the two Rht-1 semi-dwarfing genes are the major sources of variation in European winter wheat cultivars and that other small- or medium-effect QTL and potentially epistatic QTL enable fine adjustments in plant height.

Mapping Quantitative Trait Loci Controlling High Iron and Zinc Content in Self and Open Pollinated Grains of Pearl Millet [Pennisetum glaucum (L.) R. Br.

PubMed Central

Kumar, Sushil; Hash, Charles T.; Thirunavukkarasu, Nepolean; Singh, Govind; Rajaram, Vengaldas; Rathore, Abhishek; Senapathy, Senthilvel; Mahendrakar, Mahesh D.; Yadav, Rattan S.; Srivastava, Rakesh K.

2016-01-01

Pearl millet is a multipurpose grain/fodder crop of the semi-arid tropics, feeding many of the world’s poorest and most undernourished people. Genetic variation among adapted pearl millet inbreds and hybrids suggests it will be possible to improve grain micronutrient concentrations by selective breeding. Using 305 loci, a linkage map was constructed to map QTLs for grain iron [Fe] and zinc [Zn] using replicated samples of 106 pearl millet RILs (F6) derived from ICMB 841-P3 × 863B-P2. The grains of the RIL population were evaluated for Fe and Zn content using atomic absorption spectrophotometer. Grain mineral concentrations ranged from 28.4 to 124.0 ppm for Fe and 28.7 to 119.8 ppm for Zn. Similarly, grain Fe and Zn in open pollinated seeds ranged between 22.4–77.4 and 21.9–73.7 ppm, respectively. Mapping with 305 (96 SSRs; 208 DArT) markers detected seven linkage groups covering 1749 cM (Haldane) with an average intermarker distance of 5.73 cM. On the basis of two environment phenotypic data, two co-localized QTLs for Fe and Zn content on linkage group (LG) 3 were identified by composite interval mapping (CIM). Fe QTL explained 19% phenotypic variation, whereas the Zn QTL explained 36% phenotypic variation. Likewise for open pollinated seeds, the QTL analysis led to the identification of two QTLs for grain Fe content on LG3 and 5, and two QTLs for grain Zn content on LG3 and 7. The total phenotypic variance for Fe and Zn QTLs in open pollinated seeds was 16 and 42%, respectively. Analysis of QTL × QTL and QTL × QTL × environment interactions indicated no major epistasis. PMID:27933068

Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm.

PubMed

Zhou, H; Steffenson, B J; Muehlbauer, Gary; Wanyera, Ruth; Njau, Peter; Ndeda, Sylvester

2014-06-01

Loci conferring resistance to the highly virulent African stem rust race TTKSK were identified in advanced barley breeding germplasm and positioned to chromosomes 5H and 7H using an association mapping approach. African races of the stem rust pathogen (Puccinia graminis f. sp. tritici) are a serious threat to barley production worldwide because of their wide virulence. To discover and characterize resistance to African stem rust race TTKSK in US barley breeding germplasm, over 3,000 lines/cultivars were assessed for resistance at the seedling stage in the greenhouse and also the adult plant stage in the field in Kenya. Only 12 (0.3 %) and 64 (2.1 %) lines exhibited a resistance level comparable to the resistant control at the seedling and adult plant stage, respectively. To map quantitative trait loci (QTL) for resistance to race TTKSK, an association mapping approach was conducted, utilizing 3,072 single nucleotide polymorphism (SNP) markers. At the seedling stage, two neighboring SNP markers (0.8 cM apart) on chromosome 7H (11_21491 and 12_30528) were found significantly associated with resistance. The most significant one found was 12_30528; thus, the resistance QTL was named Rpg-qtl-7H-12_30528. At the adult plant stage, two SNP markers on chromosome 5H (11_11355 and 12_31427) were found significantly associated with resistance. This resistance QTL was named Rpg-qtl-5H-11_11355 for the most significant marker identified. Adult plant resistance is of paramount importance for stem rust. The marker associated with Rpg-qtl-5H-11_11355 for adult plant resistance explained only a small portion of the phenotypic variation (0.02); however, this QTL reduced disease severity up to 55.0 % under low disease pressure and up to 21.1 % under heavy disease pressure. SNP marker 11_11355 will be valuable for marker-assisted selection of adult plant stem rust resistance in barley breeding.

A large QTL for fear and anxiety mapped using an F2 cross can be dissected into multiple smaller QTLs.

PubMed

Parker, C C; Sokoloff, G; Leung, E; Kirkpatrick, S L; Palmer, A A

2013-10-01

Using chromosome substitution strains (CSS), we previously identified a large quantitative trait locus (QTL) for conditioned fear (CF) on mouse chromosome 10. Here, we used an F2 cross between CSS-10 and C57BL/6J (B6) to localize that QTL to distal chromosome 10. That QTL accounted for all the difference between CSS-10 and B6. We then produced congenic strains to fine-map that interval. We identified two congenic strains that captured some or all the QTL. The larger congenic strain (Line 1: 122.387121-129.068 Mb; build 37) appeared to account for all the difference between CSS-10 and B6. The smaller congenic strain (Line 2: 127.277-129.068 Mb) was intermediate between CSS-10 and B6. We used haplotype mapping followed by quantitative polymerase chain reaction to identify one gene that was differentially expressed in both lines relative to B6 (Rnf41) and one that was differentially expressed between only Line 1 and B6 (Shmt2). These cis-eQTLs may cause the behavioral QTLs; however, further studies are required to validate these candidate genes. More generally, our observation that a large QTL mapped using CSS and F2 crosses can be dissected into multiple smaller QTLs shows a weaknesses of two-stage approaches that seek to use coarse mapping to identify large regions followed by fine-mapping. Indeed, additional dissection of these congenic strains might result in further subdivision of these QTL regions. Despite these limitations, we have successfully fine-mapped two QTLs to small regions and identified putative candidate genes, showing that the congenic approach can be effective for fine-mapping QTLs. © 2013 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

QTL-seq for rapid identification of candidate genes for flowering time in broccoli × cabbage.

