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Sample records for anchored qtl map

  1. Mapping of pigmentation QTL on an anchored genome assembly of the cichlid fish, Metriaclima zebra.

    PubMed

    O'Quin, Claire T; Drilea, Alexi C; Conte, Matthew A; Kocher, Thomas D

    2013-04-27

    Pigmentation patterns are one of the most recognizable phenotypes across the animal kingdom. They play an important role in camouflage, communication, mate recognition and mate choice. Most progress on understanding the genetics of pigmentation has been achieved via mutational analysis, with relatively little work done to understand variation in natural populations. Pigment patterns vary dramatically among species of cichlid fish from Lake Malawi, and are thought to be important in speciation. In this study, we crossed two species, Metriaclima zebra and M. mbenjii, that differ in several aspects of their body and fin color. We genotyped 798 SNPs in 160 F2 male individuals to construct a linkage map that was used to identify quantitative trait loci (QTL) associated with the pigmentation traits of interest. We also used the linkage map to anchor portions of the M. zebra genome assembly. We constructed a linkage map consisting of 834 markers in 22 linkage groups that spanned over 1,933 cM. QTL analysis detected one QTL each for dorsal fin xanthophores, caudal fin xanthophores, and pelvic fin melanophores. Dorsal fin and caudal fin xanthophores share a QTL on LG12, while pelvic fin melanophores have a QTL on LG11. We used the mapped markers to anchor 66.5% of the M. zebra genome assembly. Within each QTL interval we identified several candidate genes that might play a role in pigment cell development. This is one of a few studies to identify QTL for natural variation in fish pigmentation. The QTL intervals we identified did not contain any pigmentation genes previously identified by mutagenesis studies in other species. We expect that further work on these intervals will identify new genes involved in pigment cell development in natural populations.

  2. Human QTL linkage mapping.

    PubMed

    Almasy, Laura; Blangero, John

    2009-06-01

    Human quantitative trait locus (QTL) linkage mapping, although based on classical statistical genetic methods that have been around for many years, has been employed for genome-wide screening for only the last 10-15 years. In this time, there have been many success stories, ranging from QTLs that have been replicated in independent studies to those for which one or more genes underlying the linkage peak have been identified to a few with specific functional variants that have been confirmed in in vitro laboratory assays. Despite these successes, there is a general perception that linkage approaches do not work for complex traits, possibly because many human QTL linkage studies have been limited in sample size and have not employed the family configurations that maximize the power to detect linkage. We predict that human QTL linkage studies will continue to be productive for the next several years, particularly in combination with RNA expression level traits that are showing evidence of regulatory QTLs of large effect sizes and in combination with high-density genome-wide SNP panels. These SNP panels are being used to identify QTLs previously localized by linkage and linkage results are being used to place informative priors on genome-wide association studies.

  3. QTL mapping using high-throughput sequencing

    USDA-ARS?s Scientific Manuscript database

    Quantitative trait locus (QTL) mapping in plants dates to the 1980’s, but earlier studies were often hindered by the expense and time required to identify large numbers of polymorphic genetic markers that differentiated the parental genotypes and then to genotype them on large segregating mapping po...

  4. 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.

  5. Data-driven assessment of eQTL mapping methods

    PubMed Central

    2010-01-01

    Background The analysis of expression quantitative trait loci (eQTL) is a potentially powerful way to detect transcriptional regulatory relationships at the genomic scale. However, eQTL data sets often go underexploited because legacy QTL methods are used to map the relationship between the expression trait and genotype. Often these methods are inappropriate for complex traits such as gene expression, particularly in the case of epistasis. Results Here we compare legacy QTL mapping methods with several modern multi-locus methods and evaluate their ability to produce eQTL that agree with independent external data in a systematic way. We found that the modern multi-locus methods (Random Forests, sparse partial least squares, lasso, and elastic net) clearly outperformed the legacy QTL methods (Haley-Knott regression and composite interval mapping) in terms of biological relevance of the mapped eQTL. In particular, we found that our new approach, based on Random Forests, showed superior performance among the multi-locus methods. Conclusions Benchmarks based on the recapitulation of experimental findings provide valuable insight when selecting the appropriate eQTL mapping method. Our battery of tests suggests that Random Forests map eQTL that are more likely to be validated by independent data, when compared to competing multi-locus and legacy eQTL mapping methods. PMID:20849587

  6. Advances in Bayesian Multiple QTL Mapping in Experimental Crosses

    PubMed Central

    Yi, Nengjun; Shriner, Daniel

    2016-01-01

    Many complex human diseases and traits of biological and/or economic importance are determined by interacting networks of multiple quantitative trait loci (QTL) and environmental factors. Mapping QTL is critical for understanding the genetic basis of complex traits, and for ultimate identification of responsible genes. A variety of sophisticated statistical methods for QTL mapping have been developed. Among these developments, the evolution of Bayesian approaches for multiple QTL mapping over the past decade has been remarkable. Bayesian methods can jointly infer the number of QTL, their genomic positions, and their genetic effects. Here, we review recently developed and still developing Bayesian methods and associated computer software for mapping multiple QTL in experimental crosses. We compare and contrast these methods to clearly describe the relationships among different Bayesian methods. We conclude this review by highlighting some areas of future research. PMID:17987056

  7. 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…

  8. 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…

  9. QTL mapping of resistance to gray leaf spot in maize.

    PubMed

    Zhang, Yan; Xu, Ling; Fan, Xingming; Tan, Jing; Chen, Wei; Xu, Mingliang

    2012-12-01

    Gray leaf spot (GLS), caused by the causal fungal pathogen Cercospora zeae-maydis, is one of the most serious foliar diseases of maize worldwide. In the current study, a highly resistant inbred line Y32 and a susceptible line Q11 were used to produce segregating populations for both genetic analysis and QTL mapping. The broad-sense heritability (H (2)) for GLS resistance was estimated to be as high as 0.85, indicating that genetic factors played key roles in phenotypic variation. In initial QTL analysis, four QTL, located on chromosomes 1, 2, 5, and 8, were detected to confer GLS resistance. Each QTL could explain 2.53-23.90 % of the total phenotypic variation, predominantly due to additive genetic effects. Two major QTL, qRgls1 and qRgls2 on chromosomes 8 and 5, were consistently detected across different locations and replicates. Compared to the previous results, qRgls2 is located in a 'hotspot' for GLS resistance; while, qRgls1 does not overlap with any other known resistance QTL. Furthermore, the major QTL-qRgls1 was fine-mapped into an interval of 1.4 Mb, flanked by the markers GZ204 and IDP5. The QTL-qRgls1 could enhance the resistance percentages by 19.70-61.28 %, suggesting its usefulness to improve maize resistance to GLS.

  10. Genetic analysis and QTL mapping of seed coat color in sesame (Sesamum indicum L.).

    PubMed

    Zhang, Haiyang; Miao, Hongmei; Wei, Libin; Li, Chun; Zhao, Ruihong; Wang, Cuiying

    2013-01-01

    Seed coat color is an important agronomic trait in sesame, as it is associated with seed biochemical properties, antioxidant content and activity and even disease resistance of sesame. Here, using a high-density linkage map, we analyzed genetic segregation and quantitative trait loci (QTL) for sesame seed coat color in six generations (P1, P2, F1, BC1, BC2 and F2). Results showed that two major genes with additive-dominant-epistatic effects and polygenes with additive-dominant-epistatic effects were responsible for controlling the seed coat color trait. Average heritability of the major genes in the BC1, BC2 and F2 populations was 89.30%, 24.00%, and 91.11% respectively, while the heritability of polygenes was low in the BC1 (5.43%), in BC2 (0.00%) and in F2 (0.89%) populations. A high-density map was constructed using 724 polymorphic markers. 653 SSR, AFLP and RSAMPL loci were anchored in 14 linkage groups (LG) spanning a total of 1,216.00 cM. The average length of each LG was 86.86 cM and the marker density was 1.86 cM per marker interval. Four QTLs for seed coat color, QTL1-1, QTL11-1, QTL11-2 and QTL13-1, whose heritability ranged from 59.33%-69.89%, were detected in F3 populations using CIM and MCIM methods. Alleles at all QTLs from the black-seeded parent tended to increase the seed coat color. Results from QTLs mapping and classical genetic analysis among the P1, P2, F1, BC1, BC2 and F2 populations were comparatively consistent. This first QTL analysis and high-density genetic linkage map for sesame provided a good foundation for further research on sesame genetics and molecular marker-assisted selection (MAS).

  11. Genetic Analysis and QTL Mapping of Seed Coat Color in Sesame (Sesamum indicum L.)

    PubMed Central

    Zhang, Haiyang; Miao, Hongmei; Wei, Libin; Li, Chun; Zhao, Ruihong; Wang, Cuiying

    2013-01-01

    Seed coat color is an important agronomic trait in sesame, as it is associated with seed biochemical properties, antioxidant content and activity and even disease resistance of sesame. Here, using a high-density linkage map, we analyzed genetic segregation and quantitative trait loci (QTL) for sesame seed coat color in six generations (P1, P2, F1, BC1, BC2 and F2). Results showed that two major genes with additive-dominant-epistatic effects and polygenes with additive-dominant-epistatic effects were responsible for controlling the seed coat color trait. Average heritability of the major genes in the BC1, BC2 and F2 populations was 89.30%, 24.00%, and 91.11% respectively, while the heritability of polygenes was low in the BC1 (5.43%), in BC2 (0.00%) and in F2 (0.89%) populations. A high-density map was constructed using 724 polymorphic markers. 653 SSR, AFLP and RSAMPL loci were anchored in 14 linkage groups (LG) spanning a total of 1,216.00 cM. The average length of each LG was 86.86 cM and the marker density was 1.86 cM per marker interval. Four QTLs for seed coat color, QTL1-1, QTL11-1, QTL11-2 and QTL13-1, whose heritability ranged from 59.33%–69.89%, were detected in F3 populations using CIM and MCIM methods. Alleles at all QTLs from the black-seeded parent tended to increase the seed coat color. Results from QTLs mapping and classical genetic analysis among the P1, P2, F1, BC1, BC2 and F2 populations were comparatively consistent. This first QTL analysis and high-density genetic linkage map for sesame provided a good foundation for further research on sesame genetics and molecular marker-assisted selection (MAS). PMID:23704951

  12. Deviance Information Criterion (DIC) in Bayesian Multiple QTL Mapping.

    PubMed

    Shriner, Daniel; Yi, Nengjun

    2009-03-15

    Mapping multiple quantitative trait loci (QTL) is commonly viewed as a problem of model selection. Various model selection criteria have been proposed, primarily in the non-Bayesian framework. The deviance information criterion (DIC) is the most popular criterion for Bayesian model selection and model comparison but has not been applied to Bayesian multiple QTL mapping. A derivation of the DIC is presented for multiple interacting QTL models and calculation of the DIC is demonstrated using posterior samples generated by Markov chain Monte Carlo (MCMC) algorithms. The DIC measures posterior predictive error by penalizing the fit of a model (deviance) by its complexity, determined by the effective number of parameters. The effective number of parameters simultaneously accounts for the sample size, the cross design, the number and lengths of chromosomes, covariates, the number of QTL, the type of QTL effects, and QTL effect sizes. The DIC provides a computationally efficient way to perform sensitivity analysis and can be used to quantitatively evaluate if including environmental effects, gene-gene interactions, and/or gene-environment interactions in the prior specification is worth the extra parameterization. The DIC has been implemented in the freely available package R/qtlbim, which greatly facilitates the general usage of Bayesian methodology for genome-wide interacting QTL analysis.

  13. 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

  14. Mapping QTL Contributing to SCMV Resistance in Tropical Maize

    USDA-ARS?s Scientific Manuscript database

    Sugarcane mosaic virus (SCMV) has been increasing in importance as a maize disease in Brazil. In this study, were mapped and characterized quantitative trait loci (QTL) associated to resistance to SCMV in a maize population consisting of 150 F2:3 families from the cross between two tropical maize i...

  15. 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

  16. Bayesian mixture structural equation modelling in multiple-trait QTL mapping

    USDA-ARS?s Scientific Manuscript database

    Quantitative trait loci (QTL) mapping often results in data on a number of traits that have well established causal relationships. Many multi-trait QTL mapping methods that account for the correlation among multiple traits have been developed to improve the statistical power and the precision of QTL...

  17. A comprehensive linkage map and QTL map for carcass traits in a cross between Giant Grey and New Zealand White rabbits.

    PubMed

    Sternstein, Ina; Reissmann, Monika; Maj, Dorota; Bieniek, Josef; Brockmann, Gudrun A

    2015-02-11

    Genomic resources for the rabbit are still limited compared to many other livestock species. The genomic sequence as well as linkage maps have gaps that hamper their use in rabbit genome research. Therefore, the aims of this study were the improvement of existing linkage maps and the mapping of quantitative trait loci (QTL) for carcass and meat quality traits. The study was performed in a F2 population of an initial cross between Giant Grey (GG) and New Zealand White (NZW) rabbits. The population consisted of 363 F2 animals derived from 9 F1 bucks and 33 F1 does. 186 microsatellite and three SNP markers were informative for mapping. Out of 189 markers, which could be assigned to linkage groups, 110 markers were genetically mapped for the first time. The average marker distance was 7.8 cM. The map across all autosomes reached a total length of 1419 cM. The maternal linkage map was 1.4 times longer than the paternal. All linkage groups could be anchored to chromosomes. On the basis of the generated genetic map, we identified a highly significant QTL (genome-wide significance p < 0.01) for different carcass weights on chromosome 7 with a peak position at 91 cM (157 Mb), a significant QTL (p < 0.05) for bone mass on chromosome 9 at 61 cM (65 Mb), and another one for drip loss on chromosome 12 at 94 cM (128 Mb). Additional suggestive QTL were found on almost all chromosomes. Several genomic loci affecting the fore, intermediate and hind parts of the carcass were identified. The identified QTL explain between 2.5 to 14.6% of the phenotypic variance in the F2 population. The results present the most comprehensive genetic map and the first genome-wide QTL mapping study for carcass and meat quality traits in rabbits. The identified QTL, in particular the major QTL on chromosome 7, provide starting points for fine mapping and candidate gene search. The data contribute to linking physical and genetic information in the rabbit genome.

  18. Multi-environment multi-QTL association mapping identifies disease resistance QTL in barley germplasm from Latin America.

    PubMed

    Gutiérrez, Lucia; Germán, Silvia; Pereyra, Silvia; Hayes, Patrick M; Pérez, Carlos A; Capettini, Flavio; Locatelli, Andres; Berberian, Natalia M; Falconi, Esteban E; Estrada, Rigoberto; Fros, Dario; Gonza, Victor; Altamirano, Hernan; Huerta-Espino, Julio; Neyra, Edgar; Orjeda, Gisella; Sandoval-Islas, Sergio; Singh, Ravi; Turkington, Kelly; Castro, Ariel J

    2015-03-01

    Multi-environment multi-QTL mixed models were used in a GWAS context to identify QTL for disease resistance. The use of mega-environments aided the interpretation of environment-specific and general QTL. Diseases represent a major constraint for barley (Hordeum vulgare L.) production in Latin America. Spot blotch (caused by Cochliobolus sativus), stripe rust (caused by Puccinia striiformis f.sp. hordei) and leaf rust (caused by Puccinia hordei) are three of the most important diseases that affect the crop in the region. Since fungicide application is not an economically or environmentally sound solution, the development of durably resistant varieties is a priority for breeding programs. Therefore, new resistance sources are needed. The objective of this work was to detect genomic regions associated with field level plant resistance to spot blotch, stripe rust, and leaf rust in Latin American germplasm. Disease severities measured in multi-environment trials across the Americas and 1,096 SNPs in a population of 360 genotypes were used to identify genomic regions associated with disease resistance. Optimized experimental design and spatial modeling were used in each trial to estimate genotypic means. Genome-Wide Association Mapping (GWAS) in each environment was used to detect Quantitative Trait Loci (QTL). All significant environment-specific QTL were subsequently included in a multi-environment-multi-QTL (MEMQ) model. Geographical origin and inflorescence type were the main determinants of population structure. Spot blotch severity was low to intermediate while leaf and stripe rust severity was high in all environments. Mega-environments were defined by locations for spot blotch and leaf rust. Significant marker-trait associations for spot blotch (9 QTL), leaf (6 QTL) and stripe rust (7 QTL) and both global and environment-specific QTL were detected that will be useful for future breeding efforts.

  19. Resisting anchoring effects: The roles of metric and mapping knowledge.

    PubMed

    Smith, Andrew R; Windschitl, Paul D

    2015-10-01

    The biasing influence of anchors on numerical estimates is well established, but the relationship between knowledge level and the susceptibility to anchoring effects is less clear. In two studies, we addressed the potential mitigating effects of having knowledge in a domain on vulnerability to anchoring effects in that domain. Of critical interest was a distinction between two forms of knowledge-metric and mapping knowledge. In Study 1, participants who had studied question-relevant information-that is, high-knowledge participants-were less influenced by anchors than were participants who had studied irrelevant information. The results from knowledge measures suggested that the reduction in anchoring was tied to increases in metric rather than mapping knowledge. In Study 2, participants studied information specifically designed to influence different types of knowledge. As we predicted, increases in metric knowledge-and not mapping knowledge-led to reduced anchoring effects. Implications for debiasing anchoring effects are discussed.

  20. An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

    PubMed Central

    Peng, Wenzhu; Xu, Jian; Zhang, Yan; Feng, Jianxin; Dong, Chuanju; Jiang, Likun; Feng, Jingyan; Chen, Baohua; Gong, Yiwen; Chen, Lin; Xu, Peng

    2016-01-01

    High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly. PMID:27225429

  1. FastMap: Fast eQTL mapping in homozygous populations

    PubMed Central

    Gatti, Daniel M.; Shabalin, Andrey A.; Lam, Tieu-Chong; Wright, Fred A.; Rusyn, Ivan; Nobel, Andrew B.

    2009-01-01

    Motivation: Gene expression Quantitative Trait Locus (eQTL) mapping measures the association between transcript expression and genotype in order to find genomic locations likely to regulate transcript expression. The availability of both gene expression and high-density genotype data has improved our ability to perform eQTL mapping in inbred mouse and other homozygous populations. However, existing eQTL mapping software does not scale well when the number of transcripts and markers are on the order of 105 and 105–106, respectively. Results: We propose a new method, FastMap, for fast and efficient eQTL mapping in homozygous inbred populations with binary allele calls. FastMap exploits the discrete nature and structure of the measured single nucleotide polymorphisms (SNPs). In particular, SNPs are organized into a Hamming distance-based tree that minimizes the number of arithmetic operations required to calculate the association of a SNP by making use of the association of its parent SNP in the tree. FastMap's tree can be used to perform both single marker mapping and haplotype association mapping over an m-SNP window. These performance enhancements also permit permutation-based significance testing. Availability: The FastMap program and source code are available at the website: http://cebc.unc.edu/fastmap86.html Contact: iir@unc.edu; nobel@email.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19091771

  2. Region-based and pathway-based QTL mapping using a p-value combination method.

    PubMed

    Yang, Hsin-Chou; Chen, Chia-Wei

    2011-11-29

    Quantitative trait locus (QTL) mapping using deep DNA sequencing data is a challenging task. In this study we performed region-based and pathway-based QTL mappings using a p-value combination method to analyze the simulated quantitative traits Q1 and Q4 and the exome sequencing data. The aims were to evaluate the performance of the QTL mapping approaches that were used and to suggest plausible strategies for QTL mapping of DNA sequencing data. We conducted single-locus QTL mappings using a linear regression model with adjustments for age and smoking status, and we also conducted region-based and pathway-based QTL mappings using a truncated product method for combining p-values from the single-locus QTL mapping. To account for the features of rare variants and common single-nucleotide polymorphisms (SNPs), we considered independently rare-variant-only, common-SNP-only, and combined analyses. An analysis of 200 simulated replications showed that the three region-based methods reasonably controlled type I error, whereas the combined analysis yielded the greatest statistical power. Rare-variant-only, common-SNP-only, and combined analyses were also applied to pathway-based QTL mappings. We found that pathway-based QTL mappings had a power of approximately 100% when the significance of the vascular endothelial growth factor pathway was evaluated, but type I errors were slightly inflated. Our approach complements single-locus QTL mapping. An integrated approach using single-locus, combined region-based, and combined pathway-based analyses should yield promising results for QTL mapping of DNA sequencing data.

  3. Conditional QTL mapping of protein content in wheat with respect to grain yield and its components.

    PubMed

    Wang, Lin; Cui, Fa; Wang, Jinping; Jun, Li; Ding, Anming; Zhao, Chunhua; Li, Xingfeng; Feng, Deshun; Gao, Jurong; Wang, Honggang

    2012-01-01

    Grain protein content in wheat (Triticum aestivum L.) is generally considered a highly heritable character that is negatively correlated with grain yield and yield-related traits. Quantitative trait loci (QTL) for protein content was mapped using data on protein content and protein content conditioned on the putatively interrelated traits to evaluate possible genetic interrelationships between protein content and yield, as well as yield-related traits. Phenotypic data were evaluated in a recombinant inbred line population with 302 lines derived from a cross between the Chinese cultivar Weimai 8 and Luohan 2. Inclusive composite interval mapping using IciMapping 3.0 was employed for mapping unconditional and conditional QTL with additives. A strong genetic relationship was found between protein content and grain yield, and yield-related traits. Unconditional QTL mapping analysis detected seven additive QTL for protein content, with additive effects ranging in absolute size from 0.1898% to 0.3407% protein content, jointly accounting for 43.45% of the trait variance. Conditional QTL mapping analysis indicated two QTL independent from yield, which can be used in marker-assisted selection for increasing yield without affecting grain protein content. Three additional QTL with minor effects were identified in the conditional mapping. Of the three QTLs, two were identified when protein content was conditioned on yield, which had pleiotropic effects on those two traits. Conditional QTL mapping can be used to dissect the genetic interrelationship between two traits at the individual QTL level for closely correlated traits. Further, conditional QTL mapping can reveal additional QTL with minor effects that are undetectable in unconditional mapping.

  4. 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...

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

    PubMed

    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

  6. 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

  7. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

    PubMed Central

    Fulop, Daniel; Ranjan, Aashish; Ofner, Itai; Covington, Michael F.; Chitwood, Daniel H.; West, Donelly; Ichihashi, Yasunori; Headland, Lauren; Zamir, Daniel; Maloof, Julin N.; Sinha, Neelima R.

    2016-01-01

    Quantitative Trait Loci (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as the S. pennellii Introgression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping. PMID:27510891

  8. QTL mapping of clubroot resistance in radish (Raphanus sativus L.).

    PubMed

    Kamei, Akito; Tsuro, Masato; Kubo, Nakao; Hayashi, Takeshi; Wang, Ning; Fujimura, Tatsuhito; Hirai, Masashi

    2010-03-01

    A QTL analysis for clubroot resistance (CR) of radish was performed using an F(2) population derived from a crossing of a CR Japanese radish and a clubroot-susceptible (CS) Chinese radish. F(3) plants obtained by selfing of F(2) plants were used for the CR tests. The potted seedlings were inoculated and the symptom was evaluated 6 weeks thereafter. The mean disease indexes of the F(3) plants were used for the phenotype of the F(2). The results of two CR tests were analyzed for the presence of QTL. A linkage map was constructed using AFLP and SSR markers; it spanned 554 cM and contained 18 linkage groups. A CR locus was observed in the top region of linkage group 1 in two tests. Therefore, the present results suggest that a large part of radish CR is controlled by a single gene or closely linked genes in this radish population, although minor effects of other genomic areas cannot be ruled out. The CR locus was named Crs1. Markers linked to Crs1 showed sequence homology to the genomic region of the top of chromosome 3 of Arabidopsis, as in the case of Crr3, a CR locus in Brassica rapa. These markers should be useful for breeding CR cultivars of radish. As Japanese radishes are known to be highly resistant or immune to clubroot, these markers may also be useful in the introgression of this CR gene to Brassica crops.

  9. QTL mapping under truncation selection in homozygous lines derived from biparental crosses.

    PubMed

    Melchinger, Albrecht E; Orsini, Elena; Schön, Chris C

    2012-02-01

    In plant breeding, a large number of progenies that will be discarded later in the breeding process must be phenotyped and marker genotyped for conducting QTL analysis. In many cases, phenotypic preselection of lines could be useful. However, in QTL analyses even moderate preselection can have a significant effect on the power of QTL detection and estimation of effects of the target traits. In this study, we provide exact formulas for quantifying the change of allele frequencies within marker classes, expectations of marker contrasts and the variance of the marker contrasts under truncation selection, for the general case of two QTL affecting the target trait and a correlated trait. We focused on homozygous lines derived at random from biparental crosses. The effects of linkage between the marker and the QTL under selection as well as the effect of selection on a correlated trait can be quantified with the given formulas. Theoretical results clearly show that depending on the magnitude of QTL effects, high selection intensities can lead to a dramatic reduction in power of QTL detection and that approximations based on the infinitesimal model deviate substantially from exact solutions. The presented formulas are valuable for choosing appropriate selection intensity when performing QTL mapping experiments on the data on phenotypically preselected traits and enable the calculation and bias correction of the effects of QTL under selection. Application of our theory to experimental data revealed that selection-induced bias of QTL effects can be successfully corrected.

  10. QTL mapping of physiological traits associated with salt tolerance in Medicago truncatula Recombinant Inbred Lines.

    PubMed

    Arraouadi, Soumaya; Badri, Mounawer; Abdelly, Chedly; Huguet, Thierry; Aouani, Mohamed Elarbi

    2012-02-01

    In this study, QTL mapping of physiological traits in the model Legume (Medicago truncatula) was performed using a set of RILs derived from LR5. Twelve parameters associated with Na+ and K+ content in leaves, stems and roots were measured. Broad-sense heritability of these traits was ranged from 0.15 to 0.83 in control and from 0.14 to 0.61 in salt stress. Variation among RILs was dependent on line, treatment and line by treatment effect. We mapped 6 QTLs in control, 2 in salt stress and 5 for sensitivity index. No major QTL was identified indicating that tolerance to salt stress is governed by several genes with low effects. Detected QTL for leaf, stem and root traits did not share the same map locations, suggesting that genes controlling transport of Na+ and K+ may be different. The maximum of QTL was observed on chromosome 1, no QTL was detected on chromosomes 5 and 6.

  11. A consensus linkage map of oil palm and a major QTL for stem height.

    PubMed

    Lee, May; Xia, Jun Hong; Zou, Zhongwei; Ye, Jian; Rahmadsyah; Alfiko, Yuzer; Jin, Jingjing; Lieando, Jessica Virginia; Purnamasari, Maria Indah; Lim, Chin Huat; Suwanto, Antonius; Wong, Limsoon; Chua, Nam-Hai; Yue, Gen Hua

    2015-02-04

    Oil palm (Elaeis guinensis Jacquin) is the most important source of vegetable oil and fat. Several linkage maps had been constructed using dominant and co-dominant markers to facilitate mapping of QTL. However, dominant markers are not easily transferable among different laboratories. We constructed a consensus linkage map for oil palm using co-dominant markers (i.e. microsatellite and SNPs) and two F1 breeding populations generated by crossing Dura and Pisifera individuals. Four hundreds and forty-four microsatellites and 36 SNPs were mapped onto 16 linkage groups. The map length was 1565.6 cM, with an average marker space of 3.72 cM. A genome-wide scan of QTL identified a major QTL for stem height on the linkage group 5, which explained 51% of the phenotypic variation. Genes in the QTL were predicted using the palm genome sequence and bioinformatic tools. The linkage map supplies a base for mapping QTL for accelerating the genetic improvement, and will be also useful in the improvement of the assembly of the genome sequences. Markers linked to the QTL may be used in selecting dwarf trees. Genes within the QTL will be characterized to understand the mechanisms underlying dwarfing.

  12. A consensus linkage map of oil palm and a major QTL for stem height

    PubMed Central

    Lee, May; Xia, Jun Hong; Zou, Zhongwei; Ye, Jian; Rahmadsyah; Alfiko, Yuzer; Jin, Jingjing; Lieando, Jessica Virginia; Purnamasari, Maria Indah; Lim, Chin Huat; Suwanto, Antonius; Wong, Limsoon; Chua, Nam-Hai; Yue, Gen Hua

    2015-01-01

    Oil palm (Elaeis guinensis Jacquin) is the most important source of vegetable oil and fat. Several linkage maps had been constructed using dominant and co-dominant markers to facilitate mapping of QTL. However, dominant markers are not easily transferable among different laboratories. We constructed a consensus linkage map for oil palm using co-dominant markers (i.e. microsatellite and SNPs) and two F1 breeding populations generated by crossing Dura and Pisifera individuals. Four hundreds and forty-four microsatellites and 36 SNPs were mapped onto 16 linkage groups. The map length was 1565.6 cM, with an average marker space of 3.72 cM. A genome-wide scan of QTL identified a major QTL for stem height on the linkage group 5, which explained 51% of the phenotypic variation. Genes in the QTL were predicted using the palm genome sequence and bioinformatic tools. The linkage map supplies a base for mapping QTL for accelerating the genetic improvement, and will be also useful in the improvement of the assembly of the genome sequences. Markers linked to the QTL may be used in selecting dwarf trees. Genes within the QTL will be characterized to understand the mechanisms underlying dwarfing. PMID:25648560

  13. Mapping QTL conferring resistance in maize to gray leaf spot disease caused by Cercospora zeina

    PubMed Central

    2014-01-01

    Background Gray leaf spot (GLS) is a globally important foliar disease of maize. Cercospora zeina, one of the two fungal species that cause the disease, is prevalent in southern Africa, China, Brazil and the eastern corn belt of the USA. Identification of QTL for GLS resistance in subtropical germplasm is important to support breeding programmes in developing countries where C. zeina limits production of this staple food crop. Results A maize RIL population (F7:S6) from a cross between CML444 and SC Malawi was field-tested under GLS disease pressure at five field sites over three seasons in KwaZulu-Natal, South Africa. Thirty QTL identified from eleven field trials (environments) were consolidated to seven QTL for GLS resistance based on their expression in at least two environments and location in the same core maize bins. Four GLS resistance alleles were derived from the more resistant parent CML444 (bin 1.10, 4.08, 9.04/9.05, 10.06/10.07), whereas the remainder were from SC Malawi (bin 6.06/6.07, 7.02/7.03, 9.06). QTLs in bin 4.08 and bin 6.06/6.07 were also detected as joint QTLs, each explained more than 11% of the phenotypic variation, and were identified in four and seven environments, respectively. Common markers were used to allocate GLS QTL from eleven previous studies to bins on the IBM2005 map, and GLS QTL “hotspots” were noted. Bin 4.08 and 7.02/7.03 GLS QTL from this study overlapped with hotspots, whereas the bin 6.06/6.07 and bin 9.06 QTLs appeared to be unique. QTL for flowering time (bin 1.07, 4.09) in this population did not correspond to QTL for GLS resistance. Conclusions QTL mapping of a RIL population from the subtropical maize parents CML444 and SC Malawi identified seven QTL for resistance to gray leaf spot disease caused by C. zeina. These QTL together with QTL from eleven studies were allocated to bins on the IBM2005 map to provide a basis for comparison. Hotspots of GLS QTL were identified on chromosomes one, two, four, five and

  14. Genome mapping by random anchoring: A discrete theoretical analysis

    NASA Astrophysics Data System (ADS)

    Zhang, M. Q.; Marr, T. G.

    1993-11-01

    As a part of the international human genome project, large-scale genomic maps of human and other model organisms are being generated. More recently, mapping using various anchoring (as opposed to the traditional "fingerprinting") strategies have been proposed based largely on mathematical models. In all of the theoretical work dealing with anchoring, an anchor has been idealized as a point on a continuous, infinite-length genome. In general, it is not desirable to make these assumptions, since in practice they may be violated under a variety of actual biological situations. Here we analyze a discrete model that can be used to predict the expected progress made when mapping by random anchoring. By virtue of keeping all three length scales (genome length, clone length, and probe length) finite, our results for the random anchoring strategy are derived in full generality, which contain previous results as special cases and hence can have broad application for planning mapping experiments or assessing the accuracy of the continuum models. Finally, we pose a challenging nonrandom anchoring model corresponding to a more efficient mapping scheme.

  15. QTL Mapping of Flowering and Fruiting Traits in Olive

    PubMed Central

    Sadok, Inès Ben; Celton, Jean-Marc; Essalouh, Laila; El Aabidine, Amal Zine; Garcia, Gilbert; Martinez, Sebastien; Grati-Kamoun, Naziha; Rebai, Ahmed; Costes, Evelyne; Khadari, Bouchaib

    2013-01-01

    One of the challenge fruit growers are facing is to balance between tree production and vegetative growth from year to year. To investigate the existence of genetic determinism for reproductive behaviour in olive tree, we studied an olive segregating population derived from a cross between ‘Olivière’ and ‘Arbequina’ cultivars. Our strategy was based on (i) an annual assessment of individual trees yield, and (ii) a decomposition of adult growth units at the crown periphery into quantitative variables related to both flowering and fruiting process in relation to their growth and branching. Genetic models, including the year, genotype effects and their interactions, were built with variance function and correlation structure of residuals when necessary. Among the progeny, trees were either ‘ON’ or ‘OFF’ for a given year and patterns of regular vs. irregular bearing were revealed. Genotype effect was significant on yield but not for flowering traits at growth unit (GU) scale, whereas the interaction between genotype and year was significant for both traits. A strong genetic effect was found for all fruiting traits without interaction with the year. Based on the new constructed genetic map, QTLs with small effects were detected, revealing multigenic control of the studied traits. Many were associated to alleles from ‘Arbequina’. Genetic correlations were found between Yield and Fruit set at GU scale suggesting a common genetic control, even though QTL co-localisations were in spe`cific years only. Most QTL were associated to flowering traits in specific years, even though reproductive traits at GU scale did not capture the bearing status of the trees in a given year. Results were also interpreted with respect to ontogenetic changes of growth and branching, and an alternative sampling strategy was proposed for capturing tree fruiting behaviour. Regular bearing progenies were identified and could constitute innovative material for selection programs

  16. Inclusive Composite Interval Mapping of QTL by Environment Interactions in Biparental Populations.

    PubMed

    Li, Shanshan; Wang, Jiankang; Zhang, Luyan

    2015-01-01

    Identification of environment-specific QTL and stable QTL having consistent genetic effects across a wide range of environments is of great importance in plant breeding. Inclusive Composite Interval Mapping (ICIM) has been proposed for additive, dominant and epistatic QTL mapping in biparental populations for single environment. In this study, ICIM was extended to QTL by environment interaction (QEI) mapping for multi-environmental trials, where the QTL average effect and QEI effects could be properly estimated. Stepwise regression was firstly applied in each environment to identify the most significant marker variables which were then used to adjust the phenotypic values. One-dimensional scanning was then conducted on the adjusted phenotypic values across the environments in order to detect QTL with either average effect or QEI effects, or both average effect and QEI effects. In this way, the genetic background could be well controlled while the conventional interval mapping was applied. An empirical method to determine the threshold of logarithm of odds was developed, and the efficiency of the ICIM QEI mapping was demonstrated in simulated populations under different genetic models. One actual recombinant inbred line population was used to compare mapping results between QEI mapping and single-environment analysis.

  17. Inclusive Composite Interval Mapping of QTL by Environment Interactions in Biparental Populations

    PubMed Central

    Li, Shanshan; Wang, Jiankang; Zhang, Luyan

    2015-01-01

    Identification of environment-specific QTL and stable QTL having consistent genetic effects across a wide range of environments is of great importance in plant breeding. Inclusive Composite Interval Mapping (ICIM) has been proposed for additive, dominant and epistatic QTL mapping in biparental populations for single environment. In this study, ICIM was extended to QTL by environment interaction (QEI) mapping for multi-environmental trials, where the QTL average effect and QEI effects could be properly estimated. Stepwise regression was firstly applied in each environment to identify the most significant marker variables which were then used to adjust the phenotypic values. One-dimensional scanning was then conducted on the adjusted phenotypic values across the environments in order to detect QTL with either average effect or QEI effects, or both average effect and QEI effects. In this way, the genetic background could be well controlled while the conventional interval mapping was applied. An empirical method to determine the threshold of logarithm of odds was developed, and the efficiency of the ICIM QEI mapping was demonstrated in simulated populations under different genetic models. One actual recombinant inbred line population was used to compare mapping results between QEI mapping and single-environment analysis. PMID:26161656

  18. Genetic linkage map construction and QTL mapping of cadmium accumulation in radish (Raphanus sativus L.).

    PubMed

    Xu, Liang; Wang, Liangju; Gong, Yiqin; Dai, Wenhao; Wang, Yan; Zhu, Xianwen; Wen, Tiancai; Liu, Liwang

    2012-08-01

    Cadmium (Cd) is a widespread soil pollutant and poses a significant threat to human health via the food chain. Large phenotypic variations in Cd concentration of radish roots and shoots have been observed. However, the genetic and molecular mechanisms of Cd accumulation in radish remain to be elucidated. In this study, a genetic linkage map was constructed using an F(2) mapping population derived from a cross between a high Cd-accumulating cultivar NAU-Dysx and a low Cd-accumulating cultivar NAU-Yh. The linkage map consisted of 523 SRAP, RAPD, SSR, ISSR, RAMP, and RGA markers and had a total length of 1,678.2 cM with a mean distance of 3.4 cM between two markers. All mapped markers distributed on nine linkage groups (LGs) having sizes between 134.7 and 236.8 cM. Four quantitative trait loci (QTLs) for root Cd accumulation were mapped on LGs 1, 4, 6, and 9, which accounted for 9.86 to 48.64 % of all phenotypic variance. Two QTLs associated with shoot Cd accumulation were detected on LG1 and 3, which accounted for 17.08 and 29.53 % of phenotypic variance, respectively. A major-effect QTL, qRCd9 (QTL for root Cd accumulation on LG9), was identified on LG 9 flanked by NAUrp011_754 and EM5me6_286 markers with a high LOD value of 23.6, which accounted for 48.64 % of the total phenotypic variance in Cd accumulation of F(2) lines. The results indicated that qRCd9 is a novel QTL responsible for controlling root Cd accumulation in radish, and the identification of specific molecular markers tightly linked to the major QTL could be further applied for marker-assisted selection (MAS) in low-Cd content radish breeding program.

  19. A statistical framework for eQTL mapping using RNA-seq data.

    PubMed

    Sun, Wei

    2012-03-01

    RNA-seq may replace gene expression microarrays in the near future. Using RNA-seq, the expression of a gene can be estimated using the total number of sequence reads mapped to that gene, known as the total read count (TReC). Traditional expression quantitative trait locus (eQTL) mapping methods, such as linear regression, can be applied to TReC measurements after they are properly normalized. In this article, we show that eQTL mapping, by directly modeling TReC using discrete distributions, has higher statistical power than the two-step approach: data normalization followed by linear regression. In addition, RNA-seq provides information on allele-specific expression (ASE) that is not available from microarrays. By combining the information from TReC and ASE, we can computationally distinguish cis- and trans-eQTL and further improve the power of cis-eQTL mapping. Both simulation and real data studies confirm the improved power of our new methods. We also discuss the design issues of RNA-seq experiments. Specifically, we show that by combining TReC and ASE measurements, it is possible to minimize cost and retain the statistical power of cis-eQTL mapping by reducing sample size while increasing the number of sequence reads per sample. In addition to RNA-seq data, our method can also be employed to study the genetic basis of other types of sequencing data, such as chromatin immunoprecipitation followed by DNA sequencing data. In this article, we focus on eQTL mapping of a single gene using the association-based method. However, our method establishes a statistical framework for future developments of eQTL mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. © 2011, The International Biometric Society.

  20. QTL mapping of powdery mildew resistance in WI 2757 cucumber (Cucumis sativus L.).

    PubMed

    He, Xiaoming; Li, Yuhong; Pandey, Sudhakar; Yandell, Brain S; Pathak, Mamta; Weng, Yiqun

    2013-08-01

    Powdery mildew (PM) is a very important disease of cucumber (Cucumis sativus L.). Resistant cultivars have been deployed in production for a long time, but the genetic mechanisms of PM resistance in cucumber are not well understood. A 3-year QTL mapping study of PM resistance was conducted with 132 F2:3 families derived from two cucumber inbred lines WI 2757 (resistant) and True Lemon (susceptible). A genetic map covering 610.4 cM in seven linkage groups was developed with 240 SSR marker loci. Multiple QTL mapping analysis of molecular marker data and disease index of the hypocotyl, cotyledon and true leaf for responses to PM inoculation identified six genomic regions in four chromosomes harboring QTL for PM resistance in WI 2757. Among the six QTL, pm1.1 and pm1.2 in chromosome 1 conferred leaf resistance. Minor QTL pm3.1 (chromosome 3) and pm4.1 (chromosome 4) contributed to disease susceptibility. The two major QTL, pm5.1 and pm5.2 were located in an interval of ~40 cM in chromosome 5 with each explaining 21.0-74.5 % phenotypic variations. Data presented herein support two recessively inherited, linked major QTL in chromosome 5 plus minor QTL in other chromosomes that control the PM resistance in WI 2757. The QTL pm5.2 for hypocotyl resistance plays the most important role in host resistance. Multiple observations in the same year revealed the importance of scoring time in the detection of PM resistance QTL. Results of this study provided new insights into phenotypic and genetic mechanisms of powdery mildew resistance in cucumber.

  1. A new simple method for improving QTL mapping under selective genotyping.

    PubMed

    Lee, Hsin-I; Ho, Hsiang-An; Kao, Chen-Hung

    2014-12-01

    The selective genotyping approach, where only individuals from the high and low extremes of the trait distribution are selected for genotyping and the remaining individuals are not genotyped, has been known as a cost-saving strategy to reduce genotyping work and can still maintain nearly equivalent efficiency to complete genotyping in QTL mapping. We propose a novel and simple statistical method based on the normal mixture model for selective genotyping when both genotyped and ungenotyped individuals are fitted in the model for QTL analysis. Compared to the existing methods, the main feature of our model is that we first provide a simple way for obtaining the distribution of QTL genotypes for the ungenotyped individuals and then use it, rather than the population distribution of QTL genotypes as in the existing methods, to fit the ungenotyped individuals in model construction. Another feature is that the proposed method is developed on the basis of a multiple-QTL model and has a simple estimation procedure similar to that for complete genotyping. As a result, the proposed method has the ability to provide better QTL resolution, analyze QTL epistasis, and tackle multiple QTL problem under selective genotyping. In addition, a truncated normal mixture model based on a multiple-QTL model is developed when only the genotyped individuals are considered in the analysis, so that the two different types of models can be compared and investigated in selective genotyping. The issue in determining threshold values for selective genotyping in QTL mapping is also discussed. Simulation studies are performed to evaluate the proposed methods, compare the different models, and study the QTL mapping properties in selective genotyping. The results show that the proposed method can provide greater QTL detection power and facilitate QTL mapping for selective genotyping. Also, selective genotyping using larger genotyping proportions may provide roughly equivalent power to complete

  2. Genetic analysis of arsenic accumulation in maize using QTL mapping

    PubMed Central

    Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

    2016-01-01

    Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars. PMID:26880701

  3. Genetic analysis of arsenic accumulation in maize using QTL mapping.

    PubMed

    Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

    2016-02-16

    Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars.

  4. Genetic analysis of arsenic accumulation in maize using QTL mapping

    NASA Astrophysics Data System (ADS)

    Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

    2016-02-01

    Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars.

  5. QTL mapping for combining ability in different population-based NCII designs: a simulation study.

    PubMed

    Li, Lanzhi; Sun, Congwei; Chen, Yuan; Dai, Zhijun; Qu, Zhen; Zheng, Xingfei; Yu, Sibin; Mou, Tongmin; Xu, Chenwu; Hu, Zhongli

    2013-12-01

    The NCII design (North Carolina mating design II) has been widely applied in studies of combining ability and heterosis. The objective of our research was to estimate how different base populations, sample sizes, testcross numbers and heritability influence QTL analyses of combining ability and heterosis. A series of Monte Carlo simulation experiments with QTL mapping were then conducted for the base population performance, testcross population phenotypic values and the general combining ability (GCA), specific combining ability (SCA) and Hmp (midparental heterosis) datasets. The results indicated that: (i) increasing the number of testers did not necessarily enhance the QTL detection power for GCA, but it was significantly related to the QTL effect. (ii) The QTLs identified in the base population may be different from those from GCA dataset. Similar phenomena can be seen from QTL detected in SCA and Hmp datasets. (iii) The QTL detection power for GCA ranked in the order of DH(RIL) based > F2 based > BC based NCII design, when the heritability was low. The recombinant inbred lines (RILs) (or DHs) allows more recombination and offers higher mapping resolution than other populations. Further, their testcross progeny can be repeatedly generated and phenotyped. Thus, RIL based (or DH based) NCII design was highly recommend for combining ability QTL analysis. Our results expect to facilitate selecting elite parental lines with high combining ability and for geneticists to research the genetic basis of combining ability.

  6. Molecular mapping in oil radish (Raphanus sativus L.) and QTL analysis of resistance against beet cyst nematode (Heterodera schachtii).

    PubMed

    Budahn, Holger; Peterka, Herbert; Mousa, Magdi Ali Ahmed; Ding, Yunhua; Zhang, Shaosong; Li, Jinbin

    2009-02-01

    The beet cyst nematode (Heterodera schachtii Schmidt) can be controlled biologically in highly infected soils of sugar beet rotations using resistant varieties of oil radish (Raphanus sativus L. ssp. oleiferus DC.) as a green crop. Resistant plants stimulate infective juveniles to invade roots, but prevent them after their penetration to complete the life cycle. The resistance trait has been transferred successfully to susceptible rapeseed by the addition of a complete radish chromosome. The aim of the study was to construct a genetic map for radish and to develop resistance-associated markers. The map with 545 RAPD, dpRAPD, AFLP and SSR markers had a length of 1,517 cM, a mean distance of 2.8 cM and consisted of nine linkage groups having sizes between 120 and 232 cM. Chromosome-specific markers for the resistance-bearing chromosome d and the other eight radish chromosomes, developed previously from a series of rapeseed-radish addition lines, were enclosed as anchor markers. Each of the extra chromosomes in the addition lines could be unambiguously assigned to one of the radish linkage groups. The QTL analysis of nematode resistance was realized in the intraspecific F(2) mapping population derived from a cross between varieties 'Pegletta' (nematode resistant) x 'Siletta Nova' (susceptible). A dominant major QTL Hs1( Rph ) explaining 46.4% of the phenotypic variability was detected in a proximal position of chromosome d. Radish chromosome-specific anchor markers with known map positions were made available for future recombination experiments to incorporate segments carrying desired genes as Hs1( Rph ) from radish into rapeseed by means of chromosome addition lines.

  7. Selective Advance for Accelerated Development of Recombinant Inbred QTL Mapping Populations

    USDA-ARS?s Scientific Manuscript database

    Recombinant inbred lines, conventionally used for QTL mapping in biparental populations of self-pollinating plant species, afford limited mapping resolution. Intercrossing during line development is sometimes used to counter this disadvantage, but is tedious. It is desirable to improve mapping resol...

  8. Fine Mapping and Evolution of a QTL Region on Cattle Chromosome 3

    ERIC Educational Resources Information Center

    Donthu, Ravikiran

    2009-01-01

    The goal of my dissertation was to fine map the milk yield and composition quantitative trait loci (QTL) mapped to cattle chromosome 3 (BTA3) by Heyen et al. (1999) and to identify candidate genes affecting these traits. To accomplish this, the region between "BL41" and "TGLA263" was mapped to the cattle genome sequence assembly Btau 3.1 and a…

  9. Fine Mapping and Evolution of a QTL Region on Cattle Chromosome 3

    ERIC Educational Resources Information Center

    Donthu, Ravikiran

    2009-01-01

    The goal of my dissertation was to fine map the milk yield and composition quantitative trait loci (QTL) mapped to cattle chromosome 3 (BTA3) by Heyen et al. (1999) and to identify candidate genes affecting these traits. To accomplish this, the region between "BL41" and "TGLA263" was mapped to the cattle genome sequence assembly Btau 3.1 and a…

  10. QTL mapping of freezing tolerance: links to fitness and adaptive trade-offs.

    PubMed

    Oakley, Christopher G; Ågren, Jon; Atchison, Rachel A; Schemske, Douglas W

    2014-09-01

    Local adaptation, defined as higher fitness of local vs. nonlocal genotypes, is commonly identified in reciprocal transplant experiments. Reciprocally adapted populations display fitness trade-offs across environments, but little is known about the traits and genes underlying fitness trade-offs in reciprocally adapted populations. We investigated the genetic basis and adaptive significance of freezing tolerance using locally adapted populations of Arabidopsis thaliana from Italy and Sweden. Previous reciprocal transplant studies of these populations indicated that subfreezing temperature is a major selective agent in Sweden. We used quantitative trait locus (QTL) mapping to identify the contribution of freezing tolerance to previously demonstrated local adaptation and genetic trade-offs. First, we compared the genomic locations of freezing tolerance QTL to those for previously published QTL for survival in Sweden, and overall fitness in the field. Then, we estimated the contributions to survival and fitness across both field sites of genotypes at locally adaptive freezing tolerance QTL. In growth chamber studies, we found seven QTL for freezing tolerance, and the Swedish genotype increased freezing tolerance for five of these QTL. Three of these colocalized with locally adaptive survival QTL in Sweden and with trade-off QTL for overall fitness. Two freezing tolerance QTL contribute to genetic trade-offs across environments for both survival and overall fitness. A major regulator of freezing tolerance, CBF2, is implicated as a candidate gene for one of the trade-off freezing tolerance QTL. Our study provides some of the first evidence of a trait and gene that mediate a fitness trade-off in nature. © 2014 John Wiley & Sons Ltd.

  11. QTL mapping for nine drought-responsive agronomic traits in bread wheat under irrigated and rain-fed environments.

    PubMed

    Gahlaut, Vijay; Jaiswal, Vandana; Tyagi, Bhudeva S; Singh, Gyanendra; Sareen, Sindhu; Balyan, Harindra S; Gupta, Pushpendra Kumar

    2017-01-01

    In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits. Two-locus analysis allowed detection of 19 main effect QTL (M-QTL) for four traits (days to anthesis, days to maturity, grain filling duration and thousand grain weight) and 19 pairs of epistatic QTL (E-QTL) for two traits (days to anthesis and thousand grain weight). Eight QTL were common in single locus analysis and two locus analysis. These QTL (identified both in single- and two-locus analysis) were distributed on 20 different chromosomes (except 4D). Important genomic regions on chromosomes 5A and 7A were also identified (5A carried QTL for seven traits and 7A carried QTL for six traits). Marker-assisted recurrent selection (MARS) involving pyramiding of important QTL reported in the present study, together with important QTL reported earlier, may be used for improvement of drought tolerance in wheat. In future, more closely linked markers for the QTL reported here may be developed through fine mapping, and the candidate genes may be identified and used for developing a better understanding of the genetic basis of drought tolerance in wheat.

  12. QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef.

    PubMed

    Zeid, M; Belay, G; Mulkey, S; Poland, J; Sorrells, M E

    2011-01-01

    Tef is a cereal crop of cultural and economic importance in Ethiopia. It is grown primarily for its grain though it is also an important source of fodder. Tef suffers from lodging that reduces both grain yield and quality. As a first step toward executing a marker-assisted breeding program for lodging resistance and grain yield improvement, a linkage map was constructed using 151 F(9) recombinant inbred lines obtained by single-seed-descent from a cross between Eragrostis tef and its wild relative Eragrostis pilosa. The map was primarily based on microsatellite (SSR) markers that were developed from SSR-enriched genomic libraries. The map consisted of 30 linkage groups and spanned a total length of 1,277.4 cM (78.7% of the genome) with an average distance of 5.7 cM between markers. This is the most saturated map for tef to date, and for the first time, all of the markers are PCR-based. Using agronomic data from 11 environments and marker data, it was possible to map quantitative trait loci (QTL) controlling lodging, grain yield and 15 other related traits. The positive effects of the QTL identified from the wild parent were mainly for earliness, reduced culm length and lodging resistance. In this population, it is now possible to combine lodging resistance and grain yield using a marker-assisted selection program targeting the QTL identified for both traits. The newly developed SSR markers will play a key role in germplasm organization, fingerprinting and monitoring the success of the hybridization process in intra-specific crosses lacking distinctive morphological markers.

  13. A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L.

    PubMed

    Liu, Liezhao; Qu, Cunmin; Wittkop, Benjamin; Yi, Bin; Xiao, Yang; He, Yajun; Snowdon, Rod J; Li, Jiana

    2013-01-01

    A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape) was constructed in a late-generation recombinant inbred line (RIL) population, using genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL), cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.

  14. A High-Density SNP Map for Accurate Mapping of Seed Fibre QTL in Brassica napus L

    PubMed Central

    Liu, Liezhao; Qu, Cunmin; Wittkop, Benjamin; Yi, Bin; Xiao, Yang; He, Yajun; Snowdon, Rod J.; Li, Jiana

    2013-01-01

    A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape) was constructed in a late-generation recombinant inbred line (RIL) population, using genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL), cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed. PMID:24386142

  15. Expression QTL mapping in grapevine--revisiting the genetic determinism of grape skin colour.

    PubMed

    Huang, Yung-Fen; Bertrand, Yves; Guiraud, Jean-Luc; Vialet, Sandrine; Launay, Amandine; Cheynier, Véronique; Terrier, Nancy; This, Patrice

    2013-06-01

    Expression quantitative locus (eQTL) mapping was proposed as a valuable approach to dissect the genetic basis of transcript variation, one of the prime causes of natural phenotypic variation. Few eQTL studies have been performed on woody species due to the difficulty in sample homogenisation. Based on previous knowledge on berry colour formation, we performed eQTL mapping in field experimentation of grapevine with appropriate sampling criteria. The transcript level of VvUFGT, a key enzyme for anthocyanin synthesis was measured by real-time qRT-PCR in grape berry on a 191-individual pseudo-F1 progeny, derived from a cross between Syrah and Grenache cultivars. Two eQTLs were identified: one, explaining 20%, of genotypic variance and co-locating with VvUFGT itself (cis-eQTL), was principally due to the contrast between Grenache alleles; the other, explaining 35% of genotypic variance, was a trans-eQTL due to Syrah allelic contrast and co-located with VvMYBAs, transcription factors known to activate the expression of VvUFGT. This study assessed and validated the feasibility of eQTL mapping approach in grapevine and offered insights and new hypotheses on grape skin colour formation.

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

    PubMed Central

    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. PMID:27176215

  17. 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.

  18. Mapping QTL for Seed Germinability under Low Temperature Using a New High-Density Genetic Map of Rice.

    PubMed

    Jiang, Ningfei; Shi, Shilai; Shi, Huan; Khanzada, Hira; Wassan, Ghulam M; Zhu, Changlan; Peng, Xiaosong; Yu, Qiuying; Chen, Xiaorong; He, Xiaopeng; Fu, Junru; Hu, Lifang; Xu, Jie; Ouyang, Linjuan; Sun, Xiaotang; Zhou, Dahu; He, Haohua; Bian, Jianmin

    2017-01-01

    Mapping major quantitative trait loci (QTL) responsible for rice seed germinability under low temperature (GULT) can provide valuable genetic source for improving cold tolerance in rice breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs) derived from a cross indica cv. Changhui 891 and japonica cv. 02428 were genotyped through re-sequencing technology. A bin map was generated which includes 3057 bins covering distance of 1266.5 cM with an average of 0.41 cM between markers. On the basis of newly constructed high-density genetic map, six QTL were detected ranging from 40 to 140 kb on Nipponbare genome. Among these, two QTL qCGR8 and qGRR11 alleles shared by 02428 could increase GULT and seed germination recovery rate after cold stress, respectively. However, qNGR1 and qNGR4 may be two major QTL affecting indica Changhui 891germination under normal condition. QTL qGRR1 and qGRR8 affected the seed germination recovery rate after cold stress and the alleles with increasing effects were shared by the Changhui 891 could improve seed germination rate after cold stress dramatically. These QTL could be a highly valuable genetic factors for cold tolerance improvement in rice lines. Moreover, the BRILs developed in this study will serve as an appropriate choice for mapping and studying genetic basis of rice complex traits.

  19. 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.

  20. An Empirical Method for Establishing Positional Confidence Intervals Tailored for Composite Interval Mapping of QTL

    PubMed Central

    Love, Tanzy M.

    2010-01-01

    Background Improved genetic resolution and availability of sequenced genomes have made positional cloning of moderate-effect QTL realistic in several systems, emphasizing the need for precise and accurate derivation of positional confidence intervals (CIs) for QTL. Support interval (SI) methods based on the shape of the QTL likelihood curve have proven adequate for standard interval mapping, but have not been shown to be appropriate for use with composite interval mapping (CIM), which is one of the most commonly used QTL mapping methods. Results Based on a non-parametric confidence interval (NPCI) method designed for use with the Haley-Knott regression method for mapping QTL, a CIM-specific method (CIM-NPCI) was developed to appropriately account for the selection of background markers during analysis of bootstrap-resampled data sets. Coverage probabilities and interval widths resulting from use of the NPCI, SI, and CIM-NPCI methods were compared in a series of simulations analyzed via CIM, wherein four genetic effects were simulated in chromosomal regions with distinct marker densities while heritability was fixed at 0.6 for a population of 200 isolines. CIM-NPCIs consistently capture the simulated QTL across these conditions while slightly narrower SIs and NPCIs fail at unacceptably high rates, especially in genomic regions where marker density is high, which is increasingly common for real studies. The effects of a known CIM bias toward locating QTL peaks at markers were also investigated for each marker density case. Evaluation of sub-simulations that varied according to the positions of simulated effects relative to the nearest markers showed that the CIM-NPCI method overcomes this bias, offering an explanation for the improved coverage probabilities when marker densities are high. Conclusions Extensive simulation studies herein demonstrate that the QTL confidence interval methods typically used to positionally evaluate CIM results can be dramatically improved

  1. Mapping Quantitative Trait Loci (QTL) for Resistance to Late Blight in Tomato.

    PubMed

    Panthee, Dilip R; Piotrowski, Ann; Ibrahem, Ragy

    2017-07-22

    Late blight caused by Phytophthora infestans (Montagne, Bary) is a devastating disease of tomato worldwide. There are three known major genes, Ph-1, Ph-2, and Ph-3, conferring resistance to late blight. In addition to these three genes, it is also believed that there are additional factors or quantitative trait loci (QTL) conferring resistance to late blight. Precise molecular mapping of all those major genes and potential QTL is important in the development of suitable molecular markers and hence, marker-assisted selection (MAS). The objective of the present study was to map the genes and QTL associated with late blight resistance in a tomato population derived from intra-specific crosses. To achieve this objective, a population, derived from the crossings of NC 1CELBR × Fla. 7775, consisting of 250 individuals at F2 and F2-derived families, were evaluated in replicated trials. These were conducted at Mountain Horticultural Crops Reseach & Extension Center (MHCREC) at Mills River, NC, and Mountain Research Staion (MRS) at Waynesville, NC in 2011, 2014, and 2015. There were two major QTL associated with late blight resistance located on chromosomes 9 and 10 with likelihood of odd (LOD) scores of more than 42 and 6, explaining 67% and 14% of the total phenotypic variation, respectively. The major QTLs are probably caused by the Ph-2 and Ph-3 genes. Furthermore, there was a minor QTL on chromosomes 12, which has not been reported before. This minor QTL may be novel and may be worth investigating further. Source of resistance to Ph-2, Ph-3, and this minor QTL traces back to line L3707, or Richter's Wild Tomato. The combination of major genes and minor QTL may provide a durable resistance to late blight in tomato.

  2. QTL mapping of grain weight in rice and the validation of the QTL qTGW3.2.

    PubMed

    Tang, Shao-qing; Shao, Gao-neng; Wei, Xiang-jin; Chen, Ming-liang; Sheng, Zhong-hua; Luo, Ju; Jiao, Gui-ai; Xie, Li-hong; Hu, Pei-song

    2013-09-15

    A recombinant inbred line (RIL) population bred from a cross between a javanica type (cv. D50) and an indica type (cv. HB277) rice was used to map seven quantitative trait loci (QTLs) for thousand grain weight (TGW). The loci were distributed on chromosomes 2, 3, 5, 6, 8 and 10. The chromosome 3 QTL qTGW3.2 was stably expressed over two years, and contributed 9-10% of the phenotypic variance. A residual heterozygous line (RHL) was selected from the RIL population and its selfed progeny was used to fine map qTGW3.2. In this "F2" population, the QTL explained about 23% of the variance, rising to nearly 33% in the subsequent "F2:3" generation. The physical location of qTGW3.2 was confined to a ~556 kb region flanked by the microsatellite loci RM16162 and RM16194. The region also contains other factors influencing certain yield-related traits, although it is also possible that qTGW3.2 affects these in a pleiotropic fashion.

  3. QTL mapping for two commercial traits in farmed saltwater crocodiles (Crocodylus porosus).

    PubMed

    Miles, L G; Isberg, S R; Thomson, P C; Glenn, T C; Lance, S L; Dalzell, P; Moran, C

    2010-04-01

    The recent generation of a genetic linkage map for the saltwater crocodile (Crocodylus porosus) has now made it possible to carry out the systematic searches necessary for the identification of quantitative trait loci (QTL) affecting traits of economic, as well as evolutionary, importance in crocodilians. In this study, we conducted genome-wide scans for two commercially important traits, inventory head length (which is highly correlated with growth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in a commercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Territory, Australia. To account for the uncommonly large difference in sex-specific recombination rates apparent in the saltwater crocodile, a duel mapping strategy was employed. This strategy employed a sib-pair analysis to take advantage of our full-sib pedigree structure, together with a half-sib analysis to account for, and take advantage of, the large difference in sex-specific recombination frequencies. Using these approaches, two putative QTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at 0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeed for any non-avian member of the Class Reptilia. Mapping of QTL is an important first step towards the identification of genes and causal mutations for commercially important traits and the development of selection tools for implementation in crocodile breeding programmes for the industry.

  4. In silico QTL mapping of basal liver iron levels in inbred mouse strains

    PubMed Central

    McLachlan, Stela; Lee, Seung-Min; Steele, Teresa M.; Hawthorne, Paula L.; Zapala, Matthew A.; Eskin, Eleazar; Schork, Nicholas J.; Anderson, Gregory J.

    2011-01-01

    Both iron deficiency and iron excess are detrimental in many organisms, and previous studies in both mice and humans suggest that genetic variation may influence iron status in mammals. However, these genetic factors are not well defined. To address this issue, we measured basal liver iron levels in 18 inbred strains of mice of both sexes on a defined iron diet and found ∼4-fold variation in liver iron in males (lowest 153 μg/g, highest 661 μg/g) and ∼3-fold variation in females (lowest 222 μg/g, highest 658 μg/g). We carried out a genome-wide association mapping to identify haplotypes underlying differences in liver iron and three other related traits (copper and zinc liver levels, and plasma diferric transferrin levels) in a subset of 14 inbred strains for which genotype information was available. We identified two putative quantitative trait loci (QTL) that contain genes with a known role in iron metabolism: Eif2ak1 and Igf2r. We also identified four putative QTL that reside in previously identified iron-related QTL and 22 novel putative QTL. The most promising putative QTL include a 0.22 Mb region on Chromosome 7 and a 0.32 Mb region on Chromosome 11 that both contain only one candidate gene, Adam12 and Gria1, respectively. Identified putative QTL are good candidates for further refinement and subsequent functional studies. PMID:21062905

  5. Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass

    PubMed Central

    Liu, Peng; Wang, Le; Wong, Sek-Man; Yue, Gen Hua

    2016-01-01

    Asian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression of Pcdhac2 was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance. PMID:27555039

  6. 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.

  7. QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

    PubMed Central

    Whitney, Kenneth D.; Broman, Karl W.; Kane, Nolan C.; Hovick, Stephen M.; Randell, Rebecca A.; Rieseberg, Loren H.

    2014-01-01

    The wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 SNP markers, and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological, and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favored in the wild. QTL for a number of other ecophysiological, phenological, and architectural traits co-localized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence. PMID:25522096

  8. A Random-Model Approach to QTL Mapping in Multiparent Advanced Generation Intercross (MAGIC) Populations.

    PubMed

    Wei, Julong; Xu, Shizhong

    2016-02-01

    Most standard QTL mapping procedures apply to populations derived from the cross of two parents. QTL detected from such biparental populations are rarely relevant to breeding programs because of the narrow genetic basis: only two alleles are involved per locus. To improve the generality and applicability of mapping results, QTL should be detected using populations initiated from multiple parents, such as the multiparent advanced generation intercross (MAGIC) populations. The greatest challenges of QTL mapping in MAGIC populations come from multiple founder alleles and control of the genetic background information. We developed a random-model methodology by treating the founder effects of each locus as random effects following a normal distribution with a locus-specific variance. We also fit a polygenic effect to the model to control the genetic background. To improve the statistical power for a scanned marker, we release the marker effect absorbed by the polygene back to the model. In contrast to the fixed-model approach, we estimate and test the variance of each locus and scan the entire genome one locus at a time using likelihood-ratio test statistics. Simulation studies showed that this method can increase statistical power and reduce type I error compared with composite interval mapping (CIM) and multiparent whole-genome average interval mapping (MPWGAIM). We demonstrated the method using a public Arabidopsis thaliana MAGIC population and a mouse MAGIC population.

  9. A Random-Model Approach to QTL Mapping in Multiparent Advanced Generation Intercross (MAGIC) Populations

    PubMed Central

    Wei, Julong; Xu, Shizhong

    2016-01-01

    Most standard QTL mapping procedures apply to populations derived from the cross of two parents. QTL detected from such biparental populations are rarely relevant to breeding programs because of the narrow genetic basis: only two alleles are involved per locus. To improve the generality and applicability of mapping results, QTL should be detected using populations initiated from multiple parents, such as the multiparent advanced generation intercross (MAGIC) populations. The greatest challenges of QTL mapping in MAGIC populations come from multiple founder alleles and control of the genetic background information. We developed a random-model methodology by treating the founder effects of each locus as random effects following a normal distribution with a locus-specific variance. We also fit a polygenic effect to the model to control the genetic background. To improve the statistical power for a scanned marker, we release the marker effect absorbed by the polygene back to the model. In contrast to the fixed-model approach, we estimate and test the variance of each locus and scan the entire genome one locus at a time using likelihood-ratio test statistics. Simulation studies showed that this method can increase statistical power and reduce type I error compared with composite interval mapping (CIM) and multiparent whole-genome average interval mapping (MPWGAIM). We demonstrated the method using a public Arabidopsis thaliana MAGIC population and a mouse MAGIC population. PMID:26715662

  10. An improved genetic model generates high-resolution mapping of QTL for protein quality in maize endosperm.

    PubMed

    Wu, Rongling; Lou, Xiang-Yang; Ma, Chang-Xing; Wang, Xuelu; Larkins, Brian A; Casella, George

    2002-08-20

    The genetic mapping of polymorphic markers in a cross between two inbred plant lines has proven to be a powerful method for detecting quantitative trait loci (QTL) underlying complex traits. However, existing methods of QTL mapping were developed for disomic inheritance of both marker and QTL loci in a diploid population. To map QTL influencing traits expressed in the endosperm, a triploid embryo-nourishing tissue resulting from double fertilization, existing QTL mapping models require modification to consider the trisomic inheritance of the endosperm and the generation difference between the mapping population and the endosperm. Such a model requires simultaneous use of two successive generations, which theoretically can lead to an increase in resolution for QTL mapping compared with the use of a single backcross or F(2) generation. Using a newly developed model based on these considerations, we demonstrate the improved resolution of QTL, influencing protein quality traits in maize endosperm. The increased resolution made possible with this approach makes identified QTL accessible to positional cloning.

  11. Identification and QTL mapping of whitefly resistance components in Solanum galapagense.

    PubMed

    Firdaus, Syarifin; van Heusden, Adriaan W; Hidayati, Nurul; Supena, Ence Darmo Jaya; Mumm, Roland; de Vos, Ric C H; Visser, Richard G F; Vosman, Ben

    2013-06-01

    Solanum galapagense is closely related to the cultivated tomato and can show a very good resistance towards whitefly. A segregating population resulting from a cross between the cultivated tomato and a whitefly resistant S. galapagense was created and used for mapping whitefly resistance and related traits, which made it possible to study the genetic basis of the resistance. Quantitative trait loci (QTL) for adult survival co-localized with type IV trichome characteristics (presence, density, gland longevity and gland size). A major QTL (Wf-1) was found for adult survival and trichome characters on Chromosome 2. This QTL explained 54.1 % of the variation in adult survival and 81.5 % of the occurrence of type IV trichomes. A minor QTL (Wf-2) for adult survival and trichome characters was identified on Chromosome 9. The major QTL was confirmed in F3 populations. Comprehensive metabolomics, based on GCMS profiling, revealed that 16 metabolites segregating in the F2 mapping population were associated with Wf-1 and/or Wf-2. Analysis of the 10 most resistant and susceptible F2 genotypes by LCMS showed that several acyl sugars were present in significantly higher concentration in the whitefly resistant genotypes, suggesting a role for these components in the resistance as well. Our results show that whitefly resistance in S. galapagense seems to inherit relatively simple compared to whitefly resistance from other sources and this offers great prospects for resistance breeding as well as elucidating the underlying molecular mechanism(s) of the resistance.

  12. Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2

    PubMed Central

    Meyers, Stacey N; Rodriguez-Zas, Sandra L; Beever, Jonathan E

    2007-01-01

    Background In a previous study, a quantitative trait locus (QTL) exhibiting large effects on both Instron shear force and taste panel tenderness was detected within the Illinois Meat Quality Pedigree (IMQP). This QTL mapped to the q arm of porcine chromosome 2 (SSC2q). Comparative analysis of SSC2q indicates that it is orthologous to a segment of human chromosome 5 (HSA5) containing a strong positional candidate gene, calpastatin (CAST). CAST polymorphisms have recently been shown to be associated with meat quality characteristics; however, the possible involvement of other genes and/or molecular variation in this region cannot be excluded, thus requiring fine-mapping of the QTL. Results Recent advances in porcine genome resources, including high-resolution radiation hybrid and bacterial artificial chromosome (BAC) physical maps, were utilized for development of novel informative markers. Marker density in the ~30-Mb region surrounding the most likely QTL position was increased by addition of eighteen new microsatellite markers, including nine publicly-available and nine novel markers. Two newly-developed markers were derived from a porcine BAC clone containing the CAST gene. Refinement of the QTL position was achieved through linkage and haplotype analyses. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with CAST markers. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing CAST markers. The presence of additional tenderness QTL on SSC2q was also suggested. Conclusion These results reinforce CAST as a strong positional candidate. Further analysis of CAST molecular variation within the IMQP F1 boars should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic

  13. Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster.

    PubMed

    Hackett, Jennifer L; Wang, Xiaofei; Smith, Brittny R; Macdonald, Stuart J

    2016-01-01

    Closely-related, and otherwise morphologically similar insect species frequently show striking divergence in the shape and/or size of male genital structures, a phenomenon thought to be driven by sexual selection. Comparative interspecific studies can help elucidate the evolutionary forces acting on genital structures to drive this rapid differentiation. However, genetic dissection of sexual trait divergence between species is frequently hampered by the difficulty generating interspecific recombinants. Intraspecific variation can be leveraged to investigate the genetics of rapidly-evolving sexual traits, and here we carry out a genetic analysis of variation in the posterior lobe within D. melanogaster. The lobe is a male-specific process emerging from the genital arch of D. melanogaster and three closely-related species, is essential for copulation, and shows radical divergence in form across species. There is also abundant variation within species in the shape and size of the lobe, and while this variation is considerably more subtle than that seen among species, it nonetheless provides the raw material for QTL mapping. We created an advanced intercross population from a pair of phenotypically-different inbred strains, and after phenotyping and genotyping-by-sequencing the recombinants, mapped several QTL contributing to various measures of lobe morphology. The additional generations of crossing over in our mapping population led to QTL intervals that are smaller than is typical for an F2 mapping design. The intervals we map overlap with a pair of lobe QTL we previously identified in an independent mapping cross, potentially suggesting a level of shared genetic control of trait variation. Our QTL additionally implicate a suite of genes that have been shown to contribute to the development of the posterior lobe. These loci are strong candidates to harbor naturally-segregating sites contributing to phenotypic variation within D. melanogaster, and may also be those

  14. Mapping QTL Contributing to Variation in Posterior Lobe Morphology between Strains of Drosophila melanogaster

    PubMed Central

    Hackett, Jennifer L.; Wang, Xiaofei; Smith, Brittny R.

    2016-01-01

    Closely-related, and otherwise morphologically similar insect species frequently show striking divergence in the shape and/or size of male genital structures, a phenomenon thought to be driven by sexual selection. Comparative interspecific studies can help elucidate the evolutionary forces acting on genital structures to drive this rapid differentiation. However, genetic dissection of sexual trait divergence between species is frequently hampered by the difficulty generating interspecific recombinants. Intraspecific variation can be leveraged to investigate the genetics of rapidly-evolving sexual traits, and here we carry out a genetic analysis of variation in the posterior lobe within D. melanogaster. The lobe is a male-specific process emerging from the genital arch of D. melanogaster and three closely-related species, is essential for copulation, and shows radical divergence in form across species. There is also abundant variation within species in the shape and size of the lobe, and while this variation is considerably more subtle than that seen among species, it nonetheless provides the raw material for QTL mapping. We created an advanced intercross population from a pair of phenotypically-different inbred strains, and after phenotyping and genotyping-by-sequencing the recombinants, mapped several QTL contributing to various measures of lobe morphology. The additional generations of crossing over in our mapping population led to QTL intervals that are smaller than is typical for an F2 mapping design. The intervals we map overlap with a pair of lobe QTL we previously identified in an independent mapping cross, potentially suggesting a level of shared genetic control of trait variation. Our QTL additionally implicate a suite of genes that have been shown to contribute to the development of the posterior lobe. These loci are strong candidates to harbor naturally-segregating sites contributing to phenotypic variation within D. melanogaster, and may also be those

  15. QTL mapping for downy mildew resistance in cucumber inbred line WI7120 (PI 330628)

    USDA-ARS?s Scientific Manuscript database

    Downy mildew (DM) is the most devastating fungal disease of cucumber worldwide. The molecular mechanism of DM resistance in cucumber is poorly understood, and use of marker-assisted breeding for DM resistance is not widely available. Here we reported QTL mapping of DM resistance with 243 F2:3 famili...

  16. High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows

    USDA-ARS?s Scientific Manuscript database

    High-resolution QTL maps of 1586 SNPs affecting 31 dairy traits (top 100 effects per trait)were constructed based on a genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped with 45,878 SNPs. The 31 traits include net merit and its 8 compnent traits, 4 calving traits, an...

  17. High Resolution QTL Maps Of 31 Traits in Contemporary U.S. Holstein Cows

    USDA-ARS?s Scientific Manuscript database

    High-resolution QTL maps of 1586 SNPs affecting 31 dairy traits (top 100 effects per trait)were constructed based on a genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped with 45,878 SNPs. The 31 traits include net merit and its 8 compnent traits, 4 calving traits, an...

  18. 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

  19. QTL Mapping of Sex Determination Loci Supports an Ancient Pathway in Ants and Honey Bees

    PubMed Central

    Miyakawa, Misato O.; Mikheyev, Alexander S.

    2015-01-01

    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

  20. 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

  1. 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.

  2. Mapping genetic determinants of viral traits with FST and quantitative trait locus (QTL) approaches.

    PubMed

    Doumayrou, Juliette; Thébaud, Gaël; Vuillaume, Florence; Peterschmitt, Michel; Urbino, Cica

    2015-10-01

    The genetic determinism of viral traits can generally be dissected using either forward or reverse genetics because the clonal reproduction of viruses does not require the use of approaches based on laboratory crosses. Nevertheless, we hypothesized that recombinant viruses could be analyzed as sexually reproducing organisms, using either a quantitative trait loci (QTL) approach or a locus-by-locus fixation index (FST). Locus-by-locus FST analysis, and four different regressions and interval mapping algorithms of QTL analysis were applied to a phenotypic and genotypic dataset previously obtained from 47 artificial recombinant genomes generated between two begomovirus species. Both approaches assigned the determinant of within-host accumulation-previously identified using standard virology approaches-to a region including the 5׳ end of the replication-associated protein (Rep) gene and the upstream intergenic region. This study provides a proof of principle that QTL and population genetics tools can be extended to characterize the genetic determinants of viral traits.

  3. 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.

  4. QTL mapping of genome regions controlling temephos resistance in larvae of the mosquito Aedes aegypti.

    PubMed

    Reyes-Solis, Guadalupe Del Carmen; Saavedra-Rodriguez, Karla; Suarez, Adriana Flores; Black, William C

    2014-10-01

    The mosquito Aedes aegypti is the principal vector of dengue and yellow fever flaviviruses. Temephos is an organophosphate insecticide used globally to suppress Ae. aegypti larval populations but resistance has evolved in many locations. Quantitative Trait Loci (QTL) controlling temephos survival in Ae. aegypti larvae were mapped in a pair of F3 advanced intercross lines arising from temephos resistant parents from Solidaridad, México and temephos susceptible parents from Iquitos, Peru. Two sets of 200 F3 larvae were exposed to a discriminating dose of temephos and then dead larvae were collected and preserved for DNA isolation every two hours up to 16 hours. Larvae surviving longer than 16 hours were considered resistant. For QTL mapping, single nucleotide polymorphisms (SNPs) were identified at 23 single copy genes and 26 microsatellite loci of known physical positions in the Ae. aegypti genome. In both reciprocal crosses, Multiple Interval Mapping identified eleven QTL associated with time until death. In the Solidaridad×Iquitos (SLD×Iq) cross twelve were associated with survival but in the reciprocal IqxSLD cross, only six QTL were survival associated. Polymorphisms at acetylcholine esterase (AchE) loci 1 and 2 were not associated with either resistance phenotype suggesting that target site insensitivity is not an organophosphate resistance mechanism in this region of México. Temephos resistance is under the control of many metabolic genes of small effect and dispersed throughout the Ae. aegypti genome.

  5. QTL Mapping of Genome Regions Controlling Temephos Resistance in Larvae of the Mosquito Aedes aegypti

    PubMed Central

    Reyes-Solis, Guadalupe del Carmen; Saavedra-Rodriguez, Karla; Suarez, Adriana Flores; Black, William C.

    2014-01-01

    Introduction The mosquito Aedes aegypti is the principal vector of dengue and yellow fever flaviviruses. Temephos is an organophosphate insecticide used globally to suppress Ae. aegypti larval populations but resistance has evolved in many locations. Methodology/Principal Findings Quantitative Trait Loci (QTL) controlling temephos survival in Ae. aegypti larvae were mapped in a pair of F3 advanced intercross lines arising from temephos resistant parents from Solidaridad, México and temephos susceptible parents from Iquitos, Peru. Two sets of 200 F3 larvae were exposed to a discriminating dose of temephos and then dead larvae were collected and preserved for DNA isolation every two hours up to 16 hours. Larvae surviving longer than 16 hours were considered resistant. For QTL mapping, single nucleotide polymorphisms (SNPs) were identified at 23 single copy genes and 26 microsatellite loci of known physical positions in the Ae. aegypti genome. In both reciprocal crosses, Multiple Interval Mapping identified eleven QTL associated with time until death. In the Solidaridad×Iquitos (SLD×Iq) cross twelve were associated with survival but in the reciprocal IqxSLD cross, only six QTL were survival associated. Polymorphisms at acetylcholine esterase (AchE) loci 1 and 2 were not associated with either resistance phenotype suggesting that target site insensitivity is not an organophosphate resistance mechanism in this region of México. Conclusions/Significance Temephos resistance is under the control of many metabolic genes of small effect and dispersed throughout the Ae. aegypti genome. PMID:25330200

  6. Factors influencing QTL mapping accuracy under complicated genetic models by computer simulation.

    PubMed

    Su, C F; Wang, W; Gong, S L; Zuo, J H; Li, S J

    2016-12-19

    The accuracy of quantitative trait loci (QTLs) identified using different sample sizes and marker densities was evaluated in different genetic models. Model I assumed one additive QTL; Model II assumed three additive QTLs plus one pair of epistatic QTLs; and Model III assumed two additive QTLs with opposite genetic effects plus two pairs of epistatic QTLs. Recombinant inbred lines (RILs) (50-1500 samples) were simulated according to the Models to study the influence of different sample sizes under different genetic models on QTL mapping accuracy. RILs with 10-100 target chromosome markers were simulated according to Models I and II to evaluate the influence of marker density on QTL mapping accuracy. Different marker densities did not significantly influence accurate estimation of genetic effects with simple additive models, but influenced QTL mapping accuracy in the additive and epistatic models. The optimum marker density was approximately 20 markers when the recombination fraction between two adjacent markers was 0.056 in the additive and epistatic models. A sample size of 150 was sufficient for detecting simple additive QTLs. Thus, a sample size of approximately 450 is needed to detect QTLs with additive and epistatic models. Sample size must be approximately 750 to detect QTLs with additive, epistatic, and combined effects between QTLs. The sample size should be increased to >750 if the genetic models of the data set become more complicated than Model III. Our results provide a theoretical basis for marker-assisted selection breeding and molecular design breeding.

  7. Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL.

    PubMed

    Thomson, Michael J; Edwards, Jeremy D; Septiningsih, Endang M; Harrington, Sandra E; McCouch, Susan R

    2006-04-01

    A quantitative trait locus (QTL), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the Oryza sativa variety Jefferson and an accession of the wild rice relative Oryza rufipogon. A series of near-isogenic lines (NILs) containing different O. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. In contrast to the late-flowering O. rufipogon parent, O. rufipogon alleles in the substitution lines caused early flowering under both short- and long-day lengths and provided evidence for at least two distinct sub-QTL: dth1.1a and dth1.1b. Potential candidate genes underlying these sub-QTL include genes with sequence similarity to Arabidopsis GI, FT, SOC1, and EMF1, and Pharbitis nil PNZIP. Evidence from families with nontarget O. rufipogon introgressions in combination with dth1.1 alleles also detected an early flowering QTL on chromosome 4 and a late-flowering QTL on chromosome 6 and provided evidence for additional sub-QTL in the dth1.1 region. The availability of a series of near-isogenic lines with alleles introgressed from a wild relative of rice provides an opportunity to better understand the molecular basis of transgressive variation in a quantitative trait.

  8. Substitution Mapping of dth1.1, a Flowering-Time Quantitative Trait Locus (QTL) Associated With Transgressive Variation in Rice, Reveals Multiple Sub-QTL

    PubMed Central

    Thomson, Michael J.; Edwards, Jeremy D.; Septiningsih, Endang M.; Harrington, Sandra E.; McCouch, Susan R.

    2006-01-01

    A quantitative trait locus (QTL), dth1.1, was associated with transgressive variation for days to heading in an advanced backcross population derived from the Oryza sativa variety Jefferson and an accession of the wild rice relative Oryza rufipogon. A series of near-isogenic lines (NILs) containing different O. rufipogon introgressions across the target region were constructed to dissect dth1.1 using substitution mapping. In contrast to the late-flowering O. rufipogon parent, O. rufipogon alleles in the substitution lines caused early flowering under both short- and long-day lengths and provided evidence for at least two distinct sub-QTL: dth1.1a and dth1.1b. Potential candidate genes underlying these sub-QTL include genes with sequence similarity to Arabidopsis GI, FT, SOC1, and EMF1, and Pharbitis nil PNZIP. Evidence from families with nontarget O. rufipogon introgressions in combination with dth1.1 alleles also detected an early flowering QTL on chromosome 4 and a late-flowering QTL on chromosome 6 and provided evidence for additional sub-QTL in the dth1.1 region. The availability of a series of near-isogenic lines with alleles introgressed from a wild relative of rice provides an opportunity to better understand the molecular basis of transgressive variation in a quantitative trait. PMID:16452146

  9. Mapping QTL main and interaction influences on milling quality in elite US rice germplasm.

    PubMed

    Nelson, J C; McClung, A M; Fjellstrom, R G; Moldenhauer, K A K; Boza, E; Jodari, F; Oard, J H; Linscombe, S; Scheffler, B E; Yeater, K M

    2011-02-01

    Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits in recombinant inbred lines (RILs) derived from crosses of common parent Cypress, a high-HR US japonica cultivar, with RT0034, a low-HR indica line (129 RILs) and LaGrue, a low-HR japonica cultivar (298 RILs), grown in two US locations in 2005-2007. Early heading increased HR in the Louisiana (LA) but not the Arkansas (AR) location. Fitting QTL-mapping models to separate QTL main and QTL × environment interaction (QEI) effects and identify epistatic interactions revealed six main-effect HR QTLs in the two crosses, at four of which Cypress contributed the increasing allele. Multi-QTL models accounted for 0.36 of genetic and 0.21 of genetic × environment interaction of HR in MY1, and corresponding proportions of 0.25 and 0.37 in MY2. The greater HR advantage of Cypress in LA than in AR corresponded to a genomewide pattern of opposition of HR-increasing QTL effects by AR-specific effects, suggesting a selection strategy for improving this cultivar for AR. Treating year-location combinations as independent environments resulted in underestimation of QEI effects, evidently owing to lower variation among years within location than between location. Identification of robust HR QTLs in elite long-grain germplasm is suggested to require more detailed attention to the interaction of plant and grain development parameters with environmental conditions than has been given to date.

  10. QTL mapping for bacterial wilt resistance in peanut (Arachis hypogaea L.).

    PubMed

    Zhao, Yongli; Zhang, Chong; Chen, Hua; Yuan, Mei; Nipper, Rick; Prakash, C S; Zhuang, Weijian; He, Guohao

    Bacterial wilt (BW) caused by Ralstonia solanacearum is a serious, global, disease of peanut (Arachis hypogaea L.), but it is especially destructive in China. Identification of DNA markers linked to the resistance to this disease will help peanut breeders efficiently develop resistant cultivars through molecular breeding. A F2 population, from a cross between disease-resistant and disease-susceptible cultivars, was used to detect quantitative trait loci (QTL) associated with the resistance to this disease in the cultivated peanut. Genome-wide SNPs were identified from restriction-site-associated DNA sequencing tags using next-generation DNA sequencing technology. SNPs linked to disease resistance were determined in two bulks of 30 resistant and 30 susceptible plants along with two parental plants using bulk segregant analysis. Polymorphic SSR and SNP markers were utilized for construction of a linkage map and for performing the QTL analysis, and a moderately dense linkage map was constructed in the F2 population. Two QTL (qBW-1 and qBW-2) detected for resistance to BW disease were located in the linkage groups LG1 and LG10 and account for 21 and 12 % of the bacterial wilt phenotypic variance. To confirm these QTL, the F8 RIL population with 223 plants was utilized for genotyping and phenotyping plants by year and location as compared to the F2 population. The QTL qBW-1 was consistent in the location of LG1 in the F8 population though the QTL qBW-2 could not be clarified due to fewer markers used and mapped in LG10. The QTL qBW-1, including four linked SNP markers and one SSR marker within 14.4-cM interval in the F8, was closely related to a disease resistance gene homolog and was considered as a candidate gene for resistance to BW. QTL identified in this study would be useful to conduct marker-assisted selection and may permit cloning of resistance genes. Our study shows that bulk segregant analysis of genome-wide SNPs is a useful approach to expedite the

  11. Advanced technologies for genomic analysis in farm animals and its application for QTL mapping.

    PubMed

    Hu, Xiaoxiang; Gao, Yu; Feng, Chungang; Liu, Qiuyue; Wang, Xiaobo; Du, Zhuo; Wang, Qingsong; Li, Ning

    2009-06-01

    Rapid progress in farm animal breeding has been made in the last few decades. Advanced technologies for genomic analysis in molecular genetics have led to the identification of genes or markers associated with genes that affect economic traits. Molecular markers, large-insert libraries and RH panels have been used to build the genetic linkage maps, physical maps and comparative maps in different farm animals. Moreover, EST sequencing, genome sequencing and SNPs maps are helping us to understand how genomes function in various organisms and further areas will be studied by DNA microarray technologies and proteomics methods. Because most economically important traits in farm animals are controlled by multiple genes and the environment, the main goal of genome research in farm animals is to map and characterize genes determining QTL. There are two main strategies to identify trait loci, candidate gene association tests and genome scan approaches. In recent years, some new concepts, such as RNAi, miRNA and eQTL, have been introduced into farm animal research, especially for QTL mapping and finding QTN. Several genes that influence important traits have already been identified or are close to being identified, and some of them have been applied in farm animal breeding programs by marker-assisted selection.

  12. QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population

    PubMed Central

    Hu, Shuaidong; Lübberstedt, Thomas; Zhao, Guangwu; Lee, Michael

    2016-01-01

    Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16h, 18°C/8h) and optimum temperature (28°C/24h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize. PMID:27031623

  13. QTL Mapping of Low-Temperature Germination Ability in the Maize IBM Syn4 RIL Population.

    PubMed

    Hu, Shuaidong; Lübberstedt, Thomas; Zhao, Guangwu; Lee, Michael

    2016-01-01

    Low temperature is the primary factor to affect maize sowing in early spring. It is, therefore, vital for maize breeding programs to improve tolerance to low temperatures at seed germination stage. However, little is known about maize QTL involved in low-temperature germination ability. 243 lines of the intermated B73×Mo17 (IBM) Syn4 recombinant inbred line (RIL) population was used for QTL analysis of low-temperature germination ability. There were significant differences in germination-related traits under both conditions of low temperature (12°C/16 h, 18°C/8 h) and optimum temperature (28°C/24 h) between the parental lines. Only three QTL were identified for controlling optimum-temperature germination rate. Six QTL controlling low-temperature germination rate were detected on chromosome 4, 5, 6, 7 and 9, and contribution rate of single QTL explained between 3.39%~11.29%. In addition, six QTL controlling low-temperature primary root length were detected in chromosome 4, 5, 6, and 9, and the contribution rate of single QTL explained between 3.96%~8.41%. Four pairs of QTL were located at the same chromosome position and together controlled germination rate and primary root length under low temperature condition. The nearest markers apart from the corresponding QTL (only 0.01 cM) were umc1303 (265.1 cM) on chromosome 4, umc1 (246.4 cM) on chromosome 5, umc62 (459.1 cM) on chromosome 6, bnl14.28a (477.4 cM) on chromosome 9, respectively. A total of 3155 candidate genes were extracted from nine separate intervals based on the Maize Genetics and Genomics Database (http://www.maizegdb.org). Five candidate genes were selected for analysis as candidates putatively affecting seed germination and seedling growth at low temperature. The results provided a basis for further fine mapping, molecular marker assisted breeding and functional study of cold-tolerance at the stage of seed germination in maize.

  14. A genome-wide SNP-based genetic map and QTL mapping for agronomic traits in Chinese cabbage

    PubMed Central

    Huang, Li; Yang, Yafei; Zhang, Fang; Cao, Jiashu

    2017-01-01

    The aim of this work was to construct a high-resolution genetic map for the dissection of complex morphological and agronomic traits in Chinese cabbage (Brassica rapa L. syn. B. campestris). Chinese cabbage, an economically important vegetable, is a good model plant for studies on the evolution of morphologic variation. Herein, two high-generation inbred Chinese cabbage lines, ‘Huangxiaoza’ and ‘Bqq094-11’, were crossed. Then restriction-site-associated DNA sequencing (RAD-seq) was performed on the parents and 120 F2 individuals. A genetic map containing 711 bins representing 3985 single nucleotide polymorphism (SNP) markers was constructed. By using WinQTL with composite interval mapping (CIM) and mixed-model based composite interval mapping (MCIM) analysis via QTLNetwork, quantitative trait loci (QTL) linked to 16 genetic traits related to plant size, color and leaf characteristics were mapped to 10 linkage groups. The high density genetic map and QTL identified for morphological and agronomic traits lay the groundwork for functional gene mapping, map-based cloning and marker-assisted selection (MAS) in Chinese cabbage. PMID:28418033

  15. Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population

    PubMed Central

    Jin, Hui; Wen, Weie; Liu, Jindong; Zhai, Shengnan; Zhang, Yan; Yan, Jun; Liu, Zhiyong; Xia, Xianchun; He, Zhonghu

    2016-01-01

    Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat. PMID:27486464

  16. QTL mapping of sake brewing characteristics of yeast.

    PubMed

    Katou, Taku; Namise, Masahiro; Kitagaki, Hiroshi; Akao, Takeshi; Shimoi, Hitoshi

    2009-04-01

    A haploid sake yeast strain derived from the commercial diploid sake yeast strain Kyokai no. 7 showed better characteristics for sake brewing compared to the haploid laboratory yeast strain X2180-1B, including higher production of ethanol and aromatic components. A hybrid of these two strains showed intermediate characteristics in most cases. After sporulation of the hybrid strain, we obtained 100 haploid segregants of the hybrid. Small-scale sake brewing tests of these segregants showed a smooth continuous distribution of the sake brewing characteristics, suggesting that these traits are determined by multiple quantitative trait loci (QTLs). To examine these sake brewing characteristics at the genomic level, we performed QTL analysis of sake brewing characteristics using 142 DNA markers that showed heterogeneity between the two parental strains. As a result, we identified 25 significant QTLs involved in the specification of sake brewing characteristics such as ethanol fermentation and the production of aromatic components.

  17. Fine mapping of a calving QTL on Bos taurus autosome 18 in Holstein cattle.

    PubMed

    Mao, X; Kadri, N K; Thomasen, J R; De Koning, D J; Sahana, G; Guldbrandtsen, B

    2016-06-01

    Decreased calving performance not only directly impacts the economic efficiency of dairy cattle farming but also influences public concern for animal welfare. Previous studies have revealed a QTL on Bos taurus autosome (BTA) 18 that has a large effect on calving traits in Holstein cattle. In this study, fine mapping of this QTL was performed using imputed high-density SNP chip (HD) genotypes followed by imputed next-generation sequencing (NGS) variants. BTA18 was scanned for seven direct calving traits in 6113 bulls with imputed HD genotypes. SNP rs136283363 (BTA18: 57 548 213) was consistently the most significantly associated SNP across all seven traits [e.g. p-value = 2.04 × 10(-59) for birth index (BI)]. To finely map the QTL region and to explore pleiotropic effects, we studied NGS variants within the targeted region (BTA18: 57 321 450-57 625 355) for associations with direct calving traits and with three conformation traits. Significant variants were prioritized, and their biological relevance to the traits was interpreted. Considering their functional relationships with direct calving traits, SIGLEC12, CD33 and CEACAM18 were proposed as candidate genes. In addition, pleiotropic effects of this QTL region on direct calving traits and conformation traits were observed. However, the extent of linkage disequilibrium combined with the lack of complete annotation and potential errors in the Bos taurus genome assembly hampered our efforts to pinpoint the causal mutation.

  18. Mapping of QTL for Tolerance to Cereal Yellow Dwarf Virus in Two-rowed Spring Barley

    PubMed Central

    Gallagher, L.; Falk, B. W.; Brown-Guedira, G.; Pellerin, E.; Dubcovsky, J.

    2016-01-01

    Cereal yellow dwarf virus (CYDV-RPV) causes a serious viral disease affecting small grain crops around the world. In the United States, it frequently is present in California where it causes significant yield losses, and when infections start early in development, plant death. CYDV is transmitted by aphids, and it has been a major impediment to developing malting barley in California. To identify chromosome locations associated with tolerance/resistance to CYDV, a segregating population of 184 recombinant inbred lines (RIL) from a cross of the California adapted malting barley line Butta 12 with the CYDV tolerant Madre Selva was used to construct a genetic map including 180 polymorphic markers mapping to 163 unique loci. Tolerance to CYDV was evaluated in replicated experiments where plants were challenged by aphid mediated inoculation with the isolate CYDV-RPV in a controlled environment. Quantitative trait loci (QTL) analysis revealed the presence of two major QTL for CYDV tolerance from Madre Selva on chromosomes 2H (Qcyd.MaBu-1) and 7H (Qcyd.MaBu-2), and 4 minor QTL from Butta 12 on chromosomes 3H, 4H, and 2H. This paper discusses the contribution of each QTL and their potential value to improve barley tolerance to CYDV. PMID:27212713

  19. Identification of exercise capacity QTL using association mapping in inbred mice.

    PubMed

    Courtney, Sean M; Massett, Michael P

    2012-10-02

    There are large interindividual differences in exercise capacity. It is well established that there is a genetic basis for these differences. However, the genetic factors underlying this variation are undefined. Therefore, the purpose of this study was to identify novel putative quantitative trait loci (QTL) for exercise capacity by measuring exercise capacity in inbred mice and performing genome-wide association mapping. Exercise capacity, defined as run time and work, was assessed in male mice (n = 6) from 34 strains of classical and wild-derived inbred mice performing a graded treadmill test. Genome-wide association mapping was performed with an efficient mixed-model association (EMMA) algorithm to identify QTL. Exercise capacity was significantly different across strains. Run time varied by 2.7-fold between the highest running strain (C58/J) and the lowest running strain (A/J). These same strains showed a 16.5-fold difference in work. Significant associations were identified for exercise time on chromosomes 1, 2, 7, 11, and 13. The QTL interval on chromosome 2 (~168 Mb) contains one gene, Nfatc2, and overlaps with a suggestive QTL for training responsiveness in humans. These results provide phenotype data on the widest range of inbred strains tested thus far and indicate that genetic background significantly influences exercise capacity. Furthermore, the novel QTLs identified in the current study provide new targets for investigating the underlying mechanisms for variation in exercise capacity.

  20. Mapping of QTL affecting incidence of blood and meat inclusions in egg layers.

    PubMed

    Honkatukia, Mervi; Tuiskula-Haavisto, Maria; Ahola, Virpi; Uimari, Pekka; Schmutz, Matthias; Preisinger, Rudolf; Cavero, David; Vennerström, Pia; Arango, Jesus; O'Sullivan, Neil; Fulton, Janet; Vilkki, Johanna

    2011-06-13

    Occurrence of blood and meat inclusions is an internal egg quality defect. Mass candling reveals most of the spots, but because brown eggshell hampers selection in brown chicken lines it has not been possible to eliminate the defect by selection. Estimated frequency of blood and meat inclusions in brown layers is about 18% whereas it is 0.5% in white egg layers. Several factors are known to increase the incidence of this fault: genetic background, low level of vitamin A and/or D, stress or infections, for instance. To study the genetic background of the defect, a mapping population of 1599 F2 hens from a cross of White Rock and Rhode Island Red lines was set up. Our histopathological analyses show that blood spots consist of mainly erythrocytes and that meat spots are accumulations of necrotic material. Linkage analysis of 27 chromosomes with 162 microsatellite markers revealed one significant quantitative trait locus (QTL) affecting blood spot and meat spot frequency. We sequenced a fragment of a candidate gene within the region, ZO-2, coding for a tight junction protein. Nine polymorphisms were detected and two of them were included in fine-mapping and association analysis. Fine-mapping defined the QTL result. To further verify the QTL, association analyses were carried out in two independent commercial breeding lines with the marker MCW241 and surrounding SNPs. Association was found mainly in a 0.8 Mb-wide chromosomal area on GGAZ. There was good agreement between the location of the QTL region on chromosome Z and the association results in the commercial breeds analyzed. Variations found in tight junction protein ZO-2 and microRNA gga-mir-1556 may predispose egg layers to blood and meat spot defects. This paper describes the first results of detailed QTL analyses of the blood and meat spots trait(s) in chickens. © 2011 Honkatukia et al; licensee BioMed Central Ltd.

  1. Approaches to interval mapping of QTL in a multigeneration pedigree: the example of porcine chromosome 4.

    PubMed

    Knott, S A; Nyström, P E; Andersson-Eklund, L; Stern, S; Marklund, L; Andersson, L; Haley, C S

    2002-02-01

    Quantitative trait loci (QTLs) have been mapped in many studies of F2 populations derived from crosses between diverse lines. One approach to confirming these effects and improving the mapping resolution is genetic chromosome dissection through a backcrossing programme. Analysis by interval mapping of the data generated is likely to provide additional power and resolution compared with treating data marker by marker. However, interval mapping approaches for such a programme are not well developed, especially where the founder lines were outbred. We explore alternative approaches to analysis using, as an example, data from chromosome 4 in an intercross between wild boar and Large White pigs where QTLs have been previously identified. A least squares interval mapping procedure was used to study growth rate and carcass traits in a subsequent second backcross generation (BC2). This procedure requires the probability of inheriting a wild boar allele for each BC2 animal for locations throughout the chromosome. Two methods for obtaining these probabilities were compared: stochastic or deterministic. The two methods gave similar probabilities for inheriting wild boar alleles and, hence, gave very similar results from the QTL analysis. The deterministic approach has the advantage of being much faster to run but requires specialized software. A QTL for fatness and for growth were confirmed and, in addition, a QTL for piglet growth from weaning at 5 weeks up to 7 weeks of age and another for carcass length were detected.

  2. 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

  3. Quantitative genomics of voluntary exercise in mice: transcriptional analysis and mapping of expression QTL in muscle.

    PubMed

    Kelly, Scott A; Nehrenberg, Derrick L; Hua, Kunjie; Garland, Theodore; Pomp, Daniel

    2014-08-15

    Motivation and ability both underlie voluntary exercise, each with a potentially unique genetic architecture. Muscle structure and function are one of many morphological and physiological systems acting to simultaneously determine exercise ability. We generated a large (n = 815) advanced intercross line of mice (G4) derived from a line selectively bred for increased wheel running (high runner) and the C57BL/6J inbred strain. We previously mapped quantitative trait loci (QTL) contributing to voluntary exercise, body composition, and changes in body composition as a result of exercise. Using brain tissue in a subset of the G4 (n = 244), we have also previously reported expression QTL (eQTL) colocalizing with the QTL for the higher-level phenotypes. Here, we examined the transcriptional landscape of hind limb muscle tissue via global mRNA expression profiles. Correlations revealed an ∼1,168% increase in significant relationships between muscle transcript expression levels and the same exercise and body composition phenotypes examined previously in the brain. The exercise trait most often significantly correlated with gene expression in the brain was running duration while in the muscle it was maximum running speed. This difference may indicate that time spent engaging in exercise behavior may be more influenced by central (neurobiological) mechanisms, while intensity of exercise may be largely controlled by peripheral mechanisms. Additionally, we used subsets of cis-acting eQTL, colocalizing with QTL, to identify candidate genes based on both positional and functional evidence. We discuss three plausible candidate genes (Insig2, Prcp, Sparc) and their potential regulatory role.

  4. 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.

  5. Mapping QTL for dollar spot resistance in creeping bentgrass (Agrostis stolonifera L.).

    PubMed

    Chakraborty, N; Curley, J; Warnke, S; Casler, M D; Jung, G

    2006-11-01

    Dollar spot caused by Sclerotinia homoeocarpa F. T. Bennett is the most economically important turf disease on golf courses in North America. Dollar spot resistance in a creeping bentgrass cultivar would greatly reduce the frequency, costs, and environmental impacts of fungicide application. Little work has been done to understand the genetics of resistance to dollar spot in creeping bentgrass. Therefore, QTL analysis was used to determine the location, number and effects of genomic regions associated with dollar spot resistance in the field. To meet this objective, field inoculations using a single isolate were performed over 2 years and multiple locations using progeny of a full sib mapping population '549 x 372'. Dollar spot resistance seems to be inherited quantitatively and broad sense heritability for resistance was estimated to be 0.88. We have detected one QTL with large effect on linkage group 7.1 with LOD values ranging from 3.4 to 8.6 and explaining 14-36% of the phenotypic variance. Several smaller effect QTL specific to rating dates, locations and years were also detected. The association of the tightly linked markers with the LG 7.1 QTL based on 106 progeny was further examined by single marker analysis on all 697 progeny. The high significance of the QTL on LG 7.1 at a sample size of 697 (P < 0.0001), along with its consistency across locations, years and ratings dates, indicated that it was stable over environments. Markers tightly linked to the QTL can be utilized for marker-assisted selection in future bentgrass breeding programs.

  6. Genome-wide QTL mapping of nine body composition and bone mineral density traits in pigs.

    PubMed

    Rothammer, Sophie; Kremer, Prisca V; Bernau, Maren; Fernandez-Figares, Ignacio; Pfister-Schär, Jennifer; Medugorac, Ivica; Scholz, Armin M

    2014-10-28

    Since the pig is one of the most important livestock animals worldwide, mapping loci that are associated with economically important traits and/or traits that influence animal welfare is extremely relevant for efficient future pig breeding. Therefore, the purpose of this study was a genome-wide mapping of quantitative trait loci (QTL) associated with nine body composition and bone mineral traits: absolute (Fat, Lean) and percentage (FatPC, LeanPC) fat and lean mass, live weight (Weight), soft tissue X-ray attenuation coefficient (R), absolute (BMC) and percentage (BMCPC) bone mineral content and bone mineral density (BMD). Data on the nine traits investigated were obtained by Dual-energy X-ray absorptiometry for 551 pigs that were between 160 and 200 days old. In addition, all pigs were genotyped using Illumina's PorcineSNP60 Genotyping BeadChip. Based on these data, a genome-wide combined linkage and linkage disequilibrium analysis was conducted. Thus, we used 44 611 sliding windows that each consisted of 20 adjacent single nucleotide polymorphisms (SNPs). For the middle of each sliding window a variance component analysis was carried out using ASReml. The underlying mixed linear model included random QTL and polygenic effects, with fixed effects of sex, housing, season and age. Using a Bonferroni-corrected genome-wide significance threshold of P < 0.001, significant peaks were identified for all traits except BMCPC. Overall, we identified 72 QTL on 16 chromosomes, of which 24 were significantly associated with one trait only and the remaining with more than one trait. For example, a QTL on chromosome 2 included the highest peak across the genome for four traits (Fat, FatPC, LeanPC and R). The nearby gene, ZNF608, is known to be associated with body mass index in humans and involved in starvation in Drosophila, which makes it an extremely good candidate gene for this QTL. Our QTL mapping approach identified 72 QTL, some of which confirmed results of previous

  7. A multiparental cross population for mapping QTL for agronomic traits in durum wheat (Triticum turgidum ssp. durum).

    PubMed

    Milner, Sara Giulia; Maccaferri, Marco; Huang, Bevan Emma; Mantovani, Paola; Massi, Andrea; Frascaroli, Elisabetta; Tuberosa, Roberto; Salvi, Silvio

    2016-02-01

    Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664 cM and including 7594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi-allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2BL and 7AS, with the former mapped independently from the photoperiod response gene Ppd-B1, while the latter overlapped with the vernalization locus VRN-A3. Additionally, 21 QTL with environment-specific effects were found. Our results indicated a prevalence of environment-specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes.

  8. Targeted linkage map densification to improve cell wall related QTL detection and interpretation in maize.

    PubMed

    Courtial, Audrey; Thomas, Justine; Reymond, Matthieu; Méchin, Valérie; Grima-Pettenati, Jacqueline; Barrière, Yves

    2013-05-01

    Several QTLs for cell wall degradability and lignin content were previously detected in the F288 × F271 maize RIL progeny, including a set of major QTLs located in bin 6.06. Unexpectedly, allelic sequencing of genes located around the bin 6.06 QTL positions revealed a monomorphous region, suggesting that these QTLs were likely "ghost" QTLs. Refining the positions of all QTLs detected in this population was thus considered, based on a linkage map densification in most important QTL regions, and in several large still unmarked regions. Re-analysis of data with an improved genetic map (173 markers instead of 108) showed that ghost QTLs located in bin 6.06 were then fractionated over two QTL positions located upstream and downstream of the monomorphic region. The area located upstream of bin 6.06 position carried the major QTLs, which explained from 37 to 59 % of the phenotypic variation for per se values and extended on only 6 cM, corresponding to a physical distance of 2.2 Mbp. Among the 92 genes present in the corresponding area of the B73 maize reference genome, nine could putatively be considered as involved in the formation of the secondary cell wall [bHLH, FKBP, laccase, fasciclin, zinc finger C2H2-type and C3HC4-type (two genes), NF-YB, and WRKY]. In addition, based on the currently improved genetic map, eight QTLs were detected in bin 4.09, while only one QTL was highlighted in the initial investigation. Moreover, significant epistatic interaction effects were shown for all traits between these QTLs located in bin 4.09 and the major QTLs located in bin 6.05. Three genes related to secondary cell wall assembly (ZmMYB42, COV1-like, PAL-like) underlay QTL support intervals in this newly identified bin 4.09 region. The current investigations, even if they were based only on one RIL progeny, illustrated the interest of a targeted marker mapping on a genetic map to improve QTL position.

  9. Glucose tolerance female-specific QTL mapped in collaborative cross mice.

    PubMed

    Abu-Toamih Atamni, Hanifa J; Ziner, Yaron; Mott, Richard; Wolf, Lior; Iraqi, Fuad A

    2017-02-01

    Type-2 diabetes (T2D) is a complex metabolic disease characterized by impaired glucose tolerance. Despite environmental high risk factors, host genetic background is a strong component of T2D development. Herein, novel highly genetically diverse strains of collaborative cross (CC) lines from mice were assessed to map quantitative trait loci (QTL) associated with variations of glucose-tolerance response. In total, 501 mice of 58 CC lines were maintained on high-fat (42 % fat) diet for 12 weeks. Thereafter, an intraperitoneal glucose tolerance test (IPGTT) was performed for 180 min. Subsequently, the values of Area under curve for the glucose at zero and 180 min (AUC0-180), were measured, and used for QTL mapping. Heritability and coefficient of variations in glucose tolerance (CVg) were calculated. One-way analysis of variation was significant (P < 0.001) for AUC0-180 between the CC lines as well between both sexes. Despite Significant variations for both sexes, QTL analysis was significant, only for females, reporting a significant female-sex-dependent QTL (~2.5 Mbp) associated with IPGTT AUC0-180 trait, located on Chromosome 8 (32-34.5 Mbp, containing 51 genes). Gene browse revealed QTL for body weight/size, genes involved in immune system, and two main protein-coding genes involved in the Glucose homeostasis, Mboat4 and Leprotl1. Heritability and coefficient of genetic variance (CVg) were 0.49 and 0.31 for females, while for males, these values 0.34 and 0.22, respectively. Our findings demonstrate the roles of genetic factors controlling glucose tolerance, which significantly differ between sexes requiring independent studies for females and males toward T2D prevention and therapy.

  10. A QTL model to map the common genetic basis for correlative phenotypic plasticity.

    PubMed

    Zhou, Tao; Lyu, Yafei; Xu, Fang; Bo, Wenhao; Zhai, Yi; Zhang, Jian; Pang, Xiaoming; Zheng, Bingsong; Wu, Rongling

    2015-01-01

    As an important mechanism for adaptation to heterogeneous environment, plastic responses of correlated traits to environmental alteration may also be genetically correlated, but less is known about the underlying genetic basis. We describe a statistical model for mapping specific quantitative trait loci (QTLs) that control the interrelationship of phenotypic plasticity between different traits. The model is constructed by a bivariate mixture setting, implemented with the EM algorithm to estimate the genetic effects of QTLs on correlative plastic response. We provide a series of procedure that test (1) how a QTL controls the phenotypic plasticity of a single trait; and (2) how the QTL determines the correlation of environment-induced changes of different traits. The model is readily extended to test how epistatic interactions among QTLs play a part in the correlations of different plastic traits. The model was validated through computer simulation and used to analyse multi-environment data of genetic mapping in winter wheat, showing its utilization in practice.

  11. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth.

    PubMed

    Zhang, Xuehai; Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Xiong, Lizhong; Yang, Wanneng; Yan, Jianbing

    2017-03-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction.

  12. 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

  13. Genetic mapping of a QTL controlling source-sink size and heading date in rice.

    PubMed

    Zhan, Xiaodeng; Sun, Bin; Lin, Zechuan; Gao, Zhiqiang; Yu, Ping; Liu, Qunen; Shen, Xihong; Zhang, Yingxin; Chen, Daibo; Cheng, Shihua; Cao, Liyong

    2015-10-25

    Source size, sink size and heading date (HD) are three important classes of traits that determine the productivity of rice. In this study, a set of recombinant inbred lines (RILs) derived from the cross between an elite indica line Big Grain1 (BG1) and a japonica line Xiaolijing (XLJ) were used to map quantitative trait loci (QTLs) for source-sink size and heading date. Totally, thirty-one QTLs for source size, twenty-two for sink size, four for heading date and seven QTL clusters which included QTLs for multiple traits were identified in three environmental trials. Thirty QTLs could be consistently detected in at least two trials and generally located in the clusters. Using a set of BC4F2 lines, the QTL cluster in C5-1-C5-2 on chromosome 5 was validated to be a major QTL pleiotropically affecting heading date, source size (flag leaf area) and panicle type (neck length of panicle, primary branching number and the ratio of secondary branching number to primary branching number), and was narrowed down to a 309.52Kb region. QTL clusters described above have a large effect on source-sink size and/or heading date, therefore they should be good resources to improve the adaptability and high yield potential of cultivars genetically.

  14. QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.).

    PubMed

    Billotte, N; Jourjon, M F; Marseillac, N; Berger, A; Flori, A; Asmady, H; Adon, B; Singh, R; Nouy, B; Potier, F; Cheah, S C; Rohde, W; Ritter, E; Courtois, B; Charrier, A; Mangin, B

    2010-05-01

    A quantitative trait locus (QTL) analysis designed for a multi-parent population was carried out and tested in oil palm (Elaeis guineensis Jacq.), which is a diploid cross-fertilising perennial species. A new extension of the MCQTL package was especially designed for crosses between heterozygous parents. The algorithm, which is now available for any allogamous species, was used to perform and compare two types of QTL search for small size families, within-family analysis and across-family analysis, using data from a 2 x 2 complete factorial mating experiment involving four parents from three selected gene pools. A consensus genetic map of the factorial design was produced using 251 microsatellite loci, the locus of the Sh major gene controlling fruit shell presence, and an AFLP marker of that gene. A set of 76 QTLs involved in 24 quantitative phenotypic traits was identified. A comparison of the QTL detection results showed that the across-family analysis proved to be efficient due to the interconnected families, but the family size issue is just partially solved. The identification of QTL markers for small progeny numbers and for marker-assisted selection strategies is discussed.

  15. QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.)

    PubMed Central

    Jourjon, M. F.; Marseillac, N.; Berger, A.; Flori, A.; Asmady, H.; Adon, B.; Singh, R.; Nouy, B.; Potier, F.; Cheah, S. C.; Rohde, W.; Ritter, E.; Courtois, B.; Charrier, A.; Mangin, B.

    2010-01-01

    A quantitative trait locus (QTL) analysis designed for a multi-parent population was carried out and tested in oil palm (Elaeis guineensis Jacq.), which is a diploid cross-fertilising perennial species. A new extension of the MCQTL package was especially designed for crosses between heterozygous parents. The algorithm, which is now available for any allogamous species, was used to perform and compare two types of QTL search for small size families, within-family analysis and across-family analysis, using data from a 2 × 2 complete factorial mating experiment involving four parents from three selected gene pools. A consensus genetic map of the factorial design was produced using 251 microsatellite loci, the locus of the Sh major gene controlling fruit shell presence, and an AFLP marker of that gene. A set of 76 QTLs involved in 24 quantitative phenotypic traits was identified. A comparison of the QTL detection results showed that the across-family analysis proved to be efficient due to the interconnected families, but the family size issue is just partially solved. The identification of QTL markers for small progeny numbers and for marker-assisted selection strategies is discussed. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1284-y) contains supplementary material, which is available to authorized users. PMID:20182696

  16. QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii.

    PubMed

    Nzuki, Inosters; Katari, Manpreet S; Bredeson, Jessen V; Masumba, Esther; Kapinga, Fortunus; Salum, Kasele; Mkamilo, Geoffrey S; Shah, Trushar; Lyons, Jessica B; Rokhsar, Daniel S; Rounsley, Steve; Myburg, Alexander A; Ferguson, Morag E

    2017-01-01

    Genetic mapping of quantitative trait loci (QTL) for resistance to cassava brown streak disease (CBSD), cassava mosaic disease (CMD), and cassava green mite (CGM) was performed using an F1 cross developed between the Tanzanian landrace, Kiroba, and a breeding line, AR37-80. The population was evaluated for two consecutive years in two sites in Tanzania. A genetic linkage map was derived from 106 F1 progeny and 1,974 SNP markers and spanned 18 chromosomes covering a distance of 1,698 cM. Fifteen significant QTL were identified; two are associated with CBSD root necrosis only, and were detected on chromosomes V and XII, while seven were associated with CBSD foliar symptoms only and were detected on chromosomes IV, VI, XVII, and XVIII. QTL on chromosomes 11 and 15 were associated with both CBSD foliar and root necrosis symptoms. Two QTL were found to be associated with CMD and were detected on chromosomes XII and XIV, while two were associated with CGM and were identified on chromosomes V and X. There are large Manihot glaziovii introgression regions in Kiroba on chromosomes I, XVII, and XVIII. The introgression segments on chromosomes XVII and XVIII overlap with QTL associated with CBSD foliar symptoms. The introgression region on chromosome I is of a different haplotype to the characteristic "Amani haplotype" found in the landrace Namikonga and others, and unlike some other genotypes, Kiroba does not have a large introgression block on chromosome IV. Kiroba is closely related to a sampled Tanzanian "tree cassava." This supports the observation that some of the QTL associated with CBSD resistance in Kiroba are different to those observed in another variety, Namikonga.