PubMed

Shu, Jinshuai; Liu, Yumei; Zhang, Lili; Li, Zhansheng; Fang, Zhiyuan; Yang, Limei; Zhuang, Mu; Zhang, Yangyong; Lv, Honghao

2018-04-01

A major QTL controlling early flowering in broccoli × cabbage was identified by marker analysis and next-generation sequencing, corresponding to GRF6 gene conditioning flowering time in Arabidopsis. Flowering is an important agronomic trait for hybrid production in broccoli and cabbage, but the genetic mechanism underlying this process is unknown. In this study, segregation analysis with BC 1 P1, BC 1 P2, F 2 , and F 2:3 populations derived from a cross between two inbred lines "195" (late-flowering) and "93219" (early flowering) suggested that flowering time is a quantitative trait. Next, employing a next-generation sequencing-based whole-genome QTL-seq strategy, we identified a major genomic region harboring a robust flowering time QTL using an F 2 mapping population, designated Ef2.1 on cabbage chromosome 2 for early flowering. Ef2.1 was further validated by indel (insertion or deletion) marker-based classical QTL mapping, explaining 51.5% (LOD = 37.67) and 54.0% (LOD = 40.5) of the phenotypic variation in F 2 and F 2:3 populations, respectively. Combined QTL-seq and classical QTL analysis narrowed down Ef1.1 to a 228-kb genomic region containing 29 genes. A cabbage gene, Bol024659, was identified in this region, which is a homolog of GRF6, a major gene regulating flowering in Arabidopsis, and was designated BolGRF6. qRT-PCR study of the expression level of BolGRF6 revealed significantly higher expression in the early flowering genotypes. Taken together, our results provide support for BolGRF6 as a possible candidate gene for early flowering in the broccoli line 93219. The identified candidate genomic regions and genes may be useful for molecular breeding to improve broccoli and cabbage flowering times.

Defeating the Warrior: genetic architecture of triticale resistance against a novel aggressive yellow rust race.

PubMed

Losert, Dominik; Maurer, Hans Peter; Leiser, Willmar L; Würschum, Tobias

2017-04-01

Genome-wide association mapping of resistance against the novel, aggressive 'Warrior' race of yellow rust in triticale revealed a genetic architecture with some medium-effect QTL and a quantitative component, which in combination confer high levels of resistance on both leaves and ears. Yellow rust is an important destructive fungal disease in small grain cereals and the exotic 'Warrior' race has recently conquered Europe. The aim of this study was to investigate the genetic architecture of yellow rust resistance in hexaploid winter triticale as the basis for a successful resistance breeding. To this end, a diverse panel of 919 genotypes was evaluated for yellow rust infection on leaves and ears in multi-location field trials and genotyped by genotyping-by-sequencing as well as for known Yr resistance loci. Genome-wide association mapping identified ten quantitative trait loci (QTL) for yellow rust resistance on the leaves and seven of these also for ear resistance. The total genotypic variance explained by the QTL amounted to 44.0% for leaf and 26.0% for ear resistance. The same three medium-effect QTL were identified for both traits on chromosomes 1B, 2B, and 7B. Interestingly, plants pyramiding the resistance allele of all three medium-effect QTL were generally most resistant, but constitute less than 5% of the investigated triticale breeding material. Nevertheless, a genome-wide prediction yielded a higher predictive ability than prediction based on these three QTL. Taken together, our results show that yellow rust resistance in winter triticale is genetically complex, including both medium-effect QTL as well as a quantitative resistance component. Resistance to the novel 'Warrior' race of this fungal pathogen is consequently best achieved by recurrent selection in the field based on identified resistant lines and can potentially be assisted by genomic approaches.

A Multi-Trait, Meta-analysis for Detecting Pleiotropic Polymorphisms for Stature, Fatness and Reproduction in Beef Cattle

PubMed Central

Bolormaa, Sunduimijid; Pryce, Jennie E.; Reverter, Antonio; Zhang, Yuandan; Barendse, William; Kemper, Kathryn; Tier, Bruce; Savin, Keith; Hayes, Ben J.; Goddard, Michael E.

2014-01-01

Polymorphisms that affect complex traits or quantitative trait loci (QTL) often affect multiple traits. We describe two novel methods (1) for finding single nucleotide polymorphisms (SNPs) significantly associated with one or more traits using a multi-trait, meta-analysis, and (2) for distinguishing between a single pleiotropic QTL and multiple linked QTL. The meta-analysis uses the effect of each SNP on each of n traits, estimated in single trait genome wide association studies (GWAS). These effects are expressed as a vector of signed t-values (t) and the error covariance matrix of these t values is approximated by the correlation matrix of t-values among the traits calculated across the SNP (V). Consequently, t'V−1t is approximately distributed as a chi-squared with n degrees of freedom. An attractive feature of the meta-analysis is that it uses estimated effects of SNPs from single trait GWAS, so it can be applied to published data where individual records are not available. We demonstrate that the multi-trait method can be used to increase the power (numbers of SNPs validated in an independent population) of GWAS in a beef cattle data set including 10,191 animals genotyped for 729,068 SNPs with 32 traits recorded, including growth and reproduction traits. We can distinguish between a single pleiotropic QTL and multiple linked QTL because multiple SNPs tagging the same QTL show the same pattern of effects across traits. We confirm this finding by demonstrating that when one SNP is included in the statistical model the other SNPs have a non-significant effect. In the beef cattle data set, cluster analysis yielded four groups of QTL with similar patterns of effects across traits within a group. A linear index was used to validate SNPs having effects on multiple traits and to identify additional SNPs belonging to these four groups. PMID:24675618

QTL and gene expression analyses identify genes affecting carcass weight and marbling on BTA14 in Hanwoo (Korean Cattle).