  17. QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii

    PubMed Central

    Nzuki, Inosters; Katari, Manpreet S.; Bredeson, Jessen V.; Masumba, Esther; Kapinga, Fortunus; Salum, Kasele; Mkamilo, Geoffrey S.; Shah, Trushar; Lyons, Jessica B.; Rokhsar, Daniel S.; Rounsley, Steve; Myburg, Alexander A.; Ferguson, Morag E.

    2017-01-01

    Genetic mapping of quantitative trait loci (QTL) for resistance to cassava brown streak disease (CBSD), cassava mosaic disease (CMD), and cassava green mite (CGM) was performed using an F1 cross developed between the Tanzanian landrace, Kiroba, and a breeding line, AR37-80. The population was evaluated for two consecutive years in two sites in Tanzania. A genetic linkage map was derived from 106 F1 progeny and 1,974 SNP markers and spanned 18 chromosomes covering a distance of 1,698 cM. Fifteen significant QTL were identified; two are associated with CBSD root necrosis only, and were detected on chromosomes V and XII, while seven were associated with CBSD foliar symptoms only and were detected on chromosomes IV, VI, XVII, and XVIII. QTL on chromosomes 11 and 15 were associated with both CBSD foliar and root necrosis symptoms. Two QTL were found to be associated with CMD and were detected on chromosomes XII and XIV, while two were associated with CGM and were identified on chromosomes V and X. There are large Manihot glaziovii introgression regions in Kiroba on chromosomes I, XVII, and XVIII. The introgression segments on chromosomes XVII and XVIII overlap with QTL associated with CBSD foliar symptoms. The introgression region on chromosome I is of a different haplotype to the characteristic “Amani haplotype” found in the landrace Namikonga and others, and unlike some other genotypes, Kiroba does not have a large introgression block on chromosome IV. Kiroba is closely related to a sampled Tanzanian “tree cassava.” This supports the observation that some of the QTL associated with CBSD resistance in Kiroba are different to those observed in another variety, Namikonga. PMID:28785268

  18. Graph-regularized dual Lasso for robust eQTL mapping

    PubMed Central

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

    2014-01-01

    Motivation: As a promising tool for dissecting the genetic basis of complex traits, expression quantitative trait loci (eQTL) mapping has attracted increasing research interest. An important issue in eQTL mapping is how to effectively integrate networks representing interactions among genetic markers and genes. Recently, several Lasso-based methods have been proposed to leverage such network information. Despite their success, existing methods have three common limitations: (i) a preprocessing step is usually needed to cluster the networks; (ii) the incompleteness of the networks and the noise in them are not considered; (iii) other available information, such as location of genetic markers and pathway information are not integrated. Results: To address the limitations of the existing methods, we propose Graph-regularized Dual Lasso (GDL), a robust approach for eQTL mapping. GDL integrates the correlation structures among genetic markers and traits simultaneously. It also takes into account the incompleteness of the networks and is robust to the noise. GDL utilizes graph-based regularizers to model the prior networks and does not require an explicit clustering step. Moreover, it enables further refinement of the partial and noisy networks. We further generalize GDL to incorporate the location of genetic makers and gene-pathway information. We perform extensive experimental evaluations using both simulated and real datasets. Experimental results demonstrate that the proposed methods can effectively integrate various available priori knowledge and significantly outperform the state-of-the-art eQTL mapping methods. Availability: Software for both C++ version and Matlab version is available at http://www.cs.unc.edu/∼weicheng/. Contact: weiwang@cs.ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24931977

  19. QTL and candidate gene mapping for polyphenolic composition in apple fruit

    PubMed Central

    2012-01-01

    Background The polyphenolic products of the phenylpropanoid pathway, including proanthocyanidins, anthocyanins and flavonols, possess antioxidant properties that may provide health benefits. To investigate the genetic architecture of control of their biosynthesis in apple fruit, various polyphenolic compounds were quantified in progeny from a 'Royal Gala' × 'Braeburn' apple population segregating for antioxidant content, using ultra high performance liquid chromatography of extracts derived from fruit cortex and skin. Results Construction of genetic maps for 'Royal Gala' and 'Braeburn' enabled detection of 79 quantitative trait loci (QTL) for content of 17 fruit polyphenolic compounds. Seven QTL clusters were stable across two years of harvest and included QTLs for content of flavanols, flavonols, anthocyanins and hydroxycinnamic acids. Alignment of the parental genetic maps with the apple whole genome sequence in silico enabled screening for co-segregation with the QTLs of a range of candidate genes coding for enzymes in the polyphenolic biosynthetic pathway. This co-location was confirmed by genetic mapping of markers derived from the gene sequences. Leucoanthocyanidin reductase (LAR1) co-located with a QTL cluster for the fruit flavanols catechin, epicatechin, procyanidin dimer and five unknown procyanidin oligomers identified near the top of linkage group (LG) 16, while hydroxy cinnamate/quinate transferase (HCT/HQT) co-located with a QTL for chlorogenic acid concentration mapping near the bottom of LG 17. Conclusion We conclude that LAR1 and HCT/HQT are likely to influence the concentration of these compounds in apple fruit and provide useful allele-specific markers for marker assisted selection of trees bearing fruit with healthy attributes. PMID:22269060

  20. Genetic mapping of a 7R Al tolerance QTL in triticale (x Triticosecale Wittmack).

    PubMed

    Niedziela, A; Bednarek, P T; Labudda, M; Mańkowski, D R; Anioł, A

    2014-02-01

    Triticale (x Triticosecale Wittmack) is a relatively new cereal crop. In Poland, triticale is grown on 12 % of arable land ( http://www.stat.gov.pl ). There is an increasing interest in its cultivation due to lowered production costs and increased adaptation to adverse environmental conditions. However, it has an insufficient tolerance to the presence of aluminum ions (Al(3+)) in the soil. The number of genes controlling aluminum tolerance in triticale and their chromosomal location is not known. Two F2 mapping biparental populations (MP1 and MP15) segregating for aluminum (Al) tolerance were tested with AFLP, SSR, DArT, and specific PCR markers. Genetic mapping enabled the construction of linkage groups representing chromosomes 7R, 5R and 2B. Obtained linkage groups were common for both mapping populations and mostly included the same markers. Composite interval mapping (CIM) allowed identification of a single QTL that mapped to the 7R chromosome and explained 25 % (MP1) and 36 % (MP15) of phenotypic variation. The B1, B26 and Xscm150 markers were 0.04 cM and 0.02 cM from the maximum of the LOD function in the MP1 and MP15, respectively and were highly associated with aluminum tolerance as indicated by Kruskal-Wallis nonparametric test. Moreover, the molecular markers B1, B26, Xrems1162 and Xscm92, previously associated with the Alt4 locus that encoded an aluminum-activated malate transporter (ScALMT1) that was involved in Al tolerance in rye (Secale cereale) also mapped within QTL. Biochemical analysis of plants represented MP1 and MP15 mapping populations confirmed that the QTL located on 7R chromosome in both mapping populations is responsible for Al tolerance.

  1. Multiparental Mapping of Plant Height and Flowering Time QTL in Partially Isogenic Sorghum Families

    PubMed Central

    Higgins, R. H.; Thurber, C. S.; Assaranurak, I.; Brown, P. J.

    2014-01-01

    Sorghum varieties suitable for grain production at temperate latitudes show dwarfism and photoperiod insensitivity, both of which are controlled by a small number of loci with large effects. We studied the genetic control of plant height and flowering time in five sorghum families (A–E), each derived from a cross between a tropical line and a partially isogenic line carrying introgressions derived from a common, temperate-adapted donor. A total of 724 F2:3 lines were phenotyped in temperate and tropical environments for plant height and flowering time and scored at 9139 SNPs using genotyping-by-sequencing. Biparental mapping was compared with multiparental mapping in different subsets of families (AB, ABC, ABCD, and ABCDE) using both a GWAS approach, which fit each QTL as a single effect across all families, and using a joint linkage approach, which fit QTL effects as nested within families. GWAS using all families (ABCDE) performed best at the cloned Dw3 locus, whereas joint linkage using all families performed best at the cloned Ma1 locus. Both multiparental approaches yielded apparently synthetic associations due to genetic heterogeneity and were highly dependent on the subset of families used. Comparison of all mapping approaches suggests that a GA2-oxidase underlies Dw1, and that a mir172a gene underlies a Dw1-linked flowering time QTL. PMID:25237111

  2. Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis)

    PubMed Central

    Sauvage, Christopher; Vagner, Marie; Derôme, Nicolas; Audet, Céline; Bernatchez, Louis

    2012-01-01

    Growth performance and reduced stress response are traits of major interest in fish production. Growth and stress-related quantitative trait loci (QTL) have been already identified in several salmonid species, but little effort has been devoted to charrs (genus Salvelinus). Moreover, most QTL studies to date focused on one or very few traits, and little investigation has been devoted to QTL identification for gene expression. Here, our objective was to identify QTL for 27 phenotypes related to growth and stress responses in brook charr (Salvelinus fontinalis), which is one of the most economically important freshwater aquaculture species in Canada. Phenotypes included 12 growth parameters, six blood and plasma variables, three hepatic variables, and one plasma hormone level as well as the relative expression measurements of five genes of interest linked to growth regulation. QTL analysis relied on a linkage map recently built from S. fontinalis consisting of both single-nucleotide polymorphism (SNP, n = 266) and microsatellite (n =81) markers in an F2 interstrain hybrid population (n = 171). We identified 63 growth-related QTL and four stress-related QTL across 18 of the 40 linkage groups of the brook charr linkage map. Percent variance explained, confidence interval, and allelic QTL effects also were investigated to provide insight into the genetic architecture of growth- and stress-related QTL. QTL related to growth performance and stress response that were identified could be classified into two groups: (1) a group composed of the numerous, small-effect QTL associated with some traits related to growth (i.e., weight) that may be under the control of a large number of genes or pleiotropic genes, and (2) a group of less numerous QTL associated with growth (i.e., gene expression) and with stress-related QTL that display a larger effect, suggesting that these QTL are under the control of a limited number of genes of major effect. This study represents a first step

  3. Arabidopsis Seed Content QTL Mapping Using High-Throughput Phenotyping: The Assets of Near Infrared Spectroscopy

    PubMed Central

    Jasinski, Sophie; Lécureuil, Alain; Durandet, Monique; Bernard-Moulin, Patrick; Guerche, Philippe

    2016-01-01

    Seed storage compounds are of crucial importance for human diet, feed and industrial uses. In oleo-proteaginous species like rapeseed, seed oil and protein are the qualitative determinants that conferred economic value to the harvested seed. To date, although the biosynthesis pathways of oil and storage protein are rather well-known, the factors that determine how these types of reserves are partitioned in seeds have to be identified. With the aim of implementing a quantitative genetics approach, requiring phenotyping of 100s of plants, our first objective was to establish near-infrared reflectance spectroscopic (NIRS) predictive equations in order to estimate oil, protein, carbon, and nitrogen content in Arabidopsis seed with high-throughput level. Our results demonstrated that NIRS is a powerful non-destructive, high-throughput method to assess the content of these four major components studied in Arabidopsis seed. With this tool in hand, we analyzed Arabidopsis natural variation for these four components and illustrated that they all displayed a wide range of variation. Finally, NIRS was used in order to map QTL for these four traits using seeds from the Arabidopsis thaliana Ct-1 × Col-0 recombinant inbred line population. Some QTL co-localized with QTL previously identified, but others mapped to chromosomal regions never identified so far for such traits. This paper illustrates the usefulness of NIRS predictive equations to perform accurate high-throughput phenotyping of Arabidopsis seed content, opening new perspectives in gene identification following QTL mapping and genome wide association studies. PMID:27891138

  4. Comprehensive QTL mapping survey dissects the complex fruit texture physiology in apple (Malus x domestica Borkh.).

    PubMed

    Longhi, Sara; Moretto, Marco; Viola, Roberto; Velasco, Riccardo; Costa, Fabrizio

    2012-02-01

    Fruit ripening is a complex physiological process in plants whereby cell wall programmed changes occur mainly to promote seed dispersal. Cell wall modification also directly regulates the textural properties, a fundamental aspect of fruit quality. In this study, two full-sib populations of apple, with 'Fuji' as the common maternal parent, crossed with 'Delearly' and 'Pink Lady', were used to understand the control of fruit texture by QTL mapping and in silico gene mining. Texture was dissected with a novel high resolution phenomics strategy, simultaneously profiling both mechanical and acoustic fruit texture components. In 'Fuji × Delearly' nine linkage groups were associated with QTLs accounting from 15.6% to 49% of the total variance, and a highly significant QTL cluster for both textural components was mapped on chromosome 10 and co-located with Md-PG1, a polygalacturonase gene that, in apple, is known to be involved in cell wall metabolism processes. In addition, other candidate genes related to Md-NOR and Md-RIN transcription factors, Md-Pel (pectate lyase), and Md-ACS1 were mapped within statistical intervals. In 'Fuji × Pink Lady', a smaller set of linkage groups associated with the QTLs identified for fruit texture (15.9-34.6% variance) was observed. The analysis of the phenotypic variance over a two-dimensional PCA plot highlighted a transgressive segregation for this progeny, revealing two QTL sets distinctively related to both mechanical and acoustic texture components. The mining of the apple genome allowed the discovery of the gene inventory underlying each QTL, and functional profile assessment unravelled specific gene expression patterns of these candidate genes.

  5. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments

    PubMed Central

    2011-01-01

    Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and

  6. Mapping of Novel QTL Regulating Grain Shattering Using Doubled Haploid Population in Rice (Oryza sativa L.)

    PubMed Central

    Lee, Gyu-Ho; Kang, In-Kyu

    2016-01-01

    The critical evolutionary step during domestication of major cereals was elimination of seed shattering because the easy-to-shatter trait in wild relatives results in a severe reduction in yield. In this study, we analyzed the QTLs associated with shattering employing a high-density genetic map in doubled haploid (DH) population of rice (Oryza sativa L.). A genetic linkage map was generated with 217 microsatellite markers spanning 2082.4 cM and covering 12 rice chromosomes with an average interval of 9.6 cM between markers based on 120 DHLs derived from a cross between Cheongcheong indica type cultivar and Nagdong japonica type cultivar. In the QTL analysis, five QTLs pertaining to the breaking tensile strength (BTS) were detected in 2013 and 2015. Two regions of the QTLs related to BTS on chromosome 1 and chromosome 6 were detected. Several important genes are distributed in 1 Mbp region of the QTL on chromosome 6 and they are related to the formation of abscission layer. We decide to name this QTL qSh6 and the candidate genes in the qSh6 region can be employed usefully in further research for cloning. PMID:27419124

  7. Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

    PubMed Central

    González-Prendes, Rayner; Quintanilla, Raquel; Cánovas, Angela; Manunza, Arianna; Figueiredo Cardoso, Tainã; Jordana, Jordi; Noguera, José Luis; Pena, Ramona N.; Amills, Marcel

    2017-01-01

    Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism. PMID:28054563

  8. Strategy for Mapping Quantitative Trait Loci (QTL) by Using Human Metapopulations

    PubMed Central

    Rudan, Igor; Biloglav, Zrinka; Carothers, Andrew D.; Wright, Alan F.; Campbell, Harry

    2006-01-01

    Aim To present a novel strategy for mapping quantitative trait loci (QTL), using human metapopulations. The strategy is based on the expectation that in geographic clusters of small and distinct human isolates, a combination of founder effect and genetic drift can dramatically increase population frequency of rare QTL variants with large effect. In such cases, the distribution of QT measurements in an “affected” isolate is expected to deviate from that observed in neighboring isolates. Methods We tested this hypothesis in 9 villages from a larger Croatian isolate resource, where 7 Mendelian disorders have been previously reported. The values of 10 physiological and biochemical QTs were measured in a random sample of 1001 individuals (100 inhabitants of each of 9 villages and 101 immigrant controls). Results Significant over- or under- representation of individuals from specific villages in extreme ends of standardized QT measurement distribution was found 10 times more frequently than expected by chance. The large majority of such clusters of individuals with extreme QT values (34/36, 94.4%) originated from the 6 villages with the most pronounced geographic isolation and endogamy. Conclusion Early epidemiological assessment supports the feasibility of the proposed strategy. Clusters of individuals with extreme QT values responsible for over-representation of single villages can usually be linked to a larger pedigree and may be useful for further QTL mapping, using linkage analysis. PMID:16909450

  9. 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

  10. Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L.) Walp.].

    PubMed

    Muchero, Wellington; Ehlers, Jeffrey D; Close, Timothy J; Roberts, Philip A

    2009-03-01

    Cowpea is an important crop for subsistence farmers in arid regions of Africa, Asia, and South America. Efforts to develop cultivars with improved productivity under drought conditions are constrained by lack of molecular markers associated with drought tolerance. Here, we report the mapping of 12 quantitative trait loci (QTL) associated with seedling drought tolerance and maturity in a cowpea recombinant inbred (RIL) population. One hundred and twenty-seven F(8) RILs developed from a cross between IT93K503-1 and CB46 were screened with 62 EcoR1 and Mse1 primer combinations to generate 306 amplified fragment length polymorphisms for use in genetic linkage mapping. The same population was phenotyped for maintenance of stem greenness (stg) and recovery dry weight (rdw) after drought stress in six greenhouse experiments. In field experiments conducted over 3 years, visual ratings and dry weights were used to phenotype drought stress-induced premature senescence in the RIL population. Kruskall-Wallis and multiple-QTL model mapping analysis were used to identify QTL associated with drought response phenotypes. Observed QTL were highly reproducible between stg and rdw under greenhouse conditions. Field studies confirmed all ten drought-response QTL observed under greenhouse conditions. Regions harboring drought-related QTL were observed on linkage groups 1, 2, 3, 5, 6, 7, 9, and 10 accounting for between 4.7 and 24.2% of the phenotypic variance (R(2)). Further, two QTL for maturity (R(2) = 14.4-28.9% and R(2) = 11.7-25.2%) mapped on linkage groups 7 and 8 separately from drought-related QTL. These results provide a platform for identification of genetic determinants of seedling drought tolerance in cowpea.

  11. 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

  12. 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.

  13. QTL mapping with near-isogenic lines in maize.

    PubMed

    Szalma, S J; Hostert, B M; Ledeaux, J R; Stuber, C W; Holland, J B

    2007-05-01

    A set of 89 near-isogenic lines (NILs) of maize was created using marker-assisted selection. Nineteen genomic regions, identified by restriction fragment length polymorphism loci and chosen to represent portions of all ten maize chromosomes, were introgressed by backcrossing three generations from donor line Tx303 into the B73 genetic background. NILs were genotyped at an additional 128 simple sequence repeat loci to estimate the size of introgressions and the amount of background introgression. Tx303 introgressions ranged in size from 10 to 150 cM, with an average of 60 cM. Across all NILs, 89% of the Tx303 genome is represented in targeted and background introgressions. The average proportion of background introgression was 2.5% (range 0-15%), significantly lower than the expected value of 9.4% for third backcross generation lines developed without marker-assisted selection. The NILs were grown in replicated field evaluations in two years to map QTLs for flowering time traits. A parallel experiment of testcrosses of each NIL to the unrelated inbred, Mo17, was conducted in the same environments to map QTLs in NIL testcross hybrids. QTLs affecting days to anthesis, days to silking, and anthesis-silk interval were detected in both inbreds and hybrids in both environments. The testing environments differed dramatically for drought stress, and different sets of QTLs were detected across environments. Furthermore, QTLs detected in inbreds were typically different from QTLs detected in hybrids, demonstrating the genetic complexity of flowering time. NILs can serve as a valuable genetic mapping resource for maize breeders and geneticists.

  14. 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

  15. Molecular mapping of Verticillium wilt resistance QTL clustered on chromosomes D7 and D9 in upland cotton.

    PubMed

    Jiang, Feng; Zhao, Jun; Zhou, Lei; Guo, WangZhen; Zhang, TianZhen

    2009-09-01

    Verticillium wilt is a destructive disease with international consequences for cotton production. Breeding broad-spectrum resistant cultivars is considered to be one of the most effective means for reducing crop losses. A resistant cotton cultivar, 60182, was crossed with a susceptible cultivar, Junmian 1, to identify markers for Verticillium resistance genes and validate the mode of its inheritance. Genetic segregation analysis for Verticillium wilt resistance was evaluated based upon infected leaf percentage in the seedling stage using major gene-polygene mixed inheritance models and joint analysis of P(1), P(2), F(1), B(1), B(2) and F(2) populations obtained from the cultivar cross. We found that resistance of upland cotton cultivar 60182 to isolates BP2, VD8 and T9, and their isoconcentration mixture was controlled by two major genes with additive-dominance-epistatic effects, and the inheritance of the major gene was dominant. Furthermore, a genetic linkage map was constructed using F(2) segregating population and resistance phenotypic data were obtained using F(2:3) families inoculated with different isolates and detected in different developmental stages. The genetic linkage map with 139 loci was comprised of 31 linkage groups covering 1165 cM, with an average distance of 8.38 cM between two markers, or 25.89% of the cotton genome length. From 60182, we found 4 QTL on chromosome D7 and 4 QTL on D9 for BP2, 5 QTL on D7 and 9 QTL on D9 for VD8, 4 QTL on D7 and 5 QTL on D9 for T9 and 3 QTL on D7 and 7 QTL on D7 for mixed pathogens. The QTL mapping results revealed that QTL clusters with high contribution rates were screened simultaneously on chromosomes D9 and D7 by multiple interval mapping (CIM), whether from resistance phenotypic data from different developmental stages or for different isolates. The result is consistent with the genetic model of two major genes in 60182 and suggests broad-spectrum resistance to both defoliating isolates of V. dahliae and

  16. High-throughput physical map anchoring via BAC-pool sequencing.

    PubMed

    Cviková, Kateřina; Cattonaro, Federica; Alaux, Michael; Stein, Nils; Mayer, Klaus Fx; Doležel, Jaroslav; Bartoš, Jan

    2015-04-11

    Physical maps created from large insert DNA libraries, typically cloned in BAC vector, are valuable resources for map-based cloning and de novo genome sequencing. The maps are most useful if contigs of overlapping DNA clones are anchored to chromosome(s), and ordered along them using molecular markers. Here we present a novel approach for anchoring physical maps, based on sequencing three-dimensional pools of BAC clones from minimum tilling path. We used physical map of wheat chromosome arm 3DS to validate the method with two different DNA sequence datasets. The first comprised 567 genes ordered along the chromosome arm based on syntenic relationship of wheat with the sequenced genomes of Brachypodium, rice and sorghum. The second dataset consisted of 7,136 SNP-containing sequences, which were mapped genetically in Aegilops tauschii, the donor of the wheat D genome. Mapping of sequence reads from individual BAC pools to the first and the second datasets enabled unambiguous anchoring 447 and 311 3DS-specific sequences, respectively, or 758 in total. We demonstrate the utility of the novel approach for BAC contig anchoring based on mass parallel sequencing of three-dimensional pools prepared from minimum tilling path of physical map. The existing genetic markers as well as any other DNA sequence could be mapped to BAC clones in a single in silico experiment. The approach reduces significantly the cost and time needed for anchoring and is applicable to any genomic project involving the construction of anchored physical map.

  17. Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication

    PubMed Central

    Fallahsharoudi, Amir; de Kock, Neil; Johnsson, Martin; Bektic, Lejla; Ubhayasekera, S. J. Kumari A.; Bergquist, Jonas; Wright, Dominic; Jensen, Per

    2016-01-01

    The stress response has been largely modified in all domesticated animals, offering a strong tool for genetic mapping. In chickens, ancestral Red Junglefowl react stronger both in terms of physiology and behavior to a brief restraint stress than domesticated White Leghorn, demonstrating modified functions of the hypothalamic–pituitary–adrenal (HPA) axis. We mapped quantitative trait loci (QTL) underlying variations in stress-induced hormone levels using 232 birds from the 12th generation of an advanced intercross between White Leghorn and Red Junglefowl, genotyped for 739 genetic markers. Plasma levels of corticosterone, dehydroepiandrosterone (DHEA), and pregnenolone (PREG) were measured using LC-MS/MS in all genotyped birds. Transcription levels of the candidate genes were measured in the adrenal glands or hypothalamus of 88 out of the 232 birds used for hormone assessment. Genes were targeted for expression analysis when they were located in a hormone QTL region and were differentially expressed in the pure breed birds. One genome-wide significant QTL on chromosome 5 and two suggestive QTL together explained 20% of the variance in corticosterone response. Two significant QTL for aldosterone on chromosome 2 and 5 (explaining 19% of the variance), and one QTL for DHEA on chromosome 4 (explaining 5% of the variance), were detected. Orthologous DNA regions to the significant corticosterone QTL have been previously associated with the physiological stress response in other species but, to our knowledge, the underlying gene(s) have not been identified. SERPINA10 had an expression QTL (eQTL) colocalized with the corticosterone QTL on chromosome 5 and PDE1C had an eQTL colocalized with the aldosterone QTL on chromosome 2. Furthermore, in both cases, the expression levels of the genes were correlated with the plasma levels of the hormones. Hence, both these genes are strong putative candidates for the domestication-induced modifications of the stress response in

  18. Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus

    PubMed Central

    Qu, Cunmin; Zhao, Huiyan; Fu, Fuyou; Zhang, Kai; Yuan, Jianglian; Liu, Liezhao; Wang, Rui; Xu, Xinfu; Lu, Kun; Li, Jia-Na

    2016-01-01

    Flavonoids are secondary metabolites that are extensively distributed in the plant kingdom and contribute to seed coat color formation in rapeseed. To decipher the genetic networks underlying flavonoid biosynthesis in rapeseed, we constructed a high-density genetic linkage map with 1089 polymorphic loci (including 464 SSR loci, 97 RAPD loci, 451 SRAP loci, and 75 IBP loci) using recombinant inbred lines (RILs). The map consists of 19 linkage groups and covers 2775 cM of the B. napus genome with an average distance of 2.54 cM between adjacent markers. We then performed expression quantitative trait locus (eQTL) analysis to detect transcript-level variation of 18 flavonoid biosynthesis pathway genes in the seeds of the 94 RILs. In total, 72 eQTLs were detected and found to be distributed among 15 different linkage groups that account for 4.11% to 52.70% of the phenotypic variance atrributed to each eQTL. Using a genetical genomics approach, four eQTL hotspots together harboring 28 eQTLs associated with 18 genes were found on chromosomes A03, A09, and C08 and had high levels of synteny with genome sequences of A. thaliana and Brassica species. Associated with the trans-eQTL hotspots on chromosomes A03, A09, and C08 were 5, 17, and 1 genes encoding transcription factors, suggesting that these genes have essential roles in the flavonoid biosynthesis pathway. Importantly, bZIP25, which is expressed specifically in seeds, MYC1, which controls flavonoid biosynthesis, and the R2R3-type gene MYB51, which is involved in the synthesis of secondary metabolites, were associated with the eQTL hotspots, and these genes might thus be involved in different flavonoid biosynthesis pathways in rapeseed. Hence, further studies of the functions of these genes will provide insight into the regulatory mechanism underlying flavonoid biosynthesis, and lay the foundation for elaborating the molecular mechanism of seed coat color formation in B. napus. PMID:27881992

  19. QTL Mapping and Candidate Gene Analysis of Telomere Length Control Factors in Maize (Zea mays L.)

    PubMed Central

    Brown, Amber N.; Lauter, Nick; Vera, Daniel L.; McLaughlin-Large, Karen A.; Steele, Tace M.; Fredette, Natalie C.; Bass, Hank W.

    2011-01-01

    Telomere length is a quantitative trait important for many cellular functions. Failure to regulate telomere length contributes to genomic instability, cellular senescence, cancer, and apoptosis in humans, but the functional significance of telomere regulation in plants is much less well understood. To gain a better understanding of telomere biology in plants, we used quantitative trait locus (QTL) mapping to identify genetic elements that control telomere length variation in maize (Zea mays L.). For this purpose, we measured the median and mean telomere lengths from 178 recombinant inbred lines of the IBM mapping population and found multiple regions that collectively accounted for 33–38% of the variation in telomere length. Two-way analysis of variance revealed interaction between the quantitative trait loci at genetic bin positions 2.09 and 5.04. Candidate genes within these and other significant QTL intervals, along with select genes known a priori to regulate telomere length, were tested for correlations between expression levels and telomere length in the IBM population and diverse inbred lines by quantitative real-time PCR. A slight but significant positive correlation between expression levels and telomere length was observed for many of the candidate genes, but Ibp2 was a notable exception, showing instead a negative correlation. A rad51-like protein (TEL-MD_5.04) was strongly supported as a candidate gene by several lines of evidence. Our results highlight the value of QTL mapping plus candidate gene expression analysis in a genetically diverse model system for telomere research. PMID:22384354

  20. An SNP-based saturated genetic map and QTL analysis of fruit-related traits in Zucchini using Genotyping-by-sequencing.

    PubMed

    Montero-Pau, Javier; Blanca, José; Esteras, Cristina; Martínez-Pérez, Eva Ma; Gómez, Pedro; Monforte, Antonio J; Cañizares, Joaquín; Picó, Belén

    2017-01-18

    Cucurbita pepo is a cucurbit with growing economic importance worldwide. Zucchini morphotype is the most important within this highly variable species. Recently, transcriptome and Simple Sequence Repeat (SSR)- and Single Nucleotide Polymorphism (SNP)-based medium density maps have been reported, however further genomic tools are needed for efficient molecular breeding in the species. Our objective is to combine currently available complete transcriptomes and the Zucchini genome sequence with high throughput genotyping methods, mapping population development and extensive phenotyping to facilitate the advance of genomic research in this species. We report the Genotyping-by-sequencing analysis of a RIL population developed from the inter subspecific cross Zucchini x Scallop (ssp. pepo x ssp. ovifera). Several thousands of SNP markers were identified and genotyped, followed by the construction of a high-density linkage map based on 7,718 SNPs (average of 386 markers/linkage group) covering 2,817.6 cM of the whole genome, which is a great improvement with respect to previous maps. A QTL analysis was performed using phenotypic data obtained from the RIL population from three environments. In total, 48 consistent QTLs for vine, flowering and fruit quality traits were detected on the basis of a multiple-environment analysis, distributed in 33 independent positions in 15 LGs, and each QTL explained 1.5-62.9% of the phenotypic variance. Eight major QTLs, which could explain greater than 20% of the phenotypic variation were detected and the underlying candidate genes identified. Here we report the first SNP saturated map in the species, anchored to the physical map. Additionally, several consistent QTLs related to early flowering, fruit shape and length, and rind and flesh color are reported as well as candidate genes for them. This information will enhance molecular breeding in C. pepo and will assist the gene cloning underlying the studied QTLs, helping to reveal the

  1. Fine Mapping of a QTL Associated with Kernel Row Number on Chromosome 1 of Maize.

    PubMed

    Calderón, Claudia I; Yandell, Brian S; Doebley, John F

    2016-01-01

    The genetic factors underlying changes in ear morphology, and particularly the inheritance of kernel row number (KRN), have been broadly investigated in diverse mapping populations in maize (Zea mays L.). In this study, we mapped a region on the long arm of chromosome 1 containing a QTL for KRN. This work was performed using a set of recombinant chromosome nearly isogenic lines (RCNILs) derived from a BC2S3 population produced using the inbred maize line W22 and teosinte (Zea mays ssp. parviglumis) as the parents. A set of 48 RCNILs was evaluated in the field during the summer of 2013 in order to perform the mapping. A QTL for KRN was found that explained approximately 51% of the phenotypic variance and had a 1.5-LOD confidence interval of 203 kb. Seven genes are described in this interval. One of these candidate genes may have been the target of domestication processes in maize and contributed to the shift from two kernel row ears in teosinte to a highly polystichous ear in maize.

  2. Construction of a genetic linkage map and QTL analysis in bambara groundnut.

    PubMed

    Ahmad, Nariman Salih; Redjeki, Endah Sri; Ho, Wai Kuan; Aliyu, Siise; Mayes, Katie; Massawe, Festo; Kilian, Andrzej; Mayes, Sean

    2016-07-01

    Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous underutilized legume that has the potential to improve food security in semi-arid Africa. So far, there are a lack of reports of controlled breeding populations that could be used for variety development and genetic studies. We report here the construction of the first genetic linkage map of bambara groundnut using a F3 population derived from a "narrow" cross between two domesticated landraces (Tiga Nicuru and DipC) with marked divergence in phenotypic traits. The map consists of 238 DArT array and SSR based markers in 21 linkage groups with a total genetic distance of 608.3 cM. In addition, phenotypic traits were evaluated for a quantitative trait loci (QTL) analysis over two generations. A total of 36 significant QTLs were detected for 19 traits. The phenotypic effect explained by a single QTL ranged from 11.6% to 49.9%. Two stable QTLs were mapped for internode length and growth habit. The identified QTLs could be useful for marker-assisted selection in bambara groundnut breeding programmes.

  3. Fine Mapping of a QTL Associated with Kernel Row Number on Chromosome 1 of Maize

    PubMed Central

    Calderón, Claudia I.; Yandell, Brian S.; Doebley, John F.

    2016-01-01

    The genetic factors underlying changes in ear morphology, and particularly the inheritance of kernel row number (KRN), have been broadly investigated in diverse mapping populations in maize (Zea mays L.). In this study, we mapped a region on the long arm of chromosome 1 containing a QTL for KRN. This work was performed using a set of recombinant chromosome nearly isogenic lines (RCNILs) derived from a BC2S3 population produced using the inbred maize line W22 and teosinte (Zea mays ssp. parviglumis) as the parents. A set of 48 RCNILs was evaluated in the field during the summer of 2013 in order to perform the mapping. A QTL for KRN was found that explained approximately 51% of the phenotypic variance and had a 1.5-LOD confidence interval of 203 kb. Seven genes are described in this interval. One of these candidate genes may have been the target of domestication processes in maize and contributed to the shift from two kernel row ears in teosinte to a highly polystichous ear in maize. PMID:26930509

  4. SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

    PubMed Central

    Chao, Shiaoman; Jellen, Eric N.; Carson, Martin L.; Rines, Howard W.; Obert, Donald E.; Lutz, Joseph D.; Shackelford, Irene; Korol, Abraham B.; Wight, Charlene P.; Gardner, Kyle M.; Hattori, Jiro; Beattie, Aaron D.; Bjørnstad, Åsmund; Bonman, J. Michael; Jannink, Jean-Luc; Sorrells, Mark E.; Brown-Guedira, Gina L.; Mitchell Fetch, Jennifer W.; Harrison, Stephen A.; Howarth, Catherine J.; Ibrahim, Amir; Kolb, Frederic L.; McMullen, Michael S.; Murphy, J. Paul; Ohm, Herbert W.; Rossnagel, Brian G.; Yan, Weikai; Miclaus, Kelci J.; Hiller, Jordan; Maughan, Peter J.; Redman Hulse, Rachel R.; Anderson, Joseph M.; Islamovic, Emir

    2013-01-01

    A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources. PMID:23533580

  5. [Studies of marker screening efficiency and corresponding influencing factors in QTL composite interval mapping].

    PubMed

    Gao, Yong-Ming; Wan, Ping

    2002-06-01

    Screening markers efficiently is the foundation of mapping QTLs by composite interval mapping. Main and interaction markers distinguished, besides using background control for genetic variation, could also be used to construct intervals of two-way searching for mapping QTLs with epistasis, which can save a lot of calculation time. Therefore, the efficiency of marker screening would affect power and precision of QTL mapping. A doubled haploid population with 200 individuals and 5 chromosomes was constructed, with 50 markers evenly distributed at 10 cM space. Among a total of 6 QTLs, one was placed on chromosome I, two linked on chromosome II, and the other three linked on chromosome IV. QTL setting included additive effects and epistatic effects of additive x additive, the corresponding QTL interaction effects were set if data were collected under multiple environments. The heritability was assumed to be 0.5 if no special declaration. The power of marker screening by stepwise regression, forward regression, and three methods for random effect prediction, e.g. best linear unbiased prediction (BLUP), linear unbiased prediction (LUP) and adjusted unbiased prediction (AUP), was studied and compared through 100 Monte Carlo simulations. The results indicated that the marker screening power by stepwise regression at 0.1, 0.05 and 0.01 significant level changed from 2% to 68%, the power changed from 2% to 72% by forward regression. The larger the QTL effects, the higher the marker screening power. While the power of marker screening by three random effect prediction was very low, the maximum was only 13%. That suggested that regression methods were much better than those by using the approaches of random effect prediction to identify efficient markers flanking QTLs, and forward selection method was more simple and efficient. The results of simulation study on heritability showed that heightening of both general heritability and interaction heritability of genotype x

  6. Genetic Analysis of Grain Filling Rate Using Conditional QTL Mapping in Maize

    PubMed Central

    Cui, Zitian; Hu, Yanmin; Wang, Bin; Tang, Jihua

    2013-01-01

    The grain filling rate (GFR) is an important dynamic trait that determines the final grain yield and is controlled by a network of genes and environment factors. To determine the genetic basis of the GFR, a conditional quantitative trait locus (QTL) analysis method was conducted using time-related phenotypic values of the GFR collected from a set of 243 immortalized F2 (IF2) population, which were evaluated at two locations over 2 years. The GFR gradually rose in the 0–15 days after pollination (DAP) and 16–22 DAP, reaching a maximum at 23–29 DAP, and then gradually decreasing. The variation of kernel weight (KW) was mainly decided by the GFR, and not by the grain filling duration (GFD). Thirty-three different unconditional QTLs were identified for the GFR at the six sampling stages over 2 years. Among them, QTLs qGFR7b, qGFR9 and qGFR6d were identified at the same stages at two locations over 2 years. In addition, 14 conditional QTLs for GFR were detected at five stages. The conditional QTL qGFR7c was identified at stage V|IV (37–43 DAP) at two locations over 2 years, and qGFR7b was detected at the sixth stage (44–50 DAP) in all four environments, except at Anyang location in 2009. QTLs qQTL7b and qQTL6f were identified by unconditional and conditional QTL mapping at the same stages, and might represent major QTLs for regulating the GFR in maize in the IF2 population. Moreover, most of the QTLs identified were co-located with QTLs from previous studies that were associated with GFR, enzyme activities of starch synthesis, soluble carbohydrates, and grain filling related genes. These results indicated that the GFR is regulated by many genes, which are specifically expressed at different grain filling stages, and the specific expression of the genes between 16–35 DAP might be very important for deciding the final kernel weight. PMID:23441180

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

    PubMed Central

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

    2005-01-01

    Background 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. Results 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. Conclusion 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. PMID:15941487

  8. Combining powers of linkage and association mapping for precise dissection of QTL controlling resistance to gray leaf spot disease in maize (Zea mays L.).

    PubMed

    Mammadov, Jafar; Sun, Xiaochun; Gao, Yanxin; Ochsenfeld, Cherie; Bakker, Erica; Ren, Ruihua; Flora, Jonathan; Wang, Xiujuan; Kumpatla, Siva; Meyer, David; Thompson, Steve

    2015-11-10

    Gray Leaf Spot (GLS causal agents Cercospora zeae-maydis and Cercospora zeina) is one of the most important foliar diseases of maize in all areas where the crop is being cultivated. Although in the USA the situation with GLS severity is not as critical as in sub-Saharan Africa or Brazil, the evidence of climate change, increasing corn monoculture as well as the narrow genetic base of North American resistant germplasm can turn the disease into a serious threat to US corn production. The development of GLS resistant cultivars is one way to control the disease. In this study we combined the high QTL detection power of genetic linkage mapping with the high resolution power of genome-wide association study (GWAS) to precisely dissect QTL controlling GLS resistance and identify closely linked molecular markers for robust marker-assisted selection and trait introgression. Using genetic linkage analysis with a small bi-parental mapping population, we identified four GLS resistance QTL on chromosomes 1, 6, 7, and 8, which were validated by GWAS. GWAS enabled us to dramatically increase the resolution within the confidence intervals of the above-mentioned QTL. Particularly, GWAS revealed that QTLGLSchr8, detected by genetic linkage mapping as a locus with major effect, was likely represented by two QTL with smaller effects. Conducted in parallel, GWAS of days-to-silking demonstrated the co-localization of flowering time QTL with GLS resistance QTL on chromosome 7 indicating that either QTLGLSchr7 is a flowering time QTL or it is a GLS resistance QTL that co-segregates with the latter. As a result, this genetic linkage - GWAS hybrid mapping system enabled us to identify one novel GLS resistance QTL (QTLGLSchr8a) and confirm with more refined positions four more previously mapped QTL (QTLGLSchr1, QTLGLSchr6, QTLGLSchr7, and QTLGLSchr8b). Through the novel Single Donor vs. Elite Panel method we were able to identify within QTL confidence intervals SNP markers that would be

  9. Integrating QTL mapping and transcriptomics identifies candidate genes underlying QTLs associated with soybean tolerance to low-phosphorus stress.

    PubMed

    Zhang, Dan; Zhang, Hengyou; Chu, Shanshan; Li, Hongyan; Chi, Yingjun; Triebwasser-Freese, Daniella; Lv, Haiyan; Yu, Deyue

    2017-01-01

    Soybean is a high phosphorus (P) demand species that is sensitive to low-P stress. Although many quantitative trait loci (QTL) for P efficiency have been identified in soybean, but few of these have been cloned and agriculturally applied mainly due to various limitations on identifying suitable P efficiency candidate genes. Here, we combined QTL mapping, transcriptome profiling, and plant transformation to identify candidate genes underlying QTLs associated with low-P tolerance and response mechanisms to low-P stress in soybean. By performing QTL linkage mapping using 152 recombinant inbred lines (RILs) that were derived from a cross between a P-efficient variety, Nannong 94-156, and P-sensitive Bogao, we identified four major QTLs underlying P efficiency. Within these four QTL regions, 34/81 candidate genes in roots/leaves were identified using comparative transcriptome analysis between two transgressive RILs, low-P tolerant genotype B20 and sensitive B18. A total of 22 phosphatase family genes were up-regulated significantly under low-P condition in B20. Overexpression of an acid phosphatase candidate gene, GmACP2, in soybean hairy roots increased P efficiency by 15.43-24.54 % compared with that in controls. Our results suggest that integrating QTL mapping and transcriptome profiling could be useful for rapidly identifying candidate genes underlying complex traits, and phosphatase-encoding genes, such as GmACP2, play important roles involving in low-P stress tolerance in soybean.

  10. eQTL mapping identify insertion and deletion specific eQTLs in multiple tissues

    PubMed Central

    Huang, Jinyan; Chen, Jun; Esparza, Jorge; Ding, Jun; Elder, James; Abecasis, Goncalo R; Lee, Young-Ae; Lathrop, G. Mark; Moffatt, Miriam F; Cookson, William O C; Liang, Liming

    2016-01-01

    GenomeC wide gene expression quantitative trait loci (eQTL) mapping have been focused on single nucleotide polymorphisms and have helped interpret findings from diseases mapping studies. The functional effect of structure variants, especially short insertions and deletions (indel) has not been well investigated. Here we imputed 1,380,133 indels based on the latest 1000 Genomes Project panel into 3 eQTL datasets from multiple tissues. Imputation of indels increased 9.9% power and identified indel specific eQTLs for 325 genes. We found introns and vicinities of UTRs were more enriched of indel eQTLs and 3.6 (singleC tissue)C 9.2%(multiC tissue) of previous identified eSNPs were taggers of eindels. Functional analyses identified epigenetics marks, gene ontology categories and disease GWAS loci affected by SNPs and indels eQTLs showing tissueC consistent or tissueC specific effects. This study provides new insights into the underlying genetic architecture of gene expression across tissues and new resource to interpret function of diseases and traits associated structure variants. PMID:25951796

  11. QTL mapping of cucumber fruit flesh thickness by SLAF-seq

    PubMed Central

    Xu, Xuewen; Lu, Lu; Zhu, Biyun; Xu, Qiang; Qi, Xiaohua; Chen, Xuehao

    2015-01-01

    Cucumber is an agriculturally and economically important vegetable crop worldwide. Fruit flesh thickness is an important trait for cucumber and also a central determinant of yield, yet little is known about the underlying mechanism of this trait. In this study, bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) was applied to finely map the gene that underlies fruit flesh thickness in cucumber. A 0.19-Mb-long quantitative trait locus on chromosome 2 controlling fruit flesh thickness (QTL fft2.1) was identified and further confirmed by simple sequence repeat (SSR) marker-based classical QTL mapping in 138 F2 individuals. Gene prediction of this 0.19-Mb region identified 20 genes. Quantitative RT-PCR revealed higher expression levels of Csa2 M058670.1 (SET domain protein-lysine methyltransferase) in D8 (thick fruit flesh parent) compared with that in XUE1 (thin fruit flesh parent) during fruit development. Sequence alignment analysis of Csa2M058670.1 from thick and thin fruit flesh cucumber lines revealed a 4-bp deletion mutation in the promoter region of this candidate gene, which may result in the loss of Csa2M058670.1 activation in thin fruit flesh lines. The data presented herein suggest that Csa2M058670.1 is a possible candidate gene for controlling flesh thickness in cucumber. PMID:26508560

  12. The mouse QTL map helps interpret human genome-wide association studies for HDL cholesterol.

    PubMed

    Leduc, Magalie S; Lyons, Malcolm; Darvishi, Katayoon; Walsh, Kenneth; Sheehan, Susan; Amend, Sarah; Cox, Allison; Orho-Melander, Marju; Kathiresan, Sekar; Paigen, Beverly; Korstanje, Ron

    2011-06-01

    Genome-wide association (GWA) studies represent a powerful strategy for identifying susceptibility genes for complex diseases in human populations but results must be confirmed and replicated. Because of the close homology between mouse and human genomes, the mouse can be used to add evidence to genes suggested by human studies. We used the mouse quantitative trait loci (QTL) map to interpret results from a GWA study for genes associated with plasma HDL cholesterol levels. We first positioned single nucleotide polymorphisms (SNPs) from a human GWA study on the genomic map for mouse HDL QTL. We then used mouse bioinformatics, sequencing, and expression studies to add evidence for one well-known HDL gene (Abca1) and three newly identified genes (Galnt2, Wwox, and Cdh13), thus supporting the results of the human study. For GWA peaks that occur in human haplotype blocks with multiple genes, we examined the homologous regions in the mouse to prioritize the genes using expression, sequencing, and bioinformatics from the mouse model, showing that some genes were unlikely candidates and adding evidence for candidate genes Mvk and Mmab in one haplotype block and Fads1 and Fads2 in the second haplotype block. Our study highlights the value of mouse genetics for evaluating genes found in human GWA studies.

  13. [The construction of the genetic map and QTL locating analysis on chromosome 2 in swine].

    PubMed

    Qu, Yan-Chun; Deng, Chang-Yan; Xiong, Yuan-Zhu; Zheng, Rong; Yu, Li; Su, Yu-Hong; Liu, Gui-Lan

    2002-01-01

    The study constructed the genetic linkage map of porcine chromosome 2 and further analysis of quantitative trait loci was conducted. The results of the study demonstrated that all 7 microsatellite loci we chose were with relatively high polymorphism, and its polymorphic information content was from 0.40182 to 0.58477. The genetic map we constructed for resource family was 152.9 cM in length, with the order of all loci highly consistent with the USDA map. All marker intervals were longer than USDA map with the interval between marker Sw2516 and Sw1201 as an exception. Furthermore, we conducted QTLs locating analysis by combining the genetic map with the phenotypic data. QTLs affecting lively estimated traits such as lean meat percentage, were located at 60-65 cM on chromosome 2, while QTLs for the height and marbling of Longissmus dorsi muscle were located at 20 cM and 55 cM, respectively Among them, QTL for estimated lean meat percentage was significant at chromosome-wise level (P < 0.01) and was responsible for 21.55% of the phenotypic variance. QTLs for the height and marbling of Longissmus dorsi muscle were responsible for 10.12% and 10.97% of the phenotypic variance, respectively. The additive and dominance effect of lively estimated traits were in the inverse tendency, while the QTL for the height of Longissmus dorsi muscle had its additive and dominance effect in the same tendency and was with advantageous allele in Large White. The QTLs we detected had relatively large effect on phenotype and built a basis for molecular marker assisted selection and breeding.

  14. QTL mapping for fruit quality in Citrus using DArTseq markers.

    PubMed

    Curtolo, Maiara; Cristofani-Yaly, Mariângela; Gazaffi, Rodrigo; Takita, Marco Aurélio; Figueira, Antonio; Machado, Marcos Antonio

    2017-04-12

    Citrus breeding programs have many limitations associated with the species biology and physiology, requiring the incorporation of new biotechnological tools to provide new breeding possibilities. Diversity Arrays Technology (DArT) markers, combined with next-generation sequencing, have wide applicability in the construction of high-resolution genetic maps and in quantitative trait locus (QTL) mapping. This study aimed to construct an integrated genetic map using full-sib progeny derived from Murcott tangor and Pera sweet orange and DArTseq™ molecular markers and to perform QTL mapping of twelve fruit quality traits. A controlled Murcott x Pera crossing was conducted at the Citrus Germplasm Repository at the Sylvio Moreira Citrus Centre of the Agronomic Institute (IAC) located in Cordeirópolis, SP, in 1997. In 2012, 278 F1 individuals out of a family of 312 confirmed hybrid individuals were analyzed for fruit traits and genotyped using the DArTseq markers. Using OneMap software to obtain the integrated genetic map, we considered only the DArT loci that showed no segregation deviation. The likelihood ratio and the genomic information from the available Citrus sinensis L. Osbeck genome were used to determine the linkage groups (LGs). The resulting integrated map contained 661 markers in 13 LGs, with a genomic coverage of 2,774 cM and a mean density of 0.23 markers/cM. The groups were assigned to the nine Citrus haploid chromosomes; however, some of the chromosomes were represented by two LGs due the lack of information for a single integration, as in cases where markers segregated in a 3:1 fashion. A total of 19 QTLs were identified through composite interval mapping (CIM) of the 12 analyzed fruit characteristics: fruit diameter (cm), height (cm), height/diameter ratio, weight (g), rind thickness (cm), segments per fruit, total soluble solids (TSS, %), total titratable acidity (TTA, %), juice content (%), number of seeds, TSS/TTA ratio and number of fruits per

  15. Novel Resampling Improves Statistical Power for Multiple-Trait QTL Mapping

    PubMed Central

    Cheng, Riyan; Doerge, R. W.; Borevitz, Justin

    2017-01-01

    Multiple-trait analysis typically employs models that associate a quantitative trait locus (QTL) with all of the traits. As a result, statistical power for QTL detection may not be optimal if the QTL contributes to the phenotypic variation in only a small proportion of the traits. Excluding QTL effects that contribute little to the test statistic can improve statistical power. In this article, we show that an optimal power can be achieved when the number of QTL effects is best estimated, and that a stringent criterion for QTL effect selection may improve power when the number of QTL effects is small but can reduce power otherwise. We investigate strategies for excluding trivial QTL effects, and propose a method that improves statistical power when the number of QTL effects is relatively small, and fairly maintains the power when the number of QTL effects is large. The proposed method first uses resampling techniques to determine the number of nontrivial QTL effects, and then selects QTL effects by the backward elimination procedure for significance test. We also propose a method for testing QTL-trait associations that are desired for biological interpretation in applications. We validate our methods using simulations and Arabidopsis thaliana transcript data. PMID:28064191

  16. Quantitative Trait Loci Mapping of the Mouse Plasma Proteome (pQTL)

    PubMed Central

    Holdt, Lesca M.; von Delft, Annette; Nicolaou, Alexandros; Baumann, Sven; Kostrzewa, Markus; Thiery, Joachim; Teupser, Daniel

    2013-01-01

    A current challenge in the era of genome-wide studies is to determine the responsible genes and mechanisms underlying newly identified loci. Screening of the plasma proteome by high-throughput mass spectrometry (MALDI-TOF MS) is considered a promising approach for identification of metabolic and disease processes. Therefore, plasma proteome screening might be particularly useful for identifying responsible genes when combined with analysis of variation in the genome. Here, we describe a proteomic quantitative trait locus (pQTL) study of plasma proteome screens in an F2 intercross of 455 mice mapped with 177 genetic markers across the genome. A total of 69 of 176 peptides revealed significant LOD scores (≥5.35) demonstrating strong genetic regulation of distinct components of the plasma proteome. Analyses were confirmed by mechanistic studies and MALDI-TOF/TOF, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses of the two strongest pQTLs: A pQTL for mass-to-charge ratio (m/z) 3494 (LOD 24.9, D11Mit151) was identified as the N-terminal 35 amino acids of hemoglobin subunit A (Hba) and caused by genetic variation in Hba. Another pQTL for m/z 8713 (LOD 36.4; D1Mit111) was caused by variation in apolipoprotein A2 (Apoa2) and cosegregated with HDL cholesterol. Taken together, we show that genome-wide plasma proteome profiling in combination with genome-wide genetic screening aids in the identification of causal genetic variants affecting abundance of plasma proteins. PMID:23172855

  17. Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

    PubMed Central

    Shao, Changwei; Niu, Yongchao; Rastas, Pasi; Liu, Yang; Xie, Zhiyuan; Li, Hengde; Wang, Lei; Jiang, Yong; Tai, Shuaishuai; Tian, Yongsheng; Sakamoto, Takashi; Chen, Songlin

    2015-01-01

    High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1–8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species. PMID:25762582

  18. Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis.

    PubMed

    Shao, Changwei; Niu, Yongchao; Rastas, Pasi; Liu, Yang; Xie, Zhiyuan; Li, Hengde; Wang, Lei; Jiang, Yong; Tai, Shuaishuai; Tian, Yongsheng; Sakamoto, Takashi; Chen, Songlin

    2015-04-01

    High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  19. Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize

    PubMed Central

    Li, Xiaopeng; Zhou, Zijian; Ding, Junqiang; Wu, Yabin; Zhou, Bo; Wang, Ruixia; Ma, Jinliang; Wang, Shiwei; Zhang, Xuecai; Xia, Zongliang; Chen, Jiafa; Wu, Jianyu

    2016-01-01

    Plant height (PH) and ear height (EH) are two very important agronomic traits related to the population density and lodging in maize. In order to better understand of the genetic basis of nature variation in PH and EH, two bi-parental populations and one genome-wide association study (GWAS) population were used to map quantitative trait loci (QTL) for both traits. Phenotypic data analysis revealed a wide normal distribution and high heritability for PH and EH in the three populations, which indicated that maize height is a highly polygenic trait. A total of 21 QTL for PH and EH in three common genomic regions (bin 1.05, 5.04/05, and 6.04/05) were identified by QTL mapping in the two bi-parental populations under multiple environments. Additionally, 41 single nucleotide polymorphisms (SNPs) were identified for PH and EH by GWAS, of which 29 SNPs were located in 19 unique candidate gene regions. Most of the candidate genes were related to plant growth and development. One QTL on Chromosome 1 was further verified in a near-isogenic line (NIL) population, and GWAS identified a C2H2 zinc finger family protein that maybe the candidate gene for this QTL. These results revealed that nature variation of PH and EH are strongly controlled by multiple genes with low effect and facilitated a better understanding of the underlying mechanism of height in maize. PMID:27379126

  20. Linkage mapping and identification of QTL affecting deoxynivalenol (DON) content (Fusarium resistance) in oats (Avena sativa L.).

    PubMed

    He, Xinyao; Skinnes, Helge; Oliver, Rebekah E; Jackson, Eric W; Bjørnstad, Asmund

    2013-10-01

    Mycotoxins caused by Fusarium spp. is a major concern on food and feed safety in oats, although Fusarium head blight (FHB) is often less apparent than in other small grain cereals. Breeding resistant cultivars is an economic and environment-friendly way to reduce toxin content, either by the identification of resistance QTL or phenotypic evaluation. Both are little explored in oats. A recombinant-inbred line population, Hurdal × Z595-7 (HZ595, with 184 lines), was used for QTL mapping and was phenotyped for 3 years. Spawn inoculation was applied and deoxynivalenol (DON) content, FHB severity, days to heading and maturity (DH and DM), and plant height (PH) were measured. The population was genotyped with DArTs, AFLPs, SSRs and selected SNPs, and a linkage map of 1,132 cM was constructed, covering all 21 oat chromosomes. A QTL for DON on chromosome 17A/7C, tentatively designated as Qdon.umb-17A/7C, was detected in all experiments using composite interval mapping, with phenotypic effects of 12.2–26.6 %. In addition, QTL for DON were also found on chromosomes 5C, 9D, 13A, 14D and unknown_3, while a QTL for FHB was found on 11A. Several of the DON/FHB QTL coincided with those for DH, DM and/or PH. A half-sib population of HZ595, Hurdal × Z615-4 (HZ615, with 91 lines), was phenotyped in 2011 for validation of QTL found in HZ595, and Qdon.umb-17A/7C was again localized with a phenotypic effect of 12.4 %. Three SNPs closely linked to Qdon.umb-17A/7C were identified in both populations, and one each for QTL on 5C, 11A and 13A were identified in HZ595. These SNPs, together with those yet to be identified, could be useful in marker-assisted selection to pyramiding resistance QTL.

  1. QTL mapping of soybean oil content for marker-assisted selection in plant breeding program.

    PubMed

    Leite, D C; Pinheiro, J B; Campos, J B; Di Mauro, A O; Unêda-Trevisoli, S H

    2016-03-18

    The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.

  2. Variable selection for large p small n regression models with incomplete data: Mapping QTL with epistases

    PubMed Central

    Zhang, Min; Zhang, Dabao; Wells, Martin T

    2008-01-01

    Background Identifying quantitative trait loci (QTL) for both additive and epistatic effects raises the statistical issue of selecting variables from a large number of candidates using a small number of observations. Missing trait and/or marker values prevent one from directly applying the classical model selection criteria such as Akaike's information criterion (AIC) and Bayesian information criterion (BIC). Results We propose a two-step Bayesian variable selection method which deals with the sparse parameter space and the small sample size issues. The regression coefficient priors are flexible enough to incorporate the characteristic of "large p small n" data. Specifically, sparseness and possible asymmetry of the significant coefficients are dealt with by developing a Gibbs sampling algorithm to stochastically search through low-dimensional subspaces for significant variables. The superior performance of the approach is demonstrated via simulation study. We also applied it to real QTL mapping datasets. Conclusion The two-step procedure coupled with Bayesian classification offers flexibility in modeling "large p small n" data, especially for the sparse and asymmetric parameter space. This approach can be extended to other settings characterized by high dimension and low sample size. PMID:18510743

  3. 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...

  4. Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays.

    PubMed

    Dell'Acqua, Matteo; Gatti, Daniel M; Pea, Giorgio; Cattonaro, Federica; Coppens, Frederik; Magris, Gabriele; Hlaing, Aye L; Aung, Htay H; Nelissen, Hilde; Baute, Joke; Frascaroli, Elisabetta; Churchill, Gary A; Inzé, Dirk; Morgante, Michele; Pè, Mario Enrico

    2015-09-11

    Maize (Zea mays) is a globally produced crop with broad genetic and phenotypic variation. New tools that improve our understanding of the genetic basis of quantitative traits are needed to guide predictive crop breeding. We have produced the first balanced multi-parental population in maize, a tool that provides high diversity and dense recombination events to allow routine quantitative trait loci (QTL) mapping in maize. We produced 1,636 MAGIC maize recombinant inbred lines derived from eight genetically diverse founder lines. The characterization of 529 MAGIC maize lines shows that the population is a balanced, evenly differentiated mosaic of the eight founders, with mapping power and resolution strengthened by high minor allele frequencies and a fast decay of linkage disequilibrium. We show how MAGIC maize may find strong candidate genes by incorporating genome sequencing and transcriptomics data. We discuss three QTL for grain yield and three for flowering time, reporting candidate genes. Power simulations show that subsets of MAGIC maize might achieve high-power and high-definition QTL mapping. We demonstrate MAGIC maize's value in identifying the genetic bases of complex traits of agronomic relevance. The design of MAGIC maize allows the accumulation of sequencing and transcriptomics layers to guide the identification of candidate genes for a number of maize traits at different developmental stages. The characterization of the full MAGIC maize population will lead to higher power and definition in QTL mapping, and lay the basis for improved understanding of maize phenotypes, heterosis included. MAGIC maize is available to researchers.

  5. Mapping and QTL analysis of drought tolerance in a spring wheat population using AFLP and DArt markers

    USDA-ARS?s Scientific Manuscript database

    Water availability is commonly the most limiting factor to crop production. This study was conducted to map quantitative trait loci (QTL) involved in drought tolerance in wheat (Triticum aestivum L.) to enable their use for marker assisted selection (MAS) in breeding. Using amplified fragment leng...

  6. Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations

    PubMed Central

    2011-01-01

    Background Common bacterial blight (CBB), incited by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Host resistance is practically the most effective and environmentally-sound approach to control CBB. Unlike conventional QTL discovery strategies, in which bi-parental populations (F2, RIL, or DH) need to be developed, association mapping-based strategies can use plant breeding populations to synchronize QTL discovery and cultivar development. Results A population of 469 dry bean lines of different market classes representing plant materials routinely developed in a bean breeding program were used. Of them, 395 lines were evaluated for CBB resistance at 14 and 21 DAI (Days After Inoculation) in the summer of 2009 in an artificially inoculated CBB nursery in south-western Ontario. All lines were genotyped using 132 SNPs (Single Nucleotide Polymorphisms) evenly distributed across the genome. Of the 132 SNPs, 26 SNPs had more than 20% missing data, 12 SNPs were monomorphic, and 17 SNPs had a MAF (Minor Allelic Frequency) of less than 0.20, therefore only 75 SNPs were used for association study, based on one SNP per locus. The best possible population structure was to assign 36% and 64% of the lines into Andean and Mesoamerican subgroups, respectively. Kinship analysis also revealed complex familial relationships among all lines, which corresponds with the known pedigree history. MLM (Mixed Linear Model) analysis, including population structure and kinship, was used to discover marker-trait associations. Eighteen and 22 markers were significantly associated with CBB rating at 14 and 21 DAI, respectively. Fourteen markers were significant for both dates and the markers UBC420, SU91, g321, g471, and g796 were highly significant (p ≤ 0.001). Furthermore, 12 significant SNP markers were co-localized with or close to the CBB-QTLs identified previously in bi-parental QTL mapping

  7. Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii

    PubMed Central

    Bai, Zhi-Yi; Han, Xue-Kai; Liu, Xiao-Jun; Li, Qing-Qing; Li, Jia-Le

    2016-01-01

    A high-density genetic map is essential for quantitative trait locus (QTL) fine mapping. In this study, 4,508 effective single nucleotide polymorphism markers (detected using specific-locus amplified fragment sequencing) and 475 microsatellites were mapped to 19 linkage groups (LGs) using a family with 157 individuals. The map spanned 2,713 cM, with an average of 259 markers and 79 loci per LG and an average inter-marker distance of 1.81 cM. To identify QTLs for pearl quality traits, 26 putatively significant QTLs were detected for 10 traits, including, three for shell width, seven for body weight, two for shell weight, two for margin mantle weight, five for inner mantle weight, and seven for shell nacre colour. Among them, five QTLs associated with shell nacre colour were mapped to LG17 and explained 19.7% to 22.8% of the trait variation; this suggests that some important genes or loci determine shell nacre colour in LG17. The linkage map and mapped QTLs for shell nacre colour would be useful for improving the quality of Hyriopsis cumingii via marker-assisted selection. PMID:27587236

  8. Genetic Mapping and QTL Analysis of Growth-Related Traits in Pinctada fucata Using Restriction-Site Associated DNA Sequencing

    PubMed Central

    Li, Yaoguo; He, Maoxian

    2014-01-01

    The pearl oyster, Pinctada fucata (P. fucata), is one of the marine bivalves that is predominantly cultured for pearl production. To obtain more genetic information for breeding purposes, we constructed a high-density linkage map of P. fucata and identified quantitative trait loci (QTL) for growth-related traits. One F1 family, which included the two parents, 48 largest progeny and 50 smallest progeny, was sampled to construct a linkage map using restriction site-associated DNA sequencing (RAD-Seq). With low coverage data, 1956.53 million clean reads and 86,342 candidate RAD loci were generated. A total of 1373 segregating SNPs were used to construct a sex-average linkage map. This spanned 1091.81 centimorgans (cM), with 14 linkage groups and an average marker interval of 1.41 cM. The genetic linkage map coverage, Coa, was 97.24%. Thirty-nine QTL-peak loci, for seven growth-related traits, were identified using the single-marker analysis, nonparametric mapping Kruskal-Wallis (KW) test. Parameters included three for shell height, six for shell length, five for shell width, four for hinge length, 11 for total weight, eight for soft tissue weight and two for shell weight. The QTL peak loci for shell height, shell length and shell weight were all located in linkage group 6. The genotype frequencies of most QTL peak loci showed significant differences between the large subpopulation and the small subpopulation (P<0.05). These results highlight the effectiveness of RAD-Seq as a tool for generation of QTL-targeted and genome-wide marker data in the non-model animal, P. fucata, and its possible utility in marker-assisted selection (MAS). PMID:25369421

  9. SNP Discovery and QTL Mapping of Sclerotinia Basal Stalk Rot Resistance in Sunflower using Genotyping-by-Sequencing.

    PubMed

    Talukder, Zahirul I; Seiler, Gerald J; Song, Qijian; Ma, Guojia; Qi, Lili

    2016-11-01

    Basal stalk rot (BSR), caused by the ascomycete fungus (Lib.) de Bary, is a serious disease of sunflower ( L.) in the cool and humid production areas of the world. Quantitative trait loci (QTL) for BSR resistance were identified in a sunflower recombinant inbred line (RIL) population derived from the cross HA 441 × RHA 439. A genotyping-by-sequencing (GBS) approach was adapted to discover single nucleotide polymorphism (SNP) markers. A genetic linkage map was developed comprised of 1053 SNP markers on 17 linkage groups (LGs) spanning 1401.36 cM. The RILs were tested in five environments (locations and years) for resistance to BSR. Quantitative trait loci were identified in each environment separately and also with integrated data across environments. A total of six QTL were identified in all five environments: one of each on LGs 4, 9, 10, 11, 16, and 17. The most significant QTL, and , were identified at multiple environments on LGs 10 and 17, explaining 31.6 and 20.2% of the observed phenotypic variance, respectively. The remaining four QTL, , , , and , were detected in only one environment on LGs 4, 9, 11, and 16, respectively. Each of these QTL explains between 6.4 and 10.5% of the observed phenotypic variation in the RIL population. Alleles conferring increased resistance were contributed by both parents. The potential of the and in marker-assisted selection (MAS) breeding are discussed. Copyright © 2016 Crop Science Society of America.

  10. Genetic Linkage Map Construction and QTL Analysis of Two Interspecific Reproductive Isolation Traits in Sponge Gourd

    PubMed Central

    Wu, Haibin; He, Xiaoli; Gong, Hao; Luo, Shaobo; Li, Mingzhu; Chen, Junqiu; Zhang, Changyuan; Yu, Ting; Huang, Wangping; Luo, Jianning

    2016-01-01

    The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 93075 [L. cylindrica (L.) Roem.]. The map spans 1436.12 CentiMorgans (cM), with an average of 8.11 cM among markers, and consists of 177 EST-SSR markers distributed in 14 linkage groups (LG) with an average of 102.58 cM per LG. Meanwhile, we conducted colinearity analysis between the sequences of EST-SSR markers and the genomic sequences of cucumber, melon and watermelon. On the basis of genetic linkage map, we conducted QTL mapping of two reproductive isolation traits in sponge gourd, which were the flowering time and hybrid male sterility. Two putative QTLs associated with flowering time (FT) were both detected on LG 1. The accumulated contribution of these two QTLs explained 38.07% of the total phenotypic variance (PV), and each QTL explained 15.36 and 22.71% of the PV respectively. Four QTLs for pollen fertility (PF) were identified on LG 1 (qPF1.1 and qPF1.2), LG 3 (qPF3) and LG 7 (qPF7), respectively. The percentage of PF explained by these QTLs varied from 2.91 to 16.79%, and all together the four QTLs accounted for 39.98% of the total PV. Our newly developed EST-SSR markers and linkage map are very useful for gene mapping, comparative genomics and molecular marker-assisted breeding. These QTLs for interspecific reproductive isolation will also contribute to the cloning of genes relating to interspecific reproductive isolation and the utilization of interspecific heterosis in sponge gourd in further studies. PMID:27458467

  11. Genetic Linkage Map Construction and QTL Analysis of Two Interspecific Reproductive Isolation Traits in Sponge Gourd.

    PubMed

    Wu, Haibin; He, Xiaoli; Gong, Hao; Luo, Shaobo; Li, Mingzhu; Chen, Junqiu; Zhang, Changyuan; Yu, Ting; Huang, Wangping; Luo, Jianning

    2016-01-01

    The hybrids between Luffa acutangula (L.) Roxb. and L.cylindrica (L.) Roem. have strong heterosis effects. However, some reproductive isolation traits hindered their normal hybridization and fructification, which was mainly caused by the flowering time and hybrid pollen sterility. In order to study the genetic basis of two interspecific reproductive isolation traits, we constructed a genetic linkage map using an F2 population derived from a cross between S1174 [L. acutangula (L.) Roxb.] and 93075 [L. cylindrica (L.) Roem.]. The map spans 1436.12 CentiMorgans (cM), with an average of 8.11 cM among markers, and consists of 177 EST-SSR markers distributed in 14 linkage groups (LG) with an average of 102.58 cM per LG. Meanwhile, we conducted colinearity analysis between the sequences of EST-SSR markers and the genomic sequences of cucumber, melon and watermelon. On the basis of genetic linkage map, we conducted QTL mapping of two reproductive isolation traits in sponge gourd, which were the flowering time and hybrid male sterility. Two putative QTLs associated with flowering time (FT) were both detected on LG 1. The accumulated contribution of these two QTLs explained 38.07% of the total phenotypic variance (PV), and each QTL explained 15.36 and 22.71% of the PV respectively. Four QTLs for pollen fertility (PF) were identified on LG 1 (qPF1.1 and qPF1.2), LG 3 (qPF3) and LG 7 (qPF7), respectively. The percentage of PF explained by these QTLs varied from 2.91 to 16.79%, and all together the four QTLs accounted for 39.98% of the total PV. Our newly developed EST-SSR markers and linkage map are very useful for gene mapping, comparative genomics and molecular marker-assisted breeding. These QTLs for interspecific reproductive isolation will also contribute to the cloning of genes relating to interspecific reproductive isolation and the utilization of interspecific heterosis in sponge gourd in further studies.

  12. A medium density genetic map and QTL for behavioral and production traits in Japanese quail.

    PubMed

    Recoquillay, Julien; Pitel, Frédérique; Arnould, Cécile; Leroux, Sophie; Dehais, Patrice; Moréno, Carole; Calandreau, Ludovic; Bertin, Aline; Gourichon, David; Bouchez, Olivier; Vignal, Alain; Fariello, Maria Ines; Minvielle, Francis; Beaumont, Catherine; Leterrier, Christine; Le Bihan-Duval, Elisabeth

    2015-01-22

    Behavioral traits such as sociability, emotional reactivity and aggressiveness are major factors in animal adaptation to breeding conditions. In order to investigate the genetic control of these traits as well as their relationships with production traits, a study was undertaken on a large second generation cross (F2) between two lines of Japanese Quail divergently selected on their social reinstatement behavior. All the birds were measured for several social behaviors (social reinstatement, response to social isolation, sexual motivation, aggression), behaviors measuring the emotional reactivity of the birds (reaction to an unknown object, tonic immobility reaction), and production traits (body weight and egg production). We report the results of the first genome-wide QTL detection based on a medium density SNP panel obtained from whole genome sequencing of a pool of individuals from each divergent line. A genetic map was constructed using 2145 markers among which 1479 could be positioned on 28 different linkage groups. The sex-averaged linkage map spanned a total of 3057 cM with an average marker spacing of 2.1 cM. With the exception of a few regions, the marker order was the same in Japanese Quail and the chicken, which confirmed a well conserved synteny between the two species. The linkage analyses performed using QTLMAP software revealed a total of 45 QTLs related either to behavioral (23) or production (22) traits. The most numerous QTLs (15) concerned social motivation traits. Interestingly, our results pinpointed putative pleiotropic regions which controlled emotional reactivity and body-weight of birds (on CJA5 and CJA8) or their social motivation and the onset of egg laying (on CJA19). This study identified several QTL regions for social and emotional behaviors in the Quail. Further research will be needed to refine the QTL and confirm or refute the role of candidate genes, which were suggested by bioinformatics analysis. It can be hoped that the

  13. A high-density genetic map for anchoring genome sequences and identifying QTLs associated with dwarf vine in pumpkin (Cucurbita maxima Duch.).

    PubMed

    Zhang, Guoyu; Ren, Yi; Sun, Honghe; Guo, Shaogui; Zhang, Fan; Zhang, Jie; Zhang, Haiying; Jia, Zhangcai; Fei, Zhangjun; Xu, Yong; Li, Haizhen

    2015-12-24

    Pumpkin (Cucurbita maxima Duch.) is an economically important crop belonging to the Cucurbitaceae family. However, very few genomic and genetic resources are available for this species. As part of our ongoing efforts to sequence the pumpkin genome, high-density genetic map is essential for anchoring and orienting the assembled scaffolds. In addition, a saturated genetic map can facilitate quantitative trait locus (QTL) mapping. A set of 186 F2 plants derived from the cross of pumpkin inbred lines Rimu and SQ026 were genotyped using the genotyping-by-sequencing approach. Using the SNPs we identified, a high-density genetic map containing 458 bin-markers was constructed, spanning a total genetic distance of 2,566.8 cM across the 20 linkage groups of C. maxima with a mean marker density of 5.60 cM. Using this map we were able to anchor 58 assembled scaffolds that covered about 194.5 Mb (71.7%) of the 271.4 Mb assembled pumpkin genome, of which 44 (183.0 Mb; 67.4%) were oriented. Furthermore, the high-density genetic map was used to identify genomic regions highly associated with an important agronomic trait, dwarf vine. Three QTLs on linkage groups (LGs) 1, 3 and 4, respectively, were recovered. One QTL, qCmB2, which was located in an interval of 0.42 Mb on LG 3, explained 21.4% phenotypic variations. Within qCmB2, one gene, Cma_004516, encoding the gibberellin (GA) 20-oxidase in the GA biosynthesis pathway, had a 1249-bp deletion in its promoter in bush type lines, and its expression level was significantly increased during the vine growth and higher in vine type lines than bush type lines, supporting Cma_004516 as a possible candidate gene controlling vine growth in pumpkin. A high-density pumpkin genetic map was constructed, which was used to successfully anchor and orient the assembled genome scaffolds, and to identify QTLs highly associated with pumpkin vine length. The map provided a valuable resource for gene cloning and marker assisted breeding in pumpkin and

  14. QTL mapping of agronomic traits in tef [Eragrostis tef (Zucc) Trotter].

    PubMed

    Yu, Ju-Kyung; Graznak, Elizabeth; Breseghello, Flavio; Tefera, Hailu; Sorrells, Mark E

    2007-06-12

    Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4x = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5). Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs) was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5) had a beneficial effect. The extensive QTL data generated for tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia.

  15. QTL mapping of agronomic traits in tef [Eragrostis tef (Zucc) Trotter

    PubMed Central

    Yu, Ju-Kyung; Graznak, Elizabeth; Breseghello, Flavio; Tefera, Hailu; Sorrells, Mark E

    2007-01-01

    Background Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5). Results Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs) was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5) had a beneficial effect. Conclusion The extensive QTL data generated for tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia. PMID:17565675

  16. QTL mapping of leafy heads by genome resequencing in the RIL population of Brassica rapa.

    PubMed

    Yu, Xiang; Wang, Han; Zhong, Weili; Bai, Jinjuan; Liu, Pinglin; He, Yuke

    2013-01-01

    Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits.

  17. A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius

    PubMed Central

    Fountain, Toby; Ravinet, Mark; Naylor, Richard; Reinhardt, Klaus; Butlin, Roger K.

    2016-01-01

    The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides, and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread. Using 334 SNP markers obtained through RAD-sequencing, we constructed the first linkage map for the species, consisting of 14 putative linkage groups (LG), with a length of 407 cM and an average marker spacing of 1.3 cM. The linkage map was used to reassemble the recently published reference genome, facilitating refinement and validation of the current genome assembly. We detected a major QTL on LG12 associated with insecticide resistance, occurring in close proximity (1.2 Mb) to a carboxylesterase encoding candidate gene for pyrethroid resistance. This provides another example of this candidate gene playing a major role in determining survival in a bed bug population following pesticide resistance evolution. The recent availability of the bed bug genome, complete with a full list of potential candidate genes related to insecticide resistance, in addition to the linkage map generated here, provides an excellent resource for future research on the development and spread of insecticide resistance in this resurging pest species. PMID:27733453

  18. A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius.

    PubMed

    Fountain, Toby; Ravinet, Mark; Naylor, Richard; Reinhardt, Klaus; Butlin, Roger K

    2016-12-07

    The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides, and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread. Using 334 SNP markers obtained through RAD-sequencing, we constructed the first linkage map for the species, consisting of 14 putative linkage groups (LG), with a length of 407 cM and an average marker spacing of 1.3 cM. The linkage map was used to reassemble the recently published reference genome, facilitating refinement and validation of the current genome assembly. We detected a major QTL on LG12 associated with insecticide resistance, occurring in close proximity (1.2 Mb) to a carboxylesterase encoding candidate gene for pyrethroid resistance. This provides another example of this candidate gene playing a major role in determining survival in a bed bug population following pesticide resistance evolution. The recent availability of the bed bug genome, complete with a full list of potential candidate genes related to insecticide resistance, in addition to the linkage map generated here, provides an excellent resource for future research on the development and spread of insecticide resistance in this resurging pest species.

  19. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes.

    PubMed

    Weng, Yiqun; Colle, Marivi; Wang, Yuhui; Yang, Luming; Rubinstein, Mor; Sherman, Amir; Ophir, Ron; Grumet, Rebecca

    2015-09-01

    QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.

  20. Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

    PubMed Central

    Wu, Xiaolei; Zhong, Guohua; Findley, Seth D; Cregan, Perry; Stacey, Gary; Nguyen, Henry T

    2008-01-01

    Background Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy and an in silico approach to anchor molecular markers onto the soybean physical map. Results A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 BstY I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (~1× genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. In parallel, the 21,700 soybean Unigene set from NCBI was used to perform in silico mapping on 80,700 Williams 82 BAC end sequences (BES). This in silico analysis yielded 9,835 positive results anchored by 4152 unigenes that contributed to 1305 contigs and 1624 singletons. Among the 1305 contigs, 305 have not been previously anchored by PCR. Therefore, 1489 (78.8%) of 1893 contigs are anchored with molecular markers. These results are being integrated with BAC fingerprints to assemble the BAC contigs. Ultimately, these efforts will lead to an integrated physical and genetic map resource. Conclusion We demonstrated that the six-dimensional soybean BAC pools can be efficiently used to anchor markers to soybean BACs despite the complexity of the soybean genome. In addition to anchoring markers, the 6-D pooling method was also effective for targeting BAC clones for investigating gene families and

  1. Genetic marker anchoring by six-dimensional pools for development of a soybean physical map.

    PubMed

    Wu, Xiaolei; Zhong, Guohua; Findley, Seth D; Cregan, Perry; Stacey, Gary; Nguyen, Henry T

    2008-01-22

    Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy and an in silico approach to anchor molecular markers onto the soybean physical map. A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 BstY I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (approximately 1x genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. In parallel, the 21,700 soybean Unigene set from NCBI was used to perform in silico mapping on 80,700 Williams 82 BAC end sequences (BES). This in silico analysis yielded 9,835 positive results anchored by 4152 unigenes that contributed to 1305 contigs and 1624 singletons. Among the 1305 contigs, 305 have not been previously anchored by PCR. Therefore, 1489 (78.8%) of 1893 contigs are anchored with molecular markers. These results are being integrated with BAC fingerprints to assemble the BAC contigs. Ultimately, these efforts will lead to an integrated physical and genetic map resource. We demonstrated that the six-dimensional soybean BAC pools can be efficiently used to anchor markers to soybean BACs despite the complexity of the soybean genome. In addition to anchoring markers, the 6-D pooling method was also effective for targeting BAC clones for investigating gene families and duplicated regions

  2. The identification and mapping of candidate genes and QTL involved in the fatty acid desaturation pathway in Brassica napus.

    PubMed

    Smooker, A M; Wells, R; Morgan, C; Beaudoin, F; Cho, K; Fraser, F; Bancroft, I

    2011-04-01

    We constructed a linkage map for the population QDH, which was derived from a cross between an oilseed rape cultivar and a resynthesised Brassica napus. The linkage map included ten markers linked to loci orthologous to those encoding fatty acid biosynthesis genes in Arabidopsis thaliana. The QDH population contains a high level of allelic variation, particularly in the C genome. We conducted quantitative trait locus (QTL) analyses, using field data obtained over 3 years, for the fatty acid composition of seed oil. The population segregates for the two major loci controlling erucic acid content, on linkage groups A8 and C3, which quantitatively affect the content of other fatty acids and is a problem generally encountered when crossing "wild" germplasm with cultivated "double low" oilseed rape cultivars. We assessed three methods for QTL analysis, interval mapping, multiple QTL mapping and single marker regression analysis of the subset of lines with low erucic acid. We found the third of these methods to be most appropriate for our main purpose, which was the study of the genetic control of the desaturation of 18-carbon fatty acids. This method enabled us to decouple the effect of the segregation of the erucic acid-controlling loci and identify 34 QTL for fatty acid content of seed oil, 14 in the A genome and 20 in the C genome. The QTL indicate the presence of 13 loci with novel alleles inherited from the progenitors of the resynthesised B. napus that might be useful for modulating the content or extent of desaturation of polyunsaturated fatty acids, only one of which coincides with the anticipated position of a candidate gene, an orthologue of FAD2.

  3. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance.

    PubMed

    Yao, Nasser; Lee, Cheng-Ruei; Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders.

  4. A High-Density Genetic Linkage Map and QTL Fine Mapping for Body Weight in Crucian Carp (Carassius auratus) Using 2b-RAD Sequencing.

    PubMed

    Liu, Haiyang; Fu, Beide; Pang, Meixia; Feng, Xiu; Yu, Xiaomu; Tong, Jingou

    2017-08-07

    A high-resolution genetic linkage map is essential for a wide range of genetics and genomics studies such as comparative genomics analysis and QTL fine mapping. Crucian carp (Carassius auratus) is widely distributed in Eurasia, and is an important aquaculture fish worldwide. In this study, a high-density genetic linkage map was constructed for crucian carp using 2b-RAD technology. The consensus map contains 8487 SNP markers, assigning to 50 linkage groups (LGs) and spanning 3762.88 cM, with an average marker interval of 0.44 cM and genome coverage of 98.8%. The female map had 4410 SNPs, and spanned 3500.42 cM (0.79 cM/marker), while the male map had 4625 SNPs and spanned 3346.33 cM (0.72 cM/marker). The average recombination ratio of female to male was 2.13:1, and significant male-biased recombination suppressions were observed in LG47 and LG49. Comparative genomics analysis revealed a clear 2:1 syntenic relationship between crucian carp LGs and chromosomes of zebrafish and grass carp, and a 1:1 correspondence, but extensive chromosomal rearrangement, between crucian carp and common carp, providing evidence that crucian carp has experienced a fourth round of whole genome duplication (4R-WGD). Eight chromosome-wide QTL for body weight at 2 months after hatch were detected on five LGs, explaining 10.1-13.2% of the phenotypic variations. Potential candidate growth-related genes, such as an EGF-like domain and TGF-β, were identified within the QTL intervals. This high-density genetic map and QTL analysis supplies a basis for genome evolutionary studies in cyprinid fishes, genome assembly, and QTL fine mapping for complex traits in crucian carp. Copyright © 2017 Liu et al.

  5. Genetic mapping of sulfur assimilation genes reveals a QTL for onion bulb pungency.

    PubMed

    McCallum, John; Pither-Joyce, Meeghan; Shaw, Martin; Kenel, Fernand; Davis, Sheree; Butler, Ruth; Scheffer, John; Jakse, Jernej; Havey, Michael J

    2007-03-01

    Onion exhibits wide genetic and environmental variation in bioactive organosulfur compounds that impart pungency and health benefits. A PCR-based molecular marker map that included candidate genes for sulfur assimilation was used to identify genomic regions affecting pungency in the cross 'W202A' x 'Texas Grano 438'. Linkage mapping revealed that genes encoding plastidic ferredoxin-sulfite reductase (SiR) and plastidic ATP sulfurylase (ATPS) are closely linked (1-2 cM) on chromosome 3. Inbred F(3) families derived from the F(2 )population used to construct the genetic map were grown in replicated trials in two environments and bulb pungency was evaluated as pyruvic acid or lachrymatory factor. Broad-sense heritability of pungency was estimated to be 0.78-0.80. QTL analysis revealed significant associations of both pungency and bulb soluble solids content with marker intervals on chromosomes 3 and 5, which have previously been reported to condition pleiotropic effects on bulb carbohydrate composition. Highly significant associations (LOD 3.7-8.7) were observed between ATPS and SiR Loci and bulb pungency but not with bulb solids content. This association was confirmed in two larger, independently derived F(2) families from the same cross. Single-locus models suggested that the partially dominant locus associated with these candidate genes controls 30-50% of genetic variation in pungency in these pedigrees. These markers may provide a practical means to select for lower pungency without correlated selection for lowered solids.

  6. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.

    PubMed

    Pfender, W F; Saha, M C; Johnson, E A; Slabaugh, M B

    2011-05-01

    A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. A susceptible and a resistant plant were crossed to produce a pseudo-testcross population of 193 F(1) individuals. Markers were produced by the restriction-site associated DNA (RAD) process, which uses massively parallel and multiplexed sequencing of reduced-representation libraries. Additional simple sequence repeat (SSR) and sequence-tagged site (STS) markers were combined with the RAD markers to produce maps for the female (738 cM) and male (721 cM) parents. Stem rust phenotypes (number of pustules per plant) were determined in replicated greenhouse trials by inoculation with a field-collected, genetically heterogeneous population of urediniospores. The F(1) progeny displayed continuous distribution of phenotypes and transgressive segregation. We detected three resistance QTL. The most prominent QTL (qLpPg1) is located near 41 cM on linkage group (LG) 7 with a 2-LOD interval of 8 cM, and accounts for 30-38% of the stem rust phenotypic variance. QTL were detected also on LG1 (qLpPg2) and LG6 (qLpPg3), each accounting for approximately 10% of phenotypic variance. Alleles of loci closely linked to these QTL originated from the resistant parent for qLpPg1 and from both parents for qLpPg2 and qLpPg3. Observed quantitative nature of the resistance may be due to partial-resistance effects against all pathogen genotypes, or qualitative effects completely preventing infection by only some genotypes in the genetically mixed inoculum. RAD markers facilitated rapid construction of new genetic maps in this outcrossing species and will enable development of sequence-based markers linked to stem rust resistance in L. perenne.

  7. QTL Analysis and Nested Association Mapping for Adult Plant Resistance to Powdery Mildew in Two Bread Wheat Populations

    PubMed Central

    Ren, Yan; Hou, Weixiu; Lan, Caixia; Basnet, Bhoja R.; Singh, Ravi P.; Zhu, Wei; Cheng, Xiyong; Cui, Dangqun; Chen, Feng

    2017-01-01

    CIMMYT wheat (Triticum aestivum L.) lines Francolin#1 and Quaiu#3 displayed effective and stable adult plant resistance (APR) to Chinese Blumeria graminis f. sp. tritici isolates in the field. To elucidate their genetic basis of resistance, two recombinant inbred line (RIL) populations of their crosses with Avocet, the susceptible parent, were phenotyped in Zhengzhou and Shangqiu in the 2014–2015 and 2015–2016 cropping seasons. These populations were also genotyped with SSR (simple sequence repeat markers) and DArT (diversity arrays technology) markers. Two common significant quantitative trait loci (QTL) on wheat chromosomes 1BL and 4BL were detected in both populations by joint and individual inclusive composite interval mapping, explaining 20.3–28.7% and 9.6–15.9% of the phenotypic variance in Avocet × Francolin#1 and 4.8–11.5% and 10.8–18.9% in Avocet × Quaiu#3, respectively. Additional QTL were mapped on chromosomes 1DL and 5BL in Avocet × Francolin#1 and on 2DL and 6BS in Avocet × Quaiu#3. Among these, QPm.heau-1DL is probably a novel APR gene contributing 6.1–8.5% of total phenotypic variance. The QTL on 1BL corresponds to the pleiotropic multi-pathogen resistance gene Yr29/Lr46/Pm39, whereas the QTL on 2DL maps to a similar region where stripe rust resistance gene Yr54 is located. The QTL identified can potentially be used for the improvement of powdery mildew and rust resistance in wheat breeding. PMID:28798752

  8. Mapping QTL for popping expansion volume in popcorn with simple sequence repeat markers.

    PubMed

    Lu, H-J; Bernardo, R; Ohm, H W

    2003-02-01

    Popping expansion volume is the most important quality trait in popcorn ( Zea mays L.), but its genetics is not well understood. The objectives of this study were to map quantitative trait loci (QTLs) responsible for popping expansion volume in a popcorn x dent corn cross, and to compare the predicted efficiencies of phenotypic selection, marker-based selection, and marker-assisted selection for popping expansion volume. Of 259 simple sequence repeat (SSR) primer pairs screened, 83 pairs were polymorphic between the H123 (dent corn) and AG19 (popcorn) parental inbreds. Popping test data were obtained for 160 S(1) families developed from the [AG19(H123 x AG19)] BC(1) population. The heritability ( h(2)) for popping expansion volume on an S(1) family mean basis was 0.73. The presence of the gametophyte factor Ga1(s) in popcorn complicates the analysis of popcorn x dent corn crosses. But, from a practical perspective, the linkage between a favorable QTL allele and Ga1(s) in popcorn will lead to selection for the favorable QTL allele. Four QTLs, on chromosomes 1S, 3S, 5S and 5L, jointly explained 45% of the phenotypic variation. Marker-based selection for popping expansion volume would require less time and work than phenotypic selection. But due to the high h(2) of popping expansion volume, marker-based selection was predicted to be only 92% as efficient as phenotypic selection. Marker-assisted selection, which comprises index selection on phenotypic and marker scores, was predicted to be 106% as efficient as phenotypic selection. Overall, our results suggest that phenotypic selection will remain the preferred method for selection in popcorn x dent corn crosses.

  9. Construction of chromosome segment substitution lines enables QTL mapping for flowering and morphological traits in Brassica rapa

    PubMed Central

    Li, Xiaonan; Wang, Wenke; Wang, Zhe; Li, Kangning; Lim, Yong Pyo; Piao, Zhongyun

    2015-01-01

    Chromosome segment substitution lines (CSSLs) represent a powerful method for precise quantitative trait loci (QTL) detection of complex agronomical traits in plants. In this study, we used a marker-assisted backcrossing strategy to develop a population consisting of 63 CSSLs, derived from backcrossing of the F1 generated from a cross between two Brassica rapa subspecies: “Chiifu” (ssp. pekinensis), the Brassica “A” genome-represented line used as the donor, and “49caixin” (ssp. parachinensis), a non-heading cultivar used as the recipient. The 63 CSSLs covered 87.95% of the B. rapa genome. Among them, 39 lines carried a single segment; 15 lines, two segments; and nine lines, three or more segments of the donor parent chromosomes. To verify the potential advantage of these CSSL lines, we used them to locate QTL for six morphology-related traits. A total of 58 QTL were located on eight chromosomes for all six traits: 17 for flowering time, 14 each for bolting time and plant height, six for plant diameter, two for leaf width, and five for flowering stalk diameter. Co-localized QTL were mainly distributed on eight genomic regions in A01, A02, A05, A06, A08, A09, and A10, present in the corresponding CSSLs. Moreover, new chromosomal fragments that harbored QTL were identified using the findings of previous studies. The CSSL population constructed in our study paves the way for fine mapping and cloning of candidate genes involved in late bolting, flowering, and plant architecture-related traits in B. rapa. Furthermore, it has great potential for future marker-aided gene/QTL pyramiding of other interesting traits in B. rapa breeding. PMID:26106405

  10. Mapping of QTL for resistance to the Mediterranean corn borer attack using the intermated B73 x Mo17 (IBM) population of maize.

    PubMed

    Ordas, Bernardo; Malvar, Rosa A; Santiago, Rogelio; Sandoya, German; Romay, Maria C; Butron, Ana

    2009-11-01

    The Mediterranean corn borer or pink stem borer (MCB, Sesamia nonagrioides Lefebvre) causes important yield losses as a consequence of stalk tunneling and direct kernel damage. B73 and Mo17 are the source of the most commercial valuable maize inbred lines in temperate zones, while the intermated B73 x Mo17 (IBM) population is an invaluable source for QTL identification. However, no or few experiments have been carried out to detect QTL for corn borer resistance in the B73 x Mo17 population. The objective of this work was to locate QTL for resistance to stem tunneling and kernel damage by MCB in the IBM population. We detected a QTL for kernel damage at bin 8.05, although the effect was small and two QTL for stalk tunneling at bins 1.06 and 9.04 in which the additive effects were 4 cm, approximately. The two QTL detected for MCB resistance were close to other QTL consistently found for European corn borer (ECB, Ostrinia nubilalis Hübner) resistance, indicating mechanisms of resistance common to both pests or gene clusters controlling resistance to different plagues. The precise mapping achieved with the IBM population will facilitate the QTL pyramiding and the positional cloning of the detected QTL.

  11. Provirus-anchored long-range (PAL) mapping of mammalian genomes

    SciTech Connect

    Kurdi-Haidar, B.; Levine, F.; Roemer, K.; LaPorte, P.; Friedman, T. )

    1993-02-01

    To design a strategy for more efficient long-range physical mapping of large mammalian genomes, we have developed a method for directional mapping from anchor points of randomly integrated retroviral proviruses containing sequences that provide unique cleavage sites in the genome. Using this method, we have determined a physical map of approximately 1.6 Mb flanking an Mo MLV-proviral integration site in mouse NIH/3T3 cells. Our results indicate that this provirus-anchored long-range (PAL) mapping strategy, which uses only two proviral sequences as univeral hybridization probes, can potentially allow rapid construction of physical maps for chromosomal regions devoid of other genetic markers. 25 refs., 4 figs., 1 tab.

  12. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth1[OPEN

    PubMed Central

    Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Yang, Wanneng

    2017-01-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. PMID:28153923

  13. Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench).

    PubMed

    Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

    2014-12-01

    For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information.

  14. Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

    PubMed Central

    Yabe, Shiori; Hara, Takashi; Ueno, Mariko; Enoki, Hiroyuki; Kimura, Tatsuro; Nishimura, Satoru; Yasui, Yasuo; Ohsawa, Ryo; Iwata, Hiroyoshi

    2014-01-01

    For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information. PMID:25914583

  15. QTL mapping and candidate genes for resistance to Fusarium ear rot and fumonisin contamination in maize.

    PubMed

    Maschietto, Valentina; Colombi, Cinzia; Pirona, Raul; Pea, Giorgio; Strozzi, Francesco; Marocco, Adriano; Rossini, Laura; Lanubile, Alessandra

    2017-01-21

    Fusarium verticillioides is a common maize pathogen causing ear rot (FER) and contamination of the grains with the fumonisin B1 (FB1) mycotoxin. Resistance to FER and FB1 contamination are quantitative traits, affected by environmental conditions, and completely resistant maize genotypes to the pathogen are so far unknown. In order to uncover genomic regions associated to reduced FER and FB1 contamination and identify molecular markers for assisted selection, an F2:3 population of 188 progenies was developed crossing CO441 (resistant) and CO354 (susceptible) genotypes. FER severity and FB1 contamination content were evaluated over 2 years and sowing dates (early and late) in ears artificially inoculated with F. verticillioides by the use of either side-needle or toothpick inoculation techniques. Weather conditions significantly changed in the two phenotyping seasons and FER and FB1 content distribution significantly differed in the F3 progenies according to the year and the sowing time. Significant positive correlations (P < 0.01) were detected between FER and FB1 contamination, ranging from 0.72 to 0.81. A low positive correlation was determined between FB1 contamination and silking time (DTS). A genetic map was generated for the cross, based on 41 microsatellite markers and 342 single nucleotide polymorphisms (SNPs) derived from Genotyping-by-Sequencing (GBS). QTL analyses revealed 15 QTLs for FER, 17 QTLs for FB1 contamination and nine QTLs for DTS. Eight QTLs located on linkage group (LG) 1, 2, 3, 6, 7 and 9 were in common between FER and FB1, making possible the selection of genotypes with both low disease severity and low fumonisin contamination. Moreover, five QTLs on LGs 1, 2, 4, 5 and 9 located close to previously reported QTLs for resistance to other mycotoxigenic fungi. Finally, 24 candidate genes for resistance to F. verticillioides are proposed combining previous transcriptomic data with QTL mapping. This study identified a set of QTLs and

  16. Genetic Analysis and QTL Mapping of Fruit Peduncle Length in Cucumber (Cucumis sativus L.)

    PubMed Central

    Zhang, Song; Wang, Ye; Zhang, Sheng-Ping; Gu, Xing-Fang

    2016-01-01

    Mechanized harvesting of cucumbers offers significant advantages compared to manual labor as both shortages and costs of labor increase. However the efficient use of machines depends on breeding plants with longer peduncles, but the genetic and molecular basis of fruit peduncle development in cucumber is not well understood. In this study, F2 populations were developed from a cross between two inbred lines, 1101 with a long peduncle and 1694 with a short peduncle. These were grown at two field sites, Hainan, with a tropical marine climate, in December 2014, and Beijing, with a warm temperate climate, in May 2015. Electron microscope examination of the pith cells in the peduncles of the two parental lines showed that line 1101 had significantly greater numbers of smaller cells compared to line 1694. The inheritance of cucumber fruit peduncle length (FPL) was investigated by the mixed major gene and polygene inheritance model. Genetic analysis indicated that FPL in cucumber is quantitatively inherited and controlled by one additive major gene and additive-dominant polygenes (D-2 model). A total of 1460 pairs of SSR (simple sequence repeat) primers were analyzed to identify quantitative trait loci (QTLs). Two similar genetic maps with 78 SSR markers which covered 720.6 cM in seven linkage groups were constructed based on two F2 populations. QTL analysis from the data collected at the two field sites showed that there are two minor QTLs on chromosome 1, named qfpl1.1 and qfpl1.2, and one major QTL on chromosome 6, named qfpl6.1. The marker UW021226, which was the closest one to qfpl6.1, had an accuracy rate of 79.0% when tested against plants selected from populations of the two parents. The results from this study provide insights into the inheritance and molecular mechanism of the variation of FPL in cucumber, and further research will be carried out to fine map qfpl6.1 to develop more accurate markers for MAS breeding. PMID:27936210

  17. Genetic Analysis and QTL Mapping of Fruit Peduncle Length in Cucumber (Cucumis sativus L.).

    PubMed

    Song, Zi-Chao; Miao, Han; Zhang, Song; Wang, Ye; Zhang, Sheng-Ping; Gu, Xing-Fang

    2016-01-01

    Mechanized harvesting of cucumbers offers significant advantages compared to manual labor as both shortages and costs of labor increase. However the efficient use of machines depends on breeding plants with longer peduncles, but the genetic and molecular basis of fruit peduncle development in cucumber is not well understood. In this study, F2 populations were developed from a cross between two inbred lines, 1101 with a long peduncle and 1694 with a short peduncle. These were grown at two field sites, Hainan, with a tropical marine climate, in December 2014, and Beijing, with a warm temperate climate, in May 2015. Electron microscope examination of the pith cells in the peduncles of the two parental lines showed that line 1101 had significantly greater numbers of smaller cells compared to line 1694. The inheritance of cucumber fruit peduncle length (FPL) was investigated by the mixed major gene and polygene inheritance model. Genetic analysis indicated that FPL in cucumber is quantitatively inherited and controlled by one additive major gene and additive-dominant polygenes (D-2 model). A total of 1460 pairs of SSR (simple sequence repeat) primers were analyzed to identify quantitative trait loci (QTLs). Two similar genetic maps with 78 SSR markers which covered 720.6 cM in seven linkage groups were constructed based on two F2 populations. QTL analysis from the data collected at the two field sites showed that there are two minor QTLs on chromosome 1, named qfpl1.1 and qfpl1.2, and one major QTL on chromosome 6, named qfpl6.1. The marker UW021226, which was the closest one to qfpl6.1, had an accuracy rate of 79.0% when tested against plants selected from populations of the two parents. The results from this study provide insights into the inheritance and molecular mechanism of the variation of FPL in cucumber, and further research will be carried out to fine map qfpl6.1 to develop more accurate markers for MAS breeding.

  18. QTL Analysis and Candidate Gene Mapping for the Polyphenol Content in Cider Apple

    PubMed Central

    Verdu, Cindy F.; Guyot, Sylvain; Childebrand, Nicolas; Bahut, Muriel; Celton, Jean-Marc; Gaillard, Sylvain; Lasserre-Zuber, Pauline; Troggio, Michela; Guilet, David; Laurens, François

    2014-01-01

    Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed. PMID:25271925

  19. QTL analysis and candidate gene mapping for the polyphenol content in cider apple.

    PubMed

    Verdu, Cindy F; Guyot, Sylvain; Childebrand, Nicolas; Bahut, Muriel; Celton, Jean-Marc; Gaillard, Sylvain; Lasserre-Zuber, Pauline; Troggio, Michela; Guilet, David; Laurens, François

    2014-01-01

    Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.

  20. High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets.

    PubMed

    Brown, Allan F; Yousef, Gad G; Chebrolu, Kranthi K; Byrd, Robert W; Everhart, Koyt W; Thomas, Aswathy; Reid, Robert W; Parkin, Isobel A P; Sharpe, Andrew G; Oliver, Rebekah; Guzman, Ivette; Jackson, Eric W

    2014-09-01

    A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.

  1. 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

  2. Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids)

    PubMed Central

    2010-01-01

    Background Azalea (Rhododendron simsii hybrids) is the most important flowering pot plant produced in Belgium, being exported world-wide. In the breeding program, flower color is the main feature for selection, only in later stages cultivation related plant quality traits are evaluated. As a result, plants with attractive flowering are kept too long in the breeding cycle. The inheritance of flower color has been well studied; information on the heritability of cultivation related quality traits is lacking. For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed. Results An integrated framework map on four individual linkage maps in Rhododendron simsii hybrids was constructed. For genotyping, mainly dominant scored AFLP (on average 364 per population) and MYB-based markers (15) were combined with co-dominant SSR (23) and EST markers (12). Linkage groups were estimated in JoinMap. A consensus grouping for the 4 mapping populations was made and applied in each individual mapping population. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment. A large portion of loci (43%) was common to at least two populations and could therefore serve as bridging markers. The different steps taken for map optimization and integration into a reference framework map for QTL mapping are discussed. Conclusions This is the first map of azalea up to our knowledge. AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis. The alignment of the 4 maps on the basis of framework markers will facilitate in turn the alignment of QTL regions detected in each of the populations. The approach we took is thoroughly different than the

  3. QTL analysis of seed dormancy in Arabidopsis using recombinant inbred lines and MQM mapping.

    PubMed

    van Der Schaar, W; Alonso-Blanco, C; Léon-Kloosterziel, K M; Jansen, R C; van Ooijen, J W; Koornneef, M

    1997-08-01

    The genetic differences for seed germination between two commonly used Arabidopsis thaliana ecotypes Ler and Col, both showing a low level of seed dormancy, were investigated. The analysis was performed with 98 recombinant inbred lines (RILs) derived from the cross between the two ecotypes, and these lines had previously been analysed for molecular marker composition by Lister and Dean (Norwich, UK). The analysis of germination was performed on seeds grown in three different maternal environments and each seed batch was tested in three different germination environments: in light, in darkness and in the presence of the gibberellin inhibitor paclobutrazol. Fourteen loci were identified using the multiple-QTL-model (MQM) procedure for mapping quantitative trait loci. At nine loci no significant interaction between the detection of the locus and environmental factors could be detected. However, three other distinct loci controlling the germination behaviour in the presence of the gibberellin inhibitor paclobutrazol had a much lower or no effect when germination was tested in water either in light or darkness. Two other loci affecting germination in darkness and/or light had practically no effect on germination in the presence of paclobutrazol.

  4. Confirmation and Fine Mapping of a Major QTL for Aflatoxin Resistance in Maize Using a Combination of Linkage and Association Mapping

    PubMed Central

    Zhang, Yu; Cui, Min; Zhang, Jimin; Zhang, Lei; Li, Chenliu; Kan, Xin; Sun, Qian; Deng, Dexiang; Yin, Zhitong

    2016-01-01

    Maize grain contamination with aflatoxin from Aspergillus flavus (A. flavus) is a serious health hazard to animals and humans. To map the quantitative trait loci (QTLs) associated with resistance to A. flavus, we employed a powerful approach that differs from previous methods in one important way: it combines the advantages of the genome-wide association analysis (GWAS) and traditional linkage mapping analysis. Linkage mapping was performed using 228 recombinant inbred lines (RILs), and a highly significant QTL that affected aflatoxin accumulation, qAA8, was mapped. This QTL spanned approximately 7 centi-Morgan (cM) on chromosome 8. The confidence interval was too large for positional cloning of the causal gene. To refine this QTL, GWAS was performed with 558,629 single nucleotide polymorphisms (SNPs) in an association population comprising 437 maize inbred lines. Twenty-five significantly associated SNPs were identified, most of which co-localised with qAA8 and explained 6.7% to 26.8% of the phenotypic variation observed. Based on the rapid linkage disequilibrium (LD) and the high density of SNPs in the association population, qAA8 was further localised to a smaller genomic region of approximately 1500 bp. A high-resolution map of the qAA8 region will be useful towards a marker-assisted selection (MAS) of A. flavus resistance and a characterisation of the causal gene. PMID:27598199

  5. Mapping a QTL conferring resistance to Fusarium head blight on chromosome 1B in winter wheat (Triticum aestivum L.)

    PubMed Central

    Nishio, Zenta; Onoe, Chihiro; Ito, Miwako; Tabiki, Tadashi; Nagasawa, Koichi; Miura, Hideho

    2016-01-01

    Fusarium head blight (FHB) is one of the most devastating diseases of wheat (Triticum aestivum L.), and the development of cultivars with FHB resistance is the most effective way to control the disease. Yumechikara is a Japanese hard red winter wheat cultivar that shows moderate resistance to FHB with superior bread-making quality. To identify quantitative trait loci (QTLs) for FHB resistance in Yumechikara, we evaluated doubled haploid lines derived from a cross between Yumechikara and a moderate susceptible cultivar, Kitahonami, for FHB resistance in a 5-year field trial, and we analyzed polymorphic molecular markers between the parents. Our analysis of these markers identified two FHB-resistance QTLs, one from Yumechikara and one from Kitahonami. The QTL from Yumechikara, which explained 36.4% of the phenotypic variation, was mapped on the distal region of chromosome 1BS, which is closely linked to the low-molecular-weight glutenin subunit gene Glu-B3 and the glume color gene Rg-B1. The other QTL (from Kitahonami) was mapped on chromosome 3BS, which explained 11.2% of the phenotypic variation. The close linkage between the FHB-resistance QTL on 1BS, Glu-B3 and Rg-B1 brings an additional value of simultaneous screening for both quality and FHB resistance using the glume color. PMID:28163582

  6. Single QTL mapping and nucleotide-level resolution of a physiologic trait in wine Saccharomyces cerevisiae strains.

    PubMed

    Marullo, Philippe; Aigle, Michel; Bely, Marina; Masneuf-Pomarède, Isabelle; Durrens, Pascal; Dubourdieu, Denis; Yvert, Gaël

    2007-09-01

    Natural Saccharomyces cerevisiae yeast strains exhibit very large genotypic and phenotypic diversity. However, the link between phenotype variation and genetic determinism is still difficult to identify, especially in wild populations. Using genome hybridization on DNA microarrays, it is now possible to identify single-feature polymorphisms among divergent yeast strains. This tool offers the possibility of applying quantitative genetics to wild yeast strains. In this instance, we studied the genetic basis for variations in acetic acid production using progeny derived from two strains from grape must isolates. The trait was quantified during alcoholic fermentation of the two strains and 108 segregants derived from their crossing. A genetic map of 2212 markers was generated using oligonucleotide microarrays, and a major quantitative trait locus (QTL) was mapped with high significance. Further investigations showed that this QTL was due to a nonsynonymous single-nucleotide polymorphism that targeted the catalytic core of asparaginase type I (ASP1) and abolished its activity. This QTL was only effective when asparagine was used as a major nitrogen source. Our results link nitrogen assimilation and CO(2) production rate to acetic acid production, as well as, on a broader scale, illustrating the specific problem of quantitative genetics when working with nonlaboratory microorganisms.

  7. From beavis to beak color: a simulation study to examine how much qtl mapping can reveal about the genetic architecture of quantitative traits.

    PubMed

    Slate, Jon

    2013-05-01

    Quantitative trait locus (QTL) mapping is frequently used in evolutionary studies to understand the genetic architecture of continuously varying traits. The majority of studies have been conducted in specially created crosses, in which genetic differences between parental lines are identified by linkage analysis. Detecting QTL segregating within populations is more problematic, especially in wild populations, because these populations typically have complicated and unbalanced multigenerational pedigrees. However, QTL mapping can still be conducted in such populations using a variance components mixed model approach, and the advent of appropriate statistical frameworks and better genotyping methods mean that the approach is gaining popularity. In this study it is shown that all studies described to date report evidence of QTL of major effect on trait variation, but that these findings are probably caused by inflated estimates of QTL effect sizes due to the Beavis effect. Using simulations I show that even the most powerful studies conducted to date are likely to give misleading descriptions of the genetic architecture of a trait. I show that an interpretation of a mapping study of beak color in the zebra finch (Taeniopygia guttata), that suggested genetic variation was determined by a small number of loci of large effect, which are possibly maintained by antagonistic pleiotropy, is likely to be incorrect. More generally, recommendations are made to how QTL mapping can be combined with other approaches to provide more accurate descriptions of a trait's genetic architecture.

  8. 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

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

    PubMed

    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.

  10. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean

    PubMed Central

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  11. QTL Mapping in Three Rice Populations Uncovers Major Genomic Regions Associated with African Rice Gall Midge Resistance

    PubMed Central

    Semagn, Kassa; Sow, Mounirou; Nwilene, Francis; Kolade, Olufisayo; Bocco, Roland; Oyetunji, Olumoye; Mitchell-Olds, Thomas; Ndjiondjop, Marie-Noëlle

    2016-01-01

    African rice gall midge (AfRGM) is one of the most destructive pests of irrigated and lowland African ecologies. This study aimed to identify the quantitative trait loci (QTL) associated with AfRGM pest incidence and resistance in three independent bi-parental rice populations (ITA306xBW348-1, ITA306xTOG7106 and ITA306xTOS14519), and to conduct meta QTL (mQTL) analysis to explore whether any genomic regions are conserved across different genetic backgrounds. Composite interval mapping (CIM) conducted on the three populations independently uncovered a total of 28 QTLs associated with pest incidence (12) and pest severity (16). The number of QTLs per population associated with AfRGM resistance varied from three in the ITA306xBW348-1 population to eight in the ITA306xTOG7106 population. Each QTL individually explained 1.3 to 34.1% of the phenotypic variance. The major genomic region for AfRGM resistance had a LOD score and R2 of 60.0 and 34.1% respectively, and mapped at 111 cM on chromosome 4 (qAfrGM4) in the ITA306xTOS14519 population. The meta-analysis reduced the number of QTLs from 28 to 17 mQTLs, each explaining 1.3 to 24.5% of phenotypic variance, and narrowed the confidence intervals by 2.2 cM. There was only one minor effect mQTL on chromosome 1 that was common in the TOS14519 and TOG7106 genetic backgrounds; all other mQTLs were background specific. We are currently fine-mapping and validating the major effect genomic region on chromosome 4 (qAfRGM4). This is the first report in mapping the genomic regions associated with the AfRGM resistance, and will be highly useful for rice breeders. PMID:27508500

  12. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean.

    PubMed

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  13. 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.

  14. A Cross-Species Gene Expression Marker-Based Genetic Map and QTL Analysis in Bambara Groundnut.

    PubMed

    Chai, Hui Hui; Ho, Wai Kuan; Graham, Neil; May, Sean; Massawe, Festo; Mayes, Sean

    2017-02-22

    Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip. A total of 753 markers grouped at an LOD (Logarithm of odds) of three, with 527 markers mapped into linkage groups. From this initial map, a spaced expression marker-based genetic map consisting of 13 linkage groups containing 218 GEMs, spanning 982.7 cM (centimorgan) of the bambara groundnut genome, was developed. Of the QTL detected, 46% were detected in both control and drought treatment populations, suggesting that they are the result of intrinsic trait differences between the parental lines used to construct the cross, with 31% detected in only one of the conditions. The present GEM map in bambara groundnut provides one technically feasible route for the translation of information and resources from major and model plant species to underutilised and resource-poor crops.

  15. A Cross-Species Gene Expression Marker-Based Genetic Map and QTL Analysis in Bambara Groundnut

    PubMed Central

    Chai, Hui Hui; Ho, Wai Kuan; Graham, Neil; May, Sean; Massawe, Festo; Mayes, Sean

    2017-01-01

    Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip. A total of 753 markers grouped at an LOD (Logarithm of odds) of three, with 527 markers mapped into linkage groups. From this initial map, a spaced expression marker-based genetic map consisting of 13 linkage groups containing 218 GEMs, spanning 982.7 cM (centimorgan) of the bambara groundnut genome, was developed. Of the QTL detected, 46% were detected in both control and drought treatment populations, suggesting that they are the result of intrinsic trait differences between the parental lines used to construct the cross, with 31% detected in only one of the conditions. The present GEM map in bambara groundnut provides one technically feasible route for the translation of information and resources from major and model plant species to underutilised and resource-poor crops. PMID:28241413

  16. Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping.