PubMed

Lee, Seung Hwan; van der Werf, J H J; Kim, Nam Kuk; Lee, Sang Hong; Gondro, C; Park, Eung Woo; Oh, Sung Jong; Gibson, J P; Thompson, J M

2011-10-01

Causal mutations affecting quantitative trait variation can be good targets for marker-assisted selection for carcass traits in beef cattle. In this study, linkage and linkage disequilibrium analysis (LDLA) for four carcass traits was undertaken using 19 markers on bovine chromosome 14. The LDLA analysis detected quantitative trait loci (QTL) for carcass weight (CWT) and eye muscle area (EMA) at the same position at around 50 cM and surrounded by the markers FABP4SNP2774C>G and FABP4_μsat3237. The QTL for marbling (MAR) was identified at the midpoint of markers BMS4513 and RM137 in a 3.5-cM marker interval. The most likely position for a second QTL for CWT was found at the midpoint of tenth marker bracket (FABP4SNP2774C>G and FABP4_μsat3237). For this marker bracket, the total number of haplotypes was 34 with a most common frequency of 0.118. Effects of haplotypes on CWT varied from a -5-kg deviation for haplotype 6 to +8 kg for haplotype 23. To determine which genes contribute to the QTL effect, gene expression analysis was performed in muscle for a wide range of phenotypes. The results demonstrate that two genes, LOC781182 (p = 0.002) and TRPS1 (p = 0.006) were upregulated with increasing CWT and EMA, whereas only LOC614744 (p = 0.04) has a significant effect on intramuscular fat (IMF) content. Two genetic markers detected in FABP4 were the most likely QTL position in this QTL study, but FABP4 did not show a significant effect on both traits (CWT and EMA) in gene expression analysis. We conclude that three genes could be potential causal genes affecting carcass traits CWT, EMA, and IMF in Hanwoo.

Quantitative trait locus for reading disability on chromosome 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardon, L.R.; Smith, S.D.; Kimberling, W.J.

1994-10-14

Interval mapping of data from two independent samples of sib pairs, at least one member of whom was reading disabled, revealed evidence for a quantitative trait locus (QTL) on chromosome 6. Results obtained from analyses of reading performance from 114 sib pairs genotyped for DNA markers localized the QTL to 6p21.3. Analyses of corresponding data from an independent sample of 50 dizygotic twin pairs provided evidence for linkage to the same region. In combination, the replicate samples yielded a x{sup 2} value of 16.73 (P = 0.0002). Examination of twin and kindred siblings with more extreme deficits in reading performancemore » yielded even stronger evidence for a QTL (x{sup 2} = 27.35, P < 0.00001). The position of the QTL was narrowly defined with a 100:1 confidence interval to a 2-centimorgan region within the human leukocyte antigen complex. 23 refs., 4 figs.« less

Fine mapping of a quantitative resistance gene for gray leaf spot of maize (Zea mays L.) derived from teosinte (Z. mays ssp. parviglumis).

PubMed

Zhang, Xinye; Yang, Qin; Rucker, Elizabeth; Thomason, Wade; Balint-Kurti, Peter

2017-06-01

In this study we mapped the QTL Qgls8 for gray leaf spot (GLS) resistance in maize to a ~130 kb region on chromosome 8 including five predicted genes. In previous work, using near isogenic line (NIL) populations in which segments of the teosinte (Zea mays ssp. parviglumis) genome had been introgressed into the background of the maize line B73, we had identified a QTL on chromosome 8, here called Qgls8, for gray leaf spot (GLS) resistance. We identified alternate teosinte alleles at this QTL, one conferring increased GLS resistance and one increased susceptibility relative to the B73 allele. Using segregating populations derived from NIL parents carrying these contrasting alleles, we were able to delimit the QTL region to a ~130 kb (based on the B73 genome) which encompassed five predicted genes.

Cortical Folding of the Primate Brain: An Interdisciplinary Examination of the Genetic Architecture, Modularity, and Evolvability of a Significant Neurological Trait in Pedigreed Baboons (Genus Papio)

PubMed Central

Atkinson, Elizabeth G.; Rogers, Jeffrey; Mahaney, Michael C.; Cox, Laura A.; Cheverud, James M.

2015-01-01

Folding of the primate brain cortex allows for improved neural processing power by increasing cortical surface area for the allocation of neurons. The arrangement of folds (sulci) and ridges (gyri) across the cerebral cortex is thought to reflect the underlying neural network. Gyrification, an adaptive trait with a unique evolutionary history, is affected by genetic factors different from those affecting brain volume. Using a large pedigreed population of ∼1000 Papio baboons, we address critical questions about the genetic architecture of primate brain folding, the interplay between genetics, brain anatomy, development, patterns of cortical–cortical connectivity, and gyrification’s potential for future evolution. Through Mantel testing and cluster analyses, we find that the baboon cortex is quite evolvable, with high integration between the genotype and phenotype. We further find significantly similar partitioning of variation between cortical development, anatomy, and connectivity, supporting the predictions of tension-based models for sulcal development. We identify a significant, moderate degree of genetic control over variation in sulcal length, with gyrus-shape features being more susceptible to environmental effects. Finally, through QTL mapping, we identify novel chromosomal regions affecting variation in brain folding. The most significant QTL contain compelling candidate genes, including gene clusters associated with Williams and Down syndromes. The QTL distribution suggests a complex genetic architecture for gyrification with both polygeny and pleiotropy. Our results provide a solid preliminary characterization of the genetic basis of primate brain folding, a unique and biomedically relevant phenotype with significant implications in primate brain evolution. PMID:25873632

Genetic Mapping in Mice Reveals the Involvement of Pcdh9 in Long-Term Social and Object Recognition and Sensorimotor Development.

PubMed

Bruining, Hilgo; Matsui, Asuka; Oguro-Ando, Asami; Kahn, René S; Van't Spijker, Heleen M; Akkermans, Guus; Stiedl, Oliver; van Engeland, Herman; Koopmans, Bastijn; van Lith, Hein A; Oppelaar, Hugo; Tieland, Liselotte; Nonkes, Lourens J; Yagi, Takeshi; Kaneko, Ryosuke; Burbach, J Peter H; Yamamoto, Nobuhiko; Kas, Martien J

2015-10-01

Quantitative genetic analysis of basic mouse behaviors is a powerful tool to identify novel genetic phenotypes contributing to neurobehavioral disorders. Here, we analyzed genetic contributions to single-trial, long-term social and nonsocial recognition and subsequently studied the functional impact of an identified candidate gene on behavioral development. Genetic mapping of single-trial social recognition was performed in chromosome substitution strains, a sophisticated tool for detecting quantitative trait loci (QTL) of complex traits. Follow-up occurred by generating and testing knockout (KO) mice of a selected QTL candidate gene. Functional characterization of these mice was performed through behavioral and neurological assessments across developmental stages and analyses of gene expression and brain morphology. Chromosome substitution strain 14 mapping studies revealed an overlapping QTL related to long-term social and object recognition harboring Pcdh9, a cell-adhesion gene previously associated with autism spectrum disorder. Specific long-term social and object recognition deficits were confirmed in homozygous (KO) Pcdh9-deficient mice, while heterozygous mice only showed long-term social recognition impairment. The recognition deficits in KO mice were not associated with alterations in perception, multi-trial discrimination learning, sociability, behavioral flexibility, or fear memory. Rather, KO mice showed additional impairments in sensorimotor development reflected by early touch-evoked biting, rotarod performance, and sensory gating deficits. This profile emerged with structural changes in deep layers of sensory cortices, where Pcdh9 is selectively expressed. This behavior-to-gene study implicates Pcdh9 in cognitive functions required for long-term social and nonsocial recognition. This role is supported by the involvement of Pcdh9 in sensory cortex development and sensorimotor phenotypes. Copyright © 2015 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach.

PubMed

Mora, Freddy; Quitral, Yerko A; Matus, Ivan; Russell, Joanne; Waugh, Robbie; Del Pozo, Alejandro

2016-01-01

This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5-22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5-35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint.

Plethysmography Phenotype QTL in Mice Before and After Allergen Sensitization and Challenge.

PubMed

Kelada, Samir N P

2016-09-08

Allergic asthma is common airway disease that is characterized in part by enhanced airway constriction in response to nonspecific stimuli. Genome-wide association studies have identified multiple loci associated with asthma risk in humans, but these studies have not accounted for gene-environment interactions, which are thought to be important factors in asthma. To identify quantitative trait loci (QTL) that regulate responses to a common human allergen, we applied a house dust mite mouse (HDM) model of allergic airway disease (AAD) to 146 incipient lines of the Collaborative Cross (CC) and the CC founder strains. We employed a longitudinal study design in which mice were phenotyped for response to the bronchoconstrictor methacholine both before and after HDM sensitization and challenge using whole body plethysmography (WBP). There was significant variation in methacholine responsiveness due to both strain and HDM treatment, as reflected by changes in the WBP parameter enhanced pause. We also found that distinct QTL regulate baseline [chromosome (Chr) 18] and post-HDM (Chr 19) methacholine responsiveness and that post-HDM airway responsiveness was correlated with other features of AAD. Finally, using invasive measurements of airway mechanics, we tested whether the Chr 19 QTL affects lung resistance per se using C57BL/6J mice and a consomic strain but found that QTL haplotype did not affect lung resistance. We conclude that aspects of baseline and allergen-induced methacholine responsiveness are associated with genetic variation, and that robust detection of airway resistance QTL in genetically diverse mice will be facilitated by direct measurement of airway mechanics. Copyright © 2016 Kelada.

Identification of Multiple QTL Hotspots in Sockeye Salmon (Oncorhynchus nerka) Using Genotyping-by-Sequencing and a Dense Linkage Map.

PubMed

Larson, Wesley A; McKinney, Garrett J; Limborg, Morten T; Everett, Meredith V; Seeb, Lisa W; Seeb, James E

2016-03-01

Understanding the genetic architecture of phenotypic traits can provide important information about the mechanisms and genomic regions involved in local adaptation and speciation. Here, we used genotyping-by-sequencing and a combination of previously published and newly generated data to construct sex-specific linkage maps for sockeye salmon (Oncorhynchus nerka). We then used the denser female linkage map to conduct quantitative trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The female linkage map consisted of 6322 loci distributed across 29 linkage groups and was 4082 cM long, and the male map contained 2179 loci found on 28 linkage groups and was 2291 cM long. We found 26 QTL: 6 for thermotolerance, 5 for length, 9 for weight, and 6 for condition factor. QTL were distributed nonrandomly across the genome and were often found in hotspots containing multiple QTL for a variety of phenotypic traits. These hotspots may represent adaptively important regions and are excellent candidates for future research. Comparing our results with studies in other salmonids revealed several regions with overlapping QTL for the same phenotypic trait, indicating these regions may be adaptively important across multiple species. Altogether, our study demonstrates the utility of genomic data for investigating the genetic basis of important phenotypic traits. Additionally, the linkage map created here will enable future research on the genetic basis of phenotypic traits in salmon. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Major Locus for Chloride Accumulation on Chromosome 5A in Bread Wheat

PubMed Central

Genc, Yusuf; Taylor, Julian; Rongala, Jay; Oldach, Klaus

2014-01-01

Chloride (Cl−) is an essential micronutrient for plant growth, but can be toxic at high concentrations resulting in reduced growth and yield. Although saline soils are generally dominated by both sodium (Na+) and Cl− ions, compared to Na+ toxicity, very little is known about physiological and genetic control mechanisms of tolerance to Cl− toxicity. In hydroponics and field studies, a bread wheat mapping population was tested to examine the relationships between physiological traits [Na+, potassium (K+) and Cl− concentration] involved in salinity tolerance (ST) and seedling growth or grain yield, and to elucidate the genetic control mechanism of plant Cl− accumulation using a quantitative trait loci (QTL) analysis approach. Plant Na+ or Cl− concentration were moderately correlated (genetically) with seedling biomass in hydroponics, but showed no correlations with grain yield in the field, indicating little value in selecting for ion concentration to improve ST. In accordance with phenotypic responses, QTL controlling Cl− accumulation differed entirely between hydroponics and field locations, and few were detected in two or more environments, demonstrating substantial QTL-by-environment interactions. The presence of several QTL for Cl− concentration indicated that uptake and accumulation was a polygenic trait. A major Cl− concentration QTL (5A; barc56/gwm186) was identified in three field environments, and accounted for 27–32% of the total genetic variance. Alignment between the 5A QTL interval and its corresponding physical genome regions in wheat and other grasses has enabled the search for candidate genes involved in Cl− transport, which is discussed. PMID:24893005

Identification of milling and baking quality QTL in multiple soft wheat mapping populations.