    PubMed

    Famoso, Adam N; Zhao, Keyan; Clark, Randy T; Tung, Chih-Wei; Wright, Mark H; Bustamante, Carlos; Kochian, Leon V; McCouch, Susan R

    2011-08-01

    Aluminum (Al) toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more Al tolerant than other cereal crops. However, the mechanisms of rice Al tolerance are largely unknown, and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions, conducted a genome-wide association (GWA) study, and conducted QTL mapping in two bi-parental populations using three estimates of Al tolerance based on root growth. Subpopulation structure explained 57% of the phenotypic variation, and the mean Al tolerance in Japonica was twice that of Indica. Forty-eight regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific. Four of these regions co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified QTLs. Three regions corresponding to induced Al-sensitive rice mutants (ART1, STAR2, Nrat1) were identified through bi-parental QTL mapping or GWA to be involved in natural variation for Al tolerance. Haplotype analysis around the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation, and sequence analysis of Nrat1 identified a trio of non-synonymous mutations predictive of Al sensitivity in our diversity panel. GWA analysis discovered more phenotype-genotype associations and provided higher resolution, but QTL mapping identified critical rare and/or subpopulation-specific alleles not detected by GWA analysis. Mapping using Indica/Japonica populations identified QTLs associated with transgressive variation where alleles from a susceptible aus or indica parent enhanced Al tolerance in a tolerant Japonica background. This work supports the hypothesis that selectively introgressing alleles across subpopulations is an efficient approach for trait enhancement in plant breeding programs and demonstrates

  17. QTL Mapping of Endocochlear Potential Differences between C57BL/6J and BALB/cJ mice.

    PubMed

    Ohlemiller, Kevin K; Kiener, Anna L; Gagnon, Patricia M

    2016-06-01

    We reported earlier that the endocochlear potential (EP) differs between C57BL/6J (B6) and BALB/cJ (BALB) mice, being lower in BALBs by about 10 mV (Ohlemiller et al. Hear Res 220: 10-26, 2006). This difference corresponds to strain differences with respect to the density of marginal cells in cochlear stria vascularis. After about 1 year of age, BALB mice also tend toward EP reduction that correlates with further marginal cell loss. We therefore suggested that early sub-clinical features of the BALB stria vascularis may predispose these mice to a condition modeling Schuknecht's strial presbycusis. We further reported (Ohlemiller et al. J Assoc Res Otolaryngol 12: 45-58, 2011) that the acute effects of a 2-h 110 dB SPL noise exposure differ between B6 and BALB mice, such that the EP remains unchanged in B6 mice, but is reduced by 40-50 mV in BALBs. In about 25 % of BALBs, the EP does not completely recover, so that permanent EP reduction may contribute to noise-induced permanent threshold shifts in BALBs. To identify genes and alleles that may promote natural EP variation as well as noise-related EP reduction in BALB mice, we have mapped related quantitative trait loci (QTLs) using 12 recombinant inbred (RI) strains formed from B6 and BALB (CxB1-CxB12). EP and strial marginal cell density were measured in B6 mice, BALB mice, their F1 hybrids, and RI mice without noise exposure, and 1-3 h after broadband noise (4-45 kHz, 110 dB SPL, 2 h). For unexposed mice, the strain distribution patterns for EP and marginal cell density were used to generate preliminary QTL maps for both EP and marginal cell density. Six QTL regions were at least statistically suggestive, including a significant QTL for marginal cell density on chromosome 12 that overlapped a weak QTL for EP variation. This region, termed Maced (Marginal cell density QTL) supports the notion of marginal cell density as a genetically influenced contributor to natural EP variation. Candidate genes for Maced

  18. Using a Candidate Gene-Based Genetic Linkage Map to Identify QTL for Winter Survival in Perennial Ryegrass

    PubMed Central

    Paina, Cristiana; Byrne, Stephen L.; Studer, Bruno; Rognli, Odd Arne; Asp, Torben

    2016-01-01

    Important agronomical traits in perennial ryegrass (Lolium perenne) breeding programs such as winter survival and heading date, are quantitative traits that are generally controlled by multiple loci. Individually, these loci have relatively small effects. The aim of this study was to develop a candidate gene based Illumina GoldenGate 1,536-plex assay, containing single nucleotide polymorphism markers designed from transcripts involved in response to cold acclimation, vernalization, and induction of flowering. The assay was used to genotype a mapping population that we have also phenotyped for winter survival to complement the heading date trait previously mapped in this population. A positive correlation was observed between strong vernalization requirement and winter survival, and some QTL for winter survival and heading date overlapped on the genetic map. Candidate genes were located in clusters along the genetic map, some of which co-localized with QTL for winter survival and heading date. These clusters of candidate genes may be used in candidate gene based association studies to identify alleles associated with winter survival and heading date. PMID:27010567

  19. QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici in a recombinant inbred line Capsicum annuum population.

    PubMed

    Naegele, R P; Ashrafi, H; Hill, T A; Chin-Wo, S Reyes; Van Deynze, A E; Hausbeck, M K

    2014-05-01

    Phytophthora capsici is an important pepper (Capsicum annuum) pathogen causing fruit and root rot, and foliar blight in field and greenhouse production. Previously, an F6 recombinant inbred line population was evaluated for fruit rot susceptibility. Continuous variation among lines and partial and isolate-specific resistance were found. In this study, Phytophthora fruit rot resistance was mapped in the same F6 population between Criollo del Morelos 334 (CM334), a landrace from Mexico, and 'Early Jalapeno' using a high-density genetic map. Isolate-specific resistance was mapped independently in 63 of the lines evaluated and the two parents. Heritability of the resistance for each isolate at 3 and 5 days postinoculation (dpi) was high (h(2) = 0.63 to 0.68 and 0.74 to 0.83, respectively). Significant additive and epistatic quantitative trait loci (QTL) were identified for resistance to isolates OP97 and 13709 (3 and 5 dpi) and 12889 (3 dpi only). Mapping of fruit traits showed potential linkage with few disease resistance QTL. The partial fruit rot resistance from CM334 suggests that this may not be an ideal source for fruit rot resistance in pepper.

  20. Using a Candidate Gene-Based Genetic Linkage Map to Identify QTL for Winter Survival in Perennial Ryegrass.

    PubMed

    Paina, Cristiana; Byrne, Stephen L; Studer, Bruno; Rognli, Odd Arne; Asp, Torben

    2016-01-01

    Important agronomical traits in perennial ryegrass (Lolium perenne) breeding programs such as winter survival and heading date, are quantitative traits that are generally controlled by multiple loci. Individually, these loci have relatively small effects. The aim of this study was to develop a candidate gene based Illumina GoldenGate 1,536-plex assay, containing single nucleotide polymorphism markers designed from transcripts involved in response to cold acclimation, vernalization, and induction of flowering. The assay was used to genotype a mapping population that we have also phenotyped for winter survival to complement the heading date trait previously mapped in this population. A positive correlation was observed between strong vernalization requirement and winter survival, and some QTL for winter survival and heading date overlapped on the genetic map. Candidate genes were located in clusters along the genetic map, some of which co-localized with QTL for winter survival and heading date. These clusters of candidate genes may be used in candidate gene based association studies to identify alleles associated with winter survival and heading date.

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

    PubMed Central

    Hadsell, Darryl L.; Hadsell, Louise A.; Olea, Walter; Rijnkels, Monique; Creighton, Chad J.; Smyth, Ian; Short, Kieran M.; Cox, Liza L.; Cox, Timothy C.

    2015-01-01

    Genetic background plays a dominant role in mammary gland development and breast cancer (BrCa). Despite this, the role of genetic diversity in mammary gland development is only partially understood. This study used strain-dependent variation in an inbred mouse mapping panel, to identify quantitative trait loci (QTL) underlying structural variation in mammary ductal development, and determined if these QTL correlated with genomic intervals conferring breast cancer susceptibility in humans. For about half of the traits, the observed variation among the complete set of strains in this study was greater (P<0.05) than that observed with previously studied strains or with strains that are in current common use for mammary gland biology. Correlations were also detected with previously reported variation in mammary tumor latency and metastasis. In silico genome-wide association (GWAS) identified 20 mammary development QTL (Mdq). Of these, 5 were syntenic with previously reported human BrCa loci. The most highly significant (P=1×10−11) association of the study was on MMU6 and contained the genes Plxna4, Plxna4os1, and Chchd3. On MMU5, a QTL was detected (p=8×10−7) that was syntenic to a human BrCa locus on h12q24.5 containing the genes Tbx3 and Tbx5. Intersection of high-association SNP (r2 >0.8) with genomic and epigenomic features, and intersection of candidate genes with gene expression and survival data from human BrCa highlighted several for further study. These results support the conclusion that genetic variation in mammary ductal development is greater than previously appreciated. They also suggest that mammary tumor latency and metastatic index may be influenced by variations in the same factors that control normal mammary ductal development and that further studies of genetically diverse mice can improve our understanding of the connection between breast development and breast cancer in humans by identifying novel susceptibility genes. PMID:25552398

  2. Construction of a potato consensus map and QTL meta-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits

    PubMed Central

    2011-01-01

    Background Integrating QTL results from independent experiments performed on related species helps to survey the genetic diversity of loci/alleles underlying complex traits, and to highlight potential targets for breeding or QTL cloning. Potato (Solanum tuberosum L.) late blight resistance has been thoroughly studied, generating mapping data for many Rpi-genes (R-genes to Phytophthora infestans) and QTLs (quantitative trait loci). Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits. Results Nineteen QTL publications for late blight resistance were considered, seven of them reported maturity QTLs. Twenty-one QTL maps and eight reference maps were compiled to construct a 2,141-marker consensus map on which QTLs were projected and clustered into meta-QTLs. The whole-genome QTL meta-analysis reduced by six-fold late blight resistance QTLs (by clustering 144 QTLs into 24 meta-QTLs), by ca. five-fold maturity QTLs (by clustering 42 QTLs into eight meta-QTLs), and by ca. two-fold QTL confidence interval mean. Late blight resistance meta-QTLs were observed on every chromosome and maturity meta-QTLs on only six chromosomes. Conclusions Meta-analysis helped to refine the genomic regions of interest frequently described, and provided the closest flanking markers. Meta-QTLs of late blight resistance and maturity juxtaposed along chromosomes IV, V and VIII, and overlapped on chromosomes VI and XI. The distribution of late blight resistance meta-QTLs is significantly independent from those of Rpi-genes, resistance gene analogs and defence-related loci. The anchorage of meta-QTLs to the potato genome sequence, recently publicly released, will especially improve the candidate gene selection to determine the genes underlying meta-QTLs. All mapping data are available from the Sol Genomics Network (SGN

  3. The peach volatilome modularity is reflected at the genetic and environmental response levels in a QTL mapping population

    PubMed Central

    2014-01-01

    Background The improvement of fruit aroma is currently one of the most sought-after objectives in peach breeding programs. To better characterize and assess the genetic potential for increasing aroma quality by breeding, a quantity trait locus (QTL) analysis approach was carried out in an F1 population segregating largely for fruit traits. Results Linkage maps were constructed using the IPSC peach 9 K Infinium ® II array, rendering dense genetic maps, except in the case of certain chromosomes, probably due to identity-by-descent of those chromosomes in the parental genotypes. The variability in compounds associated with aroma was analyzed by a metabolomic approach based on GC-MS to profile 81 volatiles across the population from two locations. Quality-related traits were also studied to assess possible pleiotropic effects. Correlation-based analysis of the volatile dataset revealed that the peach volatilome is organized into modules formed by compounds from the same biosynthetic origin or which share similar chemical structures. QTL mapping showed clustering of volatile QTL included in the same volatile modules, indicating that some are subjected to joint genetic control. The monoterpene module is controlled by a unique locus at the top of LG4, a locus previously shown to affect the levels of two terpenoid compounds. At the bottom of LG4, a locus controlling several volatiles but also melting/non-melting and maturity-related traits was found, suggesting putative pleiotropic effects. In addition, two novel loci controlling lactones and esters in linkage groups 5 and 6 were discovered. Conclusions The results presented here give light on the mode of inheritance of the peach volatilome confirming previously loci controlling the aroma of peach but also identifying novel ones. PMID:24885290

  4. Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries).

    PubMed

    Beraldi, Dario; McRae, Allan F; Gratten, Jacob; Pilkington, Jill G; Slate, Jon; Visscher, Peter M; Pemberton, Josephine M

    2007-01-01

    A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to gastrointestinal parasites and ectoparasitic keds segregating in the free-living Soay sheep population on St. Kilda (UK). The mapping panel consisted of a single pedigree of 882 individuals of which 588 were genotyped. The Soay linkage map used for the scans comprised 251 markers covering the whole genome at average spacing of 15cM. The traits here investigated were the strongyle faecal egg count (FEC), the coccidia faecal oocyst count (FOC) and a count of keds (Melophagus ovinus). QTL mapping was performed by means of variance component analysis so that the genetic parameters of the study traits were also estimated and compared with previous studies in Soay and domestic sheep. Strongyle FEC and coccidia FOC showed moderate heritability (h(2)=0.26 and 0.22, respectively) in lambs but low heritability in adults (h(2)<0.10). Ked count appeared to have very low h(2) in both lambs and adults. Genome scans were performed for the traits with moderate heritability and two genomic regions reached the level of suggestive linkage for coccidia FOC in lambs (logarithm of the odds=2.68 and 2.21 on chromosomes 3 and X, respectively). We believe this is the first study to report a QTL search for parasite resistance in a free-living animal population and therefore may represent a useful reference for similar studies aimed at understanding the genetics of host-parasite co-evolution in the wild.

  5. Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing.

    PubMed

    Liu, Nianxi; Li, Mu; Hu, Xiangbao; Ma, Qibin; Mu, Yinghui; Tan, Zhiyuan; Xia, Qiuju; Zhang, Gengyun; Nian, Hai

    2017-06-19

    One of the overarching goals of soybean breeding is to develop lines that combine increased yield with improved quality characteristics. High-density-marker QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped a recombinant inbred line (RIL) population (Zhonghuang 24 × Huaxia 3) using a restriction-site associated DNA sequencing (RAD-seq) approach. A high-density soybean genetic map was constructed and used to identify several QTLs that were shown to influence six yield-related and two quality traits. A total of 47,472 single-nucleotide polymorphisms (SNPs) were detected for the RILs that were integrated into 2639 recombination bin units, with an average distance of 1.00 cM between adjacent markers. Forty seven QTLs for yield-related traits and 13 QTLs for grain quality traits were found to be distributed on 16 chromosomes in the 2 year studies. Among them, 18 QTLs were stable, and were identified in both analyses. Twenty six QTLs were identified for the first time, with a single QTL (qNN19a) in a 56 kb region explaining 32.56% of phenotypic variation, and an additional 10 of these were novel, stable QTLs. Moreover, 8 QTL hotpots on four different chromosomes were identified for the correlated traits. With RAD-sequencing, some novel QTLs and important QTL clusters for both yield-related and quality traits were identified based on a new, high-density bin linkage map. Three predicted genes were selected as candidates that likely have a direct or indirect influence on both yield and quality in soybean. Our findings will be helpful for understanding common genetic control mechanisms of co-localized traits and to select cultivars for further analysis to predictably modulate soybean yield and quality simultaneously.

  6. Genome-Wide Association Mapping in the Global Diversity Set Reveals New QTL Controlling Root System and Related Shoot Variation in Barley

    PubMed Central

    Reinert, Stephan; Kortz, Annika; Léon, Jens; Naz, Ali A.

    2016-01-01

    The fibrous root system is a visible sign of ecological adaptation among barley natural populations. In the present study, we utilized rich barley diversity to dissect the genetic basis of root system variation and its link with shoot attributes under well-water and drought conditions. Genome-wide association mapping of phenotype data using a dense genetic map (5892 SNP markers) revealed 17 putative QTL for root and shoot traits. Among these, at 14 loci the preeminence of exotic QTL alleles resulted in trait improvements. The most promising QTL were quantified using haplotype analysis at local and global genome levels. The strongest QTL was found on chromosome 1H which accounted for root dry weight and tiller number simultaneously. Candidate gene analysis across the targeted region detected a crucial amino acid substitution mutation in the conserved domain of a WRKY29 transcription factor among genotypes bearing major and minor QTL alleles. Similarly, the drought inducible QTL QRdw.5H (5H, 95.0 cM) seems to underlie 37 amino acid deletion and substitution mutations in the conserved domain of two related genes CBF10B and CBF10A, respectively. The identification and further characterization of these candidate genes will be essential to decipher genetics behind developmental and natural adaptation mechanisms of barley. PMID:27486472

  7. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes

    USDA-ARS?s Scientific Manuscript database

    Fruit size is an important quality trait in cucumber of different market classes. The genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using three mapping populations developed from cross betwee...

  8. 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.

  9. Genetic mapping of QTL for resistance to Fusarium head blight spread (type 2 resistance) in a Triticum dicoccoides × Triticum durum backcross-derived population.

    PubMed

    Buerstmayr, Maria; Alimari, Abdallah; Steiner, Barbara; Buerstmayr, Hermann

    2013-11-01

    Improvement of resistance to Fusarium head blight (FHB) is a continuous challenge for durum wheat breeders, particularly due to the limited genetic variation within this crop species. We accordingly generated a backcross-derived mapping population using the type 2 FHB resistant Triticum dicoccoides line Mt. Gerizim #36 as donor and the modern Austrian T. durum cultivar Helidur as recipient; 103 BC1F6:7 lines were phenotyped for type 2 FHB resistance using single-spikelet inoculations and genotyped with 421 DNA markers (SSR and AFLP). QTL mapping revealed two highly significant QTL, mapping to chromosomes 3A and 6B, respectively. For both QTL the T. dicoccoides allele improved type 2 FHB resistance. Recombinant lines with both favorable alleles fixed conferred high resistance to FHB similar to that observed in the T. dicoccoides parent. The results appear directly applicable for durum wheat resistance breeding.

  10. A High-Resolution InDel (Insertion–Deletion) Markers-Anchored Consensus Genetic Map Identifies Major QTLs Governing Pod Number and Seed Yield in Chickpea

    PubMed Central

    Srivastava, Rishi; Singh, Mohar; Bajaj, Deepak; Parida, Swarup K.

    2016-01-01

    Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome next-generation resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 × ILWC 46) and (Pusa 256 × ILWC 46)] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82,360 InDel markers with reference to kabuli genome and 13,891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations) InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97%) and intra-specific polymorphic potential (58–87%) among a diverse panel of cultivated desi, kabuli, and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM) genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as anchors, three major

  11. Identification of quantitative trait locus (QTL) linked to dorsal fin length from preliminary linkage map of molly fish, Poecilia sp.

    PubMed

    Keong, Bun Poh; Siraj, Siti Shapor; Daud, Siti Khalijah; Panandam, Jothi Malar; Rahman, Arina Nadia Abdul

    2014-02-15

    A preliminary linkage map was constructed by applying backcross and testcross strategy using microsatellite (SSR) markers developed for Xiphophorus and Poecilia reticulata in ornamental fish, molly Poecilia sp. The linkage map having 18 SSR loci consisted of four linkage groups that spanned a map size of 516.1cM. Association between genotypes and phenotypes was tested in a random fashion and QTL for dorsal fin length was found to be linked to locus Msb069 on linkage group 2. Coincidentally, locus Msb069 was also reported as putative homologue primer pairs containing SSRs repeat motif which encoded hSMP-1, a sex determining locus. Dorsal fin length particularly in males of Poecilia latipinna is an important feature during courtship display. Therefore, we speculate that both dorsal fin length and putative hSMP-1 gene formed a close proximity to male sexual characteristics.

  12. Mapping QTL of Root Morphological Traits at Different Growth Stages in Rice

    USDA-ARS?s Scientific Manuscript database

    Roots are a vital organ for absorbing soil moisture and nutrients and influencing drought resistance. The identification of quantitative trait loci (QTL) with molecular markers may allow the estimation of parameters of genetic architecture and improve root traits by molecular marker-assisted selecti...

  13. Mapping of Fusarium Head Blight resistance QTL in winter wheat cultivar NC-Neuse

    USDA-ARS?s Scientific Manuscript database

    Fusarium Head Blight (FHB), primarily caused by Fusarium graminearum, can significantly reduce the grain quality of wheat (Triticum aestivum L.) due to mycotoxin contamination. The objective of this study was to identify quantitative trait loci (QTL) for FHB resistance in the moderately resistant so...

  14. An Empirical Method for Establishing Positional Confidence Intervals Tailored for Composite Interval Mapping of QTL

    USDA-ARS?s Scientific Manuscript database

    Improved genetic resolution and availability of sequenced genomes have made positional cloning of moderate-effect QTL (quantitative trait loci) realistic in several systems, emphasizing the need for precise and accurate derivation of positional confidence intervals (CIs). Support interval (SI) meth...

  15. QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.).

    PubMed

    Burton, Amy L; Johnson, James M; Foerster, Jillian M; Hirsch, Candice N; Buell, C R; Hanlon, Meredith T; Kaeppler, Shawn M; Brown, Kathleen M; Lynch, Jonathan P

    2014-11-01

    QTL were identified for root architectural traits in maize. Root architectural traits, including the number, length, orientation, and branching of the principal root classes, influence plant function by determining the spatial and temporal domains of soil exploration. To characterize phenotypic patterns and their genetic control, three recombinant inbred populations of maize were grown for 28 days in solid media in a greenhouse and evaluated for 21 root architectural traits, including length, number, diameter, and branching of seminal, primary and nodal roots, dry weight of embryonic and nodal systems, and diameter of the nodal root system. Significant phenotypic variation was observed for all traits. Strong correlations were observed among traits in the same root class, particularly for the length of the main root axis and the length of lateral roots. In a principal component analysis, relationships among traits differed slightly for the three families, though vectors grouped together for traits within a given root class, indicating opportunities for more efficient phenotyping. Allometric analysis showed that trajectories of growth for specific traits differ in the three populations. In total, 15 quantitative trait loci (QTL) were identified. QTL are reported for length in multiple root classes, diameter and number of seminal roots, and dry weight of the embryonic and nodal root systems. Phenotypic variation explained by individual QTL ranged from 0.44% (number of seminal roots, NyH population) to 13.5% (shoot dry weight, OhW population). Identification of QTL for root architectural traits may be useful for developing genotypes that are better suited to specific soil environments.

  16. Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice.

    PubMed

    Ding, Xipeng; Li, Xiaokai; Xiong, Lizhong

    2011-09-01

    Drought stress is a major limiting factor for crop production and breeding for drought resistance is very challenging due to the complex nature of this trait. Previous studies in rice suggest that the upland japonica variety IRAT109 shows better drought resistance than the lowland indica variety Zhenshan 97. Numerous quantitative trait loci (QTL) have been previously mapped using a recombinant inbred line population derived from these two genotypes. In this study, near-isogenic lines (NILs) for 17 drought resistance-related QTL were constructed and phenotypic variations of these NILs were investigated under drought and normal conditions. Fourteen of these NILs showed significant phenotypic differences relative to the recurrent parent under at least one of the conditions and nine NILs showed significant differences under both conditions. After eliminating the effect of heading date on drought resistance, only four NILs carrying seven QTL (four for the same grain yield-related traits and three for the same or similar root traits QTL) showed differences consistent with the original QTL mapping results. One of these lines (N19) contains qFSR4, a QTL on chromosome 4 controlling root volume per tiller and co-segregating with flag leaf width and spikelet number per panicle. Using a population derived from N19, qFSR4 was mapped to a 38-kb region containing three open reading frames including the previously characterized NARROW LEAF 1 (NAL1) gene. NAL1, which controls leaf width and also affects vein patterning and polar auxin transport, is the most promising candidate genes for qFSR4. Our results underscore the importance of the development of NILs to confirm the identification of QTL affecting complex traits such as drought resistance.

  17. Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding

    PubMed Central

    2012-01-01

    Background Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for several traits involved in peanut productivity and adaptation as well as domestication. Results A total of 95 QTLs were mapped in the two water treatments. About half of the QTL positive effects were associated with alleles of the wild parent and several QTLs involved in yield components were specific to the water-limited treatment. QTLs detected for the same trait mapped to non-homeologous genomic regions, suggesting differential control in subgenomes as a consequence of polyploidization. The noteworthy clustering of QTLs for traits involved in seed and pod size and in plant and pod morphology suggests, as in many crops, that a small number of loci have contributed to peanut domestication. Conclusion In our study, we have identified QTLs that differentiated cultivated peanut from its wild relatives as well as wild alleles that contributed positive variation to several traits involved in peanut productivity and adaptation. These findings offer novel opportunities for peanut improvement using wild relatives. PMID:22340522

  18. Genetic Architecture of Resistance to Alternaria brassicae in Arabidopsis thaliana: QTL Mapping Reveals Two Major Resistance-Conferring Loci

    PubMed Central

    Rajarammohan, Sivasubramanian; Kumar, Amarendra; Gupta, Vibha; Pental, Deepak; Pradhan, Akshay K.; Kaur, Jagreet

    2017-01-01

    Alternaria brassicae, a necrotrophic fungal pathogen, causes Alternaria blight, one of the most important diseases of oleiferous Brassica crops. The current study utilized Arabidopsis as a model to decipher the genetic architecture of defense against A. brassicae. Significant phenotypic variation that was largely genetically determined was observed among Arabidopsis accessions in response to pathogen challenge. Three biparental mapping populations were developed from three resistant accessions viz. CIBC-5, Ei-2, and Cvi-0 and two susceptible accessions – Gre-0 and Zdr-1 (commonly crossed to CIBC-5 and Ei-2). A total of six quantitative trait locus (QTLs) governing resistance to A. brassicae were identified, five of which were population-specific while one QTL was common between all the three mapping populations. Interestingly, the common QTL had varying phenotypic contributions in different populations, which can be attributed to the genetic background of the parental accessions. The presence of both common and population-specific QTLs indicate that resistance to A. brassicae is quantitative, and that different genes may mediate resistance to the pathogen in different accessions. Two of the QTLs had moderate-to-large effects, one of which explained nearly 50% of the variation. The large effect QTLs may therefore contain genes that could play a significant role in conferring resistance even in heterologous hosts. PMID:28286515

  19. Molecular mapping and validation of a major QTL conferring resistance to a defoliating isolate of verticillium wilt in cotton (Gossypium hirsutum L.).

    PubMed

    Zhang, Xingju; Yuan, Yanchao; 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.

  20. 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

  1. Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13.

    PubMed

    Olsen, Hanne Gro; Knutsen, Tim Martin; Kohler, Achim; Svendsen, Morten; Gidskehaug, Lars; Grove, Harald; Nome, Torfinn; Sodeland, Marte; Sundsaasen, Kristil Kindem; Kent, Matthew Peter; Martens, Harald; Lien, Sigbjørn

    2017-02-13

    Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offers potential to improve milk fat composition, there is strong interest to understand more about the genetic factors that influence the biosynthesis of bovine milk and the molecular mechanisms that regulate milk fat synthesis and secretion. For this reason, the work reported here aimed at identifying genetic variants that affect milk fatty acid composition in Norwegian Red cattle. Milk fatty acid composition was predicted from the nation-wide recording scheme using Fourier transform infrared spectroscopy data and applied to estimate heritabilities for 36 individual and combined fatty acid traits. The recordings were used to generate daughter yield deviations that were first applied in a genome-wide association (GWAS) study with 17,343 markers to identify quantitative trait loci (QTL) affecting fatty acid composition, and next on high-density and sequence-level datasets to fine-map the most significant QTL on BTA13 (BTA for Bos taurus chromosome). The initial GWAS revealed 200 significant associations, with the strongest signals on BTA1, 13 and 15. The BTA13 QTL highlighted a strong functional candidate gene for de novo synthesis of short- and medium-chained saturated fatty acids; acyl-CoA synthetase short-chain family member 2. However, subsequent fine-mapping using single nucleotide polymorphisms (SNPs) from a high-density chip and variants detected by resequencing showed that the effect was more likely caused by a second nearby gene; nuclear receptor coactivator 6 (NCOA6). These findings were confirmed with results from haplotype studies. NCOA6 is a nuclear receptor that interacts with transcription factors such as PPARγ, which is a major regulator of bovine milk fat synthesis. An initial GWAS revealed a highly significant QTL for de novo-synthesized fatty

  2. The Identification of Two Head Smut Resistance-Related QTL in Maize by the Joint Approach of Linkage Mapping and Association Analysis.

    PubMed

    Li, Yong-xiang; Wu, Xun; Jaqueth, Jennifer; Zhang, Dengfeng; Cui, Donghui; Li, Chunhui; Hu, Guanghui; Dong, Huaiyu; Song, Yan-chun; Shi, Yun-su; Wang, Tianyu; Li, Bailin; Li, Yu

    2015-01-01

    Head smut, caused by the fungus Sphacelotheca reiliana (Kühn) Clint, is a devastating threat to maize production. In this study, QTL mapping of head smut resistance was performed using a recombinant inbred line (RIL) population from a cross between a resistant line "QI319" and a susceptible line "Huangzaosi" (HZS) with a genetic map constructed from genotyping-by-sequencing (GBS) data and composed of 1638 bin markers. Two head smut resistance QTL were identified, located on Chromosome 2 (q2.09HR) and Chromosome 5 (q5.03HR), q2.09HR is co-localized with a previously reported QTL for head smut resistance, and the effect of q5.03HR has been validated in backcross populations. It was also observed that pyramiding the resistant alleles of both QTL enhanced the level of resistance to head smut. A genome-wide association study (GWAS) using 277 diverse inbred lines was processed to validate the mapped QTL and to identify additional head smut resistance associations. A total of 58 associated SNPs were detected, which were distributed in 31 independent regions. SNPs with significant association to head smut resistance were detected within the q2.09HR and q5.03HR regions, confirming the linkage mapping results. It was also observed that both additive and epistastic effects determine the genetic architecture of head smut resistance in maize. As shown in this study, the combined strategy of linkage mapping and association analysis is a powerful approach in QTL dissection for disease resistance in maize.

  3. QTL for several metabolic traits map to loci controlling growth and body composition in an F2 intercross between high- and low-growth chicken lines.

    PubMed

    Nadaf, Javad; Pitel, Frédérique; Gilbert, Hélène; Duclos, Michel J; Vignoles, Florence; Beaumont, Catherine; Vignal, Alain; Porter, Tom E; Cogburn, Larry A; Aggrey, Samuel E; Simon, Jean; Le Bihan-Duval, Elisabeth

    2009-08-07

    Quantitative trait loci (QTL) for metabolic and body composition traits were mapped at 7 and 9 wk, respectively, in an F(2) intercross between high-growth and low-growth chicken lines. These lines also diverged for abdominal fat percentage (AFP) and plasma insulin-like growth factor-I (IGF-I), insulin, and glucose levels. Genotypings were performed with 129 microsatellite markers covering 21 chromosomes. A total of 21 QTL with genomewide level of significance were detected by single-trait analyses for body weight (BW), breast muscle weight (BMW) and percentage (BMP), AF weight (AFW) and percentage (AFP), shank length (ShL) and diameter (ShD), fasting plasma glucose level (Gluc), and body temperature (T(b)). Other suggestive QTL were identified for these parameters and for plasma IGF-I and nonesterified fatty acid levels. QTL controlling adiposity and Gluc were colocalized on GGA3 and GGA5 and QTL for BW, ShL and ShD, adiposity, and T(b) on GGA4. Multitrait analyses revealed two QTL controlling Gluc and AFP on GGA5 and Gluc and T(b) on GGA26. Significant effects of the reciprocal cross were observed on BW, ShD, BMW, and Gluc, which may result from mtDNA and/or maternal effects. Most QTL regions for Gluc and adiposity harbor genes for which alleles have been associated with increased susceptibility to diabetes and/or obesity in humans. Identification of genes responsible for these metabolic QTL will increase our understanding of the constitutive "hyperglycemia" found in chickens. Furthermore, a comparative approach could provide new information on the genetic causes of diabetes and obesity in humans.

  4. 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 F6-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

  5. A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber

    PubMed Central

    Zhu, Wen-Ying; Huang, Long; Chen, Long; Yang, Jian-Tao; Wu, Jia-Ni; Qu, Mei-Ling; Yao, Dan-Qing; Guo, Chun-Li; Lian, Hong-Li; He, Huan-Le; Pan, Jun-Song; Cai, Run

    2016-01-01

    High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected. PMID:27148281

  6. Uncovering the genetic architecture of Colletotrichum lindemuthianum resistance through QTL mapping and epistatic interaction analysis in common bean.

    PubMed

    González, Ana M; Yuste-Lisbona, Fernando J; Rodiño, A Paula; De Ron, Antonio M; Capel, Carmen; García-Alcázar, Manuel; Lozano, Rafael; Santalla, Marta

    2015-01-01

    Colletotrichum lindemuthianum is a hemibiotrophic fungal pathogen that causes anthracnose disease in common bean. Despite the genetics of anthracnose resistance has been studied for a long time, few quantitative trait loci (QTLs) studies have been conducted on this species. The present work examines the genetic basis of quantitative resistance to races 23 and 1545 of C. lindemuthianum in different organs (stem, leaf and petiole). A population of 185 recombinant inbred lines (RIL) derived from the cross PMB0225 × PHA1037 was evaluated for anthracnose resistance under natural and artificial photoperiod growth conditions. Using multi-environment QTL mapping approach, 10 and 16 main effect QTLs were identified for resistance to anthracnose races 23 and 1545, respectively. The homologous genomic regions corresponding to 17 of the 26 main effect QTLs detected were positive for the presence of resistance-associated gene cluster encoding nucleotide-binding and leucine-rich repeat (NL) proteins. Among them, it is worth noting that the main effect QTLs detected on linkage group 05 for resistance to race 1545 in stem, petiole and leaf were located within a 1.2 Mb region. The NL gene Phvul.005G117900 is located in this region, which can be considered an important candidate gene for the non-organ-specific QTL identified here. Furthermore, a total of 39 epistatic QTL (E-QTLs) (21 for resistance to race 23 and 18 for resistance to race 1545) involved in 20 epistatic interactions (eleven and nine interactions for resistance to races 23 and 1545, respectively) were identified. None of the main and epistatic QTLs detected displayed significant environment interaction effects. The present research provides essential information not only for the better understanding of the plant-pathogen interaction but also for the application of genomic assisted breeding for anthracnose resistance improvement in common bean through application of marker-assisted selection (MAS).

  7. Uncovering the genetic architecture of Colletotrichum lindemuthianum resistance through QTL mapping and epistatic interaction analysis in common bean

    PubMed Central

    González, Ana M.; Yuste-Lisbona, Fernando J.; Rodiño, A. Paula; De Ron, Antonio M.; Capel, Carmen; García-Alcázar, Manuel; Lozano, Rafael; Santalla, Marta

    2015-01-01

    Colletotrichum lindemuthianum is a hemibiotrophic fungal pathogen that causes anthracnose disease in common bean. Despite the genetics of anthracnose resistance has been studied for a long time, few quantitative trait loci (QTLs) studies have been conducted on this species. The present work examines the genetic basis of quantitative resistance to races 23 and 1545 of C. lindemuthianum in different organs (stem, leaf and petiole). A population of 185 recombinant inbred lines (RIL) derived from the cross PMB0225 × PHA1037 was evaluated for anthracnose resistance under natural and artificial photoperiod growth conditions. Using multi-environment QTL mapping approach, 10 and 16 main effect QTLs were identified for resistance to anthracnose races 23 and 1545, respectively. The homologous genomic regions corresponding to 17 of the 26 main effect QTLs detected were positive for the presence of resistance-associated gene cluster encoding nucleotide-binding and leucine-rich repeat (NL) proteins. Among them, it is worth noting that the main effect QTLs detected on linkage group 05 for resistance to race 1545 in stem, petiole and leaf were located within a 1.2 Mb region. The NL gene Phvul.005G117900 is located in this region, which can be considered an important candidate gene for the non-organ-specific QTL identified here. Furthermore, a total of 39 epistatic QTL (E-QTLs) (21 for resistance to race 23 and 18 for resistance to race 1545) involved in 20 epistatic interactions (eleven and nine interactions for resistance to races 23 and 1545, respectively) were identified. None of the main and epistatic QTLs detected displayed significant environment interaction effects. The present research provides essential information not only for the better understanding of the plant-pathogen interaction but also for the application of genomic assisted breeding for anthracnose resistance improvement in common bean through application of marker-assisted selection (MAS). PMID:25852706

  8. QTL mapping and epistatic interaction analysis in asparagus bean for several characterized and novel horticulturally important traits

    PubMed Central

    2013-01-01

    Background Asparagus bean (Vigna. unguiculata. ssp sesquipedalis) is a subspecies and special vegetable type of cowpea (Vigna. unguiculata L. Walp.) important in Asia. Genetic basis of horticulturally important traits of asparagus bean is still poorly understood, hindering the utilization of targeted, DNA marker-assisted breeding in this crop. Here we report the identification of quantitative trait loci (QTLs) and epistatic interactions for four horticultural traits, namely, days to first flowering (FLD), nodes to first flower (NFF), leaf senescence (LS) and pod number per plant (PN) using a recombinant inbred line (RIL) population of asparagus bean. Results A similar genetic mode of one major QTL plus a few minor QTLs was found to dominate each of the four traits, with the number of QTLs for individual traits ranging from three to four. These QTLs were distributed on 7 of the 11 chromosomes. Major QTLs for FLD, NFF and LS were co-localized on LG 11, indicative of tight linkage. Genome wide epistasis analysis detected two and one interactive locus pairs that significantly affect FLD and LS, respectively, and the epistatic QTLs for FLD appeared to work in different ways. Synteny based comparison of QTL locations revealed conservation of chromosome regions controlling these traits in related legume crops. Conclusion Major, minor, and epistatic QTLs were found to contribute to the inheritance of the FLD, NFF, LS, and PN. Positions of many of these QTLs are conserved among closely related legume species, indicating common mechanisms they share. To our best knowledge, this is the first QTL mapping report using an asparagus bean × asparagus bean intervarietal population and provides marker-trait associations for marker-assisted approaches to selection. PMID:23375055

  9. Construction of a high-density genetic map and lint percentage and cottonseed nutrient trait QTL identification in upland cotton (Gossypium hirsutum L.).

    PubMed

    Liu, Dexin; Liu, Fang; Shan, Xiaoru; Zhang, Jian; Tang, Shiyi; Fang, Xiaomei; Liu, Xueying; Wang, Wenwen; Tan, Zhaoyun; Teng, Zhonghua; Zhang, Zhengsheng; Liu, Dajun

    2015-10-01

    Upland cotton plays a critical role not only in the textile industry, but also in the production of important secondary metabolites, such as oil and proteins. Construction of a high-density linkage map and identifying yield and seed trait quantitative trail loci (QTL) are prerequisites for molecular marker-assisted selective breeding projects. Here, we update a high-density upland cotton genetic map from recombinant inbred lines. A total of 25,313 SSR primer pairs were screened for polymorphism between Yumian 1 and T586, and 1712 SSR primer pairs were used to genotype the mapping population and construct a map. An additional 1166 loci have been added to our previously published map with 509 SSR markers. The updated genetic map spans a total recombinant length of 3338.2 cM and contains 1675 SSR loci and nine morphological markers, with an average interval of 1.98 cM between adjacent markers. Green lint (Lg) mapped on chromosome 15 in a previous report is mapped in an interval of 2.6 cM on chromosome 21. Based on the map and phenotypic data from multiple environments, 79 lint percentage and seed nutrient trait QTL are detected. These include 8 lint percentage, 13 crude protein, 15 crude oil, 8 linoleic, 10 oleic, 13 palmitic, and 12 stearic acid content QTL. They explain 3.5-62.7 % of the phenotypic variation observed. Four morphological markers identified have a major impact on lint percentage and cottonseed nutrients traits. In this study, our genetic map provides new sights into the tetraploid cotton genome. Furthermore, the stable QTL and morphological markers could be used for fine-mapping and map-based cloning.

  10. Fine mapping Fhb4, a major QTL conditioning resistance to Fusarium infection in bread wheat (Triticum aestivum L.).

    PubMed

    Xue, Shulin; Li, Guoqiang; Jia, Haiyan; Xu, Feng; Lin, Feng; Tang, Mingzhi; Wang, Yao; An, Xia; Xu, Haibin; Zhang, Lixia; Kong, Zhongxin; Ma, Zhengqiang

    2010-06-01

    Qfhi.nau-4B is a major quantitative trait locus (QTL) against Fusarium graminearum infection identified in the Fusarium head blight-resistant germplasm Wangshuibai. To fine map this QTL, a recombinant inbred line (RIL) population of 530 lines derived from Nanda2419 x Wangshuibai and the BC(3)F(2) population derived from the cross of a Qfhi.nau-4B near isogenic line (NIL) with susceptible cultivar Mianyang 99-323 as the recurrent parent were screened for recombinants occurred between microsatellite markers Xbarc20 and Xwmc349 that flank Qfhi.nau-4B. A total of 95 recombinants were obtained, including 45 RIL recombinants obtained through reverse-selection of Qfhi.nau-5A and 50 NIL recombinants from the BC(3)F(2) population. Genotyping these recombinant lines with 22 markers mapping to the Xbarc20 and Xwmc349 interval revealed fourteen genotypes of the RIL recombinants as well as of the NIL recombinants. Two-year field evaluation of their resistance to Fusarium infection showed that these lines could be clearly classified into two groups according to percentage of infected spikes. The more resistant class had over 60% less infection than the susceptible class and were common to have Wangshuibai chromatin in the 1.7-cM interval flanked by Xhbg226 and Xgwm149. None of the susceptible recombinants had this Wangshuibai chromatin. Qfhi.nau-4B was thus confined between Xhbg226 and Xgwm149 and named Fhb4. The interval harboring Fhb4 was mapped to 4BL5-0.86-1.00 bin using Chinese Spring deletion lines, a region with about 5.7 times higher recombination rate than the genome average. This study established the basis for map-based cloning of Fhb4.

  11. Wide-genome QTL mapping of fruit quality traits in a tomato RIL population derived from the wild-relative species Solanum pimpinellifolium L.

    PubMed

    Capel, Carmen; Fernández del Carmen, Asunción; Alba, Juan Manuel; Lima-Silva, Viviana; Hernández-Gras, Francesc; Salinas, María; Boronat, Albert; Angosto, Trinidad; Botella, Miguel A; Fernández-Muñoz, Rafael; Granell, Antonio; Capel, Juan; Lozano, Rafael

    2015-10-01

    QTL and candidate genes associated to fruit quality traits have been identified in a tomato genetic map derived from Solanum pimpinellifolium L., providing molecular tools for marker-assisted breeding. The study of genetic, physiological, and molecular pathways involved in fruit development and ripening has considered tomato as the model fleshy-fruited species par excellence. Fruit quality traits regarding organoleptic and nutritional properties are major goals for tomato breeding programs since they largely decide the acceptance of tomato in both fresh and processing markets. Here we report the genetic mapping of single-locus and epistatic quantitative trait loci (QTL) associated to the fruit size and content of sugars, acids, vitamins, and carotenoids from the characterization of a RIL population derived from the wild-relative Solanum pimpinellifolium TO-937. A genetic map composed of 353 molecular markers including 13 genes regulating fruit and developmental traits was generated, which spanned 1007 cM with an average distance between markers of 2.8 cM. Genetic analyses indicated that fruit quality traits analyzed in this work exhibited transgressive segregation and that additive and epistatic effects are the major genetic basis of fruit quality traits. Moreover, most mapped QTL showed environment interaction effects. FrW7.1 fruit size QTL co-localized with QTL involved in soluble solid, vitamin C, and glucose contents, dry weight/fresh weight, and most importantly with the Sucrose Phosphate Synthase gene, suggesting that polymorphisms in this gene could influence genetic variation in several fruit quality traits. In addition, 1-deoxy-D-xylulose 5-phosphate synthase and Tocopherol cyclase genes were identified as candidate genes underlying QTL variation in beta-carotene and vitamin C. Together, our results provide useful genetic and molecular information regarding fruit quality and new chances for tomato breeding by implementing marker-assisted selection.

  12. 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.

  13. 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

  14. An anchored framework BAC map of mouse chromosome 11 assembled using multiplex oligonucleotide hybridization.

    PubMed

    Cai, W W; Reneker, J; Chow, C W; Vaishnav, M; Bradley, A

    1998-12-15

    Despite abundant library resources for many organisms, physical mapping of these organisms has been seriously limited due to lack of efficient library screening techniques. We have developed a highly efficient strategy for large-scale screening of genomic libraries based on multiplex oligonucleotide hybridization on high-density genomic filters. We have applied this strategy to generate a bacterial artificial chromosome (BAC) anchored map of mouse chromosome 11. Using the MIT mouse SSLP data, 320 pairs of oligonucleotide probes were designed with an "overgo" computer program that selects new primer sequences that avoid the microsatellite repeat. BACs identified by these probes are automatically anchored to the chromosome. Ninety-two percent of the probes identified positive clones from a 5.9-fold coverage mouse BAC library with an average of 7 positive clones per marker. An average of 4.2 clones was confirmed for 204 markers by PCR. Our data show that a large number of clones can be efficiently isolated from a large genomic library using this strategy with minimal effort. This strategy will have wide application for large-scale mapping and sequencing of human and other large genomes.

  15. A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation.

    PubMed

    Cavagnaro, Pablo F; Iorizzo, Massimo; Yildiz, Mehtap; Senalik, Douglas; Parsons, Joshua; Ellison, Shelby; Simon, Philipp W

    2014-12-16

    Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. Informative, saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have not been developed. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root color visually, quantified root anthocyanin pigments by high performance liquid chromatography in segregating F2, F3 and F4 generations of a mapping population, mapped quantitative trait loci (QTL) onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations. Root pigmentation, scored visually as presence or absence of purple coloration, segregated in a pattern consistent with a two gene model in an F2, and progeny testing of F3-F4 families confirmed the proposed genetic model. Purple petiole pigmentation was conditioned by a single dominant gene that co-segregates with one of the genes conditioning root pigmentation. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color.All five anthocyanin glycosides previously reported in carrot, as well as RTPE, varied quantitatively in the F2 population. For the purpose of QTL analysis, a high resolution gene-derived SNP-based linkage map of carrot was constructed with 894 markers covering 635.1 cM with a 1.3 cM map resolution. A total of 15 significant QTL for all anthocyanin pigments and for RTPE mapped to six chromosomes. Eight QTL with the largest phenotypic effects mapped to two regions of chromosome 3 with co-localized QTL for several anthocyanin glycosides and for RTPE. A single dominant gene conditioning anthocyanin acylation was identified and mapped.Comparative mapping with two other carrot populations segregating for purple color indicated that carrot anthocyanin

  16. Plasticity of primary and secondary growth dynamics in Eucalyptus hybrids: a quantitative genetics and QTL mapping perspective

    PubMed Central

    2013-01-01

    Background The genetic basis of growth traits has been widely studied in forest trees. Quantitative trait locus (QTL) studies have highlighted the presence of both stable and unstable genomic regions accounting for biomass production with respect to tree age and genetic background, but results remain scarce regarding the interplay between QTLs and the environment. In this study, our main objective was to dissect the genetic architecture of the growth trajectory with emphasis on genotype x environment interaction by measuring primary and secondary growth covering intervals connected with environmental variations. Results Three different trials with the same family of Eucalyptus urophylla x E. grandis hybrids (with different genotypes) were planted in the Republic of Congo, corresponding to two QTL mapping experiments and one clonal test. Height and radial growths were monitored at regular intervals from the seedling stage to five years old. The correlation between growth increments and an aridity index revealed that growth before two years old (r = 0.5; 0.69) was more responsive to changes in water availability than late growth (r = 0.39; 0.42) for both height and circumference. We found a regular increase in heritability with time for cumulative growth for both height [0.06 - 0.33] and circumference [0.06 - 0.38]. Heritabilities for incremental growth were more heterogeneous over time even if ranges of variation were similar (height [0-0.31]; circumference [0.19 to 0.48]). Within the trials, QTL analysis revealed collocations between primary and secondary growth QTLs as well as between early growth increments and final growth QTLs. Between trials, few common QTLs were detected highlighting a strong environmental effect on the genetic architecture of growth, validated by significant QTL x E interactions. Conclusion These results suggest that early growth responses to water availability determine the genetic architecture of total growth at the mature stage

  17. Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

    PubMed Central

    Cubillos, Francisco A.; Brice, Claire; Molinet, Jennifer; Tisné, Sebastién; Abarca, Valentina; Tapia, Sebastián M.; Oporto, Christian; García, Verónica; Liti, Gianni; Martínez, Claudio

    2017-01-01

    Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics. PMID:28592651

  18. Using a set of TeQing-into-Lemont chromosome segment substitution lines for fine mapping QTL: Case studies on sheath blight resistance, spreading culm, and mesocotyl elongation

    USDA-ARS?s Scientific Manuscript database

    A set of backcross introgression lines containing portions of the TeQing genome now introgressed into a Lemont genetic background allows us to fine map rice QTL, and measure their breeding value within U.S. rice genetic and field environments....

  19. High Resolution QTL Map Of Body Conformation Traits From Genome-Wide Association Analysis In Contemporary U.S. Holstein Cows

    USDA-ARS?s Scientific Manuscript database

    A QTL map of 1,005 SNP markers affecting 18 body conformation traits (top 100 effects per trait) was constructed based on a genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped with the BovineSNP50 (45,878 SNPs). The top 100 effects for each trait explained 38-56% of t...

  20. High Resolution QTL Map Of Net Merit Component Traits And Calving Traits From Genome-Wide Association Analysis In Contemporary U.S. Holstein Cows

    USDA-ARS?s Scientific Manuscript database

    A QTL map of 725 SNPs affecting 13 dairy traits (top 100 effects per trait) was constructed based on a genome-wide association analysis of 1,654 contemporary U.S. Holstein cows genotyped with 45,878 SNPs. The 13 traits were net merit (NM$), its 8 component traits and 4 calving traits. The top 100 ef...

  1. QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis)

    USDA-ARS?s Scientific Manuscript database

    Flowering time and fruit size are two important traits in domestication and crop evolution in cucumber, but little is known about their genetic basis. In this paper, we reported QTL mapping on flowering time and fruit size inn populations derived from the cross between a small fruited, early floweri...

  2. Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing.

    PubMed

    Celik, Ibrahim; Gurbuz, Nergiz; Uncu, Ali Tevfik; Frary, Anne; Doganlar, Sami

    2017-01-03

    Solanum pimpinellifolium has high breeding potential for fruit quality traits and has been used as a donor in tomato breeding programs. Unlocking the genetic potential of S. pimpinellifolium requires high-throughput polymorphism identification protocols for QTL mapping and introgression of favourable alleles into cultivated tomato by both positive and background selection. In this study we identified SNP loci using a genotyping by sequencing (GBS) approach in an IBL mapping population derived from the cross between a high yielding fresh market tomato and S. pimpinellifolium (LA1589) as the recurrent and donor parents, respectively. A total of 120,983,088 reads were generated by the Illumina HiSeq next-generation sequencing platform. From these reads 448,539 sequence tags were generated. A majority of the sequence tags (84.4%) were uniquely aligned to the tomato genome. A total of 3.125 unique SNP loci were identified as a result of tag alignment to the genome assembly and were used in QTL analysis of 11 fruit quality traits. As a result, 37 QTLs were identified. S. pimpinellifolium contributed favourable alleles for 16 QTLs (43.2%), thus confirming the high breeding potential of this wild species. The present work introduced a set of SNPs at sufficiently high density for QTL mapping in populations derived from S. pimpinellifolium (LA1589). Moreover, this study demonstrated the high efficiency of the GBS approach for SNP identification, genotyping and QTL mapping in an interspecific tomato population.

  3. Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping.

    PubMed

    Khan, M Awais; Zhao, Youfu Frank; Korban, Schuyler S

    2013-07-01

    Fire blight, incited by the enterobacterium Erwinia amylovora, is a destructive disease of Rosaceae, particularly of apples and pears. There are reports on the molecular mechanisms underlying E. amylovora pathogenesis and how the host activates its resistance mechanism. The host's resistance mechanism is quantitatively controlled, although some major genes might also be involved. Thus far, quantitative trait loci (QTL) mapping and differential expression studies have been used to elucidate those genes and/or genomic regions underlying quantitative resistance present in the apple genome. In this study, an effort is undertaken to dissect the genetic basis of fire blight resistance in apple using both QTL and genome-wide association mapping. On the basis of an F1 pedigree of 'Coop 16' × 'Coop 17' and a genome-wide association study (GWAS) mapping population of Malus accessions (species, old and new cultivars and selections), new QTLs and associations have been identified. A total of three QTLs for resistance to fire blight, with above 95% significant logarithm of odds threshold value of 2.5, have been identified on linkage groups (LGs) 02, 06, and 15 of the apple genome with phenotypic variation explained values of 14.7, 20.1 and 17.4, respectively. Although elevated P-values with signals for marker-trait associations are observed for some LGs, these are not found to be significant. However, a total of 34 significant associations, with P-values ≥0.02, have been detected including 8 for lesion length at 7 days following inoculation (PL1), 14 for lesion length at 14 days following inoculation (PL2), and 12 for shoot length. © 2013 Scandinavian Plant Physiology Society.

  4. Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.).

    PubMed

    Pandit, Awadhesh; Rai, Vandna; Bal, Subhashis; Sinha, Shikha; Kumar, Vinod; Chauhan, Mahesh; Gautam, Raj K; Singh, Rakesh; Sharma, Prakash C; Singh, Ashok K; Gaikwad, Kishor; Sharma, Tilak R; Mohapatra, Trilochan; Singh, Nagendra K

    2010-08-01

    Identification of genes for quantitative traits is difficult using any single approach due to complex inheritance of the traits and limited resolving power of the individual techniques. Here a combination of genetic mapping and bulked transcriptome profiling was used to narrow down the number of differentially expressed salt-responsive genes in rice in order to identify functional polymorphism of genes underlying the quantitative trait loci (QTL). A population of recombinant inbred lines (RILs) derived from cross between salt-tolerant variety CSR 27 and salt-sensitive variety MI 48 was used to map QTL for salt ion concentrations in different tissues and salt stress susceptibility index (SSI) for spikelet fertility, grain weight, and grain yield. Eight significant QTL intervals were mapped on chromosomes 1, 8, and 12 for the salt ion concentrations and a QTL controlling SSI for spikelet fertility was co-located in one of these intervals on chromosome 8. However, there were total 2,681 genes in these QTL intervals, making it difficult to pinpoint the genes responsible for the functional differences for the traits. Similarly, transcriptome profiling of the seedlings of tolerant and sensitive parents grown under control and salt-stress conditions showed 798 and 2,407 differentially expressed gene probes, respectively. By analyzing pools of RNA extracted from ten each of extremely tolerant and extremely sensitive RILs to normalize the background noise, the number of differentially expressed genes under salt stress was drastically reduced to 30 only. Two of these genes, an integral transmembrane protein DUF6 and a cation chloride cotransporter, were not only co-located in the QTL intervals but also showed the expected distortion of allele frequencies in the extreme tolerant and sensitive RILs, and therefore are suitable for future validation studies and development of functional markers for salt tolerance in rice to facilitate marker-assisted breeding.

  5. 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.

  6. Genome-wide linkage mapping of QTL for black point reaction in bread wheat (Triticum aestivum L.).

    PubMed

    Liu, Jindong; He, Zhonghu; Wu, Ling; Bai, Bin; Wen, Weie; Xie, Chaojie; Xia, Xianchun

    2016-11-01

    Nine QTL for black point resistance in wheat were identified using a RIL population derived from a Linmai 2/Zhong 892 cross and 90K SNP assay. Black point, discoloration of the embryo end of the grain, downgrades wheat grain quality leading to significant economic losses to the wheat industry. The availability of molecular markers will accelerate improvement of black point resistance in wheat breeding. The aims of this study were to identify quantitative trait loci (QTL) for black point resistance and tightly linked molecular markers, and to search for candidate genes using a high-density genetic linkage map of wheat. A recombinant inbred line (RIL) population derived from the cross Linmai 2/Zhong 892 was evaluated for black point reaction during the 2011-2012, 2012-2013 and 2013-2014 cropping seasons, providing data for seven environments. A high-density linkage map was constructed by genotyping the RILs with the wheat 90K single nucleotide polymorphism (SNP) chip. Composite interval mapping detected nine QTL on chromosomes 2AL, 2BL, 3AL, 3BL, 5AS, 6A, 7AL (2) and 7BS, designated as QBp.caas-2AL, QBp.caas-2BL, QBp.caas-3AL, QBp.caas-3BL, QBp.caas-5AS, QBp.caas-6A, QBp.caas-7AL.1, QBp.caas-7AL.2 and QBp.caas-7BS, respectively. All resistance alleles, except for QBp.caas-7AL.1 from Linmai 2, were contributed by Zhong 892. QBp.caas-3BL, QBp.caas-5AS, QBp.caas-7AL.1, QBp.caas-7AL.2 and QBp.caas-7BS probably represent new loci for black point resistance. Sequences of tightly linked SNPs were used to survey wheat and related cereal genomes identifying three candidate genes for black point resistance. The tightly linked SNP markers can be used in marker-assisted breeding in combination with the kompetitive allele specific PCR technique to improve black point resistance.

  7. Genome anchored QTLs for biomass productivity in Hybrid Populus: Heterosis and detection across Contrasting Environments.

    SciTech Connect

    Muchero, Wellington; Sewell, Mitchell; Gunter, Lee E; Tschaplinski, Timothy J; Yin, Tongming; DiFazio, Steven P; Tuskan, Gerald A

    2013-01-01

    Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs) in an interspecific F2 population derived from an outbred Populus trichocarpa P. deltoides parental cross. Three years of phenotypic data for stem growth traits (height and diameter) were collected from two parental, two F1 and 339 F2 trees in a clonal trial replicated both within and among two environmentally contrasting sites in the North American Pacific Northwest. A genetic linkage map comprised of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring QTL using the Multiple-QTL Model (MQM) package of the statistical program MapQTL 6. A total of twelve QTLs, nine putative and three suggestive, were identified with eight of these being identified at both sites in at least one experiment. Of these, three putative QTL BM-1, BM-2, BM-7, on LGs I, II, and XIV, respectively, were identified in all three years for both height and diameter. Two QTLs BM-2 and BM-7, on LG II and XIV, respectively, exhibited significant evidence of over-dominance in all three years for both traits. Conversely a QTL on BM-6 LG XIII exhibited out-breeding depression in two years for both height and diameter. The remaining nine QTLs showed difference levels of dominance and additive effects. Seven of the nine QTL were successfully anchored and QTL peak positions were estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known physical positions positions. QTL BM-7 on LG XIV had been anchored on the genome assembly in a previous study, therefore eight QTLs identified in this study were assigned genome assembly positions. Physical distances encompassed by each QTL regions ranged from 1.3 to 8.8 Mb.

  8. Mapping a major QTL responsible for dwarf architecture in Brassica napus using a single-nucleotide polymorphism marker approach.