PubMed

Cabrera, Antonio; Guttieri, Mary; Smith, Nathan; Souza, Edward; Sturbaum, Anne; Hua, Duc; Griffey, Carl; Barnett, Marla; Murphy, Paul; Ohm, Herb; Uphaus, Jim; Sorrells, Mark; Heffner, Elliot; Brown-Guedira, Gina; Van Sanford, David; Sneller, Clay

2015-11-01

Two mapping approaches were use to identify and validate milling and baking quality QTL in soft wheat. Two LG were consistently found important for multiple traits and we recommend the use marker-assisted selection on specific markers reported here. Wheat-derived food products require a range of characteristics. Identification and understanding of the genetic components controlling end-use quality of wheat is important for crop improvement. We assessed the underlying genetics controlling specific milling and baking quality parameters of soft wheat including flour yield, softness equivalent, flour protein, sucrose, sodium carbonate, water absorption and lactic acid, solvent retention capacities in a diversity panel and five bi-parental mapping populations. The populations were genotyped with SSR and DArT markers, with markers specific for the 1BL.1RS translocation and sucrose synthase gene. Association analysis and composite interval mapping were performed to identify quantitative trait loci (QTL). High heritability was observed for each of the traits evaluated, trait correlations were consistent over populations, and transgressive segregants were common in all bi-parental populations. A total of 26 regions were identified as potential QTL in the diversity panel and 74 QTL were identified across all five bi-parental mapping populations. Collinearity of QTL from chromosomes 1B and 2B was observed across mapping populations and was consistent with results from the association analysis in the diversity panel. Multiple regression analysis showed the importance of the two 1B and 2B regions and marker-assisted selection for the favorable alleles at these regions should improve quality.

Plethysmography Phenotype QTL in Mice Before and After Allergen Sensitization and Challenge

DOE PAGES

Kelada, Samir N. P.

2016-07-22

Allergic asthma is common airway disease that is characterized in part by enhanced airway constriction in response to nonspecific stimuli. Genome-wide association studies have identified multiple loci associated with asthma risk in humans, but these studies have not accounted for gene–environment interactions, which are thought to be important factors in asthma. To identify quantitative trait loci (QTL) that regulate responses to a common human allergen, we applied a house dust mite mouse (HDM) model of allergic airway disease (AAD) to 146 incipient lines of the Collaborative Cross (CC) and the CC founder strains. We employed a longitudinal study design inmore » which mice were phenotyped for response to the bronchoconstrictor methacholine both before and after HDM sensitization and challenge using whole body plethysmography (WBP). There was significant variation in methacholine responsiveness due to both strain and HDM treatment, as reflected by changes in the WBP parameter enhanced pause. We also found that distinct QTL regulate baseline [chromosome (Chr) 18] and post-HDM (Chr 19) methacholine responsiveness and that post-HDM airway responsiveness was correlated with other features of AAD. Finally, using invasive measurements of airway mechanics, we tested whether the Chr 19 QTL affects lung resistance per se using C57BL/6J mice and a consomic strain but found that QTL haplotype did not affect lung resistance. We conclude that aspects of baseline and allergen-induced methacholine responsiveness are associated with genetic variation, and that robust detection of airway resistance QTL in genetically diverse mice will be facilitated by direct measurement of airway mechanics.« less

Plethysmography Phenotype QTL in Mice Before and After Allergen Sensitization and Challenge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelada, Samir N. P.

Allergic asthma is common airway disease that is characterized in part by enhanced airway constriction in response to nonspecific stimuli. Genome-wide association studies have identified multiple loci associated with asthma risk in humans, but these studies have not accounted for gene–environment interactions, which are thought to be important factors in asthma. To identify quantitative trait loci (QTL) that regulate responses to a common human allergen, we applied a house dust mite mouse (HDM) model of allergic airway disease (AAD) to 146 incipient lines of the Collaborative Cross (CC) and the CC founder strains. We employed a longitudinal study design inmore » which mice were phenotyped for response to the bronchoconstrictor methacholine both before and after HDM sensitization and challenge using whole body plethysmography (WBP). There was significant variation in methacholine responsiveness due to both strain and HDM treatment, as reflected by changes in the WBP parameter enhanced pause. We also found that distinct QTL regulate baseline [chromosome (Chr) 18] and post-HDM (Chr 19) methacholine responsiveness and that post-HDM airway responsiveness was correlated with other features of AAD. Finally, using invasive measurements of airway mechanics, we tested whether the Chr 19 QTL affects lung resistance per se using C57BL/6J mice and a consomic strain but found that QTL haplotype did not affect lung resistance. We conclude that aspects of baseline and allergen-induced methacholine responsiveness are associated with genetic variation, and that robust detection of airway resistance QTL in genetically diverse mice will be facilitated by direct measurement of airway mechanics.« less

Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16

PubMed Central

Khan, Sabaz Ali; Chibon, Pierre-Yves; de Vos, Ric C.H.; Schipper, Bert A.; Walraven, Evert; Beekwilder, Jules; van Dijk, Thijs; Finkers, Richard; Visser, Richard G.F.; van de Weg, Eric W.; Bovy, Arnaud; Cestaro, Alessandro; Velasco, Riccardo; Jacobsen, Evert; Schouten, Henk J.

2012-01-01

Apple (Malus×domestica Borkh) is among the main sources of phenolic compounds in the human diet. The genetic basis of the quantitative variations of these potentially beneficial phenolic compounds was investigated. A segregating F1 population was used to map metabolite quantitative trait loci (mQTLs). Untargeted metabolic profiling of peel and flesh tissues of ripe fruits was performed using liquid chromatography–mass spectrometry (LC-MS), resulting in the detection of 418 metabolites in peel and 254 in flesh. In mQTL mapping using MetaNetwork, 669 significant mQTLs were detected: 488 in the peel and 181 in the flesh. Four linkage groups (LGs), LG1, LG8, LG13, and LG16, were found to contain mQTL hotspots, mainly regulating metabolites that belong to the phenylpropanoid pathway. The genetics of annotated metabolites was studied in more detail using MapQTL®. A number of quercetin conjugates had mQTLs on LG1 or LG13. The most important mQTL hotspot with the largest number of metabolites was detected on LG16: mQTLs for 33 peel-related and 17 flesh-related phenolic compounds. Structural genes involved in the phenylpropanoid biosynthetic pathway were located, using the apple genome sequence. The structural gene leucoanthocyanidin reductase (LAR1) was in the mQTL hotspot on LG16, as were seven transcription factor genes. The authors believe that this is the first time that a QTL analysis was performed on such a high number of metabolites in an outbreeding plant species. PMID:22330898