    PubMed

    Wang, Yankun; Chen, Wenjing; Chu, Pu; Wan, Shubei; Yang, Mao; Wang, Mingming; Guan, Rongzhan

    2016-08-18

    Key genes related to plant type traits have played very important roles in the "green revolution" by increasing lodging resistance and elevating the harvest indices of crop cultivars. Although there have been numerous achievements in the development of dwarfism and plant type in Brassica napus breeding, exploring new materials conferring oilseed rape with efficient plant types that provide higher yields is still of significance in breeding, as well as in elucidating the mechanisms underlying plant development. Here, we report a new dwarf architecture with down-curved leaf mutant (Bndwf/dcl1) isolated from an ethyl methanesulphonate (EMS)-mutagenized B. napus line, together with its inheritance and gene mapping, and pleiotropic effects of the mapped locus on plant-type traits. We constructed a high-density single-nucleotide polymorphism (SNP) map using a backcross population derived from the Bndwf/dcl1 mutant and the canola cultivar 'zhongshuang11' ('ZS11') and mapped the dwarf architecture with the down-curved leaf dominant locus, BnDWF/DCL1, in a 6.58-cM interval between SNP marker bins M46180 and M49962 on the linkage group (LG) C05 of B. napus. Further mapping with other materials derived from Bndwf/dcl1 narrowed the interval harbouring BnDWF/DCL1 to 175 kb in length and this interval contained 16 annotated genes. Quantitative trait locus (QTL) mappings with the backcross population for plant type traits, including plant height, branching height, main raceme length and average branching interval, indicated that the mapped QTLs for plant type traits were located at the same position as the BnDWF/DCL1 locus. This study suggests that the BnDWF/DCL1 locus is a major pleiotropic locus/QTL in B. napus, which may reduce plant height, alter plant type traits and change leaf shape, and thus may lead to compact plant architecture. Accordingly, this locus may have substantial breeding potential for increasing planting density.

  9. QTL mapping and phenotypic variation of root anatomical traits in maize (Zea mays L.).

    PubMed

    Burton, Amy L; Johnson, James; Foerster, Jillian; Hanlon, Meredith T; Kaeppler, Shawn M; Lynch, Jonathan P; Brown, Kathleen M

    2015-01-01

    Root anatomical trait variation is described for three maize RIL populations. Six quantitative trait loci (QTL) are presented for anatomical traits: root cross-sectional area, % living cortical area, aerenchyma area, and stele area. Root anatomy is directly related to plant performance, influencing resource acquisition and transport, the metabolic cost of growth, and the mechanical strength of the root system. Ten root anatomical traits were measured in greenhouse-grown plants from three recombinant inbred populations of maize [intermated B73 × Mo17 (IBM), Oh43 × W64a (OhW), and Ny821 × H99 (NyH)]. Traits included areas of cross section, stele, cortex, aerenchyma, and cortical cells, percentages of the cortex occupied by aerenchyma, and cortical cell file number. Significant phenotypic variation was observed for each of the traits, with maximum values typically seven to ten times greater than minimum values. Means and ranges were similar for the OhW and NyH populations for all traits, while the IBM population had lower mean values for the majority of traits, but a 50% greater range of variation for aerenchyma area. A principal component analysis showed a similar trait structure for the three families, with clustering of area and count traits. Strong correlations were observed among area traits in the cortex, stele, and cross-section. The aerenchyma and percent living cortical area traits were independent of other traits. Six QTL were identified for four of the traits. The phenotypic variation explained by the QTL ranged from 4.7% (root cross-sectional area, OhW population) to 12.0% (percent living cortical area, IBM population). Genetic variation for root anatomical traits can be harnessed to increase abiotic stress tolerance and provide insights into mechanisms controlling phenotypic variation for root anatomy.

  10. High-Density SNP Map Construction and QTL Identification for the Apetalous Character in Brassica napus L.

    PubMed Central

    Wang, Xiaodong; Yu, Kunjiang; Li, Hongge; Peng, Qi; Chen, Feng; Zhang, Wei; Chen, Song; Hu, Maolong; Zhang, Jiefu

    2015-01-01

    The apetalous genotype is a morphological ideotype for increasing seed yield and should be of considerable agricultural use; however, only a few studies have focused on the genetic control of this trait in Brassica napus. In the present study, a recombinant inbred line, the AH population, containing 189 individuals was derived from a cross between an apetalous line ‘APL01’ and a normally petalled variety ‘Holly’. The Brassica 60 K Infinium BeadChip Array harboring 52,157 single nucleotide polymorphism (SNP) markers was used to genotype the AH individuals. A high-density genetic linkage map was constructed based on 2,755 bins involving 11,458 SNPs and 57 simple sequence repeats, and was used to identify loci associated with petalous degree (PDgr). The linkage map covered 2,027.53 cM, with an average marker interval of 0.72 cM. The AH map had good collinearity with the B. napus reference genome, indicating its high quality and accuracy. After phenotypic analyses across five different experiments, a total of 19 identified quantitative trait loci (QTLs) distributed across chromosomes A3, A5, A6, A9 and C8 were obtained, and these QTLs were further integrated into nine consensus QTLs by a meta-analysis. Interestingly, the major QTL qPD.C8-2 was consistently detected in all five experiments, and qPD.A9-2 and qPD.C8-3 were stably expressed in four experiments. Comparative mapping between the AH map and the B. napus reference genome suggested that there were 328 genes underlying the confidence intervals of the three steady QTLs. Based on the Gene Ontology assignments of 52 genes to the regulation of floral development in published studies, 146 genes were considered as potential candidate genes for PDgr. The current study carried out a QTL analysis for PDgr using a high-density SNP map in B. napus, providing novel targets for improving seed yield. These results advanced our understanding of the genetic control of PDgr regulation in B. napus. PMID:26779193

  11. Genetic map construction and quantitative trait locus (QTL) detection of growth-related traits in Litopenaeus vannamei for selective breeding applications.

    PubMed

    Andriantahina, Farafidy; Liu, Xiaolin; Huang, Hao

    2013-01-01

    Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL) have been regarded as useful for marker-assisted selection (MAS) in complex traits as growth. Using an intermediate F2 cross of slow and fast growth parents, a genetic linkage map of Pacific whiteleg shrimp, Litopenaeusvannamei, based on amplified fragment length polymorphisms (AFLP) and simple sequence repeats (SSR) markers was constructed. Meanwhile, QTL analysis was performed for growth-related traits. The linkage map consisted of 451 marker loci (429 AFLPs and 22 SSRs) which formed 49 linkage groups with an average marker space of 7.6 cM; they spanned a total length of 3627.6 cM, covering 79.50% of estimated genome size. 14 QTLs were identified for growth-related traits, including three QTLs for body weight (BW), total length (TL) and partial carapace length (PCL), two QTLs for body length (BL), one QTL for first abdominal segment depth (FASD), third abdominal segment depth (TASD) and first abdominal segment width (FASW), which explained 2.62 to 61.42% of phenotypic variation. Moreover, comparison of linkage maps between L. vannamei and Penaeusjaponicus was applied, providing a new insight into the genetic base of QTL affecting the growth-related traits. The new results will be useful for conducting MAS breeding schemes in L. vannamei .

  12. mQTL.NMR: an integrated suite for genetic mapping of quantitative variations of (1)H NMR-based metabolic profiles.

    PubMed

    Hedjazi, Lyamine; Gauguier, Dominique; Zalloua, Pierre A; Nicholson, Jeremy K; Dumas, Marc-Emmanuel; Cazier, Jean-Baptiste

    2015-04-21

    High-throughput (1)H nuclear magnetic resonance (NMR) is an increasingly popular robust approach for qualitative and quantitative metabolic profiling, which can be used in conjunction with genomic techniques to discover novel genetic associations through metabotype quantitative trait locus (mQTL) mapping. There is therefore a crucial necessity to develop specialized tools for an accurate detection and unbiased interpretability of the genetically determined metabolic signals. Here we introduce and implement a combined chemoinformatic approach for objective and systematic analysis of untargeted (1)H NMR-based metabolic profiles in quantitative genetic contexts. The R/Bioconductor mQTL.NMR package was designed to (i) perform a series of preprocessing steps restoring spectral dependency in collinear NMR data sets to reduce the multiple testing burden, (ii) carry out robust and accurate mQTL mapping in human cohorts as well as in rodent models, (iii) statistically enhance structural assignment of genetically determined metabolites, and (iv) illustrate results with a series of visualization tools. Built-in flexibility and implementation in the powerful R/Bioconductor framework allow key preprocessing steps such as peak alignment, normalization, or dimensionality reduction to be tailored to specific problems. The mQTL.NMR package is freely available with its source code through the Comprehensive R/Bioconductor repository and its own website ( http://www.ican-institute.org/tools/ ). It represents a significant advance to facilitate untargeted metabolomic data processing and quantitative analysis and their genetic mapping.

  13. Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism.

    PubMed

    Bardol, N; Ventelon, M; Mangin, B; Jasson, S; Loywick, V; Couton, F; Derue, C; Blanchard, P; Charcosset, A; Moreau, Laurence

    2013-11-01

    Advancements in genotyping are rapidly decreasing marker costs and increasing marker density. This opens new possibilities for mapping quantitative trait loci (QTL), in particular by combining linkage disequilibrium information and linkage analysis (LDLA). In this study, we compared different approaches to detect QTL for four traits of agronomical importance in two large multi-parental datasets of maize (Zea mays L.) of 895 and 928 testcross progenies composed of 7 and 21 biparental families, respectively, and genotyped with 491 markers. We compared to traditional linkage-based methods two LDLA models relying on the dense genotyping of parental lines with 17,728 SNP: one based on a clustering approach of parental line segments into ancestral alleles and one based on single marker information. The two LDLA models generally identified more QTL (60 and 52 QTL in total) than classical linkage models (49 and 44 QTL in total). However, they performed inconsistently over datasets and traits suggesting that a compromise must be found between the reduction of allele number for increasing statistical power and the adequacy of the model to potentially complex allelic variation. For some QTL, the model exclusively based on linkage analysis, which assumed that each parental line carried a different QTL allele, was able to capture remaining variation not explained by LDLA models. These complementarities between models clearly suggest that the different QTL mapping approaches must be considered to capture the different levels of allelic variation at QTL involved in complex traits.

  14. QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis).

    PubMed

    Pan, Yupeng; Qu, Shuping; Bo, Kailiang; Gao, Meiling; Haider, Kristin R; Weng, Yiqun

    2017-07-01

    QTL analysis revealed 11 QTL underlying flowering time and fruit size variation in the semi-wild Xishuangbanna cucumber, of which, FT6.2 and FS5.2 played the most important roles in determining photoperiod-dependent flowering time and round-fruit shape, respectively. Flowering time and fruit size are two important traits in domestication and diversifying selection in cucumber, but their genetic basis is not well understood. Here we reported QTL mapping results on flowering time and fruit size with F2 and F2:3 segregating populations derived from the cross between WI7200, a small fruited, early flowering primitive cultivated cucumber and WI7167, a round-fruited, later flowering semi-wild Xishuangbanna (XIS) cucumber. A linkage map with 267 microsatellite marker loci was developed with 138 F2 plants. Phenotypic data of male and female flowering time, fruit length and diameter and three other traits (mature fruit weight and number, and seedling hypocotyl length) were collected in multiple environments. Three flowering time QTL, FT1.1, FT5.1 and FT6.2 were identified, in which FT6.2 played the most important role in conferring less photoperiod sensitive early flowering during domestication whereas FT1.1 seemed more influential in regulating flowering time within the cultivated cucumber. Eight consensus fruit size QTL distributed in 7 chromosomes were detected, each of which contributed to both longitudinal and radial growth in cucumber fruit development. Among them, FS5.2 on chromosome 5 exhibited the largest effect on the determination of round fruit shape that was characteristic of the WI7167 XIS cucumber. Possible roles of these flowering time and fruit size QTL in domestication of cucumber and crop evolution of the semi-wild XIS cucumber, as well as the genetic basis of round fruit shape in cucumber are discussed.

  15. QTL mapping in eggplant reveals clusters of yield-related loci and orthology with the tomato genome.

    PubMed

    Portis, Ezio; Barchi, Lorenzo; Toppino, Laura; Lanteri, Sergio; Acciarri, Nazzareno; Felicioni, Nazzareno; Fusari, Fabio; Barbierato, Valeria; Cericola, Fabio; Valè, Giampiero; Rotino, Giuseppe Leonardo

    2014-01-01

    In spite of its widespread cultivation and nutritional and economic importance, the eggplant (Solanum melongena L.) genome has not been extensively explored. A lack of knowledge of the patterns of inheritance of key agronomic traits has hindered the exploitation of marker technologies to accelerate its genetic improvement. An already established F2 intraspecific population of eggplant bred from the cross '305E40' x '67/3' was phenotyped for 20 agronomically relevant traits at two sites. Up to seven quantitative trait loci (QTL) per trait were identified and the percentage of the phenotypic variance (PV) explained per QTL ranged from 4 to 93%. Not all the QTL were detectable at both sites, but for each trait at least one major QTL (PV explained ≥ 10%) was identified. Although no detectable QTL x environment interaction was found, some QTL identified were location-specific. Many of the fruit-related QTL clustered within specific chromosomal regions, reflecting either linkage and/or pleiotropy. Evidence for putative tomato orthologous QTL/genes was obtained for several of the eggplant QTL. Information regarding the inheritance of key agronomic traits was obtained. Some of the QTL, along with their respective linked markers, may be useful in the context of marker-assisted breeding.

  16. QTL Mapping in Eggplant Reveals Clusters of Yield-Related Loci and Orthology with the Tomato Genome

    PubMed Central

    Portis, Ezio; Barchi, Lorenzo; Toppino, Laura; Lanteri, Sergio; Acciarri, Nazzareno; Felicioni, Nazzareno; Fusari, Fabio; Barbierato, Valeria; Cericola, Fabio; Valè, Giampiero; Rotino, Giuseppe Leonardo

    2014-01-01

    In spite of its widespread cultivation and nutritional and economic importance, the eggplant (Solanum melongena L.) genome has not been extensively explored. A lack of knowledge of the patterns of inheritance of key agronomic traits has hindered the exploitation of marker technologies to accelerate its genetic improvement. An already established F2 intraspecific population of eggplant bred from the cross ‘305E40’ x ‘67/3’ was phenotyped for 20 agronomically relevant traits at two sites. Up to seven quantitative trait loci (QTL) per trait were identified and the percentage of the phenotypic variance (PV) explained per QTL ranged from 4 to 93%. Not all the QTL were detectable at both sites, but for each trait at least one major QTL (PV explained ≥10%) was identified. Although no detectable QTL x environment interaction was found, some QTL identified were location-specific. Many of the fruit-related QTL clustered within specific chromosomal regions, reflecting either linkage and/or pleiotropy. Evidence for putative tomato orthologous QTL/genes was obtained for several of the eggplant QTL. Information regarding the inheritance of key agronomic traits was obtained. Some of the QTL, along with their respective linked markers, may be useful in the context of marker-assisted breeding. PMID:24586828

  17. Leaf Rubisco turnover in a perennial ryegrass (Lolium perenne L.) mapping population: genetic variation, identification of associated QTL, and correlation with plant morphology and yield.

    PubMed

    Khaembah, Edith N; Irving, Louis J; Thom, Errol R; Faville, Marty J; Easton, H Sydney; Matthew, Cory

    2013-03-01

    This study tested the hypotheses that: (i) genetic variation in Rubisco turnover may exist in perennial ryegrass (Lolium perenne L.); (ii) such variation might affect nitrogen use efficiency and plant yield; and (iii) genetic control of Rubisco turnover might be amenable to identification by quantitative trait loci (QTL) mapping. A set of 135 full-sib F1 perennial ryegrass plants derived from a pair cross between genotypes from the cultivars 'Grasslands Impact' and 'Grasslands Samson' was studied to test these hypotheses. Leaf Rubisco concentration at different leaf ages was measured and modelled as a log-normal curve described by three mathematical parameters: D (peak Rubisco concentration), G (time of D), and F (curve standard deviation). Herbage dry matter (DM) yield and morphological traits (tiller weight (TW), tiller number (TN), leaf lamina length (LL), and an index of competitive ability (PI)) were also measured. The progeny exhibited continuous variation for all traits. Simple correlation and principal component analyses indicated that plant productivity was associated with peak Rubisco concentration and not Rubisco turnover. Lower DM was associated with higher leaf Rubisco concentration indicating that Rubisco turnover effects on plant productivity may relate to energy cost of Rubisco synthesis rather than photosynthetic capacity. QTL detection by a multiple QTL model identified seven significant QTL for Rubisco turnover and nine QTL for DM and morphological traits. An indication of the genetic interdependence of DM and the measures of Rubisco turnover was the support interval overlap involving QTL for D and QTL for TN on linkage group 5 in a cluster involving QTL for DM and PI. In this region, alleles associated with increased TN, DM, and PI were associated with decreased D, indicating that this region may regulate Rubisco concentration and plant productivity via increased tillering. A second cluster involving QTL for LL, TN, PI and DM was found on

  18. Mapping QTLs and QTL x environment interaction for CIMMYT maize drought stress program using factorial regression and partial least squares methods.

    PubMed

    Vargas, Mateo; van Eeuwijk, Fred A; Crossa, Jose; Ribaut, Jean-Marcel

    2006-04-01

    The study of QTL x environment interaction (QEI) is important for understanding genotype x environment interaction (GEI) in many quantitative traits. For modeling GEI and QEI, factorial regression (FR) models form a powerful class of models. In FR models, covariables (contrasts) defined on the levels of the genotypic and/or environmental factor(s) are used to describe main effects and interactions. In FR models for QTL expression, considerable numbers of genotypic covariables can occur as for each putative QTL an additional covariable needs to be introduced. For large numbers of genotypic and/or environmental covariables, least square estimation breaks down and partial least squares (PLS) estimation procedures become an attractive alternative. In this paper we develop methodology for analyzing QEI by FR for estimating effects and locations of QTLs and QEI and interpreting QEI in terms of environmental variables. A randomization test for the main effects of QTLs and QEI is presented. A population of F2 derived F3 families was evaluated in eight environments differing in drought stress and soil nitrogen content and the traits yield and anthesis silking interval (ASI) were measured. For grain yield, chromosomes 1 and 10 showed significant QEI, whereas in chromosomes 3 and 8 only main effect QTLs were observed. For ASI, QTL main effects were observed on chromosomes 1, 2, 6, 8, and 10, whereas QEI was observed only on chromosome 8. The assessment of the QEI at chromosome 1 for grain yield showed that the QTL main effect explained 35.8% of the QTL + QEI variability, while QEI explained 64.2%. Minimum temperature during flowering time explained 77.6% of the QEI. The QEI analysis at chromosome 10 showed that the QTL main effect explained 59.8% of the QTL + QEI variability, while QEI explained 40.2%. Maximum temperature during flowering time explained 23.8% of the QEI. Results of this study show the possibilities of using FR for mapping QTL and for dissecting QEI in terms

  19. 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.

  20. Construction of a genetic linkage map and QTL analysis of erucic acid content and glucosinolate components in yellow mustard (Sinapis alba L.)

    PubMed Central

    2013-01-01

    Background Yellow mustard (Sinapis alba L.) is an important condiment crop for the spice trade in the world. It has lagged behind oilseed Brassica species in molecular marker development and application. Intron length polymorphism (ILP) markers are highly polymorphic, co-dominant and cost-effective. The cross-species applicability of ILP markers from Brassica species and Arabidopsis makes them possible to be used for genetic linkage mapping and further QTL analysis of agronomic traits in yellow mustard. Results A total of 250 ILP and 14 SSR markers were mapped on 12 linkage groups and designated as Sal01-12 in yellow mustard. The constructed map covered a total genetic length of 890.4 cM with an average marker interval of 3.3 cM. The QTL for erucic content co-localized with the fatty acid elongase 1 (FAE1) gene on Sal03. The self-(in)compatibility gene was assigned to Sal08. The 4-hydroxybenzyl, 3-indolylmethyl and 4-hydroxy-3-indolylmethyl glucosinolate contents were each controlled by one major QTL, all of which were located on Sal02. Two QTLs, accounting for the respective 20.4% and 19.2% of the total variation of 2-hydroxy-3-butenyl glucosinolate content, were identified and mapped to Sal02 and Sal11. Comparative synteny analysis revealed that yellow mustard was phylogenetically related to Arabidopsis thaliana and had undergone extensive chromosomal rearrangements during speciation. Conclusion The linkage map based on ILP and SSR markers was constructed and used for QTL analysis of seed quality traits in yellow mustard. The markers tightly linked with the genes for different glucosinolate components will be used for marker-assisted selection and map-based cloning. The ILP markers and linkage map provide useful molecular tools for yellow mustard breeding. PMID:24066707

  1. QTL mapping of partial resistance in winter wheat to Stagonospora nodorum blotch.

    PubMed

    Czembor, Pawel C; Arseniuk, Edward; Czaplicki, Andrzej; Song, Qijiang; Cregan, Perry B; Ueng, Peter P

    2003-08-01

    Stagonospora nodorum blotch is an important foliar and glume disease in cereals. Inheritance of resistance in wheat appears to be quantitative. To date, breeding of partially resistant cultivars has been the only effective way to combat this pathogen. The partial resistance components, namely length of incubation period, disease severity, and length of latent period, were evaluated on a population of doubled haploids derived from a cross between the partially resistant Triticum aestivum 'Liwilla' and susceptible Triticum aestivum 'Begra'. Experiments were conducted in a controlled environment and the fifth leaf was examined. Molecular analyses were based on bulked segregant analyses using 240 microsatellite markers. Four QTLs were significantly associated with partial resistance components and were located on chromosomes 2B, 3B, 5B, and 5D. The percentage of phenotypic variance explained by a single QTL ranged from 14 to 21% for incubation period, from 16 to 37% for disease severity, and from 13 to 28% for latent period,

  2. Multi-environment QTL mapping reveals genetic architecture of fruit cracking in a tomato RIL Solanum lycopersicum × S. pimpinellifolium population.

    PubMed

    Capel, Carmen; Yuste-Lisbona, Fernando J; López-Casado, Gloria; Angosto, Trinidad; Cuartero, Jesús; Lozano, Rafael; Capel, Juan

    2017-01-01

    QTL and codominant genetic markers for fruit cracking have been identified in a tomato genetic map derived from a RIL population, providing molecular tools for marker-assisted breeding of this trait. In tomato, as well as in other fleshy fruits, one of the main disorders that widely limit quality and production is fruit cracking or splitting of the epidermis that is observed on the fruit skin and flesh at any stage of fruit growth and maturation. To elucidate the genetic basis of fruit cracking, a quantitative trait loci (QTL) analysis was conducted in 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 cracking during three consecutive growing seasons. Construction of a high-density linkage map based on codominant markers, covering more than 1000 cM of the whole genome, led to the identification of both main and epistatic QTL controlling fruit cracking on the basis of a single-environment as well as multiple-environment analysis. This information will enhance molecular breeding for novel cracking resistant varieties and simultaneously assist the identification of genes underlying these QTL, helping to reveal the genetic basis of fruit cracking in tomato.

  3. Construction of chromosome segment substitution lines in peanut (Arachis hypogaea L.) using a wild synthetic and QTL mapping for plant morphology.

    PubMed

    Fonceka, Daniel; Tossim, Hodo-Abalo; Rivallan, Ronan; Vignes, Hélène; Lacut, Elodie; de Bellis, Fabien; Faye, Issa; Ndoye, Ousmane; Leal-Bertioli, Soraya C M; Valls, José F M; Bertioli, David J; Glaszmann, Jean-Christophe; Courtois, Brigitte; Rami, Jean-François

    2012-01-01

    Chromosome segment substitution lines (CSSLs) are powerful QTL mapping populations that have been used to elucidate the molecular basis of interesting traits of wild species. Cultivated peanut is an allotetraploid with limited genetic diversity. Capturing the genetic diversity from peanut wild relatives is an important objective in many peanut breeding programs. In this study, we used a marker-assisted backcrossing strategy to produce a population of 122 CSSLs from the cross between the wild synthetic allotetraploid (A. ipaënsis×A. duranensis)(4x) and the cultivated Fleur11 variety. The 122 CSSLs offered a broad coverage of the peanut genome, with target wild chromosome segments averaging 39.2 cM in length. As a demonstration of the utility of these lines, four traits were evaluated in a subset of 80 CSSLs. A total of 28 lines showed significant differences from Fleur11. The line×trait significant associations were assigned to 42 QTLs: 14 for plant growth habit, 15 for height of the main stem, 12 for plant spread and one for flower color. Among the 42 QTLs, 37 were assigned to genomic regions and three QTL positions were considered putative. One important finding arising from this QTL analysis is that peanut growth habit is a complex trait that is governed by several QTLs with different effects. The CSSL population developed in this study has proved efficient for deciphering the molecular basis of trait variations and will be useful to the peanut scientific community for future QTL mapping studies.

  4. QTL Mapping for Phosphorus Efficiency and Morphological Traits at Seedling and Maturity Stages in Wheat

    PubMed Central

    Yuan, Yuanyuan; Gao, Minggang; Zhang, Mingxia; Zheng, Honghua; Zhou, Xiuwen; Guo, Ying; Zhao, Yan; Kong, Fangmei; Li, Sishen

    2017-01-01

    Phosphorus (P) efficiency (PE), which comprises phosphorus uptake (PupE) and utilization efficiency (PutE), is considered as one of the most important factors for crop yield. In the present study, 11 seedling traits and 13 maturity traits related to wheat PE and morphology were investigated using a set of recombinant inbred lines (RILs) derived from the cross of “TN 18 × LM 6,” under hydroponic culture trials and field trials at low P (LP) and normal P (NP) levels in two different years, respectively. The LP input reduced of biomass, yield and PupE traits, but increased PutE traits. A total of 163 QTLs for seedling and maturity traits under different P levels and their AV, and 15 QTLs for relative traits were detected on 21 chromosomes. Of these, 49 and 63 QTLs for were detected specially in LP and NP treatments, respectively. We found 11 relatively high-frequency QTLs (RHF-QTLs) and four important QTL clusters, which may be the potential targets for marker-assisted selection (MAS) in wheat breeding programs for PE. Favorable relationships for breeding programs were found in the four important QTL clusters, which allow the possibility of improving the morphological traits and PutE simultaneously. A total of 29 markers which associated with 51 QTLs were found highly homologous with EST sequences, which suggested that they were potential functional loci. We suggested that the four biomass traits (SDW, RDW, TDW, and RSDW), five yield traits (SN, PH, TGW, GWP, and StWP) and two relative traits (Rstwp and Rgwp) can be considered as the primary indexes for the evaluation of PE for they are easy to identify on a large-scale. PMID:28484481

  5. 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 F2 population derived from a cross between two commercial F1 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 F1 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 F2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.

  6. Genetic architecture of sexual selection: QTL mapping of male song and female receiver traits in an acoustic moth.

    PubMed

    Limousin, Denis; Streiff, Réjane; Courtois, Brigitte; Dupuy, Virginie; Alem, Sylvain; Greenfield, Michael D

    2012-01-01

    Models of indirect (genetic) benefits sexual selection predict linkage disequilibria between genes that influence male traits and female preferences, owing to non-random mate choice or physical linkage. Such linkage disequilibria can accelerate the evolution of traits and preferences to exaggerated levels. Both theory and recent empirical findings on species recognition suggest that such linkage disequilibria may result from physical linkage or pleiotropy, but very little work has addressed this possibility within the context of sexual selection. We studied the genetic architecture of sexually selected traits by analyzing signals and preferences in an acoustic moth, Achroia grisella, in which males attract females with a train of ultrasound pulses and females prefer loud songs and a fast pulse rhythm. Both male signal characters and female preferences are repeatable and heritable traits. Moreover, female choice is based largely on male song, while males do not appear to provide direct benefits at mating. Thus, some genetic correlation between song and preference traits is expected. We employed a standard crossing design between inbred lines and used AFLP markers to build a linkage map for this species and locate quantitative trait loci (QTL) that influence male song and female preference. Our analyses mostly revealed QTLs of moderate strength that influence various male signal and female receiver traits, but one QTL was found that exerts a major influence on the pulse-pair rate of male song, a critical trait in female attraction. However, we found no evidence of specific co-localization of QTLs influencing male signal and female receiver traits on the same linkage groups. This finding suggests that the sexual selection process would proceed at a modest rate in A. grisella and that evolution toward exaggerated character states may be tempered. We suggest that this equilibrium state may be more the norm than the exception among animal species.

  7. Genetic Architecture of Sexual Selection: QTL Mapping of Male Song and Female Receiver Traits in an Acoustic Moth

    PubMed Central

    Limousin, Denis; Streiff, Réjane; Courtois, Brigitte; Dupuy, Virginie; Alem, Sylvain; Greenfield, Michael D.

    2012-01-01

    Models of indirect (genetic) benefits sexual selection predict linkage disequilibria between genes that influence male traits and female preferences, owing to non-random mate choice or physical linkage. Such linkage disequilibria can accelerate the evolution of traits and preferences to exaggerated levels. Both theory and recent empirical findings on species recognition suggest that such linkage disequilibria may result from physical linkage or pleiotropy, but very little work has addressed this possibility within the context of sexual selection. We studied the genetic architecture of sexually selected traits by analyzing signals and preferences in an acoustic moth, Achroia grisella, in which males attract females with a train of ultrasound pulses and females prefer loud songs and a fast pulse rhythm. Both male signal characters and female preferences are repeatable and heritable traits. Moreover, female choice is based largely on male song, while males do not appear to provide direct benefits at mating. Thus, some genetic correlation between song and preference traits is expected. We employed a standard crossing design between inbred lines and used AFLP markers to build a linkage map for this species and locate quantitative trait loci (QTL) that influence male song and female preference. Our analyses mostly revealed QTLs of moderate strength that influence various male signal and female receiver traits, but one QTL was found that exerts a major influence on the pulse-pair rate of male song, a critical trait in female attraction. However, we found no evidence of specific co-localization of QTLs influencing male signal and female receiver traits on the same linkage groups. This finding suggests that the sexual selection process would proceed at a modest rate in A. grisella and that evolution toward exaggerated character states may be tempered. We suggest that this equilibrium state may be more the norm than the exception among animal species. PMID:22957082

  8. A resistance-like gene identified by EST mapping and its association with a QTL controlling Fusarium head blight infection on wheat chromosome 3BS.

    PubMed

    Shen, Xiaorong; Francki, Michael G; Ohm, Herbert W

    2006-06-01

    Fusarium head blight (FHB) is a major disease in the wheat growing regions of the world. A quantitative trait locus (QTL) on the short arm of chromosome 3B controls much of the variation for resistance. The cloning of candidate disease-resistance genes for FHB QTLs on chromosome 3B can provide further elucidation of the mechanisms that control resistance. However, rearrangements and divergence during plant genome evolution often hampers the identification of sequences with similarity to known disease-resistance genes. This study focuses on the use of wheat expressed sequence tags (ESTs) that map to the region on chromosome 3B containing the QTL for FHB resistance and low-stringency BLAST searching to identify sequences with similarity to known disease-resistance genes. One EST rich with leucine repeats and low similarity to a protein kinase domain of the barley Rpg1 gene was identified. Genetic mapping using a Ning894037 x Alondra recombinant inbred (RI) population showed that this EST mapped to the QTL on the short arm of chromosome 3B and may represent a portion of a newly diverged gene contributing to FHB resistance. The EST is a new marker suitable for marker-assisted selection and provides a starting point to begin map-based cloning for chromosome walking and investigate new diverged genes at this locus.

  9. QTL mapping of 1000-kernel weight, kernel length, and kernel width in bread wheat (Triticum aestivum L.).

    PubMed

    Ramya, P; Chaubal, A; Kulkarni, K; Gupta, L; Kadoo, N; Dhaliwal, H S; Chhuneja, P; Lagu, M; Gupta, V

    2010-01-01

    Kernel size and morphology influence the market value and milling yield of bread wheat (Triticum aestivum L.). The objective of this study was to identify quantitative trait loci (QTLs) controlling kernel traits in hexaploid wheat. We recorded 1000-kernel weight, kernel length, and kernel width for 185 recombinant inbred lines from the cross Rye Selection 111 × Chinese Spring grown in 2 agro-climatic regions in India for many years. Composite interval mapping (CIM) was employed for QTL detection using a linkage map with 169 simple sequence repeat (SSR) markers. For 1000-kernel weight, 10 QTLs were identified on wheat chromosomes 1A, 1D, 2B, 2D, 4B, 5B, and 6B, whereas 6 QTLs for kernel length were detected on 1A, 2B, 2D, 5A, 5B and 5D. Chromosomes 1D, 2B, 2D, 4B, 5B and 5D had 9 QTLs for kernel width. Chromosomal regions with QTLs detected consistently for multiple year-location combinations were identified for each trait. Pleiotropic QTLs were found on chromosomes 2B, 2D, 4B, and 5B. The identified genomic regions controlling wheat kernel size and shape can be targeted during further studies for their genetic dissection.

  10. Mapping of QTL for the seed storage proteins cruciferin and napin in a winter oilseed rape doubled haploid population and their inheritance in relation to other seed traits.

    PubMed

    Schatzki, Jörg; Ecke, Wolfgang; Becker, Heiko C; Möllers, Christian

    2014-05-01

    Cruciferin (cru) and napin (nap) were negatively correlated and the cru/nap ratio was closely negative correlated with glucosinolate content indicating a link between the two biosynthetic pathways. Canola-type oilseed rape (Brassica napus L.) is an economically important oilseed crop in temperate zones. Apart from the oil, the canola protein shows potential as a value-added food and nutraceutical ingredient. The two major storage protein groups occurring in oilseed rape are the 2 S napins and 12 S cruciferins. The aim of the present study was to analyse the genetic variation and the inheritance of napin and cruciferin content of the seed protein in the winter oilseed rape doubled haploid population Express 617 × R53 and to determine correlations to other seed traits. Seed samples were obtained from field experiments performed in 2 years at two locations with two replicates in Germany. A previously developed molecular marker map of the DH population was used to map quantitative trait loci (QTL) of the relevant traits. The results indicated highly significant effects of the year and the genotype on napin and cruciferin content as well as on the ratio of cruciferin to napin. Heritabilities were comparatively high with 0.79 for napin and 0.77 for cruciferin. Napin and cruciferin showed a significant negative correlation (-0.36**) and a close negative correlation of the cru/nap ratio to glucosinolate content was observed (-0.81**). Three QTL for napin and two QTL for cruciferin were detected, together explaining 47 and 35 % of the phenotypic variance. A major QTL for glucosinolate content was detected on linkage group N19 whose confidence interval overlapped with QTL for napin and cruciferin content. Results indicate a relationship between seed protein composition and glucosinolate content.

  11. A Consensus Microsatellite-Based Linkage Map for the Hermaphroditic Bay Scallop (Argopecten irradians) and Its Application in Size-Related QTL Analysis

    PubMed Central

    Li, Hongjun; Liu, Xiao; Zhang, Guofan

    2012-01-01

    Bay scallop (Argopecten irradians) is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color) markers were mapped to 16 linkage groups (LGs), which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13∶1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL), shell height (SH), shell width (SW) and total weight (TW) were measured for quantitative trait loci (QTL) analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively) were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH) was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS) in bay scallop. PMID:23077533

  12. QTL mapping with different genetic systems for nine non-essential amino acids of cottonseeds.

    PubMed

    Liu, Haiying; Quampah, Alfred; Chen, Jinhong; Li, Jinrong; Huang, Zhuangrong; He, Qiuling; Shi, Chunhai; Zhu, Shuijin

    2017-03-18

    Amino acid is an important nutrient resource for both human and animals. Using a set of 188 RILs population derived from an elite hybrid cross of upland cotton cultivars 'HS46' × 'MARCABUCAG8US-1-88' and their immortal F2 (IF2) with reciprocal backcrosses BC1F1 and BC2F1 (BC) populations in two environments, the QTLs located on the embryo genome and maternal plant genome for nine amino acids of cottonseed were studied across environments. The QTL Network-CL-2.0-seed software was used to analyze the QTLs and their genetic effects for nine amino acids. A total of 56 QTLs for nine amino acids were detected in both populations, with many having over 5% of phenotypic variation. Ten of the total QTLs could be simultaneously found in the IF2 and BC populations. For most QTLs, the genetic effects from embryo genome were more important than those from maternal plant genome for the performance of nine amino acids. Significant embryo additive main effects and maternal additive main effect with their environment interaction effects from many QTLs were also found in present experiment. Some QTLs with larger phenotypic variation were important for improving the amino-acid contents in cottonseeds.

  13. QTL mapping of leukocyte telomere length in American Indians: The Strong Heart Family Study

    PubMed Central

    Lin, Jue; Matsuguchi, Tet; Blackburn, Elizabeth; Best, Lyle G.; Lee, Elisa T.; MacCluer, Jean W.; Cole, Shelley A.; Zhao, Jinying

    2013-01-01

    Telomeres play a central role in cellular senescence and are associated with a variety of age-related disorders such as dementia, Alzheimer's disease and atherosclerosis. Telomere length varies greatly among individuals of the same age, and is heritable. Here we performed a genome-wide linkage scan to identify quantitative trait loci (QTL) influencing leukocyte telomere length (LTL) measured by quantitative PCR in 3,665 American Indians (aged 14 – 93 years) from 94 large, multi-generational families. All participants were recruited by the Strong Heart Family Study (SHFS), a prospective study to identify genetic factors for cardiovascular disease and its risk factors in American Indians residing in Oklahoma, Arizona and Dakota. LTL heritability was estimated to be between 51% and 62%, suggesting a strong genetic predisposition to interindividual variation of LTL in this population. Significant QTLs were localized to chromosome 13 (Logarithm of odds score (LOD) = 3.9) at 13q12.11, to 18q22.2 (LOD = 3.2) and to 3p14.1 (LOD = 3.0) for Oklahoma. This is the first study to identify susceptibility loci influencing leukocyte telomere variation in American Indians, a minority group suffering from a disproportionately high rate of type 2 diabetes and other age-related disorders. PMID:24036517

  14. QTL mapping of leukocyte telomere length in American Indians: the Strong Heart Family Study.

    PubMed

    Zhu, Yun; Voruganti, V Saroja; Lin, Jue; Matsuguchi, Tet; Blackburn, Elizabeth; Best, Lyle G; Lee, Elisa T; MacCluer, Jean W; Cole, Shelley A; Zhao, Jinying

    2013-09-01

    Telomeres play a central role in cellular senescence and are associated with a variety of age-related disorders such as dementia, Alzheimer's disease and atherosclerosis. Telomere length varies greatly among individuals of the same age, and is heritable. Here we performed a genome-wide linkage scan to identify quantitative trait loci (QTL) influencing leukocyte telomere length (LTL) measured by quantitative PCR in 3,665 American Indians (aged 14-93 years) from 94 large, multi-generational families. All participants were recruited by the Strong Heart Family Study (SHFS), a prospective study to identify genetic factors for cardiovascular disease and its risk factors in American Indians residing in Oklahoma, Arizona and Dakota. LTL heritability was estimated to be between 51% and 62%, suggesting a strong genetic predisposition to interindividual variation of LTL in this population. Significant QTLs were localized to chromosome 13 (Logarithm of odds score (LOD)=3.9) at 13q12.11, to 18q22.2 (LOD=3.2) and to 3p14.1 (LOD=3.0) for Oklahoma. This is the first study to identify susceptibility loci influencing leukocyte telomere variation in American Indians, a minority group suffering from a disproportionately high rate of type 2 diabetes and other age-related disorders.

  15. QTL mapping of protein content and seed characteristics under water-stress conditions in sunflower.

    PubMed

    Ebrahimi, A; Maury, P; Berger, M; Calmon, A; Grieu, P; Sarrafi, A

    2009-05-01

    The purpose of this study was to identify genomic regions controlling seed protein content, kernel and hull weights, and seed density in water-stress conditions in sunflower (Helianthus annuus L.). The experiments consisted of a split-plot design (water treatment and recombinant inbred lines) with three blocks in two environments (greenhouse and field). High significant variation was observed between genotypes for all traits as well as for water treatment x genotype interaction. Several specific and nonspecific QTLs were detected for all traits under well-watered and water-stress conditions. Two SSR markers, ORS671_2 and HA2714, linked to protein content were identified that have no interaction with water treatments in greenhouse conditions. We also detected the E35M60_4 marker associated with kernel weight that had no interaction with water treatments. A specific QTL for protein content was detected with important phenotypic variance (17%) under water-stress conditions. Overlapping QTLs for protein content and seed density were identified in linkage group 15. This region probably has a peliotropic effect on protein content and seed density. QTLs for protein content colocated with grain weight traits were also identified.

  16. 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

  17. QTL mapping of ten agronomic traits on the soybean ( Glycine max L. Merr.) genetic map and their association with EST markers.

    PubMed

    Zhang, W-K; Wang, Y-J; Luo, G-Z; Zhang, J-S; He, C-Y; Wu, X-L; Gai, J-Y; Chen, S-Y

    2004-04-01

    A set of 184 recombinant inbred lines (RILs) derived from soybean vars. Kefeng No.1 x Nannong 1138-2 was used to construct a genetic linkage map. The two parents exhibit contrasting characteristics for most of the traits that were mapped. Using restricted fragment length polymorphisms (RFLPs), simple sequence repeats (SSRs) and expressed sequence tags (ESTs), we mapped 452 markers onto 21 linkage groups and covered 3595.9 cM of the soybean genome. All of the linkage groups except linkage group F were consistent with those of the consensus map of Cregan et al. (1999). Linkage group F was divided into two linkage groups, F1 and F2. The map consisted of 189 RFLPs, 219 SSRs, 40 ESTs, three R gene loci and one phenotype marker. Ten agronomic traits-days to flowering, days to maturity, plant height, number of nodes on main stem, lodging, number of pods per node, protein content, oil content, 100-seed weight, and plot yield-were studied. Using winqtlcart, we detected 63 quantitative trait loci (QTLs) that had LOD>3 for nine of the agronomic traits (only exception being seed oil content) and mapped these on 12 linkage groups. Most of the QTLs were clustered, especially on groups B1 and C2. Some QTLs were mapped to the same loci. This pleiotropism was common for most of the QTLs, and one QTL could influence at most five traits. Seven EST markers were found to be linked closely with or located at the same loci as the QTLs. EST marker GmKF059a, encoding a repressor protein and mapped on group C2, accounted for about 20% of the total variation of days to flowering, plant height, lodging and nodes on the main stem, respectively.

  18. Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci.

    PubMed

    Brandt, Monika; Ahsan, Muhammad; Honaker, Christa F; Siegel, Paul B; Carlborg, Örjan

    2017-01-05

    The Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high- and low-weight lines show a >12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines. Copyright © 2017 Brandt et al.

  19. QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance.

    PubMed

    Almeida, Gustavo Dias; Makumbi, Dan; Magorokosho, Cosmos; Nair, Sudha; Borém, Aluízio; Ribaut, Jean-Marcel; Bänziger, Marianne; Prasanna, Boddupalli M; Crossa, Jose; Babu, Raman

    2013-03-01

    Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be 'adaptive' to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes.

  20. QTL mapping for a trade-off between leaf and bud production in a recombinant inbred population of Microseris douglasii and M. bigelovii (Asteraceae, Lactuceae): a potential preadaptation for the colonization of serpentine soils.

    PubMed

    Gailing, O; Macnair, M R; Bachmann, K

    2004-07-01

    The different response to growth on serpentine soil is a major autecological difference between the annual asteracean species Microseris douglasii and M. bigelovii, with nearly non-overlapping distribution ranges in California. Early flowering and seed set is regarded as a crucial character contributing to escape drought and thus is strongly correlated with survival and reproductive success on serpentine as naturally toxic soil. M. bigelovii (strain C94) from non-serpentine soil produces more leaves at the expense of bud production in the first growing phase than M. douglasii (B14) from serpentine soil. A QTL mapping study for this trade-off and for other growth-related traits was performed after six generations of inbreeding (F7) from a single interspecific hybrid between B14 and C94 on plants that were grown on serpentine and alternatively on normal potting soil. The trade-off is mainly correlated with markers on one map region on linkage group 03a (lg03a) with major phenotypic effects (phenotypic variance explained [PVE] = 18.8 - 31.7 %). Plants with the M. douglasii allele in QTL-B1 (QTL-NL1) produce more buds but fewer leaves in the first 119 days on both soil types. Three modifier QTL could be mapped for bud and leaf production. In one modifier (QTL-B2 = QTL-NL4) the M. douglasii allele is again associated with more buds but fewer leaves. QTL mapped for bud set in the F6 co-localize with QTL-B1 (major QTL) and QTL-B3. Two additional QTL for leaf length and red coloration of leaves could be mapped to one map region on lg03a. Co-localization of the two QTL loci with major phenotypic effects on bud and leaf production strongly suggests that a major genetic locus controls the trade-off between the two adaptive traits. The importance of mutational changes in major genes for the adaptation to stressful environments is discussed.

  1. Regression-based multi-trait QTL mapping using a structural equation model

    USDA-ARS?s Scientific Manuscript database

    Quantitative trait locus mapping often results in data on a number of traits that have well established causal relationships. Many multi-trait quantitative trait locus mapping methods that account for the correlation among the multiple traits have been developed to improve the statistical power and ...

  2. Joint QTL linkage mapping for multiple-cross mating design sharing one common parent

    USDA-ARS?s Scientific Manuscript database

    Nested association mapping (NAM) is a novel genetic mating design that combines the advantages of linkage analysis and association mapping. This design provides opportunities to study the inheritance of complex traits, but also requires more advanced statistical methods. In this paper, we present th...

  3. QTL mapping of the production of wine aroma compounds by yeast.

    PubMed

    Steyer, Damien; Ambroset, Chloe; Brion, Christian; Claudel, Patricia; Delobel, Pierre; Sanchez, Isabelle; Erny, Claude; Blondin, Bruno; Karst, Francis; Legras, Jean-Luc

    2012-10-30

    Wine aroma results from the combination of numerous volatile compounds, some produced by yeast and others produced in the grapes and further metabolized by yeast. However, little is known about the consequences of the genetic variation of yeast on the production of these volatile metabolites, or on the metabolic pathways involved in the metabolism of grape compounds. As a tool to decipher how wine aroma develops, we analyzed, under two experimental conditions, the production of 44 compounds by a population of 30 segregants from a cross between a laboratory strain and an industrial strain genotyped at high density. We detected eight genomic regions explaining the diversity concerning 15 compounds, some produced de novo by yeast, such as nerolidol, ethyl esters and phenyl ethanol, and others derived from grape compounds such as citronellol, and cis-rose oxide. In three of these eight regions, we identified genes involved in the phenotype. Hemizygote comparison allowed the attribution of differences in the production of nerolidol and 2-phenyl ethanol to the PDR8 and ABZ1 genes, respectively. Deletion of a PLB2 gene confirmed its involvement in the production of ethyl esters. A comparison of allelic variants of PDR8 and ABZ1 in a set of available sequences revealed that both genes present a higher than expected number of non-synonymous mutations indicating possible balancing selection. This study illustrates the value of QTL analysis for the analysis of metabolic traits, and in particular the production of wine aromas. It also identifies the particular role of the PDR8 gene in the production of farnesyldiphosphate derivatives, of ABZ1 in the production of numerous compounds and of PLB2 in ethyl ester synthesis. This work also provides a basis for elucidating the metabolism of various grape compounds, such as citronellol and cis-rose oxide.

  4. A high-density genetic map identifies a novel major QTL for boron efficiency in oilseed rape (Brassica napus L.).

    PubMed

    Zhang, Didi; Hua, Yingpeng; Wang, Xiaohua; Zhao, Hua; Shi, Lei; Xu, Fangsen

    2014-01-01

    Low boron (B) seriously limits the growth of oilseed rape (Brassica napus L.), a high B demand species that is sensitive to low B conditions. Significant genotypic variations in response to B deficiency have been observed among B. napus cultivars. To reveal the genetic basis for B efficiency in B. napus, quantitative trait loci (QTLs) for the plant growth traits, B uptake traits and the B efficiency coefficient (BEC) were analyzed using a doubled haploid (DH) population derived from a cross between a B-efficient parent, Qingyou 10, and a B-inefficient parent, Westar 10. A high-density genetic map was constructed based on single nucleotide polymorphisms (SNPs) assayed using Brassica 60 K Infinium BeadChip Array, simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). The linkage map covered a total length of 2139.5 cM, with 19 linkage groups (LGs) and an average distance of 1.6 cM between adjacent markers. Based on hydroponic evaluation of six B efficiency traits measured in three separate repeated trials, a total of 52 QTLs were identified, accounting for 6.14-46.27% of the phenotypic variation. A major QTL for BEC, qBEC-A3a, was co-located on A3 with other QTLs for plant growth and B uptake traits under low B stress. Using a subset of substitution lines, qBEC-A3a was validated and narrowed down to the interval between CNU384 and BnGMS436. The results of this study provide a novel major locus located on A3 for B efficiency in B. napus that will be suitable for fine mapping and marker-assisted selection breeding for B efficiency in B. napus.

  5. A High-Density Genetic Map Identifies a Novel Major QTL for Boron Efficiency in Oilseed Rape (Brassica napus L.)

    PubMed Central

    Wang, Xiaohua; Zhao, Hua; Shi, Lei; Xu, Fangsen

    2014-01-01

    Low boron (B) seriously limits the growth of oilseed rape (Brassica napus L.), a high B demand species that is sensitive to low B conditions. Significant genotypic variations in response to B deficiency have been observed among B. napus cultivars. To reveal the genetic basis for B efficiency in B. napus, quantitative trait loci (QTLs) for the plant growth traits, B uptake traits and the B efficiency coefficient (BEC) were analyzed using a doubled haploid (DH) population derived from a cross between a B-efficient parent, Qingyou 10, and a B-inefficient parent, Westar 10. A high-density genetic map was constructed based on single nucleotide polymorphisms (SNPs) assayed using Brassica 60 K Infinium BeadChip Array, simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). The linkage map covered a total length of 2139.5 cM, with 19 linkage groups (LGs) and an average distance of 1.6 cM between adjacent markers. Based on hydroponic evaluation of six B efficiency traits measured in three separate repeated trials, a total of 52 QTLs were identified, accounting for 6.14–46.27% of the phenotypic variation. A major QTL for BEC, qBEC-A3a, was co-located on A3 with other QTLs for plant growth and B uptake traits under low B stress. Using a subset of substitution lines, qBEC-A3a was validated and narrowed down to the interval between CNU384 and BnGMS436. The results of this study provide a novel major locus located on A3 for B efficiency in B. napus that will be suitable for fine mapping and marker-assisted selection breeding for B efficiency in B. napus. PMID:25375356

  6. 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.

  7. Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum.

    PubMed

    Gelli, Malleswari; Konda, Anji Reddy; Liu, Kan; Zhang, Chi; Clemente, Thomas E; Holding, David R; Dweikat, Ismail M

    2017-07-11

    (TFIIIC) and dwarfing gene (DW2) encoding multidrug resistance-associated protein-9 homolog showed abundant expression in CK60 parent, similar to earlier study. The validated QTLs among different mapping populations would be the most reliable and stable QTLs across germplasm. The DEG transcripts found in the validated QTL regions will serve as future candidate genes for enhancing NUE in sorghum using molecular approaches.

  8. 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

  9. 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.

  10. Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population.

    PubMed

    Uemoto, Y; Nakano, H; Kikuchi, T; Sato, S; Ishida, M; Shibata, T; Kadowaki, H; Kobayashi, E; Suzuki, K

    2012-04-01

    The stearoyl-CoA desaturase (delta-9-desaturase; SCD) gene is a candidate gene for fatty acid composition. It is located on pig SSC14 in a region where quantitative trait loci (QTL) for fatty acid composition were previously detected in a Duroc purebred population. The objective of the present study was to fine map the QTL, to identify polymorphisms of the pig SCD gene and to examine the effects of SCD polymorphisms on fatty acid composition and melting point of fat in the population. The pigs were examined for fatty acid composition and melting point of inner and outer subcutaneous fat and inter- and intramuscular fat; the number of pigs examined was 479-521. Two SNPs (g.-353C>T and g.-233T>C) were identified in the promoter region of the SCD gene and were completely linked in the pigs from the base generation. In all pigs, 19 microsatellite markers and SCD haplotypes were then genotyped. Different statistical models were applied to evaluate the effects of QTL and the possible causality of the SCD gene variants with respect to the QTL. The results show that all significant QTL for C14:0, C18:0, C18:1 and melting point of fat were detected in the same region, located near the SCD gene. The results also show a significant association between SCD haplotypes and fatty acid composition and fat melting point in this population. These results indicate that the haplotype of the SCD gene has a strong effect on fatty acid composition and melting point of fat. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

  11. Mapping and confirmation of a major left ventricular mass QTL on rat chromosome 1 by contrasting SHRSP and F344 rats.

    PubMed

    Grabowski, Katja; Koplin, Gerold; Aliu, Bujar; Schulte, Leonard; Schulz, Angela; Kreutz, Reinhold

    2013-09-16

    An abnormal increase in left ventricular (LV) mass, i.e., LV hypertrophy (LVH), represents an important target organ damage in arterial hypertension and has been associated with poor clinical outcome. Genetic factors are contributing to variation in LV mass in addition to blood pressure and other factors such as dietary salt intake. We set out to map quantitative trait loci (QTL) for LV mass by comparing the spontaneously hypertensive stroke-prone (SHRSP) rat with LVH and normotensive Fischer rats (F344) with contrasting low LV mass. To this end we performed a genome-wide QTL mapping analysis in 232 F2 animals derived from SHRSP and F344 exposed to high-salt (4% in chow) intake for 8 wk. We mapped one major QTL for LV mass on rat chromosome 1 (RNO1) that demonstrated strong linkage (peak logarithm of odds score 8.4) to relative LV weight (RLVW) and accounted for ∼19% of the variance of this phenotype in F2 rats. We therefore generated a consomic SHRSP-1(F344) strain in which RNO1 from F344 was introgressed into the SHRSP background. Consomic and SHRSP animals showed similar blood pressures during conventional intra-arterial measurements, while RLVW was already significantly lower (-17.7%, P<0.05) in SHRSP-1(F344) in response to a normal-salt diet; a similar significant reduction of LV mass was also observed in consomic rats after high-salt intake (P<0.05 vs. SHRSP). Thus, a major QTL on RNO1 was confirmed with significant impact on LV mass in the hypertensive background of SHRSP.

  12. Cloning of a phosphatidylinositol 4-kinase gene based on fiber strength transcriptome QTL mapping in the cotton species Gossypium barbadense.

    PubMed

    Liu, H W; Shi, R F; Wang, X F; Pan, Y X; Zang, G Y; Ma, Z Y

    2012-09-25

    Sea Island cotton (Gossypium barbadense) is highly valued for its superior fiber qualities, especially fiber strength. Based on a transcript-derived fragment originated from transcriptome QTL mapping, a fiber strength related candidate gene of phosphatidylinositol 4-kinase cDNA, designated as GbPI4K, was first cloned, and its expression was characterized in the secondary cell wall thickening stage of G. barbadense fibers. The ORF of GbPI4K was found to be 1926 bp in length and encoded a predicted protein of 641 amino acid residues. The putative protein contained a clear PI3/4K kinase catalytic domain and fell into the plant type II PI4K cluster in phylogenetic analysis. In this study, the expression of cotton PI4K protein was also induced in Escherichia coli BL21 (DE3) as a fused protein. Semi-quantitative RT-PCR analysis showed that the gene expressed in the root, hypocotyl and leaf of the cotton plants. Real-time RT-PCR indicated that this gene in Sea Island cotton fibers expressed 10 days longer than that in Upland cotton fibers, and the main expression difference of PI4K between Sea Island cotton and Upland cotton in fibers was located in the secondary cell wall thickening stage of the fiber. Further analysis indicated that PI4K is a crucial factor in the ability of Rac proteins to regulate phospholipid signaling pathways.

  13. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species

    USDA-ARS?s Scientific Manuscript database

    For the first time in many years a comprehensive genome map for cultivated oat has been constructed using a combination of single nucleotide polymorphism (SNP) markers and validated with a collection of cytogenetically defined germplasm lines. The markers were able to help distinguish the three geno...

  14. Genome-Wide Identification of QTL for Seed Yield and Yield-Related Traits and Construction of a High-Density Consensus Map for QTL Comparison in Brassica napus

    PubMed Central

    Zhao, Weiguo; Wang, Xiaodong; Wang, Hao; Tian, Jianhua; Li, Baojun; Chen, Li; Chao, Hongbo; Long, Yan; Xiang, Jun; Gan, Jianping; Liang, Wusheng; Li, Maoteng

    2016-01-01

    Seed yield (SY) is the most important trait in rapeseed, is determined by multiple seed yield-related traits (SYRTs) and is also easily subject to environmental influence. Many quantitative trait loci (QTLs) for SY and SYRTs have been reported in Brassica napus; however, no studies have focused on seven agronomic traits simultaneously affecting SY. Genome-wide QTL analysis for SY and seven SYRTs in eight environments was conducted in a doubled haploid population containing 348 lines. Totally, 18 and 208 QTLs for SY and SYRTs were observed, respectively, and then these QTLs were integrated into 144 consensus QTLs using a meta-analysis. Three major QTLs for SY were observed, including cqSY-C6-2 and cqSY-C6-3 that were expressed stably in winter cultivation area for 3 years and cqSY-A2-2 only expressed in spring rapeseed area. Trait-by-trait meta-analysis revealed that the 144 consensus QTLs were integrated into 72 pleiotropic unique QTLs. Among them, all the unique QTLs affected SY, except for uq.A6-1, including uq.A2-3, uq.C1-2, uq.C1-3, uq.C6-1, uq.C6-5, and uq.C6-6 could also affect more than two SYRTs. According to the constructed high-density consensus map and QTL comparison from literatures, 36 QTLs from five populations were co-localized with QTLs identified in this study. In addition, 13 orthologous genes were observed, including five each gene for SY and thousand seed weight, and one gene each for biomass yield, branch height, and plant height. The genomic information of these QTLs will be valuable in hybrid cultivar breeding and in analyzing QTL expression in different environments. PMID:26858737

  15. Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter.

    PubMed

    Wang, Jing; Zhang, Kaichun; Zhang, Xiaoming; Yan, Guohua; Zhou, Yu; Feng, Laibao; Ni, Yang; Duan, Xuwei

    2015-01-01

    A cross between the sweet cherry (Prunus avium) cultivars 'Wanhongzhu' and 'Lapins' was performed to create a mapping population suitable for the construction of a linkage map. The specific-locus amplified fragment (SLAF) sequencing technique used as a single nucleotide polymorphism (SNP) discovery platform and generated 701 informative genotypic assays; these, along with 16 microsatellites (SSRs) and the incompatibility (S) gene, were used to build a map which comprised 8 linkage groups (LGs) and covered a genetic distance of 849.0 cM. The mean inter-marker distance was 1.18 cM and there were few gaps > 5 cM in length. Marker collinearity was maintained with the established peach genomic sequence. The map was used to show that trunk diameter (TD) is under the control of 4 loci, mapping to 3 different LGs. Different locus influenced TD at a varying stage of the tree's development. The high density 'W×L' genetic linkage map has the potential to enable high-resolution identification of QTLs of agronomically relevant traits, and accelerate sweet cherry breeding.