Genetic Control of Fruit Vitamin C Contents1

PubMed Central

Davey, Mark W.; Kenis, Katrien; Keulemans, Johan

2006-01-01

An F1 progeny derived from a cross between the apple (Malus x domestica) cultivars Telamon and Braeburn was used to identify quantitative trait loci (QTL) linked to the vitamin C (l-ascorbate [l-AA]) contents of fruit skin and flesh (cortex) tissues. We identified up to three highly significant QTLs for both the mean l-AA and the mean total l-AA contents of fruit flesh on both parental genetic linkage maps, confirming the quantitative nature of these traits. These QTLs account for up to a maximum of 60% of the total population variation observed in the progeny, and with a maximal individual contribution of 31% per QTL. QTLs common to both parents were identified on linkage groups (LGs) 6, 10, and 11 of the Malus reference map, while each parent also had additional unique QTLs on other LGs. Interestingly, one strong QTL on LG-17 of the Telamon linkage map colocalized with a highly significant QTL associated with flesh browning, and a minor QTL for dehydroascorbate content, supporting earlier work that links fruit l-AA contents with the susceptibility of hardfruit to postharvest browning. We also found significant minor QTLs for skin l-AA and total l-AA (l-AA + dehydroascorbate) contents in Telamon. Currently, little is known about the genetic determinants underlying tissue l-AA homeostasis, but the presence of major, highly significant QTL in both these apple genotypes under field conditions suggests the existence of common control mechanisms, allelic heterozygosity, and helps outline strategies and the potential for the molecular breeding of these traits. PMID:16844833

Identification of QTLs conferring resistance to downy mildews of maize in Asia.

PubMed

George, M L C; Prasanna, B M; Rathore, R S; Setty, T A S; Kasim, F; Azrai, M; Vasal, S; Balla, O; Hautea, D; Canama, A; Regalado, E; Vargas, M; Khairallah, M; Jeffers, D; Hoisington, D

2003-08-01

Downy mildew is one of the most destructive diseases of maize in subtropical and tropical regions in Asia. As a prerequisite for improving downy mildew resistance in maize, we analyzed quantitative trait loci (QTLs) involved in resistance to the important downy mildew pathogens--Peronosclerospora sorghi (sorghum downy mildew) and P. heteropogoni (Rajasthan downy mildew) in India, P. maydis (Java downy mildew) in Indonesia, P. zeae in Thailand and P. philippinensis in the Philippines--using a recombinant inbred line population derived from a cross between Ki3 (downy mildew resistant) and CML139 (susceptible). Resistance was evaluated as percentage disease incidence in replicated field trials at five downy mildew 'hotspots' in the four countries. Heritability estimates of individual environments ranged from 0.58 to 0.75 with an across environment heritability of 0.50. Composite interval mapping was applied for QTL detection using a previously constructed restriction fragment length polymorphism linkage map. The investigation resulted in the identification of six genomic regions on chromosomes 1, 2, 6, 7 and 10 involved in the resistance to the downy mildews under study, explaining, in total, 26-57% of the phenotypic variance for disease response. Most QTL alleles conferring resistance to the downy mildews were from Ki3. All QTLs showed significant QTL x environment interactions, suggesting that the expression of the QTL may be environment-dependent. A strong QTL on chromosome 6 was stable across environments, significantly affecting disease resistance at the five locations in four Asian countries. Simple-sequence repeat markers tightly linked to this QTL were identified for potential use in marker-assisted selection.

SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach

PubMed Central

Mora, Freddy; Quitral, Yerko A.; Matus, Ivan; Russell, Joanne; Waugh, Robbie; del Pozo, Alejandro

2016-01-01

This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5–22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5–35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint. PMID:27446139

Exploring new alleles for frost tolerance in winter rye.

PubMed

Erath, Wiltrud; Bauer, Eva; Fowler, D Brian; Gordillo, Andres; Korzun, Viktor; Ponomareva, Mira; Schmidt, Malthe; Schmiedchen, Brigitta; Wilde, Peer; Schön, Chris-Carolin

2017-10-01

Rye genetic resources provide a valuable source of new alleles for the improvement of frost tolerance in rye breeding programs. Frost tolerance is a must-have trait for winter cereal production in northern and continental cropping areas. Genetic resources should harbor promising alleles for the improvement of frost tolerance of winter rye elite lines. For frost tolerance breeding, the identification of quantitative trait loci (QTL) and the choice of optimum genome-based selection methods are essential. We identified genomic regions involved in frost tolerance of winter rye by QTL mapping in a biparental population derived from a highly frost tolerant selection from the Canadian cultivar Puma and the European elite line Lo157. Lines per se and their testcrosses were phenotyped in a controlled freeze test and in multi-location field trials in Russia and Canada. Three QTL on chromosomes 4R, 5R, and 7R were consistently detected across environments. The QTL on 5R is congruent with the genomic region harboring the Frost resistance locus 2 (Fr-2) in Triticeae. The Puma allele at the Fr-R2 locus was found to significantly increase frost tolerance. A comparison of predictive ability obtained from the QTL-based model with different whole-genome prediction models revealed that besides a few large, also small QTL effects contribute to the genomic variance of frost tolerance in rye. Genomic prediction models assigning a high weight to the Fr-R2 locus allow increasing the selection intensity for frost tolerance by genome-based pre-selection of promising candidates.

Validation of consensus quantitative trait loci associated with resistance to multiple foliar pathogens of maize.

PubMed

Asea, Godfrey; Vivek, Bindiganavile S; Bigirwa, George; Lipps, Patrick E; Pratt, Richard C

2009-05-01

Maize production in sub-Saharan Africa incurs serious losses to epiphytotics of foliar diseases. Quantitative trait loci conditioning partial resistance (rQTL) to infection by causal agents of gray leaf spot (GLS), northern corn leaf blight (NCLB), and maize streak have been reported. Our objectives were to identify simple-sequence repeat (SSR) molecular markers linked to consensus rQTL and one recently identified rQTL associated with GLS, and to determine their suitability as tools for selection of improved host resistance. We conducted evaluations of disease severity phenotypes in separate field nurseries, each containing 410 F2:3 families derived from a cross between maize inbred CML202 (NCLB and maize streak resistant) and VP31 (a GLS-resistant breeding line) that possess complimentary rQTL. F2:3 families were selected for resistance based on genotypic (SSR marker), phenotypic, or combined data and the selected F3:4 families were reevaluated. Phenotypic values associated with SSR markers for consensus rQTL in bins 4.08 for GLS, 5.04 for NCLB, and 1.04 for maize streak significantly reduced disease severity in both generations based on single-factor analysis of variance and marker-interval analysis. These results were consistent with the presence of homozygous resistant parent alleles, except in bin 8.06, where markers were contributed by the NCLB-susceptible parent. Only one marker associated with resistance could be confirmed in bins 2.09 (GLS) and 3.06 (NCLB), illustrating the need for more robust rQTL discovery, fine-mapping, and validation prior to undertaking marker-based selection.