  16. Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter

    PubMed Central

    Wang, Jing; Zhang, Kaichun; Zhang, Xiaoming; Yan, Guohua; Zhou, Yu; Feng, Laibao; Ni, Yang; Duan, Xuwei

    2015-01-01

    A cross between the sweet cherry (Prunus avium) cultivars ‘Wanhongzhu’ and ‘Lapins’ was performed to create a mapping population suitable for the construction of a linkage map. The specific-locus amplified fragment (SLAF) sequencing technique used as a single nucleotide polymorphism (SNP) discovery platform and generated 701 informative genotypic assays; these, along with 16 microsatellites (SSRs) and the incompatibility (S) gene, were used to build a map which comprised 8 linkage groups (LGs) and covered a genetic distance of 849.0 cM. The mean inter-marker distance was 1.18 cM and there were few gaps > 5 cM in length. Marker collinearity was maintained with the established peach genomic sequence. The map was used to show that trunk diameter (TD) is under the control of 4 loci, mapping to 3 different LGs. Different locus influenced TD at a varying stage of the tree’s development. The high density ‘W×L’ genetic linkage map has the potential to enable high-resolution identification of QTLs of agronomically relevant traits, and accelerate sweet cherry breeding. PMID:26516760

  17. Fast Genome-Wide QTL Association Mapping on Pedigree and Population Data.

    PubMed

    Zhou, Hua; Blangero, John; Dyer, Thomas D; Chan, Kei-Hang K; Lange, Kenneth; Sobel, Eric M

    2017-04-01

    Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and pedigree data. Even datasets thought to consist of only unrelated individuals may include cryptic relationships that can lead to false positives if not discovered and controlled for. In addition, family designs possess compelling advantages. They are better equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects. Pedigrees selected for extreme trait values often segregate a single gene with strong effect. Finally, many pedigrees are available as an important legacy from the era of linkage analysis. Unfortunately, pedigree likelihoods are notoriously hard to compute. In this paper, we reexamine the computational bottlenecks and implement ultra-fast pedigree-based GWAS analysis. Kinship coefficients can either be based on explicitly provided pedigrees or automatically estimated from dense markers. Our strategy (a) works for random sample data, pedigree data, or a mix of both; (b) entails no loss of power; (c) allows for any number of covariate adjustments, including correction for population stratification; (d) allows for testing SNPs under additive, dominant, and recessive models; and (e) accommodates both univariate and multivariate quantitative traits. On a typical personal computer (six CPU cores at 2.67 GHz), analyzing a univariate HDL (high-density lipoprotein) trait from the San Antonio Family Heart Study (935,392 SNPs on 1,388 individuals in 124 pedigrees) takes less than 2 min and 1.5 GB of memory. Complete multivariate QTL analysis of the three time-points of the longitudinal HDL multivariate trait takes less than 5 min and 1.5 GB of memory. The algorithm is implemented as the Ped-GWAS Analysis (Option 29) in the Mendel statistical genetics package, which is

  18. Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm

    PubMed Central

    Chen, Jiafa; Shrestha, Rosemary; Ding, Junqiang; Zheng, Hongjian; Mu, Chunhua; Wu, Jianyu; Mahuku, George

    2016-01-01

    Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1–4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize. PMID:27742723

  19. Genetic linkage map construction and QTL identification of juvenile growth traits in Torreya grandis

    PubMed Central

    2014-01-01

    Torreya grandis Fort. ex Lindl, a conifer species widely distributed in Southeastern China, is of high economic value by producing edible, nutrient seeds. However, knowledge about the genome structure and organization of this species is poorly understood, thereby limiting the effective use of its gene resources. Here, we report on a first genetic linkage map for Torreya grandis using 96 progeny randomly chosen from a half-sib family of a commercially cultivated variety of this species, Torreya grandis Fort. ex Lindl cv. Merrillii. The map contains 262 molecular markers, i.e., 75 random amplified polymorphic DNAs (RAPD), 119 inter-simple sequence repeats (ISSR) and 62 amplified fragments length polymorphisms (AFLP), and spans a total of 7,139.9 cM, separated by 10 linkage groups. The linkage map was used to map quantitative trait loci (QTLs) associated with juvenile growth traits by functional mapping. We identified four basal diameter-related QTLs on linkage groups 1, 5 and 9; four height-related QTLs on linkage groups 1, 2, 5 and 8. It was observed that the genetic effects of QTLs on growth traits vary with age, suggesting the dynamic behavior of growth QTLs. Part of the QTLs was found to display a pleiotropic effect on basal diameter growth and height growth. PMID:25079139

  20. QTL analyses for seed iron and zinc concentrations in an intra-genepool population of Andean common beans (Phaseolus vulgaris L.).

    PubMed

    Blair, Matthew W; Astudillo, Carohna; Rengifo, Judith; Beebe, Steve E; Graham, Robin

    2011-02-01

    Legumes provide essential micronutrients that are found only in low amounts in the cereals or root crops. An ongoing project at CIAT has shown that the legume common bean is variable in the amount of seed minerals (iron, zinc, and other elements), vitamins, and sulfur amino acids that they contain and that these traits are likely to be inherited quantitatively. In this study we analyzed iron and zinc concentrations in an Andean recombinant inbred line (RIL) population of 100 lines derived from a cross between G21242, a Colombian cream-mottled climbing bean with high seed iron/zinc and G21078, an Argentinean cream seeded climbing bean with low seed iron/zinc. The population was planted across three environments; seed from each genotype was analyzed with two analytical methods, and quantitative trait loci (QTL) were detected using composite interval mapping and single-point analyses. A complete genetic map was created for the cross using a total of 74 microsatellite markers to anchor the map to previously published reference maps and 42 RAPD markers. In total, nine seed mineral QTL were identified on five linkage groups (LGs) with the most important being new loci on b02 and other QTL on b06, b08, and b07 near phaseolin. Seed weight QTL were associated with these on b02 and b08. These Andean-derived QTL are candidates for marker-assisted selection either in combination with QTL from the Mesoamerican genepool or with other QTL found in inter and intra-genepool crosses, and the genetic map can be used to anchor other intra-genepool studies.

  1. QTL mapping of forage yield and forage yield component traits in Sorghum bicolor x S. sudanense.

    PubMed

    Liu, Y L; Wang, L H; Li, J Q; Zhan, Q W; Zhang, Q; Li, J F; Fan, F F

    2015-04-22

    The sorghum-sudangrass hybrid (Sorghum bicolor x S. sudanense) is an important forage crop. However, little is known about the genetic mechanisms related to forage yield and the 4 forage yield component traits in this forage crop. In this study, a linkage map was constructed with 124 assigned SSR markers using an F2 mapping population derived from the crossing of sorghum Tx623A and sudangrass Sa. Nine quantitative trait loci (QTLs) were detected for forage yield and the 4 forage yield component traits using inclusive composite interval mapping. Five fresh weight QTLs were identified and contributed >50% of the total phenotypic variance. Of these QTLs, all showed additive and dominant effects, but most exhibited mainly dominant effects. These results will provide useful information for improvements in sorghum-sudangrass hybrid breeding.

  2. Integrating Small RNA Sequencing with QTL Mapping for Identification of miRNAs and Their Target Genes Associated with Heat Tolerance at the Flowering Stage in Rice

    PubMed Central

    Liu, Qing; Yang, Tifeng; Yu, Ting; Zhang, Shaohong; Mao, Xingxue; Zhao, Junliang; Wang, Xiaofei; Dong, Jingfang; Liu, Bin

    2017-01-01

    Although, microRNAs (miRNAs) have been reported to be associated with heat tolerance at the seedling stage in rice, their involvement in heat tolerance at the flowering stage is still unknown. In this study, small RNA profiling was conducted in a heat-tolerant variety Gan-Xiang-Nuo (GXN) and a heat-sensitive variety Hua-Jing-Xian-74 (HJX), respectively. Totally, 102 miRNAs were differentially expressed (DE) under heat stress. Compared to HJX, GXN had more DE miRNAs and its DE miRNAs changed earlier under heat stress. Plant Ontology (PO) analysis of the target genes revealed that many DE miRNAs were involved in flower development. As a parallel experiment, QTL mapping was also conducted and four QTLs for heat tolerance at the flowering stage were identified using chromosome single-segment substitution lines derived from GXN and HJX. Further, through integrating analysis of DE miRNAs with QTLs, we identified 8 target genes corresponding to 26 miRNAs within the four QTL regions. Some meaningful target genes such as LOC_Os12g42400, SGT1, and pectinesterase were within the QTL regions. The negative correlation between miR169r-5p and its target gene LOC_Os12g42400 was confirmed under heat stress, and overexpression of miR169r-5p enhanced heat tolerance at flowering stage in rice. Our results demonstrate that the integrated analysis of genome-wide miRNA profiling with QTL mapping can facilitate identification of miRNAs and their target genes associated with the target traits and the limited candidates identified in this study offer an important source for further functional analysis and molecular breeding for heat tolerance in rice. PMID:28174587

  3. Genetic dissection of heterosis using epistatic QTL mapping in partial NCII mating design

    USDA-ARS?s Scientific Manuscript database

    Heterosis refers to the phenomenon in which hybrid F1 exhibits enhanced growth or agronomic performance. However, theoretical studies on the genetic basis of heterosis were based on bi-parental segregation populations instead of multiple-parental hybrid F1 populations. In simulation study, we mapped...

  4. The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease

    PubMed Central

    Eitam, Harel; Yishay, Moran; Schiavini, Fausta; Soller, Morris; Bagnato, Alessandro; Shabtay, Ariel

    2016-01-01

    Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle, caused by multiple pathogens that become more virulent in response to stress. As clinical signs often go undetected and various preventive strategies failed, identification of genes affecting BRD is essential for selection for resistance. Selective DNA pooling (SDP) was applied in a genome wide association study (GWAS) to map BRD QTLs in Israeli Holstein male calves. Kosher scoring of lung adhesions was used to allocate 122 and 62 animals to High (Glatt Kosher) and Low (Non-Kosher) resistant groups, respectively. Genotyping was performed using the Illumina BovineHD BeadChip according to the Infinium protocol. Moving average of -logP was used to map QTLs and Log drop was used to define their boundaries (QTLRs). The combined procedure was efficient for high resolution mapping. Nineteen QTLRs distributed over 13 autosomes were found, some overlapping previous studies. The QTLRs contain polymorphic functional and expression candidate genes to affect kosher status, with putative immunological and wound healing activities. Kosher phenotyping was shown to be a reliable means to map QTLs affecting BRD morbidity. PMID:27077383

  5. The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease.

    PubMed

    Lipkin, Ehud; Strillacci, Maria Giuseppina; Eitam, Harel; Yishay, Moran; Schiavini, Fausta; Soller, Morris; Bagnato, Alessandro; Shabtay, Ariel

    2016-01-01

    Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle, caused by multiple pathogens that become more virulent in response to stress. As clinical signs often go undetected and various preventive strategies failed, identification of genes affecting BRD is essential for selection for resistance. Selective DNA pooling (SDP) was applied in a genome wide association study (GWAS) to map BRD QTLs in Israeli Holstein male calves. Kosher scoring of lung adhesions was used to allocate 122 and 62 animals to High (Glatt Kosher) and Low (Non-Kosher) resistant groups, respectively. Genotyping was performed using the Illumina BovineHD BeadChip according to the Infinium protocol. Moving average of -logP was used to map QTLs and Log drop was used to define their boundaries (QTLRs). The combined procedure was efficient for high resolution mapping. Nineteen QTLRs distributed over 13 autosomes were found, some overlapping previous studies. The QTLRs contain polymorphic functional and expression candidate genes to affect kosher status, with putative immunological and wound healing activities. Kosher phenotyping was shown to be a reliable means to map QTLs affecting BRD morbidity.

  6. Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat

    USDA-ARS?s Scientific Manuscript database

    Since the dawn of wheat cytogenetics, chromosome 3B has been known to harbor a gene(s) that, when removed, caused chromosome desynapsis and gametic sterility. The lack of natural genetic diversity for this gene(s) has prevented any attempts to fine map and further characterize it. Here, gamma radiat...

  7. Precision QTL mapping of downy mildew resistance in Hop (Humulus lupulus L.)

    USDA-ARS?s Scientific Manuscript database

    Hop Downy mildew (DM) is an obligate parasite causing severe losses in hop if not controlled. Resistance to this pathogen is a primary goal for hop breeding programs. The objective of this study was to identify QTLs linked to DM resistance. Next-generation-sequencing was performed on a mapping po...

  8. A statistical model for QTL mapping in polysomic autotetraploids underlying double reduction

    USDA-ARS?s Scientific Manuscript database

    Technical Abstract: As a group of economically important species, linkage mapping of polysomic autotetraploids, including potato, sugarcane and rose, is difficult to conduct due to their unique meiotic property of double reduction that allows sister chromatids to enter into the same gamete. We desc...

  9. A linkage map of transcribed single nucleotide polymorphisms in rohu (Labeo rohita) and QTL associated with resistance to Aeromonas hydrophila

    PubMed Central

    2014-01-01

    Background Production of carp dominates world aquaculture. More than 1.1 million tonnes of rohu carp, Labeo rohita (Hamilton), were produced in 2010. Aeromonas hydrophila is a bacterial pathogen causing aeromoniasis in rohu, and is a major problem for carp production worldwide. There is a need to better understand the genetic mechanisms affecting resistance to this disease, and to develop tools that can be used with selective breeding to improve resistance. Here we use a 6 K SNP array to genotype 21 full-sibling families of L. rohita that were experimentally challenged intra-peritoneally with a virulent strain of A. hydrophila to scan the genome for quantitative trait loci associated with disease resistance. Results In all, 3193 SNPs were found to be informative and were used to create a linkage map and to scan for QTL affecting resistance to A. hydrophila. The linkage map consisted of 25 linkage groups, corresponding to the number of haploid chromosomes in L. rohita. Male and female linkage maps were similar in terms of order, coverage (1384 and 1393 cM, respectively) and average interval distances (1.32 and 1.35 cM, respectively). Forty-one percent of the SNPs were annotated with gene identity using BLAST (cut off E-score of 0.001). Twenty-one SNPs mapping to ten linkage groups showed significant associations with the traits hours of survival and dead or alive (P <0.05 after Bonferroni correction). Of the SNPs showing significant or suggestive associations with the traits, several were homologous to genes of known immune function or were in close linkage to such genes. Genes of interest included heat shock proteins (70, 60, 105 and “small heat shock proteins”), mucin (5b precursor and 2), lectin (receptor and CD22), tributyltin-binding protein, major histocompatibility loci (I and II), complement protein component c7-1, perforin 1, ubiquitin (ligase, factor e4b isoform 2 and conjugation enzyme e2 c), proteasome subunit, T-cell antigen receptor and

  10. QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium.

    PubMed

    Ma, Xuexia; Ding, Yezhang; Zhou, Baoliang; Guo, Wangzhen; Lv, Yanhui; Zhu, Xiefei; Zhang, Tianzhen

    2008-12-01

    Asiatic cotton (Gossypium arboreum L.) is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species was replaced by the New World allotetraploid cotton G. hirsutum L. Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs. In addition, G. arboreum serves as a model for genomic research in Gossypium. In the present study, we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 13 linkage groups. The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci. A population containing 176 F(2:3) families was used to perform quantitative trait loci (QTL) mapping for 17 phenotypes using Multiple QTL Model (MQM) of MapQTL ver 5.0. Overall, 108 QTLs were detected on 13 chromosomes. Thirty-one QTLs for yield and its components were detected in the F2 population. Forty-one QTLs for yield and its components were detected in the F(2:3) families with a total of 43 QTLs for fiber qualities. Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F2 and F(2:3). Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals. These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes.

  11. Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea.

    PubMed

    Saxena, Rachit K; Singh, Vikas K; Kale, Sandip M; Tathineni, Revathi; Parupalli, Swathi; Kumar, Vinay; Garg, Vanika; Das, Roma R; Sharma, Mamta; Yamini, K N; Muniswamy, S; Ghanta, Anuradha; Rathore, Abhishek; Kumar, C V Sameer; Saxena, K B; Kishor, P B Kavi; Varshney, Rajeev K

    2017-05-15

    Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL_A and ICPL 20096 × ICPL 332 designated as PRIL_B) and one F2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL_A, PRIL_B and F2, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.

  12. Powdery mildew resistance in roses: QTL mapping in different environments using selective genotyping.

    PubMed

    Linde, M; Hattendorf, A; Kaufmann, H; Debener, Th

    2006-10-01

    Podosphaera pannosa, the causal agent of rose powdery mildew, hampers the production of cut roses throughout the world. A major tool to control this disease is the use of resistant plant material. Single resistance genes, like Rpp1, may be overcome within a few years by high risk pathogens like powdery mildews. Durable resistance could be achieved using quantitative resistances. Here we describe mapping of QTLs for resistance to P. pannosa in six different environments (artificial and natural infections in the greenhouse over 3 years and natural infections in the field over 2 years). AFLPs, RGAs and other marker types were used to construct an integrated linkage map for the diploid population 97/7 containing 233 markers. In a selective genotyping procedure, marker segregation was analysed for 170 of the up to 270 phenotyped individuals. We identified seven linkage groups with an average length of 60 cM, corresponding to seven rose chromosomes in the haploid set. Using an LOD significance threshold of 3.9 we detected a total of 28 QTLs for the nine powdery mildew disease scores under analysis. Using the data from artificial inoculations with powdery mildew race 9, three resistance QTLs explaining about 84% of the variability were mapped. Twelve and 15 QTLs were detected for resistance to naturally occurring infections in the greenhouse and in the field, respectively, over several years.

  13. Resistance loci affecting distinct stages of fungal pathogenesis: use of introgression lines for QTL mapping and characterization in the maize - Setosphaeria turcica pathosystem

    PubMed Central

    2010-01-01

    Background Studies on host-pathogen interactions in a range of pathosystems have revealed an array of mechanisms by which plants reduce the efficiency of pathogenesis. While R-gene mediated resistance confers highly effective defense responses against pathogen invasion, quantitative resistance is associated with intermediate levels of resistance that reduces disease progress. To test the hypothesis that specific loci affect distinct stages of fungal pathogenesis, a set of maize introgression lines was used for mapping and characterization of quantitative trait loci (QTL) conditioning resistance to Setosphaeria turcica, the causal agent of northern leaf blight (NLB). To better understand the nature of quantitative resistance, the identified QTL were further tested for three secondary hypotheses: (1) that disease QTL differ by host developmental stage; (2) that their performance changes across environments; and (3) that they condition broad-spectrum resistance. Results Among a set of 82 introgression lines, seven lines were confirmed as more resistant or susceptible than B73. Two NLB QTL were validated in BC4F2 segregating populations and advanced introgression lines. These loci, designated qNLB1.02 and qNLB1.06, were investigated in detail by comparing the introgression lines with B73 for a series of macroscopic and microscopic disease components targeting different stages of NLB development. Repeated greenhouse and field trials revealed that qNLB1.06Tx303 (the Tx303 allele at bin 1.06) reduces the efficiency of fungal penetration, while qNLB1.02B73 (the B73 allele at bin 1.02) enhances the accumulation of callose and phenolics surrounding infection sites, reduces hyphal growth into the vascular bundle and impairs the subsequent necrotrophic colonization in the leaves. The QTL were equally effective in both juvenile and adult plants; qNLB1.06Tx303 showed greater effectiveness in the field than in the greenhouse. In addition to NLB resistance, qNLB1.02B73 was

  14. Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree

    PubMed Central

    DeWoody, Jennifer; Viger, Maud; Lakatos, Ferenc; Tuba, Katalin; Taylor, Gail; Smulders, Marinus J. M.

    2013-01-01

    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001) but negatively correlated with skeletonizer damage (P<0.01) in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast-growing forest tree

  15. Insight into the genetic components of community genetics: QTL mapping of insect association in a fast-growing forest tree.

    PubMed

    DeWoody, Jennifer; Viger, Maud; Lakatos, Ferenc; Tuba, Katalin; Taylor, Gail; Smulders, Marinus J M

    2013-01-01

    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001) but negatively correlated with skeletonizer damage (P<0.01) in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast-growing forest tree.

  16. High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

    PubMed Central

    Gaur, Rashmi; Jeena, Ganga; Shah, Niraj; Gupta, Shefali; Pradhan, Seema; Tyagi, Akhilesh K; Jain, Mukesh; Chattopadhyay, Debasis; Bhatia, Sabhyata

    2015-01-01

    This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties. PMID:26303721

  17. High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea.

    PubMed

    Gaur, Rashmi; Jeena, Ganga; Shah, Niraj; Gupta, Shefali; Pradhan, Seema; Tyagi, Akhilesh K; Jain, Mukesh; Chattopadhyay, Debasis; Bhatia, Sabhyata

    2015-08-25

    This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties.

  18. Validation and fine mapping of lyc12.1, a QTL for increased tomato fruit lycopene content.

    PubMed

    Kinkade, Matthew P; Foolad, Majid R

    2013-08-01

    Lycopene content is a key component of tomato (Solanum lycopersicum L.) fruit quality, and is a focus of many tomato-breeding programs. Two QTLs for increased fruit lycopene content, inherited from a high-lycopene S. pimpinellifolium accession, were previously detected on tomato chromosomes 7 and 12 using a S. lycopersicum × S. pimpinellifolium RIL population, and were identified as potential targets for marker-assisted selection and positional cloning. To validate the phenotypic effect of these two QTLs, a BC2 population was developed from a cross between a select RIL and the S. lycopersicum recurrent parent. The BC2 population was field-grown and evaluated for fruit lycopene content using HPLC. Statistical analyses revealed that while lyc7.1 did not significantly increase lycopene content in the heterozygous condition, individuals harboring lyc12.1 in the heterozygous condition contained 70.3 % higher lycopene than the recurrent parent. To eliminate the potential pleiotropic effect of fruit size and minimize the physical size of the lyc12.1 introgression, a marker-assisted backcross program was undertaken and produced a BC3S1 NIL population (n = 1,500) segregating for lyc12.1. Lycopene contents from lyc12.1 homozygous and heterozygous recombinants in this population were measured and lyc12.1 was localized to a 1.5 cM region. Furthermore, we determined that lyc12.1 was delimited to a ~1.5 Mb sequence of tomato chromosome 12, and provided some insight into potential candidate genes in the region. The derived sub-NILs will be useful for transferring of lyc12.1 to other tomato genetic backgrounds and for further fine-mapping and cloning of the QTL.

  19. An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits.

    PubMed

    Routtu, Jarkko; Hall, Matthew D; Albere, Brian; Beisel, Christian; Bergeron, R Daniel; Chaturvedi, Anurag; Choi, Jeong-Hyeon; Colbourne, John; De Meester, Luc; Stephens, Melissa T; Stelzer, Claus-Peter; Solorzano, Eleanne; Thomas, W Kelley; Pfrender, Michael E; Ebert, Dieter

    2014-11-27

    Although Daphnia is increasingly recognized as a model for ecological genomics and biomedical research, there is, as of yet, no high-resolution genetic map for the genus. Such a map would provide an important tool for mapping phenotypes and assembling the genome. Here we estimate the genome size of Daphnia magna and describe the construction of an SNP array based linkage map. We then test the suitability of the map for life history and behavioural trait mapping. The two parent genotypes used to produce the map derived from D. magna populations with and without fish predation, respectively and are therefore expected to show divergent behaviour and life-histories. Using flow cytometry we estimated the genome size of D. magna to be about 238 mb. We developed an SNP array tailored to type SNPs in a D. magna F2 panel and used it to construct a D. magna linkage map, which included 1,324 informative markers. The map produced ten linkage groups ranging from 108.9 to 203.6 cM, with an average distance between markers of 1.13 cM and a total map length of 1,483.6 cM (Kosambi corrected). The physical length per cM is estimated to be 160 kb. Mapping infertility genes, life history traits and behavioural traits on this map revealed several significant QTL peaks and showed a complex pattern of underlying genetics, with different traits showing strongly different genetic architectures. The new linkage map of D. magna constructed here allowed us to characterize genetic differences among parent genotypes from populations with ecological differences. The QTL effect plots are partially consistent with our expectation of local adaptation under contrasting predation regimes. Furthermore, the new genetic map will be an important tool for the Daphnia research community and will contribute to the physical map of the D. magna genome project and the further mapping of phenotypic traits. The clones used to produce the linkage map are maintained in a stock collection and can be used for

  20. 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

  1. A microsatellite-based, physically anchored linkage map for the gray, short-tailed opossum (Monodelphis domestica).

    PubMed

    Samollow, Paul B; Gouin, Nicolas; Miethke, Pat; Mahaney, Susan M; Kenney, Margaret; VandeBerg, John L; Graves, Jennifer A Marshall; Kammerer, Candace M

    2007-01-01

    The genome of the gray, short-tailed opossum, Monodelphis domestica, will be the first of any marsupial to be fully sequenced. The utility of this sequence will be greatly enhanced by construction and integration of detailed genetic and physical maps. Therefore, it is important to verify the unusual recombinational characteristics that were suggested by the 'first-generation' M. domestica linkage map; specifically, very low levels of recombination and severely reduced female recombination, both of which are contrary to patterns in other vertebrates. We constructed a new linkage map based on a different genetic cross, using a new and much larger set of map markers, and physically anchored and oriented the linkage groups onto chromosomes via fluorescence in-situ hybridization mapping. This map includes 150 loci in eight autosomal linkage groups corresponding to the eight autosome pairs, and spans 86-89% of the autosomal genome. The sex-averaged autosomal map covers 715 cM, with a full-length estimate of 866 cM; the shortest full-length linkage map reported for any vertebrate. The sex-specific maps confirmed severely reduced female recombination in all linkage groups, and an overall F/M map ratio = 0.54. These results greatly extend earlier findings, and provide an improved microsatellite-based linkage map for this species.

  2. QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping

    PubMed Central

    Dang, Xiaojing; Liu, Erbao; Liang, Yinfeng; Liu, Qiangming; Breria, Caleb M.; Hong, Delin

    2016-01-01

    Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL), stigma brush-shaped part length (SBPL) and stigma non-brush-shaped part length (SNBPL) were found. Significant positive correlations were identified among stigma traits. In total, 2072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs) for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL, and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future. PMID:27555858

  3. 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

  4. A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.).

    PubMed

    Topdar, N; Kundu, A; Sinha, M K; Sarkar, D; Das, M; Banerjee, S; Kar, C S; Satya, P; Balyan, H S; Mahapatra, B S; Gupta, P K

    2013-01-01

    We report the first complete microsatellite genetic map of jute (Corchorus olitorius L.; 2n = 2x = 14) using an F6 recombinant inbred population. Of the 403 microsatellite markers screened, 82 were mapped on the seven linkage groups (LGs) that covered a total genetic distance of 799.9 cM, with an average marker interval of 10.7 cM. LG5 had the longest and LG7 the shortest genetic lengths, whereas LG1 had the maximum and LG7 the minimum number of markers. Segregation distortion of microsatellite loci was high (61%), with the majority of them (76%) skewed towards the female parent. Genomewide non-parametric single-marker analysis in combination with multiple quantitative trait loci (QTL)-models (MQM) mapping detected 26 definitive QTLs for bast fibre quality, yield and yield-related traits. These were unevenly distributed on six LGs, as colocalized clusters, at genomic sectors marked by 15 microsatellite loci. LG1 was the QTL-richest map sector, with the densest colocalized clusters of QTLs governing fibre yield, yield-related traits and tensile strength. Expectedly, favorable QTLs were derived from the desirable parents, except for nearly all of those of fibre fineness, which might be due to the creation of new gene combinations. Our results will be a good starting point for further genome analyses in jute.

  5. QTL analysis for some quantitative traits in bread wheat*

    PubMed Central

    Pushpendra, Kumar Gupta; Harindra, Singh Balyan; Pawan, Laxminarayan Kulwal; Neeraj, Kumar; Ajay, Kumar; Reyazul, Rouf Mir; Amita, Mohan; Jitendra, Kumar

    2007-01-01

    Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) suggested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection. PMID:17973342

  6. Construction of high-resolution genetic maps of Zoysia matrella (L.) Merrill and applications to comparative genomic analysis and QTL mapping of resistance to fall armyworm.

    PubMed

    Huang, Xiaoen; Wang, Fangfang; Singh, Ratnesh; Reinert, James A; Engelke, M C; Genovesi, Anthony D; Chandra, Ambika; Yu, Qingyi

    2016-08-08

    Zoysia matrella, widely used in lawns and sports fields, is of great economic and ecological value. Z. matrella is an allotetraploid species (2n = 4x = 40) in the genus zoysia under the subfamily Chloridoideae. Despite its ecological impacts and economic importance, the subfamily Chloridoideae has received little attention in genomics studies. As a result, limited genetic and genomic information are available for this subfamily, which have impeded progress in understanding evolutionary history of grasses in this important lineage. The lack of a high-resolution genetic map has hampered efforts to improve zoysiagrass using molecular genetic tools. We used restriction site-associated DNA sequencing (RADSeq) approach and a segregating population developed from the cross between Z. matrella cultivars 'Diamond' and 'Cavalier' to construct high-resolution genetic maps of Z. matrella. The genetic map of Diamond consists of 2,375 Single Nucleotide Polymorphism (SNP) markers mapped on 20 linkage groups (LGs) with a total length of 1754.48 cM and an average distance between adjacent markers at 0.74 cM. The genetic map of Cavalier contains 3,563 SNP markers on 20 LGs, covering 1824.92 cM, with an average distance between adjacent markers at 0.51 cM. A higher level of genome collinearity between Z. matrella and rice than that between Z. matrella and sorghum was revealed by comparative genomic analysis. Pairwise comparison revealed that two independent nested chromosome fusion events occurred after Z. matrella and sorghum split from a common ancestor. The high-resolution linkage maps were applied into mapping QTLs associated with fall armyworm (FAW) resistance and six loci located on LGs 8 and 20 were detected to be significantly associated with FAW resistance. The high-resolution linkage maps provide anchor points for comparative genomics analysis between Z. matrella and other grass species. Our comparative genomic analysis suggested that the chromosome number

  7. QTL mapping of wheat plant architectural characteristics and their genetic relationship with seven QTLs conferring resistance to sheath blight

    PubMed Central

    Guo, Yan; Du, Ziyi; Chen, Jiang; Zhang, Zhongjun

    2017-01-01

    Sheath blight is one of the most devastating wheat diseases worldwide. Breeding resistant cultivars is the most powerful strategy to defeat the disease. Plant resistance on “disease escape” works through modulation of morphological traits and shows sustainable resistance to disease. Plant architectural traits have been reported to play a significant role in disease response. Therefore, exploring the genetic relationship between plant architecture and disease resistance is of importance to the understanding of plant resistance via “disease escape”. Using an F9 population of 266 RILs (Recombinant Inbred Lines) derived from the cross of Luke × AQ24788-83, we have generated a linkage map of 631 markers on 21 chromosomes. In this study, we present the QTL identification of fourteen plant architectural characteristics and heading time from two years and analyze their genetic relationships with seven previously published QTLs to sheath blight (QSBs, QSe.cau), including plant height (PH), the space between the flag leaf and penultimate leaf (fdR), heading date (Hd), and other traits. Twelve stable QTLs of the morphological traits were identified with good consistency across five replicates. For the seven previously published QSBs, we found no significant association with plant height. However, some of the QSBs displayed strong associations with plant architectural traits and heading date. Especially, QfdR.cau-1AS, QHd.cau-2BS, QfdR.cau-5DL, and QfdR.cau-6BL were respectively mapped to the same regions as QSe.cau-1AS, QSe.cau-2BS, QSe.cau-5DL, and QSe.cau-6BL. Taken together, we have demonstrated that plant height did not exert a direct influence on the resistance to sheath blight conferred by the seven QSBs and that the plant architecture and heading date did exhibit a tight relationship with the resistance. Therefore, this study provides a novel evidence to help understand sheath blight resistance in wheat. In addition, the linked morphological characteristics

  8. Detecting the QTL-allele system conferring flowering date in a nested association mapping population of soybean using a novel procedure.

    PubMed

    Li, Shuguang; Cao, Yongce; He, Jianbo; Zhao, Tuanjie; Gai, Junyi

    2017-08-10

    The RTM-GWAS was chosen among five procedures to identify DTF QTL-allele constitution in a soybean NAM population; 139 QTLs with 496 alleles accounting for 81.7% of phenotypic variance were detected. Flowering date (days to flowering, DTF) is an ecological trait in soybean, closely related to its ability to adapt to areas. A nested association mapping (NAM) population consisting of four RIL populations (LM, ZM, MT and MW with M8206 as their common parent) was established and tested for their DTF under five environments. Using restriction-site-associated DNA sequencing the population was genotyped with SNP markers. The restricted two-stage multi-locus (RTM) genome-wide association study (GWAS) (RTM-GWAS) with SNP linkage disequilibrium block (SNPLDB) as multi-allele genomic markers performed the best among the five mapping procedures with software publicly available. It identified the greatest number of quantitative trait loci (QTLs) (139) and alleles (496) on 20 chromosomes covering almost all of the QTLs detected by four other mapping procedures. The RTM-GWAS provided the detected QTLs with highest genetic contribution but without overflowing and missing heritability problems (81.7% genetic contribution vs. heritability of 97.6%), while SNPLDB markers matched the NAM population property of multiple alleles per locus. The 139 QTLs with 496 alleles were organized into a QTL-allele matrix, showing the corresponding DTF genetic architecture of the five parents and the NAM population. All lines and parents comprised both positive and negative alleles, implying a great potential of recombination for early and late DTF improvement. From the detected QTL-allele system, 126 candidate genes were annotated and χ (2) tested as a DTF candidate gene system involving nine biological processes, indicating the trait a complex, involving several biological processes rather than only a handful of major genes.

  9. 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.

  10. QTL mapping - Current status and challenges: Comment on "Mapping complex traits as a dynamic system" by L. Sun and R. Wu

    NASA Astrophysics Data System (ADS)

    Liu, Nianjun

    2015-06-01

    One of the important objectives of genetic study is to understand the underlying mechanism of complex traits. However, complex traits are complex in terms of their mechanisms. First, multiple genetic variants are involved in different ways. In addition to the main effects (such as additive and dominant effects), these genetic variants may interact with each other [1-4], they may have pleiotropic effects [5,6], there may be genomic imprinting (a phenomenon where some genes are expressed or repressed depending on their parental origin) [7-9] and epigenetic effects [10-14]. In addition, environment often fits in via gene by environment interaction [15,16]. A more complicated genetic interaction between QTLs is from different genomes, i.e. the genome-genome interaction which may involve genomes from the same organisms or even different organisms [17-19]. Biology is multifactorial and dynamic. Complex traits are closely related to developmental changes in an organism's ontogeny, giving time an important role in the formation of complex traits. From the point of view of ecology, the formation of complex traits is extremely complex involving not only the genes of an individual but also the genotypes of its neighbors that co-occur with it [17,18,20-23]. Such complexity makes QTL mapping very challenging.

  11. A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea

    PubMed Central

    Bajaj, Deepak; Upadhyaya, Hari D.; Khan, Yusuf; Das, Shouvik; Badoni, Saurabh; Shree, Tanima; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Singh, Sube; Sharma, Shivali; Tyagi, Akhilesh K.; Chattopdhyay, Debasis; Parida, Swarup K.

    2015-01-01

    High experimental validation/genotyping success rate (94–96%) and intra-specific polymorphic potential (82–96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8–25.8% with LOD: 7.0–13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1–171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea. PMID:25786576

  12. Fine mapping of qGW1, a major QTL for grain weight in sorghum.

    PubMed

    Han, Lijie; Chen, Jun; Mace, Emma S; Liu, Yishan; Zhu, Mengjiao; Yuyama, Nana; Jordan, David R; Cai, Hongwei

    2015-09-01

    We detected seven QTLs for 100-grain weight in sorghum using an F 2 population, and delimited qGW1 to a 101-kb region on the short arm of chromosome 1, which contained 13 putative genes. Sorghum is one of the most important cereal crops. Breeding high-yielding sorghum varieties will have a profound impact on global food security. Grain weight is an important component of grain yield. It is a quantitative trait controlled by multiple quantitative trait loci (QTLs); however, the genetic basis of grain weight in sorghum is not well understood. In the present study, using an F2 population derived from a cross between the grain sorghum variety SA2313 (Sorghum bicolor) and the Sudan-grass variety Hiro-1 (S. bicolor), we detected seven QTLs for 100-grain weight. One of them, qGW1, was detected consistently over 2 years and contributed between 20 and 40 % of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants from a fine-mapping F3 population, we delimited qGW1 to a 101-kb region on the short arm of chromosome 1, containing 13 predicted gene models, one of which was found to be under purifying selection during domestication. However, none of the grain size candidate genes shared sequence similarity with previously cloned grain weight-related genes from rice. This study will facilitate isolation of the gene underlying qGW1 and advance our understanding of the regulatory mechanisms of grain weight. SSR markers linked to the qGW1 locus can be used for improving sorghum grain yield through marker-assisted selection.

  13. Fine Mapping Identifies a New QTL for Brown Rice Rate in Rice (Oryza Sativa L.).

    PubMed

    Ren, Deyong; Rao, Yuchun; Huang, Lichao; Leng, Yujia; Hu, Jiang; Lu, Mei; Zhang, Guangheng; Zhu, Li; Gao, Zhenyu; Dong, Guojun; Guo, Longbiao; Qian, Qian; Zeng, Dali

    2016-12-01

    High yield and quality determine the commercial potential of rice variety. Brown rice rate (BRR) is a key factor ensuring grain yield and quality in rice. So far, there were few reports about the genes that directly controlled the BRR in rice. Therefore, dissecting the genetic mechanism of the BRR genes can facilitate improving effective rice supply or edible grain yield. A double haploid population derived from the cross between Taichung Native 1 (TN1) (an indica variety) and Chunjiang 06 (CJ06) (a japonica variety) was used to investigate the genetic basis of grain milling and appearance traits affecting the BRR. By using a constructed molecular linkage map, four quantitative trait loci (QTLs) for the BRR were detected on chromosomes 1, 8, 9, and 10, respectively. In addition, three QTLs for appearance traits, including grain weight and grain length/width ratio, were detected on chromosomes 6, 9 and 10, respectively. Chromosome segment substitution lines (CSSLs) were established at the qBRR-10 locus. Finally, the qBRR-10 was narrowed to a 39.5 kb region on chromosome 10. In this region, two candidate genes, LOC_Os10g32124 and LOC_Os10g32190, showed significantly differential expression in TN1 and CSSL1-2 compared with CJ06. Histocytological analysis suggested that cell size and hull thickness may be important factors for the BRR. In the study, the qBRR-10 affected the BRR and was finally located to a region between two markers, P13 and P14. Two candidate genes were selected based on the expression difference between two parents, which facilitated the further cloning of the qBRR-10 gene and largely contributed to improve the grain yield and quality in rice.

  14. QTL mapping of temperature sensitivity reveals candidate genes for thermal adaptation and growth morphology in the plant pathogenic fungus Zymoseptoria tritici.

    PubMed

    Lendenmann, M H; Croll, D; Palma-Guerrero, J; Stewart, E L; McDonald, B A

    2016-04-01

    Different thermal environments impose strong, differential selection on populations, leading to local adaptation, but the genetic basis of thermal adaptation is poorly understood. We used quantitative trait locus (QTL) mapping in the fungal wheat pathogen Zymoseptoria tritici to study the genetic architecture of thermal adaptation and identify candidate genes. Four wild-type strains originating from the same thermal environment were crossed to generate two mapping populations with 263 (cross 1) and 261 (cross 2) progeny. Restriction site-associated DNA sequencing was used to genotype 9745 (cross 1) and 7333 (cross 2) single-nucleotide polymorphism markers segregating within the mapping population. Temperature sensitivity was assessed using digital image analysis of colonies growing at two different temperatures. We identified four QTLs for temperature sensitivity, with unique QTLs found in each cross. One QTL had a logarithm of odds score >11 and contained only six candidate genes, including PBS2, encoding a mitogen-activated protein kinase kinase associated with low temperature tolerance in Saccharomyces cerevisiae. This and other QTLs showed evidence for pleiotropy among growth rate, melanization and growth morphology, suggesting that many traits can be correlated with thermal adaptation in fungi. Higher temperatures were highly correlated with a shift to filamentous growth among the progeny in both crosses. We show that thermal adaptation has a complex genetic architecture, with natural populations of Z. tritici harboring significant genetic variation for this trait. We conclude that Z. tritici populations have the potential to adapt rapidly to climate change and expand into new climatic zones.

  15. Candidate Genes Within Tissue Culture Regeneration QTL Revisited with a Linkage Map Based on Transcript Derived Markers

    USDA-ARS?s Scientific Manuscript database

    Green plant regeneration from tissue culture is under the genetic control of multiple genes. Candidate genes for regeneration have been identified in multiple species using QTL and microarray analyses, and some of these genes have been verified as improving regeneration through transformation. Multi...

  16. SNP discovery and QTL mapping of Sclerotinia basal stalk rot resistance in sunflower using genotyping-by-sequencing (GBS)

    USDA-ARS?s Scientific Manuscript database

    Basal stalk rot (BSR) caused by the ascomycete fungus Sclerotinia sclerotiorum (Lib.) de Bary is a serious disease of sunflower (Helianthus annuus L.) in the cool and humid production areas of the world. Quantitative trait loci (QTL) for BSR resistance were identified in a sunflower recombinant inbr...

  17. Application of a Bayesian non-linear model hybrid scheme to sequence data for genomic prediction and QTL mapping.

    PubMed

    Wang, Tingting; Chen, Yi-Ping Phoebe; MacLeod, Iona M; Pryce, Jennie E; Goddard, Michael E; Hayes, Ben J

    2017-08-15

    Using whole genome sequence data might improve genomic prediction accuracy, when compared with high-density SNP arrays, and could lead to identification of casual mutations affecting complex traits. For some traits, the most accurate genomic predictions are achieved with non-linear Bayesian methods. However, as the number of variants and the size of the reference population increase, the computational time required to implement these Bayesian methods (typically with Monte Carlo Markov Chain sampling) becomes unfeasibly long. Here, we applied a new method, HyB_BR (for Hybrid BayesR), which implements a mixture model of normal distributions and hybridizes an Expectation-Maximization (EM) algorithm followed by Markov Chain Monte Carlo (MCMC) sampling, to genomic prediction in a large dairy cattle population with imputed whole genome sequence data. The imputed whole genome sequence data included 994,019 variant genotypes of 16,214 Holstein and Jersey bulls and cows. Traits included fat yield, milk volume, protein kg, fat% and protein% in milk, as well as fertility and heat tolerance. HyB_BR achieved genomic prediction accuracies as high as the full MCMC implementation of BayesR, both for predicting a validation set of Holstein and Jersey bulls (multi-breed prediction) and a validation set of Australian Red bulls (across-breed prediction). HyB_BR had a ten fold reduction in compute time, compared with the MCMC implementation of BayesR (48 hours versus 594 hours). We also demonstrate that in many cases HyB_BR identified sequence variants with a high posterior probability of affecting the milk production or fertility traits that were similar to those identified in BayesR. For heat tolerance, both HyB_BR and BayesR found variants in or close to promising candidate genes associated with this trait and not detected by previous studies. The results demonstrate that HyB_BR is a feasible method for simultaneous genomic prediction and QTL mapping with whole genome sequence in

  18. High-density ddRAD linkage and yield-related QTL mapping delimits a chromosomal region responsible for oil content in rapeseed (Brassica napus L.).

    PubMed

    Chen, Jun; Wang, Bo; Zhang, Yueli; Yue, Xiaopeng; Li, Zhaohong; Liu, Kede

    2017-06-01

    Rapeseed (Brassica napus L.) is one of the most important oil crops almost all over the world. Seed-related traits, including oil content (OC), silique length (SL), seeds per silique (SS), and seed weight (SW), are primary targets for oil yield improvement. To dissect the genetic basis of these traits, 192 recombinant inbred lines (RILs) were derived from two parents with distinct oil content and silique length. High-density linkage map with a total length of 1610.4 cM were constructed using 1,329 double-digestion restriction site associated DNA (ddRAD) markers, 107 insertion/deletions (INDELs), and 90 well-distributed simple sequence repeats (SSRs) markers. A total of 37 consensus quantitative trait loci (QTLs) were detected for the four traits, with individual QTL explained 3.1-12.8% of the phenotypic variations. Interestingly, one OC consensus QTL (cqOCA10b) on chromosome A10 was consistently detected in all three environments, and explained 9.8% to 12.8% of the OC variation. The locus was further delimited into an approximately 614 kb genomic region, in which the flanking markers could be further evaluated for marker-assisted selection in rapeseed OC improvement and the candidate genes targeted for map-based cloning and genetic manipulation.

  19. Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean.

    PubMed

    Sonah, Humira; O'Donoughue, Louise; Cober, Elroy; Rajcan, Istvan; Belzile, François

    2015-02-01

    Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>47,000 SNPs) for a panel of 304 short-season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  20. Genetic analysis for rice seedling vigor and fine mapping of a major QTL qSSL1b for seedling shoot length

    PubMed Central

    Zhang, Anpeng; Liu, Chaolei; Chen, Guang; Hong, Kai; Gao, Yang; Tian, Peng; Peng, Youlin; Zhang, Bin; Ruan, Banpu; Jiang, Hongzhen; Guo, Longbiao; Qian, Qian; Gao, Zhenyu

    2017-01-01

    Seedling vigor is an important agricultural trait as direct-seeded rice technology becomes widely applied. In order to investigate the genetic mechanisms underlying seedling vigor in rice, seeds of 132 recombinant inbred lines (RILs) derived from 93-11 and PA64s, harvested from Lingshui and Hangzhou were cultivated in the nutrient solution, and four indices for seedling vigor were measured including seedling shoot length (SSL), seedling root length (SRL), seedling wet weight (SWW) and seedling dry weight (SDW). Significant correlations were observed among the indices, and also between 1000-seed weight (TSW) and SWW or SDW. Combined with a high-resolution genetic map generated from sequencing of the RILs, 65 quantitative trait loci (QTLs) were detected on all chromosomes with interval of 1.93 Mb on average. Among 57 QTLs for seedling vigor, 28 were detected from seeds harvested in both sites and 33 were first identified. With BC3F2 derived from 93-11 and a CSSL harboring segments from PA64s in 93-11 background, a major QTL for SSL, qSSL1b was fine mapped within 80.5 kb between two InDel markers. Our study provides a platform for further cloning of the QTL and dissecting the molecular basis for seedling vigor at early seedling stage in rice. PMID:28744184

  1. Genetic analysis for rice seedling vigor and fine mapping of a major QTL qSSL1b for seedling shoot length.

    PubMed

    Zhang, Anpeng; Liu, Chaolei; Chen, Guang; Hong, Kai; Gao, Yang; Tian, Peng; Peng, Youlin; Zhang, Bin; Ruan, Banpu; Jiang, Hongzhen; Guo, Longbiao; Qian, Qian; Gao, Zhenyu

    2017-06-01

    Seedling vigor is an important agricultural trait as direct-seeded rice technology becomes widely applied. In order to investigate the genetic mechanisms underlying seedling vigor in rice, seeds of 132 recombinant inbred lines (RILs) derived from 93-11 and PA64s, harvested from Lingshui and Hangzhou were cultivated in the nutrient solution, and four indices for seedling vigor were measured including seedling shoot length (SSL), seedling root length (SRL), seedling wet weight (SWW) and seedling dry weight (SDW). Significant correlations were observed among the indices, and also between 1000-seed weight (TSW) and SWW or SDW. Combined with a high-resolution genetic map generated from sequencing of the RILs, 65 quantitative trait loci (QTLs) were detected on all chromosomes with interval of 1.93 Mb on average. Among 57 QTLs for seedling vigor, 28 were detected from seeds harvested in both sites and 33 were first identified. With BC3F2 derived from 93-11 and a CSSL harboring segments from PA64s in 93-11 background, a major QTL for SSL, qSSL1b was fine mapped within 80.5 kb between two InDel markers. Our study provides a platform for further cloning of the QTL and dissecting the molecular basis for seedling vigor at early seedling stage in rice.

  2. Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1.

    PubMed

    Chen, Mingliang; Luo, Ju; Shao, Gaoneng; Wei, Xiangjin; Tang, Shaoqing; Sheng, Zhonghua; Song, Jian; Hu, Peisong

    2012-05-01

    Leaf width is an important agricultural trait in rice. QTL mapping in a recombinant inbred line population derived from the cross between the javanica cultivar D50 (narrow-leaved) and the indica cultivar HB277 (wide-leaved) identified five QTLs controlling flag leaf width. Fine mapping of the major QTL qFLW4 narrowed its location to a 74.8 kb interval between the SSR loci RM17483 and RM17486, a region which also contains the gene NAL1 (Narrow leaf 1). There was no difference in the level of NAL1 expression between cvs. D50 and HB277, but an analysis of the NAL1 transcripts showed that while most (if not all) of those produced in cv. D50 were full-length, two-thirds of those in HB277 were non-functional due to either loss or gain of sequence. The inference was that NAL1 is probably synonymous with qFLW4, and that the functional difference between the two alleles was due to alternative splicing. The analysis of expression of other known genes involved in the determination of leaf width provided no evidence of their having any clear functional association with qFLW4/NAL1.

  3. Facilitating the Interpretation of English Language Proficiency Scores: Combining Scale Anchoring and Test Score Mapping Methodologies

    ERIC Educational Resources Information Center

    Powers, Donald; Schedl, Mary; Papageorgiou, Spiros

    2017-01-01

    The aim of this study was to develop, for the benefit of both test takers and test score users, enhanced "TOEFL ITP"® test score reports that go beyond the simple numerical scores that are currently reported. To do so, we applied traditional scale anchoring (proficiency scaling) to item difficulty data in order to develop performance…

  4. AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond

    PubMed Central

    Hu, Zhi-Liang; Fritz, Eric Ryan; Reecy, James M.

    2007-01-01

    The Animal Quantitative Trait Loci (QTL) database (AnimalQTLdb) is designed to house all publicly available QTL data on livestock animal species from which researchers can easily locate and compare QTL within species. The database tools are also added to link the QTL data to other types of genomic information, such as radiation hybrid (RH) maps, finger printed contig (FPC) physical maps, linkage maps and comparative maps to the human genome, etc. Currently, this database contains data on 1287 pig, 630 cattle and 657 chicken QTL, which are dynamically linked to respective RH, FPC and human comparative maps. We plan to apply the tool to other animal species, and add more structural genome information for alignment, in an attempt to aid comparative structural genome studies (). PMID:17135205

  5. Genome-Wide Linkage Mapping of QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Population Linmai 2 × Zhong 892

    PubMed Central

    Liu, Jindong; He, Zhonghu; Wu, Ling; Bai, Bin; Wen, Weie; Xie, Chaojie; Xia, Xianchun

    2015-01-01

    Stripe rust is one of the most devastating diseases of wheat (Triticum aestivum) worldwide. Adult-plant resistance (APR) is an efficient approach to provide long-term protection of wheat from the disease. The Chinese winter wheat cultivar Zhong 892 has a moderate level of APR to stripe rust in the field. To determine the inheritance of the APR resistance in this cultivar, 273 F6 recombinant inbred lines (RILs) were developed from a cross between Linmai 2 and Zhong 892. The RILs were evaluated for maximum disease severity (MDS) in two sites during the 2011–2012, 2012–2013 and 2013–2014 cropping seasons, providing data for five environments. Illumina 90k SNP (single nucleotide polymorphism) chips were used to genotype the RILs and their parents. Composite interval mapping (CIM) detected eight QTL, namely QYr.caas-2AL, QYr.caas-2BL.3, QYr.caas-3AS, QYr.caas-3BS, QYr.caas-5DL, QYr.caas-6AL, QYr.caas-7AL and QYr.caas-7DS.1, respectively. All except QYr.caas-2BL.3 resistance alleles were contributed by Zhong 892. QYr.caas-3AS and QYr.caas-3BS conferred stable resistance to stripe rust in all environments, explaining 6.2–17.4% and 5.0–11.5% of the phenotypic variances, respectively. The genome scan of SNP sequences tightly linked to QTL for APR against annotated proteins in wheat and related cereals genomes identified two candidate genes (autophagy-related gene and disease resistance gene RGA1), significantly associated with stripe rust resistance. These QTL and their closely linked SNP markers, in combination with kompetitive allele specific PCR (KASP) technology, are potentially useful for improving stripe rust resistances in wheat breeding. PMID:26714310

  6. High-density genetic linkage map construction by F2 populations and QTL analysis of early-maturity traits in upland cotton (Gossypium hirsutum L.).

    PubMed

    Li, Libei; Zhao, Shuqi; Su, Junji; Fan, Shuli; Pang, Chaoyou; Wei, Hengling; Wang, Hantao; Gu, Lijiao; Zhang, Chi; Liu, Guoyuan; Yu, Dingwei; Liu, Qibao; Zhang, Xianlong; Yu, Shuxun

    2017-01-01

    Due to China's rapidly increasing population, the total arable land area has dramatically decreased; as a consequence, the competition for farming land allocated for grain and cotton production has become fierce. Therefore, to overcome the existing contradiction between cotton grain and fiber production and the limited farming land, development of early-maturing cultivars is necessary. In this research, a high-density linkage map of upland cotton was constructed using genotyping by sequencing (GBS) to discover single nucleotide polymorphism (SNP) markers associated with early maturity in 170 F2 individuals derived from a cross between LU28 and ZHONG213. The high-density genetic map, which was composed of 3978 SNP markers across the 26 cotton chromosomes, spanned 2480 cM with an average genetic distance of 0.62 cM. Collinearity analysis showed that the genetic map was of high quality and accurate and agreed well with the Gossypium hirsutum reference genome. Based on this high-density linkage map, QTL analysis was performed on cotton early-maturity traits, including FT, FBP, WGP, NFFB, HNFFB and PH. A total 47 QTLs for the six traits were detected; each of these QTLs explained between 2.61% and 32.57% of the observed phenotypic variation. A major region controlling early-maturity traits in Gossypium hirsutum was identified for FT, FBP, WGP, NFFB and HNFFB on chromosome D03. QTL analyses revealed that phenotypic variation explained (PVE) ranged from 10.42% to 32.57%. Two potential candidate genes, Gh_D03G0885 and Gh_D03G0922, were predicted in a stable QTL region and had higher expression levels in the early-maturity variety ZHONG213 than in the late-maturity variety LU28. However, further evidence is required for functional validation. This study could provide useful information for the dissection of early-maturity traits and guide valuable genetic loci for molecular-assisted selection (MAS) in cotton breeding.

  7. High-density genetic linkage map construction by F2 populations and QTL analysis of early-maturity traits in upland cotton (Gossypium hirsutum L.)

    PubMed Central

    Li, Libei; Zhao, Shuqi; Su, Junji; Fan, Shuli; Pang, Chaoyou; Wei, Hengling; Wang, Hantao; Gu, Lijiao; Zhang, Chi; Liu, Guoyuan; Yu, Dingwei; Liu, Qibao; Zhang, Xianlong

    2017-01-01

    Due to China’s rapidly increasing population, the total arable land area has dramatically decreased; as a consequence, the competition for farming land allocated for grain and cotton production has become fierce. Therefore, to overcome the existing contradiction between cotton grain and fiber production and the limited farming land, development of early-maturing cultivars is necessary. In this research, a high-density linkage map of upland cotton was constructed using genotyping by sequencing (GBS) to discover single nucleotide polymorphism (SNP) markers associated with early maturity in 170 F2 individuals derived from a cross between LU28 and ZHONG213. The high-density genetic map, which was composed of 3978 SNP markers across the 26 cotton chromosomes, spanned 2480 cM with an average genetic distance of 0.62 cM. Collinearity analysis showed that the genetic map was of high quality and accurate and agreed well with the Gossypium hirsutum reference genome. Based on this high-density linkage map, QTL analysis was performed on cotton early-maturity traits, including FT, FBP, WGP, NFFB, HNFFB and PH. A total 47 QTLs for the six traits were detected; each of these QTLs explained between 2.61% and 32.57% of the observed phenotypic variation. A major region controlling early-maturity traits in Gossypium hirsutum was identified for FT, FBP, WGP, NFFB and HNFFB on chromosome D03. QTL analyses revealed that phenotypic variation explained (PVE) ranged from 10.42% to 32.57%. Two potential candidate genes, Gh_D03G0885 and Gh_D03G0922, were predicted in a stable QTL region and had higher expression levels in the early-maturity variety ZHONG213 than in the late-maturity variety LU28. However, further evidence is required for functional validation. This study could provide useful information for the dissection of early-maturity traits and guide valuable genetic loci for molecular-assisted selection (MAS) in cotton breeding. PMID:28809947

  8. Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.

    PubMed

    Poursarebani, Naser; Nussbaumer, Thomas; Simková, Hana; Safář, Jan; Witsenboer, Hanneke; van Oeveren, Jan; Doležel, Jaroslav; Mayer, Klaus F X; Stein, Nils; Schnurbusch, Thorsten

    2014-07-01

    Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A using whole-genome profiling (WGP™). The bacterial artificial chromosome (BAC) contig assembly tools fingerprinted contig (fpc) and linear topological contig (ltc) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that ltc created a highly robust assembly compared with those formed by fpc. The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP™ tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to the 'decoration' of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the sequencing of wheat chromosome 6A, and is of immediate use for map-based isolation of agronomically important genes/quantitative trait loci located on this chromosome.