Support for the reproductive ground plan hypothesis of social evolution and major QTL for ovary traits of Africanized worker honey bees (Apis mellifera L.)

PubMed Central

2011-01-01

Background The reproductive ground plan hypothesis of social evolution suggests that reproductive controls of a solitary ancestor have been co-opted during social evolution, facilitating the division of labor among social insect workers. Despite substantial empirical support, the generality of this hypothesis is not universally accepted. Thus, we investigated the prediction of particular genes with pleiotropic effects on ovarian traits and social behavior in worker honey bees as a stringent test of the reproductive ground plan hypothesis. We complemented these tests with a comprehensive genome scan for additional quantitative trait loci (QTL) to gain a better understanding of the genetic architecture of the ovary size of honey bee workers, a morphological trait that is significant for understanding social insect caste evolution and general insect biology. Results Back-crossing hybrid European x Africanized honey bee queens to the Africanized parent colony generated two study populations with extraordinarily large worker ovaries. Despite the transgressive ovary phenotypes, several previously mapped QTL for social foraging behavior demonstrated ovary size effects, confirming the prediction of pleiotropic genetic effects on reproductive traits and social behavior. One major QTL for ovary size was detected in each backcross, along with several smaller effects and two QTL for ovary asymmetry. One of the main ovary size QTL coincided with a major QTL for ovary activation, explaining 3/4 of the phenotypic variance, although no simple positive correlation between ovary size and activation was observed. Conclusions Our results provide strong support for the reproductive ground plan hypothesis of evolution in study populations that are independent of the genetic stocks that originally led to the formulation of this hypothesis. As predicted, worker ovary size is genetically linked to multiple correlated traits of the complex division of labor in worker honey bees, known as the pollen hoarding syndrome. The genetic architecture of worker ovary size presumably consists of a combination of trait-specific loci and general regulators that affect the whole behavioral syndrome and may even play a role in caste determination. Several promising candidate genes in the QTL intervals await further study to clarify their potential role in social insect evolution and the regulation of insect fertility in general. PMID:21489230

Adjusting data to body size: a comparison of methods as applied to quantitative trait loci analysis of musculoskeletal phenotypes.

PubMed

Lang, Dean H; Sharkey, Neil A; Lionikas, Arimantas; Mack, Holly A; Larsson, Lars; Vogler, George P; Vandenbergh, David J; Blizard, David A; Stout, Joseph T; Stitt, Joseph P; McClearn, Gerald E

2005-05-01

The aim of this study was to compare three methods of adjusting skeletal data for body size and examine their use in QTL analyses. It was found that dividing skeletal phenotypes by body mass index induced erroneous QTL results. The preferred method of body size adjustment was multiple regression. Many skeletal studies have reported strong correlations between phenotypes for muscle, bone, and body size, and these correlations add to the difficulty in identifying genetic influence on skeletal traits that are not mediated through overall body size. Quantitative trait loci (QTL) identified for skeletal phenotypes often map to the same chromosome regions as QTLs for body size. The actions of a QTL identified as influencing BMD could therefore be mediated through the generalized actions of growth on body size or muscle mass. Three methods of adjusting skeletal phenotypes to body size were performed on morphologic, structural, and compositional measurements of the femur and tibia in 200-day-old C57BL/6J x DBA/2 (BXD) second generation (F(2)) mice (n = 400). A common method of removing the size effect has been through the use of ratios. This technique and two alternative techniques using simple and multiple regression were performed on muscle and skeletal data before QTL analyses, and the differences in QTL results were examined. The use of ratios to remove the size effect was shown to increase the size effect by inducing spurious correlations, thereby leading to inaccurate QTL results. Adjustments for body size using multiple regression eliminated these problems. Multiple regression should be used to remove the variance of co-factors related to skeletal phenotypes to allow for the study of genetic influence independent of correlated phenotypes. However, to better understand the genetic influence, adjusted and unadjusted skeletal QTL results should be compared. Additional insight can be gained by observing the difference in LOD score between the adjusted and nonadjusted phenotypes. Identifying QTLs that exert their effects on skeletal phenotypes through body size-related pathways as well as those having a more direct and independent influence on bone are equally important in deciphering the complex physiologic pathways responsible for the maintenance of bone health.

Targeted Recombinant Progeny: a design for ultra-high resolution mapping of Quantitative Trait Loci in crosses between inbred or pure lines.

PubMed

Heifetz, Eliyahu M; Soller, Morris

2015-07-07

High-resolution mapping of the loci (QTN) responsible for genetic variation in quantitative traits is essential for positional cloning of candidate genes, and for effective marker assisted selection. The confidence interval (QTL) flanking the point estimate of QTN-location is proportional to the number of individuals in the mapping population carrying chromosomes recombinant in the given interval. Consequently, many designs for high resolution QTN mapping are based on increasing the proportion of recombinants in the mapping population. The "Targeted Recombinant Progeny" (TRP) design is a new design for high resolution mapping of a target QTN in crosses between pure, or inbred lines. It is a three-generation procedure generating a large number of recombinant individuals within a QTL previously shown to contain a QTN. This is achieved by having individuals that carry chromosomes recombinant across the target QTL interval as parents of a large mapping population; most of whom will therefore carry recombinant chromosomes targeted to the given QTL. The TRP design is particularly useful for high resolution mapping of QTN that differentiate inbred or pure lines, and hence are not amenable to high resolution mapping by genome-wide association tests. In the absence of residual polygenic variation, population sizes required for achieving given mapping resolution by the TRP-F2 design relative to a standard F2 design ranged from 0.289 for a QTN with standardized allele substitution effect = 0.2, mapped to an initial QTL of 0.2 Morgan to 0.041 for equivalent QTN mapped to an initial QTL of 0.02 M. In the presence of residual polygenic variation, the relative effectiveness of the TRP design ranges from 1.068 to 0.151 for the same initial QTL intervals and QTN effect. Thus even in the presence of polygenic variation, the TRP can still provide major savings. Simulation showed that mapping by TRP should be based on 30-50 markers spanning the initial interval; and on at least 50 or more G2 families representing this number of recombination points,. The TRP design can be an effective procedure for achieving high and ultra-high mapping resolution of a target QTN previously mapped to a known confidence interval (QTL).

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.

PubMed

Zych, Konrad; Li, Yang; van der Velde, Joeri K; Joosen, Ronny V L; Ligterink, Wilco; Jansen, Ritsert C; Arends, Danny

2015-02-19

Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers. The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping. We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population. The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under "GNU GPL v3". The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl .

The identification of QTL controlling ergot sclerotia size in hexaploid wheat implicates a role for the Rht dwarfing alleles.

PubMed

Gordon, Anna; Basler, Ryan; Bansept-Basler, Pauline; Fanstone, Vicky; Harinarayan, Lakshmi; Grant, Paul K; Birchmore, Richard; Bayles, Rosemary A; Boyd, Lesley A; O'Sullivan, Donal M

2015-12-01

Four QTL conferring resistance to ergot were identified in the UK winter wheat varieties 'Robigus' and 'Solstice'. Two QTL co-located with semi-dwarfing alleles at the Rht loci Rht - 1B and Rht - 1D implicating a role of these DELLA proteins in infection success of Claviceps purpurea. The fungal pathogen Claviceps purpurea infects ovaries of a broad range of temperate grasses and cereals, including hexaploid wheat, causing a disease commonly known as ergot. Sclerotia produced in place of seed carry a cocktail of harmful alkaloid compounds that result in a range of symptoms in humans and animals, causing ergotism. Following a field assessment of C. purpurea infection in winter wheat, two varieties 'Robigus' and 'Solstice' were selected which consistently produced the largest differential effect on ergot sclerotia weights. They were crossed to produce a doubled haploid mapping population, and a marker map, consisting of 714 genetic loci and a total length of 2895 cM was produced. Four ergot reducing QTL were identified using both sclerotia weight and size as phenotypic parameters; QCp.niab.2A and QCp.niab.4B being detected in the wheat variety 'Robigus', and QCp.niab.6A and QCp.niab.4D in the variety 'Solstice'. The ergot resistance QTL QCp.niab.4B and QCp.niab.4D peaks mapped to the same markers as the known reduced height (Rht) loci on chromosomes 4B and 4D, Rht-B1 and Rht-D1, respectively. In both cases, the reduction in sclerotia weight and size was associated with the semi-dwarfing alleles, Rht-B1b from 'Robigus' and Rht-D1b from 'Solstice'. Two-dimensional, two-QTL scans identified significant additive interactions between QTL QCp.niab.4B and QCp.niab.4D, and between QCp.niab.2A and QCp.niab.4B when looking at sclerotia size, but not between QCp.niab.2A and QCp.niab.4D. The two plant height QTL, QPh.niab.4B and QPh.niab.4D, which mapped to the same locations as QCp.niab.4B and QCp.niab.4D, also displayed significant genetic interactions.

Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle.

PubMed

Seabury, Christopher M; Oldeschulte, David L; Saatchi, Mahdi; Beever, Jonathan E; Decker, Jared E; Halley, Yvette A; Bhattarai, Eric K; Molaei, Maral; Freetly, Harvey C; Hansen, Stephanie L; Yampara-Iquise, Helen; Johnson, Kristen A; Kerley, Monty S; Kim, JaeWoo; Loy, Daniel D; Marques, Elisa; Neibergs, Holly L; Schnabel, Robert D; Shike, Daniel W; Spangler, Matthew L; Weaber, Robert L; Garrick, Dorian J; Taylor, Jeremy F

2017-05-18

Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P-value threshold (P ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL (n = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL (n = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

Identifying Rare FHB-Resistant Segregants in Intransigent Backcross and F2 Winter Wheat Populations.

PubMed

Clark, Anthony J; Sarti-Dvorjak, Daniela; Brown-Guedira, Gina; Dong, Yanhong; Baik, Byung-Kee; Van Sanford, David A

2016-01-01

Fusarium head blight (FHB), caused mainly by Fusarium graminearum Schwabe [telomorph: Gibberella zeae Schwein.(Petch)] in the US, is one of the most destructive diseases of wheat (Triticum aestivum L. and T. durum L.). Infected grain is usually contaminated with deoxynivalenol (DON), a serious mycotoxin. The challenge in FHB resistance breeding is combining resistance with superior agronomic and quality characteristics. Exotic QTL are widely used to improve FHB resistance. Success depends on the genetic background into which the QTL are introgressed, whether through backcrossing or forward crossing; QTL expression is impossible to predict. In this study four high-yielding soft red winter wheat breeding lines with little or no scab resistance were each crossed to a donor parent (VA01W-476) with resistance alleles at two QTL: Fhb1 (chromosome 3BS) and QFhs.nau-2DL (chromosome 2DL) to generate backcross and F2 progeny. F2 individuals were genotyped and assigned to 4 groups according to presence/ absence of resistance alleles at one or both QTL. The effectiveness of these QTL in reducing FHB rating, incidence, index, severity, Fusarium-damaged kernels (FDK) and DON, in F2-derived lines was assessed over 2 years. Fhb1 showed an average reduction in DON of 17.5%, and conferred significant resistance in 3 of 4 populations. QFhs.nau-2DL reduced DON 6.7% on average and conferred significant resistance in 2 of 4 populations. The combination of Fhb1 and QFhs.nau-2DL resistance reduced DON 25.5% across all populations. Double resistant lines had significantly reduced DON compared to double susceptible lines in 3 populations. Backcross derived progeny were planted in replicated yield trials (2011 and 2012) and in a scab nursery in 2012. Several top yielding lines performed well in the scab nursery, with acceptable DON concentrations, even though the average effect of either QTL in this population was not significant. Population selection is often viewed as an "all or nothing" process: if the average resistance level is insufficient, the population is discarded. These results indicate that it may be possible to find rare segregants which combine scab resistance, superior agronomic performance and acceptable quality even in populations in which the average effect of the QTL is muted or negligible.