  9. Anchoring Linkage Groups of the Rosa Genetic Map to Physical Chromosomes with Tyramide-FISH and EST-SNP Markers

    PubMed Central

    Kirov, Ilya; Van Laere, Katrijn; De Riek, Jan; De Keyser, Ellen; Van Roy, Nadine; Khrustaleva, Ludmila

    2014-01-01

    In order to anchor Rosa linkage groups to physical chromosomes, a combination of the Tyramide-FISH technology and the modern molecular marker system based on High Resolution Melting (HRM) is an efficient approach. Although, Tyramide-FISH is a very promising technique for the visualization of short DNA probes, it is very challenging for plant species with small chromosomes such as Rosa. In this study, we successfully applied the Tyramide-FISH technique for Rosa and compared different detection systems. An indirect detection system exploiting biotinylated tyramides was shown to be the most suitable technique for reliable signal detection. Three gene fragments with a size of 1100 pb–1700 bp (Phenylalanine Ammonia Lyase, Pyrroline-5-Carboxylate Synthase and Orcinol O-Methyl Transferase) have been physically mapped on chromosomes 7, 4 and 1, respectively, of Rosa wichurana. The signal frequency was between 25% and 40%. HRM markers of these 3 gene fragments were used to include the gene fragments on the existing genetic linkage map of Rosa wichurana. As a result, three linkage groups could be anchored to their physical chromosomes. The information was used to check for synteny between the Rosa chromosomes and Fragaria. PMID:24755945

  10. Anchoring linkage groups of the Rosa genetic map to physical chromosomes with tyramide-FISH and EST-SNP markers.

    PubMed

    Kirov, Ilya; Van Laere, Katrijn; De Riek, Jan; De Keyser, Ellen; Van Roy, Nadine; Khrustaleva, Ludmila

    2014-01-01

    In order to anchor Rosa linkage groups to physical chromosomes, a combination of the Tyramide-FISH technology and the modern molecular marker system based on High Resolution Melting (HRM) is an efficient approach. Although, Tyramide-FISH is a very promising technique for the visualization of short DNA probes, it is very challenging for plant species with small chromosomes such as Rosa. In this study, we successfully applied the Tyramide-FISH technique for Rosa and compared different detection systems. An indirect detection system exploiting biotinylated tyramides was shown to be the most suitable technique for reliable signal detection. Three gene fragments with a size of 1100 pb-1700 bp (Phenylalanine Ammonia Lyase, Pyrroline-5-Carboxylate Synthase and Orcinol O-Methyl Transferase) have been physically mapped on chromosomes 7, 4 and 1, respectively, of Rosa wichurana. The signal frequency was between 25% and 40%. HRM markers of these 3 gene fragments were used to include the gene fragments on the existing genetic linkage map of Rosa wichurana. As a result, three linkage groups could be anchored to their physical chromosomes. The information was used to check for synteny between the Rosa chromosomes and Fragaria.

  11. Mapping and introgression of QTL involved in fruit shape transgressive segregation into ‘piel de sapo’ melon (cucumis melo l.) [corrected].

    PubMed

    Díaz, Aurora; Zarouri, Belkacem; Fergany, Mohamed; Eduardo, Iban; Alvarez, José M; Picó, Belén; Monforte, Antonio J

    2014-01-01

    A mapping F2 population from the cross 'Piel de Sapo' × PI124112 was selectively genotyped to study the genetic control of morphological fruit traits by QTL (Quantitative Trait Loci) analysis. Ten QTL were identified, five for FL (Fruit Length), two for FD (Fruit Diameter) and three for FS (Fruit Shape). At least one robust QTL per character was found, flqs8.1 (LOD = 16.85, R2 = 34%), fdqs12.1 (LOD = 3.47, R2 = 11%) and fsqs8.1 (LOD = 14.85, R2 = 41%). flqs2.1 and fsqs2.1 cosegregate with gene a (andromonoecious), responsible for flower sex determination and with pleiotropic effects on FS. They display a positive additive effect (a) value, so the PI124112 allele causes an increase in FL and FS, producing more elongated fruits. Conversely, the negative a value for flqs8.1 and fsqs8.1 indicates a decrease in FL and FS, what results in rounder fruits, even if PI124112 produces very elongated melons. This is explained by a significant epistatic interaction between fsqs2.1 and fsqs8.1, where the effects of the alleles at locus a are attenuated by the additive PI124112 allele at fsqs8.1. Roundest fruits are produced by homozygous for PI124112 at fsqs8.1 that do not carry any dominant A allele at locus a (PiPiaa). A significant interaction between fsqs8.1 and fsqs12.1 was also detected, with the alleles at fsqs12.1 producing more elongated fruits. fsqs8.1 seems to be allelic to QTL discovered in other populations where the exotic alleles produce elongated fruits. This model has been validated in assays with backcross lines along 3 years and ultimately obtaining a fsqs8.1-NIL (Near Isogenic Line) in 'Piel de Sapo' background which yields round melons.

  12. Mapping and Introgression of QTL Involved in Fruit Shape Transgressive Segregation into ‘Piel de Sapo’ Melon (Cucucumis melo L.)

    PubMed Central

    Díaz, Aurora; Zarouri, Belkacem; Fergany, Mohamed; Eduardo, Iban; Álvarez, José M.; Picó, Belén; Monforte, Antonio J.

    2014-01-01

    A mapping F2 population from the cross ‘Piel de Sapo’ × PI124112 was selectively genotyped to study the genetic control of morphological fruit traits by QTL (Quantitative Trait Loci) analysis. Ten QTL were identified, five for FL (Fruit Length), two for FD (Fruit Diameter) and three for FS (Fruit Shape). At least one robust QTL per character was found, flqs8.1 (LOD = 16.85, R2 = 34%), fdqs12.1 (LOD = 3.47, R2 = 11%) and fsqs8.1 (LOD = 14.85, R2 = 41%). flqs2.1 and fsqs2.1 cosegregate with gene a (andromonoecious), responsible for flower sex determination and with pleiotropic effects on FS. They display a positive additive effect (a) value, so the PI124112 allele causes an increase in FL and FS, producing more elongated fruits. Conversely, the negative a value for flqs8.1 and fsqs8.1 indicates a decrease in FL and FS, what results in rounder fruits, even if PI124112 produces very elongated melons. This is explained by a significant epistatic interaction between fsqs2.1 and fsqs8.1, where the effects of the alleles at locus a are attenuated by the additive PI124112 allele at fsqs8.1. Roundest fruits are produced by homozygous for PI124112 at fsqs8.1 that do not carry any dominant A allele at locus a (PiPiaa). A significant interaction between fsqs8.1 and fsqs12.1 was also detected, with the alleles at fsqs12.1 producing more elongated fruits. fsqs8.1 seems to be allelic to QTL discovered in other populations where the exotic alleles produce elongated fruits. This model has been validated in assays with backcross lines along 3 years and ultimately obtaining a fsqs8.1-NIL (Near Isogenic Line) in ‘Piel de Sapo’ background which yields round melons. PMID:25126852

  13. Mapping of a major QTL associated with protein content on chromosome 2B in hard red winter wheat (Triticum aestivum L.)

    PubMed Central

    Terasawa, Yohei; Ito, Miwako; Tabiki, Tadashi; Nagasawa, Koichi; Hatta, Koichi; Nishio, Zenta

    2016-01-01

    A quantitative trait locus (QTL) controlling wheat grain protein content (GPC) and flour protein content (FPC) was identified using doubled haploid (DH) lines developed from a cross between the hard red winter wheat variety ‘Yumechikara’ with a high protein content used for bread making, and the soft red winter wheat ‘Kitahonami’ with a low protein content used for Japanese white salted noodles. A single major QTL, QGpc.2B-yume, was identified on the short arm of wheat chromosome 2B for both the GPC and FPC over 3 years of testing. QGpc.2B-yume was mapped on the flanking region of microsatellite marker Xgpw4382. The DH lines grouped by the haplotype of the closest flanking microsatellite marker Xgpw4382 showed differences of 1.0% and 1.1% in mean GPC and FPC, respectively. Yield-component-related traits were not affected by the haplotype of QGpc.2B-yume, and major North American hard red winter wheat varieties showed the high-protein haplotype. Unlike Gpc-B1 derived from tetraploid wheat, QGpc.2B-yume has no negative effects on yield-component-related traits and should be useful for wheat breeding to increase GPC and FPC. PMID:27795672

  14. Genetic Analysis in Maize Foundation Parents with Mapping Population and Testcross Population: Ye478 Carried More Favorable Alleles and Using QTL Information Could Improve Foundation Parents.

    PubMed

    Liu, Yinghong; Hou, Xianbin; Xiao, Qianlin; Yi, Qiang; Bian, Shaowei; Hu, Yufeng; Liu, Hanmei; Zhang, Junjie; Hao, Xiaoqin; Cheng, Weidong; Li, Yu; Huang, Yubi

    2016-01-01

    The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs) and general combining ability (GCA) of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further, analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight) was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations.

  15. Mapping of a major QTL associated with protein content on chromosome 2B in hard red winter wheat (Triticum aestivum L.).

    PubMed

    Terasawa, Yohei; Ito, Miwako; Tabiki, Tadashi; Nagasawa, Koichi; Hatta, Koichi; Nishio, Zenta

    2016-09-01

    A quantitative trait locus (QTL) controlling wheat grain protein content (GPC) and flour protein content (FPC) was identified using doubled haploid (DH) lines developed from a cross between the hard red winter wheat variety 'Yumechikara' with a high protein content used for bread making, and the soft red winter wheat 'Kitahonami' with a low protein content used for Japanese white salted noodles. A single major QTL, QGpc.2B-yume, was identified on the short arm of wheat chromosome 2B for both the GPC and FPC over 3 years of testing. QGpc.2B-yume was mapped on the flanking region of microsatellite marker Xgpw4382. The DH lines grouped by the haplotype of the closest flanking microsatellite marker Xgpw4382 showed differences of 1.0% and 1.1% in mean GPC and FPC, respectively. Yield-component-related traits were not affected by the haplotype of QGpc.2B-yume, and major North American hard red winter wheat varieties showed the high-protein haplotype. Unlike Gpc-B1 derived from tetraploid wheat, QGpc.2B-yume has no negative effects on yield-component-related traits and should be useful for wheat breeding to increase GPC and FPC.

  16. QTL for resistance in Lolium perenne to a mixed population of Puccinia graminis subsp. graminicola: use of RAD (restriction site associated DNA) markers to rapidly populate a new linkage map

    USDA-ARS?s Scientific Manuscript database

    A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. Susceptible and resistant plants were crossed to produce a pseudo-testcross population. Markers were produced by the Restriction-sit...

  17. QTL mapping & quantitative disease resistance to TSWV and leaf spots in a recombinant inbred line population SunOleic 97R and C94022 of peanut (Arachis hypogaea L.)

    USDA-ARS?s Scientific Manuscript database

    Peanut is susceptible to a range of diseases, such as Tomato spotted wilt virus (TSWV), early leaf spot (ELS) and late leaf spot (LLS). Breeding line NC94022 has been identified with the highest resistance to TSWV in the field. Quantitative trait loci (QTL) mapping is a highly effective approach fo...

  18. Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Six Economic Traits Using an F2 Population of the Hybrid from Saccharina longissima and Saccharina japonica.

    PubMed

    Zhang, Jing; Liu, Tao; Feng, Rongfang; Liu, Cui; Chi, Shan

    2015-01-01

    Saccharina (Laminaria) is one of the most important economic seaweeds. Previously, four genetic linkage maps of Saccharina have been constructed and five QTLs have been identified. However, they were not enough for its breeding. In this work, Saccharina longissima (♀) and Saccharina japonica (♂), which showed obvious differences in morphology and genetics, were applied in hybridization to yield the F2 mapping population with 102 individuals. Using these 102 F2 hybrids, the genetic linkage map of Saccharina was constructed by MapMaker software based on 37 amplified fragment length polymorphisms (AFLPs), 22 sequence-related amplified polymorphisms (SRAPs) and 139 simple sequence repeats (SSRs) markers. Meanwhile, QTL analysis was performed for six economic traits. The linkage map constructed in this research consisted of 422 marker loci (137 AFLPs, 57 SRAPs and 228 SSRs), which formed 45 linkage groups (LGs) with an average marker space of 7.92 cM; they spanned a total length of 2233.1 cM, covering the whole estimated genome size. A total of 29 QTLs were identified for six economic traits, which explained 1.06 to 64.00% of phenotypic variation, including three QTLs for frond length (FL) and raw weight (RW), five QTLs for frond width (FW), two QTLs for frond fascia width (FFW) and frond thickness (FT), and fourteen QTLs for base shape (BS). The results of this research will improve the breeding efficiency and be beneficial for marker-assisted selection (MAS) schemes in Saccharina breeding.

  19. Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Six Economic Traits Using an F2 Population of the Hybrid from Saccharina longissima and Saccharina japonica

    PubMed Central

    Zhang, Jing; Liu, Tao; Feng, Rongfang; Liu, Cui; Chi, Shan

    2015-01-01

    Saccharina (Laminaria) is one of the most important economic seaweeds. Previously, four genetic linkage maps of Saccharina have been constructed and five QTLs have been identified. However, they were not enough for its breeding. In this work, Saccharina longissima (♀) and Saccharina japonica (♂), which showed obvious differences in morphology and genetics, were applied in hybridization to yield the F2 mapping population with 102 individuals. Using these 102 F2 hybrids, the genetic linkage map of Saccharina was constructed by MapMaker software based on 37 amplified fragment length polymorphisms (AFLPs), 22 sequence-related amplified polymorphisms (SRAPs) and 139 simple sequence repeats (SSRs) markers. Meanwhile, QTL analysis was performed for six economic traits. The linkage map constructed in this research consisted of 422 marker loci (137 AFLPs, 57 SRAPs and 228 SSRs), which formed 45 linkage groups (LGs) with an average marker space of 7.92 cM; they spanned a total length of 2233.1 cM, covering the whole estimated genome size. A total of 29 QTLs were identified for six economic traits, which explained 1.06 to 64.00% of phenotypic variation, including three QTLs for frond length (FL) and raw weight (RW), five QTLs for frond width (FW), two QTLs for frond fascia width (FFW) and frond thickness (FT), and fourteen QTLs for base shape (BS). The results of this research will improve the breeding efficiency and be beneficial for marker-assisted selection (MAS) schemes in Saccharina breeding. PMID:26010152

  20. An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps.

    PubMed

    Mimura, Yutaka; Inoue, Takahiro; Minamiyama, Yasuhiro; Kubo, Nakao

    2012-03-01

    Of the Capsicum peppers (Capsicum spp.), cultivated C. annuum is the most commercially important, but has lacked an intraspecific linkage map based on sequence-specific PCR markers in accord with haploid chromosome numbers. We constructed a linkage map of pepper using a doubled haploid (DH) population derived from a cross between two C. annuum genotypes, a bell-type cultivar 'California Wonder' and a Malaysian small-fruited cultivar 'LS2341 (JP187992)', which is used as a source of resistance to bacterial wilt (Ralstonia solanacearum). A set of 253 markers (151 SSRs, 90 AFLPs, 10 CAPSs and 2 sequence-tagged sites) was on the map which we constructed, spanning 1,336 cM. This is the first SSR-based map to consist of 12 linkage groups, corresponding to the haploid chromosome number in an intraspecific cross of C. annuum. As this map has a lot of PCR-based anchor markers, it is easy to compare it to other pepper genetic maps. Therefore, this map and the newly developed markers will be useful for cultivated C. annuum breeding.

  1. A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome

    USDA-ARS?s Scientific Manuscript database

    As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high-density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of ...

  2. Saturation Mapping of a Major Effect QTL for Stripe Rust Resistance on Wheat Chromosome 2B in Cultivar Napo 63 Using SNP Genotyping Arrays

    PubMed Central

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

    2017-01-01

    Stripe rust or yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat (Triticum aestivum L.). Widespread deployment of resistant cultivars is the best means of achieving durable disease control. The red grain, spring wheat cultivar Napo 63 produced by CIMMYT in the 1960s shows a high level of adult-plant resistance to stripe rust in the field. To elucidate the genetic basis of resistance in this cultivar we evaluated 224 F2:3 lines and 175 F2:6 recombinant inbred lines (RILs) derived from a cross between Napo 63 and the Pst-susceptible line Avocet S. The maximum disease severity (MDS) data of F2:3 lines and the relative area under the disease progress curve (rAUDPC) data of RILs were collected during the 2014–2015 and 2015–2016 wheat growing seasons, respectively. Combined bulked segregant analysis and 90K single nucleotide polymorphism (SNP) arrays placed 275 of 511 polymorphic SNPs on chromosome 2B. Sixty four KASP markers selected from the 275 SNPs and 76 SSR markers on 2B were used to identify a chromosome region associated with rust response. A major effect QTL, named Qyrnap.nwafu-2BS, was identified by inclusive composite interval mapping and was preliminarily mapped to a 5.46 cM interval flanked by KASP markers 90K-AN34 and 90K-AN36 in chromosome 2BS. Fourteen KASP markers more closely linked to the locus were developed following a 660K SNP array analysis. The QTL region was finally narrowed to a 0.9 cM interval flanked by KASP markers 660K-AN21 and 660K-AN57 in bin region 2BS-1-0.53. The resistance of Napo 63 was stable across all environments, and as a QTL, explained an average 66.1% of the phenotypic variance in MDS of F2:3 lines and 55.7% of the phenotypic variance in rAUDPC of F5:6 RILs. The short genetic interval and flanking KASP markers developed in the study will facilitate marker-assisted selection, gene pyramiding, and eventual positional cloning of Qyrnap.nwafu-2BS. PMID:28491075

  3. QTL mapping of slow-rusting, adult plant resistance to race Ug99 of stem rust fungus in PBW343/Muu RIL population.

    PubMed

    Singh, Sukhwinder; Singh, Ravi P; Bhavani, Sridhar; Huerta-Espino, Julio; Eugenio, Lopez-Vera Eric

    2013-05-01

    Races of stem rust fungus pose a major threat to wheat production worldwide. We mapped adult plant resistance (APR) to Ug99 in 141 lines of a PBW343/Muu recombinant inbred lines (RILs) population by phenotyping them for three seasons at Njoro, Kenya in field trials and genotyping them with Diversity Arrays Technology (DArT) markers. Moderately susceptible parent PBW343 and APR parent Muu displayed mean stem rust severities of 66.6 and 5 %, respectively. The mean disease severity of RILs ranged from 1 to 100 %, with an average of 23.3 %. Variance components for stem rust severity were highly significant (p < 0.001) for RILs and seasons and the heritability (h (2)) for the disease ranged between 0.78 and 0.89. Quantitative trait loci (QTL) analysis identified four consistent genomic regions on chromosomes 2BS, 3BS, 5BL, and 7AS; three contributed by Muu (QSr.cim-2BS, QSr.cim-3BS and QSr.cim-7AS) and one (QSr.cim-5BL) derived from PBW343. RILs with flanking markers for these QTLs had significantly lower severities than those lacking the markers, and combinations of QTLs had an additive effect, significantly enhancing APR. The QTL identified on chromosome 3BS mapped to the matching region as the known APR gene Sr2. Four additional QTLs on chromosomes 1D, 3A, 4B, and 6A reduced disease severity significantly at least once in three seasons. Our results show a complex nature of APR to stem rust where Sr2 and other minor slow rusting resistance genes can confer a higher level of resistance when present together.

  4. Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.).

    PubMed

    Liu, Xueying; Teng, Zhonghua; Wang, Jinxia; Wu, Tiantian; Zhang, Zhiqin; Deng, Xianping; Fang, Xiaomei; Tan, Zhaoyun; Ali, Iftikhar; Liu, Dexin; Zhang, Jian; Liu, Dajun; Liu, Fang; Zhang, Zhengsheng

    2017-07-21

    Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population. Genetic linkage analysis was conducted on 726 loci obtained from the 712 polymorphic SSR markers, along with 1379 SSR loci obtained in our previous study, and a high-density genetic map with 2051 loci was constructed, which spanned 3508.29 cM with an average distance of 1.71 cM between adjacent markers. Marker orders on the linkage map are highly consistent with the corresponding physical orders on a G. hirsutum genome sequence. Based on fiber quality and yield component trait data collected from six environments, 113 QTLs were identified through two analytical methods. Among these 113 QTLs, 50 were considered stable (detected in multiple environments or for which phenotypic variance explained by additive effect was greater than environment effect), and 18 of these 50 were identified with stability by both methods. These 18 QTLs, including eleven for fiber quality and seven for yield component traits, could be priorities for MAS.

  5. Genetic architecture of sensory exploitation: QTL mapping of female and male receiver traits in an acoustic moth.

    PubMed

    Alem, S; Streiff, R; Courtois, B; Zenboudji, S; Limousin, D; Greenfield, M D

    2013-12-01

    The evolution of extravagant sexual traits by sensory exploitation occurs if males incidentally evolve features that stimulate females owing to a pre-existing environmental response that arose in the context of natural selection. The sensory exploitation process is thus expected to leave a specific genetic imprint, a pleiotropic control of the original environmental response and the novel sexual response in females. However, females may be subsequently selected to improve their discrimination of environmental and sexual stimuli. Accordingly, responses may have diverged and the original genetic architecture may have been modified. These possibilities may be considered by studying the genetic architecture of responses to male signals and to the environmental stimuli that were purportedly 'exploited' by those signals. However, no previous study has addressed the genetic control of sensory exploitation. We investigated this question in an acoustic pyralid moth, Achroia grisella, in which a male ultrasonic song attracts females and perception of ultrasound likely arose in the context of detecting predatory bats. We examined the genetic architecture of female response to bat echolocation signals and to male song via a cartographic study of quantitative trait loci (QTL) influencing these receiver traits. We found several QTL for both traits, but none of them were colocalized on the same chromosomes. These results indicate that - to the extent to which male A. grisella song originated by the process of sensory exploitation - some modification of the female responses occurred since the origin of the male signal.

  6. The age related markers lipofuscin and apoptosis show different genetic architecture by QTL mapping in short-lived Nothobranchius fish

    PubMed Central

    Ng'oma, Enoch; Reichwald, Kathrin; Dorn, Alexander; Wittig, Michael; Balschun, Tobias; Franke, Andre; Platzer, Matthias; Cellerino, Allesandro

    2014-01-01

    Annual fish of the genus Nothobranchius show large variations in lifespan and expression of age-related phenotypes between closely related populations. We studied N. kadleci and its sister species N. furzeri GRZ strain, and found that N.kadleci is longer-lived than the N. furzeri. Lipofuscin and apoptosis measured in the liver increased with age in N. kadleci with different profiles: lipofuscin increased linearly, while apoptosis declined in the oldest animals. More lipofuscin (P < 0.001) and apoptosis (P < 0.001) was observed in N. furzeri than in N. kadleci at 16w age. Lipofuscin and apoptotic cells were then quantified in hybrids from the mating of N. furzeri to N. kadleci. F1 individuals showed heterosis for lipofuscin but additive effects for apoptosis. These two age-related phenotypes were not correlated in F2 hybrids. Quantitative trait loci analysis of 287 F2 fish using 237 markers identified two QTL accounting for 10% of lipofuscin variance (P < 0.001) with overdominance effect. Apoptotic cells revealed three significant- and two suggestive QTL explaining 19% of variance (P < 0.001), showing additive and dominance effects, and two interacting loci. Our results show that lipofuscin and apoptosis are markers of different age-dependent biological processes controlled by different genetic mechanisms. PMID:25093339

  7. A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata) Using Genotyping-by-Sequencing

    PubMed Central

    Wang, Jinpeng; Li, Li; Zhang, Guofan

    2016-01-01

    Oysters are among the most important species in global aquaculture. Crassostrea gigas, and its subspecies C. angulata, are the major cultured species. To determine the genetic basis of growth-related traits in oysters, we constructed a second-generation linkage map from 3367 single-nucleotide polymorphisms (SNPs) based on genotyping-by-sequencing, genotyped from a C. gigas × C. angulata hybrid family. These 3367 SNPs were distributed on 1695 markers, which were assigned to 10 linkage groups. The genetic linkage map had a total length of 1084.3 cM, with an average of 0.8 cM between markers; it thus represents the densest genetic map constructed for oysters to date. Twenty-seven quantitative trait loci (QTL) for five growth-related traits were detected. These QTL could explain 4.2–7.7% (mean = 5.4%) of the phenotypic variation. In total, 50.8% of phenotypic variance for shell width, 7.7% for mass weight, and 34.1% for soft tissue weight were explained. The detected QTL were distributed among eight linkage groups, and more than half (16) were concentrated within narrow regions in their respective linkage groups. Thirty-eight annotated genes were identified within the QTL regions, two of which are key genes for carbohydrate metabolism. Other genes were found to participate in assembly and regulation of the actin cytoskeleton, signal transduction, and regulation of cell differentiation and development. The newly developed high-density genetic map, and the QTL and candidate genes identified provide a valuable genetic resource and a basis for marker-assisted selection for C. gigas and C. angulata. PMID:26994291

  8. The ACS Exams Institute Undergraduate Chemistry Anchoring Concepts Content Map II: Organic Chemistry

    ERIC Educational Resources Information Center

    Raker, Jeffrey; Holme, Thomas; Murphy, Kristen

    2013-01-01

    As a way to assist chemistry departments with programmatic assessment of undergraduate chemistry curricula, the ACS Examinations Institute is devising a map of the content taught throughout the undergraduate curriculum. The structure of the map is hierarchal, with large grain size at the top and more content detail as one moves "down"…

  9. The ACS Exams Institute Undergraduate Chemistry Anchoring Concepts Content Map II: Organic Chemistry

    ERIC Educational Resources Information Center

    Raker, Jeffrey; Holme, Thomas; Murphy, Kristen

    2013-01-01

    As a way to assist chemistry departments with programmatic assessment of undergraduate chemistry curricula, the ACS Examinations Institute is devising a map of the content taught throughout the undergraduate curriculum. The structure of the map is hierarchal, with large grain size at the top and more content detail as one moves "down"…

  10. SNP identification from RNA sequencing and linkage map construction of rubber tree for anchoring the draft genome.

    PubMed

    Shearman, Jeremy R; Sangsrakru, Duangjai; Jomchai, Nukoon; Ruang-Areerate, Panthita; Sonthirod, Chutima; Naktang, Chaiwat; Theerawattanasuk, Kanikar; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke

    2015-01-01

    Hevea brasiliensis, or rubber tree, is an important crop species that accounts for the majority of natural latex production. The rubber tree nuclear genome consists of 18 chromosomes and is roughly 2.15 Gb. The current rubber tree reference genome assembly consists of 1,150,326 scaffolds ranging from 200 to 531,465 bp and totalling 1.1 Gb. Only 143 scaffolds, totalling 7.6 Mb, have been placed into linkage groups. We have performed RNA-seq on 6 varieties of rubber tree to identify SNPs and InDels and used this information to perform target sequence enrichment and high throughput sequencing to genotype a set of SNPs in 149 rubber tree offspring from a cross between RRIM 600 and RRII 105 rubber tree varieties. We used this information to generate a linkage map allowing for the anchoring of 24,424 contigs from 3,009 scaffolds, totalling 115 Mb or 10.4% of the published sequence, into 18 linkage groups. Each linkage group contains between 319 and 1367 SNPs, or 60 to 194 non-redundant marker positions, and ranges from 156 to 336 cM in length. This linkage map includes 20,143 of the 69,300 predicted genes from rubber tree and will be useful for mapping studies and improving the reference genome assembly.

  11. Genetic map construction and quantitative trait loci (QTL) mapping for nitrogen use efficiency and its relationship with productivity and quality of the biennial crop Belgian endive (Cichorium intybus L.).

    PubMed

    Cassan, Laurent; Moreau, Laurence; Segouin, Samuel; Bellamy, Annick; Falque, Mathieu; Limami, Anis M

    2010-10-15

    A genetic study of the biennial crop Belgian endive (Cichorium intybus) was carried out to examine the effect of nitrogen nutrition during the vegetative phase in the control of the productivity and quality of the chicon (etiolated bud), a crop that grows during the second phase of development (forcing process). A population of 302 recombinant inbred lines (RIL) was obtained from the cross between contrasting lines "NS1" and "NR2". A genetic map was constructed and QTLs of several physiological and agronomical traits were mapped under two levels of nitrogen fertilization during the vegetative phase (N- and N+). The agronomical traits showed high broad sense heritability, whereas the physiological traits were characterized by low broad sense heritability. Nitrogen reserves mobilization during the forcing process was negatively correlated with nitrogen reserves content of the tuberized root and common QTLs were detected for these traits. The chicon productivity and quality were not correlated, but showed one common QTL. This study revealed that chicon productivity and quality were genetically associated with nitrogen reserves mobilization that exerts opposite effects on both traits. Chicon productivity was positively correlated with N reserves mobilization under N- and N+ and a common QTL with the same additive effects was detected for both traits. Chicon quality was negatively correlated with N reserves mobilization under N- and N+ and a common QTL with opposite additive effects was detected for both traits. These results lead to the conclusion that N reserves mobilization is a more effective trait than N reserves content in predicting chicon productivity and quality. Finally, this study revealed agronomical and physiological QTLs utilizable by breeders via marker-assisted selection to aid the optimization of chicon quality under adapted N fertilization. Copyright (c) 2010 Elsevier GmbH. All rights reserved.

  12. Dissecting the genetic architecture of Fusarium verticillioides seed rot resistance in maize by combining QTL mapping and genome-wide association analysis

    PubMed Central

    Ju, Ming; Zhou, Zijian; Mu, Cong; Zhang, Xuecai; Gao, Jingyang; Liang, Yakun; Chen, Jiafa; Wu, Yabin; Li, Xiaopeng; Wang, Shiwei; Wen, Jingjing; Yang, Luming; Wu, Jianyu

    2017-01-01

    Fusarium verticillioides can be transmitted via seeds and cause systemic infection in maize (Zea mays L.); its mycotoxin has harmful effects on animal and human health. We combined QTL mapping in recombinant inbred line (RIL) populations with a genome-wide association study (GWAS) of 217 diverse maize lines using 224,152 single nucleotide polymorphisms (SNPs) under controlled conditions to determine the genetic architecture of F. verticillioides seed rot (FSR) resistance. Our study identified 8 quantitative trait loci (QTLs) and 43 genes associated with 57 SNPs that were correlated with FSR resistance through linkage mapping and GWAS, respectively. Among these, there were three candidate genes, namely GRMZM2G0081223, AC213654.3_FG004, and GRMZM2G099255, which were detected in both linkage mapping and GWAS. Furthermore, the near-isogenic lines (NILs) containing GRMZM2G0081223, which also had a susceptible parent background, were found to have a significantly improved level of resistance. In addition, the expression profile of the three candidate genes revealed that they all respond to the infection following inoculation with F. verticillioides. These genetic analyses indicate that FSR resistance is controlled by loci with minor effect, and the polymerization breeding of lines with beneficial alleles and candidate genes could improve FSR resistance in maize. PMID:28422143

  13. Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch

    PubMed Central

    Bielenberg, Douglas Gary; Rauh, Bradley; Fan, Shenghua; Gasic, Ksenija; Abbott, Albert Glenn; Reighard, Gregory Lynn; Okie, William R.; Wells, Christina Elizabeth

    2015-01-01

    Low-cost, high throughput genotyping methods are crucial to marker discovery and marker-assisted breeding efforts, but have not been available for many ‘specialty crops’ such as fruit and nut trees. Here we apply the Genotyping-By-Sequencing (GBS) method developed for cereals to the discovery of single nucleotide polymorphisms (SNPs) in a peach F2 mapping population. Peach is a genetic and genomic model within the Rosaceae and will provide a template for the use of this method with other members of this family. Our F2 mapping population of 57 genotypes segregates for bloom time (BD) and chilling requirement (CR) and we have extensively phenotyped this population. The population derives from a selfed F1 progeny of a cross between ‘Hakuho’ (high CR) and ‘UFGold’ (low CR). We were able to successfully employ GBS and the TASSEL GBS pipeline without modification of the original methodology using the ApeKI restriction enzyme and multiplexing at an equivalent of 96 samples per Illumina HiSeq 2000 lane. We obtained hundreds of SNP markers which were then used to construct a genetic linkage map and identify quantitative trait loci (QTL) for BD and CR. PMID:26430886

  14. Genotyping by Sequencing for SNP-Based Linkage Map Construction and QTL Analysis of Chilling Requirement and Bloom Date in Peach [Prunus persica (L.) Batsch].

    PubMed

    Bielenberg, Douglas Gary; Rauh, Bradley; Fan, Shenghua; Gasic, Ksenija; Abbott, Albert Glenn; Reighard, Gregory Lynn; Okie, William R; Wells, Christina Elizabeth

    2015-01-01

    Low-cost, high throughput genotyping methods are crucial to marker discovery and marker-assisted breeding efforts, but have not been available for many 'specialty crops' such as fruit and nut trees. Here we apply the Genotyping-By-Sequencing (GBS) method developed for cereals to the discovery of single nucleotide polymorphisms (SNPs) in a peach F2 mapping population. Peach is a genetic and genomic model within the Rosaceae and will provide a template for the use of this method with other members of this family. Our F2 mapping population of 57 genotypes segregates for bloom time (BD) and chilling requirement (CR) and we have extensively phenotyped this population. The population derives from a selfed F1 progeny of a cross between 'Hakuho' (high CR) and 'UFGold' (low CR). We were able to successfully employ GBS and the TASSEL GBS pipeline without modification of the original methodology using the ApeKI restriction enzyme and multiplexing at an equivalent of 96 samples per Illumina HiSeq 2000 lane. We obtained hundreds of SNP markers which were then used to construct a genetic linkage map and identify quantitative trait loci (QTL) for BD and CR.

  15. seeQTL: a searchable database for human eQTLs.

    PubMed

    Xia, Kai; Shabalin, Andrey A; Huang, Shunping; Madar, Vered; Zhou, Yi-Hui; Wang, Wei; Zou, Fei; Sun, Wei; Sullivan, Patrick F; Wright, Fred A

    2012-02-01

    seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots. seeQTL is freely available for non-commercial use at http://www.bios.unc.edu/research/genomic_software/seeQTL/. fred_wright@unc.edu; kxia@bios.unc.edu Supplementary data are available at Bioinformatics online.

  16. seeQTL: a searchable database for human eQTLs

    PubMed Central

    Xia, Kai; Shabalin, Andrey A.; Huang, Shunping; Madar, Vered; Zhou, Yi-Hui; Wang, Wei; Zou, Fei; Sun, Wei; Sullivan, Patrick F.; Wright, Fred A.

    2012-01-01

    Summary: seeQTL is a comprehensive and versatile eQTL database, including various eQTL studies and a meta-analysis of HapMap eQTL information. The database presents eQTL association results in a convenient browser, using both segmented local-association plots and genome-wide Manhattan plots. Availability and implementation: seeQTL is freely available for non-commercial use at http://www.bios.unc.edu/research/genomic_software/seeQTL/. Contact: fred_wright@unc.edu; kxia@bios.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22171328

  17. Microsatellite Discovery from BAC End Sequences and Genetic Mapping to Anchor the Soybean Physical and Genetic Maps

    USDA-ARS?s Scientific Manuscript database

    Physical maps can be an invaluable resource for improving and assessing the quality of a whole-genome sequence assembly. Here we report the identification and screening of 3,290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the physical map of the cultivar Williams 8...

  18. QTL mapping of root traits in phosphorus-deficient soils reveals important genomic regions for improving NDVI and grain yield in barley.

    PubMed

    Gong, Xue; McDonald, Glenn

    2017-06-07

    Major QTLs for root rhizosheath size are not correlated with grain yield or yield response to phosphorus. Important QTLs were found to improve phosphorus efficiency. Root traits are important for phosphorus (P) acquisition, but they are often difficult to characterize and their breeding values are seldom assessed under field conditions. This has shed doubts on using seedling-based criteria of root traits to select and breed for P efficiency. Eight root traits were assessed under controlled conditions in a barley doubled-haploid population in soils differing in P levels. The population was also phenotyped for grain yield, normalized difference vegetation index (NDVI), grain P uptake and P utilization efficiency at maturity (PutEGY) under field conditions. Several quantitative traits loci (QTLs) from the root screening and the field trials were co-incident. QTLs for root rhizosheath size and root diameter explained the highest phenotypic variation in comparison to QTLs for other root traits. Shared QTLs were found between root diameter and grain yield, and total root length and PutEGY. A common major QTL for rhizosheath size and NDVI was mapped to the HvMATE gene marker on chromosome 4H. Collocations between major QTLs for NDVI and grain yield were detected on chromosomes 6H and 7H. When results from BIP and MET were combined, QTLs detected for grain yield were also those QTLs found for NDVI. QTLs qGY5H, qGY6H and qGY7Hb on 7H were robust QTLs in improving P efficiency. A selection of multiple loci may be needed to optimize the breeding outcomes due to the QTL x Environment interaction. We suggest that rhizosheath size alone is not a reliable trait to predict P efficiency or grain yield.

  19. Genetic Analysis in Maize Foundation Parents with Mapping Population and Testcross Population: Ye478 Carried More Favorable Alleles and Using QTL Information Could Improve Foundation Parents

    PubMed Central

    Liu, Yinghong; Hou, Xianbin; Xiao, Qianlin; Yi, Qiang; Bian, Shaowei; Hu, Yufeng; Liu, Hanmei; Zhang, Junjie; Hao, Xiaoqin; Cheng, Weidong; Li, Yu; Huang, Yubi

    2016-01-01

    The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs) and general combining ability (GCA) of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further, analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight) was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations. PMID:27721817

  20. Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.).

    PubMed

    Blair, M W; Pedraza, F; Buendia, H F; Gaitán-Solís, E; Beebe, S E; Gepts, P; Tohme, J

    2003-11-01

    A total of 150 microsatellite markers developed for common bean ( Phaseolus vulgaris L.) were tested for parental polymorphism and used to determine the positions of 100 genetic loci on an integrated genetic map of the species. The value of these single-copy markers was evident in their ability to link two existing RFLP-based genetic maps with a base map developed for the Mesoamerican x Andean population, DOR364 x G19833. Two types of microsatellites were mapped, based respectively on gene-coding and anonymous genomic-sequences. Gene-based microsatellites proved to be less polymorphic (46.3%) than anonymous genomic microsatellites (64.3%) between the parents of two inter-genepool crosses. The majority of the microsatellites produced single bands and detected single loci, however four of the gene-based and three of the genomic microsatellites produced consistent double or multiple banding patterns and detected more than one locus. Microsatellite loci were found on each of the 11 chromosomes of common bean, the number per chromosome ranging from 5 to 17 with an average of ten microsatellites each. Total map length for the base map was 1,720 cM and the average chromosome length was 156.4 cM, with an average distance between microsatellite loci of 19.5 cM. The development of new microsatellites from sequences in the Genbank database and the implication of these results for genetic mapping, quantitative trait locus analysis and marker-assisted selection in common bean are described.

  1. Cytogenetic anchoring of radiation hybrid and virtual maps of sheep chromosome X and comparison of X chromosomes in sheep, cattle, and human.

    PubMed

    Goldammer, Tom; Brunner, Ronald M; Rebl, Alexander; Wu, Chun Hua; Nomura, Ko; Hadfield, Tracy; Maddox, Jill F; Cockett, Noelle E

    2009-01-01

    A comprehensive physical map was generated for Ovis aries chromosome X (OARX) based on a cytogenomics approach. DNA probes were prepared from bacterial artificial chromosome (BAC) clones from the CHORI-243 sheep library and were assigned to G-banded metaphase spreads via fluorescence in-situ hybridization (FISH). A total of 22 BACs gave a single hybridization signal to the X chromosome and were assigned out of 32 tested. The positioned BACs contained 16 genes and a microsatellite marker which represent new cytogenetically mapped loci in the sheep genome. The gene and microsatellite loci serve to anchor between the existing radiation hybrid (RH) and virtual sheep genome (VSG) maps to the cytogenetic OARX map, whilst the BACs themselves also serve as anchors between the VSG and the cytogenetic maps. An additional 17 links between the RH and cytogenetic maps are provided by BAC end sequence (BES) derived markers that have also been positioned on the RH map. Comparison of the map orders for the cytogenetic, RH, and virtual maps reveals that the orders for the cytogenetic and RH maps are most similar, with only one locus, represented by BAC CH243-330E18, mapping to relatively different positions. Several discrepancies, including an inverted segment are found when comparing both the cytogenetic and RH maps with the virtual map. These discrepancies highlight the value of using physical mapping methods to inform the process of future in silico map construction. A detailed comparative analysis of sheep, human, and cattle mapping data allowed the construction of a comparative map that confirms and expands the knowledge about evolutionary conservation and break points between the X chromosomes of the three mammalian species.

  2. A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B.

    PubMed

    Kobayashi, Fuminori; Wu, Jianzhong; Kanamori, Hiroyuki; Tanaka, Tsuyoshi; Katagiri, Satoshi; Karasawa, Wataru; Kaneko, Satoko; Watanabe, Shota; Sakaguchi, Toyotaka; Hanawa, Yumiko; Fujisawa, Hiroko; Kurita, Kanako; Abe, Chikako; Iehisa, Julio C M; Ohno, Ryoko; Šafář, Jan; Šimková, Hana; Mukai, Yoshiyuki; Hamada, Masao; Saito, Mika; Ishikawa, Goro; Katayose, Yuichi; Endo, Takashi R; Takumi, Shigeo; Nakamura, Toshiki; Sato, Kazuhiro; Ogihara, Yasunari; Hayakawa, Katsuyuki; Doležel, Jaroslav; Nasuda, Shuhei; Matsumoto, Takashi; Handa, Hirokazu

    2015-08-12

    A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with the goal of revealing the structural features of the third largest chromosome in wheat. We assembled 689 informative BAC contigs (hereafter reffered to as contigs) representing 91% of the entire physical length of wheat chromosome 6B. The contigs were integrated into a radiation hybrid (RH) map of chromosome 6B, with one linkage group consisting of 448 loci with 653 markers. The order and direction of 480 contigs, corresponding to 87% of the total length of 6B, were determined. We also characterized the contigs that contained a part of the nucleolus organizer region or centromere based on their positions on the RH map and the assembled BAC clone sequences. Analysis of the virtual gene order along 6B using the information collected for the integrated map revealed the presence of several chromosomal rearrangements, indicating evolutionary events that occurred on chromosome 6B. We constructed a reliable physical map of chromosome 6B, enabling us to analyze its genomic structure and evolutionary progression. More importantly, the physical map should provide a high-quality and map-based reference sequence that will serve as a resource for wheat chromosome 6B.

  3. An extended anchored linkage map and virtual mapping for the American mink genome based on homology to human and dog.

    PubMed

    Anistoroaei, R; Ansari, S; Farid, A; Benkel, B; Karlskov-Mortensen, P; Christensen, K

    2009-09-01

    In this report we present an extended linkage map of the American mink (Neovison vison) consisting of 157 microsatellite markers and comprising at least one linkage group for each of the autosomes. Each linkage group has been assigned to a chromosome and oriented by fluorescence in situ hybridization (FISH) and/or by means of human/dog/mink comparative homology. The average interval between markers is 8.5 cM and the linkage groups collectively span 1340 cM. In addition, 217 and 275 mink microsatellites have been placed on human and dog genomes, respectively. In conjunction with the existing comparative human/dog/mink data, these assignments represent useful virtual maps for the American mink genome. Comparison of the current human/dog assembled sequential map with the existing Zoo-FISH-based human/dog/mink maps helped to refine the human/dog/mink comparative map. Furthermore, comparison of the human and dog genome assemblies revealed a number of large synteny blocks, some of which are corroborated by data from the mink linkage map.

  4. A GBS-SNP-based linkage map and quantitative trait loci (QTL) associated with resistance to Fusarium oxysporum f. sp. niveum race 2 identified in Citrullus lanatus var. citroides.

    PubMed

    Branham, Sandra E; Levi, Amnon; Farnham, Mark W; Patrick Wechter, W

    2017-02-01

    A major QTL for resistance to Fusarium oxysporum f. sp. niveum race 2 was mapped to a narrow 1.2 Mb interval using a high-density GBS-SNP linkage map, the first map of Citrullus lanatus var. citroides. Fusarium wilt, a fungal disease caused by Fusarium oxysporum f. sp. niveum (Fon), devastates watermelon crop production worldwide. Several races, which are differentiated by host range, of the pathogen exist. Resistance to Fon race 2, a particularly virulent strain prevalent in the United States, does not exist in edible cultivars of the sweet cultivated watermelon Citrullus lanatus var. lanatus (Cll) and has been well described in a few plant introductions of the wild subspecies of watermelon, C. lanatus var. citroides (Clc). Clc provides a vital source of genetic diversity, as well as resistance to numerous diseases. Unfortunately, both genetic diversity and disease resistance are lacking in Cll due to the narrow genetic base. Despite the importance of Clc to continued watermelon improvement, intra-variety genetic studies are lacking. Here, we present the first Clc genetic linkage map, generated with 2495 single nucleotide polymorphisms developed through genotyping-by-sequencing, and use it to identify quantitative trait loci associated with Fon race 2 resistance. Multiple QTL mapping in a Clc F2:3 population (N = 173) identified one major and four minor QTL. The major QTL explained 43% of the variation in Fon race 2 resistance and was delimited to a 1.2-Mb interval on chromosome 9, a region spanning 44 genes.

  5. The ACS Exams Institute Undergraduate Chemistry Anchoring Concepts Content Map I: General Chemistry

    ERIC Educational Resources Information Center

    Holme, Thomas; Murphy, Kristen

    2012-01-01

    To provide tools for programmatic assessment related to the use of ACS Exams in undergraduate chemistry courses, the ACS Exams Institute has built a content map that applies to the entire undergraduate curriculum. At the top two levels, the grain size of the content classification is large and spans the entire undergraduate curriculum. At the…

  6. The ACS Exams Institute Undergraduate Chemistry Anchoring Concepts Content Map I: General Chemistry

    ERIC Educational Resources Information Center

    Holme, Thomas; Murphy, Kristen

    2012-01-01

    To provide tools for programmatic assessment related to the use of ACS Exams in undergraduate chemistry courses, the ACS Exams Institute has built a content map that applies to the entire undergraduate curriculum. At the top two levels, the grain size of the content classification is large and spans the entire undergraduate curriculum. At the…

  7. Joint QTL analyses for partial resistance to Phytophthora sojae using six nested inbred populations with heterogeneous conditions

    USDA-ARS?s Scientific Manuscript database

    Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect these QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred li...

  8. Characterization of three maize bacterial artificial chromosome libraries toward anchoring of the physical map to the genetic map using high-density bacterial artificial chromosome filter hybridization.

    PubMed

    Yim, Young-Sun; Davis, Georgia L; Duru, Ngozi A; Musket, Theresa A; Linton, Eric W; Messing, Joachim W; McMullen, Michael D; Soderlund, Carol A; Polacco, Mary L; Gardiner, Jack M; Coe, Edward H

    2002-12-01

    Three maize (Zea mays) bacterial artificial chromosome (BAC) libraries were constructed from inbred line B73. High-density filter sets from all three libraries, made using different restriction enzymes (HindIII, EcoRI, and MboI, respectively), were evaluated with a set of complex probes including the 185-bp knob repeat, ribosomal DNA, two telomere-associated repeat sequences, four centromere repeats, the mitochondrial genome, a multifragment chloroplast DNA probe, and bacteriophage lambda. The results indicate that the libraries are of high quality with low contamination by organellar and lambda-sequences. The use of libraries from multiple enzymes increased the chance of recovering each region of the genome. Ninety maize restriction fragment-length polymorphism core markers were hybridized to filters of the HindIII library, representing 6x coverage of the genome, to initiate development of a framework for anchoring BAC contigs to the intermated B73 x Mo17 genetic map and to mark the bin boundaries on the physical map. All of the clones used as hybridization probes detected at least three BACs. Twenty-two single-copy number core markers identified an average of 7.4 +/- 3.3 positive clones, consistent with the expectation of six clones. This information is integrated into fingerprinting data generated by the Arizona Genomics Institute to assemble the BAC contigs using fingerprint contig and contributed to the process of physical map construction.

  9. Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology

    PubMed Central

    2014-01-01

    Background The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causative mutations in a QTL region. For this, a concordance analysis was applied for a leg conformation trait in dairy cattle. Several QTL were detected for which the QTL status (homozygous or heterozygous for the QTL) was inferred for each individual. Subsequently, the inferred QTL status was used in a concordance analysis to reduce the number of candidate mutations. Methods Twenty QTL for rear leg set side view were mapped using Bayes C. Marker effects estimated during QTL mapping were used to infer the QTL status for each individual. Subsequently, polymorphisms present in the QTL regions were extracted from the whole-genome sequences of 71 Holstein bulls. Only polymorphisms for which the status was concordant with the QTL status were kept as candidate causative mutations. Results QTL status could be inferred for 15 of the 20 QTL. The number of concordant polymorphisms differed between QTL and depended on the number of QTL statuses that could be inferred and the linkage disequilibrium in the QTL region. For some QTL, the concordance analysis was efficient and narrowed down to a limited number of candidate mutations located in one or two genes, while for other QTL a large number of genes contained concordant polymorphisms. Conclusions For regions for which the concordance analysis could be performed, we were able to reduce the number of candidate mutations. For part of the QTL, the concordant analyses narrowed QTL regions down to a limited number of genes, of which some are known for their role in limb or skeletal development in humans and mice. Mutations in these genes are good candidates for QTN (quantitative trait nucleotides) influencing rear leg set side view. PMID:24884971

  10. Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing.

    PubMed

    Glazer, Andrew M; Killingbeck, Emily E; Mitros, Therese; Rokhsar, Daniel S; Miller, Craig T

    2015-06-03

    Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis. Copyright © 2015 Glazer et al.

  11. Genetic mapping and QTL analysis of disease resistance traits in peanut population Tifrunner x GT-C20

    USDA-ARS?s Scientific Manuscript database

    A genetic map of peanut (Arachis hypogaea L.) with 426 SSR markers was constructed using a population of 162 recombinant inbred lines (RILs) from a cross between ‘Tifrunner’ and ‘GT-C20’. Linkage groups (LGs) were assigned to chromosomes using published peanut reference maps. The total length of the...

  12. An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803

    PubMed Central

    Mitschke, Jan; Georg, Jens; Scholz, Ingeborg; Sharma, Cynthia M.; Dienst, Dennis; Bantscheff, Jens; Voß, Björn; Steglich, Claudia; Wilde, Annegret; Vogel, Jörg; Hess, Wolfgang R.

    2011-01-01

    There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ∼64% of all TSS give rise to antisense or ncRNAs in a genome that is to 87% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5′ annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research. PMID:21245330

  13. Mapping of a blood pressure QTL on chromosome 17 in American Indians of the strong heart family study.

    PubMed

    Franceschini, Nora; Tao, Ran; Liu, Lan; Rutherford, Sue; Haack, Karin; Almasy, Laura; Göring, Harald Hh; Laston, Sandra; Lee, Elisa T; Best, Lyle G; Fabsitz, Richard; Cole, Shelley A; North, Kari E

    2014-11-11

    Blood pressure (BP) is a complex trait, with a heritability of 30 to 40%. Several genome wide associated BP loci explain only a small fraction of the phenotypic variation. Family studies can provide an important tool for gene discovery by utilizing trait and genetic transmission information among relative-pairs. We have previously described a quantitative trait locus at chromosome 17q25.3 influencing systolic BP in American Indians of the Strong Heart Family Study (SHFS). This locus has been reported to associate with variation in BP traits in family studies of Europeans, African Americans and Hispanics. To follow-up persuasive linkage findings at this locus, we performed comprehensive genotyping in the 1-LOD unit support interval region surrounding this QTL using a multi-step strategy. We first genotyped 1,334 single nucleotide polymorphisms (SNPs) in 928 individuals from families that showed evidence of linkage for BP. We then genotyped a second panel of 306 SNPs in all SHFS participants (N = 3,807) for genes that displayed the strongest evidence of association in the region, and, in a third step, included additional genotyping to better cover the genes of interest and to interrogate plausible candidate genes in the region. Three genes had multiple SNPs marginally associated with systolic BP (TBC1D16, HRNBP3 and AZI1). In BQTN analysis, used to estimate the posterior probability that any variant in each gene had an effect on the phenotype, AZI1 showed the most prominent findings (posterior probability of 0.66). Importantly, upon correction for multiple testing, none of our study findings could be distinguished from chance. Our findings demonstrate the difficulty of follow-up studies of linkage studies for complex traits, particularly in the context of low powered studies and rare variants underlying linkage peaks.

  14. Metabolomic Quantitative Trait Loci (mQTL) Mapping Implicates the Ubiquitin Proteasome System in Cardiovascular Disease Pathogenesis

    PubMed Central

    Kraus, William E.; Muoio, Deborah M.; Stevens, Robert; Craig, Damian; Bain, James R.; Grass, Elizabeth; Haynes, Carol; Kwee, Lydia; Qin, Xuejun; Slentz, Dorothy H.; Krupp, Deidre; Muehlbauer, Michael; Hauser, Elizabeth R.; Gregory, Simon G.; Newgard, Christopher B.; Shah, Svati H.

    2015-01-01

    Levels of certain circulating short-chain dicarboxylacylcarnitine (SCDA), long-chain dicarboxylacylcarnitine (LCDA) and medium chain acylcarnitine (MCA) metabolites are heritable and predict cardiovascular disease (CVD) events. Little is known about the biological pathways that influence levels of most of these metabolites. Here, we analyzed genetics, epigenetics, and transcriptomics with metabolomics in samples from a large CVD cohort to identify novel genetic markers for CVD and to better understand the role of metabolites in CVD pathogenesis. Using genomewide association in the CATHGEN cohort (N = 1490), we observed associations of several metabolites with genetic loci. Our strongest findings were for SCDA metabolite levels with variants in genes that regulate components of endoplasmic reticulum (ER) stress (USP3, HERC1, STIM1, SEL1L, FBXO25, SUGT1) These findings were validated in a second cohort of CATHGEN subjects (N = 2022, combined p = 8.4x10-6–2.3x10-10). Importantly, variants in these genes independently predicted CVD events. Association of genomewide methylation profiles with SCDA metabolites identified two ER stress genes as differentially methylated (BRSK2 and HOOK2). Expression quantitative trait loci (eQTL) pathway analyses driven by gene variants and SCDA metabolites corroborated perturbations in ER stress and highlighted the ubiquitin proteasome system (UPS) arm. Moreover, culture of human kidney cells in the presence of levels of fatty acids found in individuals with cardiometabolic disease, induced accumulation of SCDA metabolites in parallel with increases in the ER stress marker BiP. Thus, our integrative strategy implicates the UPS arm of the ER stress pathway in CVD pathogenesis, and identifies novel genetic loci associated with CVD event risk. PMID:26540294

  15. Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses

    PubMed Central

    2014-01-01

    Background Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and strawberry. Early studies on lactone biosynthesis suggest that several enzymatic pathways could be responsible for the diversity of lactones, but detailed information on them remained elusive. In this study, we have integrated genetic mapping and genome-wide transcriptome analysis to investigate the molecular basis of natural variation in γ-decalactone content in strawberry fruit. Results As a result, the fatty acid desaturase FaFAD1 was identified as the gene underlying the locus at LGIII-2 that controls γ-decalactone production in ripening fruit. The FaFAD1 gene is specifically expressed in ripe fruits and its expression fully correlates with the presence of γ-decalactone in all 95 individuals of the mapping population. In addition, we show that the level of expression of FaFAH1, with similarity to cytochrome p450 hydroxylases, significantly correlates with the content of γ-decalactone in the mapping population. The analysis of expression quantitative trait loci (eQTL) suggests that the product of this gene also has a regulatory role in the biosynthetic pathway of lactones. Conclusions Altogether, this study provides mechanistic information of how the production of γ-decalactone is naturally controlled in strawberry, and proposes enzymatic activities necessary for the formation of this VOC in plants. PMID:24742100

  16. Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses.

    PubMed

    Sánchez-Sevilla, José F; Cruz-Rus, Eduardo; Valpuesta, Victoriano; Botella, Miguel A; Amaya, Iraida

    2014-04-17

    Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and strawberry. Early studies on lactone biosynthesis suggest that several enzymatic pathways could be responsible for the diversity of lactones, but detailed information on them remained elusive. In this study, we have integrated genetic mapping and genome-wide transcriptome analysis to investigate the molecular basis of natural variation in γ-decalactone content in strawberry fruit. As a result, the fatty acid desaturase FaFAD1 was identified as the gene underlying the locus at LGIII-2 that controls γ-decalactone production in ripening fruit. The FaFAD1 gene is specifically expressed in ripe fruits and its expression fully correlates with the presence of γ-decalactone in all 95 individuals of the mapping population. In addition, we show that the level of expression of FaFAH1, with similarity to cytochrome p450 hydroxylases, significantly correlates with the content of γ-decalactone in the mapping population. The analysis of expression quantitative trait loci (eQTL) suggests that the product of this gene also has a regulatory role in the biosynthetic pathway of lactones. Altogether, this study provides mechanistic information of how the production of γ-decalactone is naturally controlled in strawberry, and proposes enzymatic activities necessary for the formation of this VOC in plants.

  17. Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts.

    PubMed

    Belheouane, Meriem; Gupta, Yask; Künzel, Sven; Ibrahim, Saleh; Baines, John F

    2017-06-06

    Recent studies highlight the utility of quantitative trait locus (QTL) mapping for determining the contribution of host genetics to interindividual variation in the microbiota. We previously demonstrated that similar to the gut microbiota, abundances of bacterial taxa in the skin are significantly influenced by host genetic variation. In this study, we analyzed the skin microbiota of mice from the 15th generation of an advanced intercross line using a novel approach of extending bacterial trait mapping to both the 16S rRNA gene copy (DNA) and transcript (RNA) levels, which reflect relative bacterial cell number and activity, respectively. Remarkably, the combination of highly recombined individuals and 53,203 informative SNPs allowed the identification of genomic intervals as small as <0.1 megabases containing single genes. Furthermore, the inclusion of 16S rRNA transcript-level mapping dramatically increased the number of significant associations detected, with five versus 21 significant SNP-bacterial trait associations based on DNA- compared to RNA-level profiling, respectively. Importantly, the genomic intervals identified contain many genes involved in skin inflammation and cancer and are further supported by the bacterial traits they influence, which in some cases have known genotoxic or probiotic capabilities. These results indicate that profiling based on the relative activity levels of bacterial community members greatly enhances the capability of detecting interactions between the host and its associated microbes. Finally, the identification of several genes involved in skin cancer suggests that similar to colon carcinogenesis, the resident microbiota may play a role in skin cancer susceptibility and its potential prevention and/or treatment.

  18. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution.

    PubMed

    Quraishi, Umar Masood; Abrouk, Michael; Murat, Florent; Pont, Caroline; Foucrier, Séverine; Desmaizieres, Gregory; Confolent, Carole; Rivière, Nathalie; Charmet, Gilles; Paux, Etienne; Murigneux, Alain; Guerreiro, Laurent; Lafarge, Stéphane; Le Gouis, Jacques; Feuillet, Catherine; Salse, Jerome

    2011-03-01

    Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cere