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1

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

ERIC Educational Resources Information Center

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…

Donthu, Ravikiran

2009-01-01

2

An entropy-based index for fine-scale mapping of QTL.  

PubMed

By comparing the entropy and conditional entropy in a marker, an entropy-based index for fine-scale linkage-disequilibrium gene mapping is presented using high-density marker maps in extreme samples for quantitative trait. The entropy-based index is the function of LD between the marker and the trait locus and does not depend on marker allele frequencies across the loci. It is parallel to Hardy-Weinberg disequilibrium (HWD) measure for QTL fine mapping, but its power of fine mapping QTL is higher than that of HWD measure. Through simulations, the fine mapping performance of this entropy-based index is investigated extensively under various genetic parameters. The results show that the indices presented here are both robust and powerful. PMID:17498636

Xiang, Yang; Li, Yumei; Liu, Zaiming; Sun, Zhenqiu

2007-04-01

3

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

PubMed Central

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 improvement of pork products. Furthermore, additional resources have been generated for the targeted investigation of other putative QTL on SSC2q, which may lead to further advancements in pork quality. PMID:17935628

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

2007-01-01

4

Robust indices of Hardy-Weinberg disequilibrium for QTL fine mapping.  

PubMed

Hardy-Weinberg disequilibrium (HWD) measures have been proposed using dense markers to fine map a quantitative trait locus (QTL) to regions < approximately 1 cM. Earlier HWD measures may introduce bias in the fine mapping because they are dependent on marker allele frequencies across loci. Hence, HWD indices that do not depend on marker allele frequencies are desired for fine mapping. Based on our earlier work, here we present four new HWD indices that do not depend on marker allele frequencies. Two are for use when marker allele frequencies in a study population are known, and two are for use when marker allele frequencies in a study population are not known and are only known in the extreme samples. The new measures are a function of the genetic distance between the marker locus and a QTL. Through simulations, we investigated and compared the fine mapping performance of the new HWD measures with that of the earlier ones. Our results show that when marker allele frequencies vary across loci, the new measures presented here are more robust and powerful. PMID:15031618

Deng, Hong-Wen; Li, Yu-Mei; Li, Miao-Xin; Liu, Peng-Yuan

2003-01-01

5

Fine-mapping of muscle weight QTL in LG/J and SM/J intercrosses1 Lionikas A1  

E-print Network

). Because of the world's growing geriatric population, age-related loss of strength and55 muscle massFine-mapping of muscle weight QTL in LG/J and SM/J intercrosses1 2 Lionikas A1 , Cheng R3 , Lim JE5 and Cancer Biology, Duke University Medical Center, Durham, NC 2770813 14 15 16 Running title: Muscle weight

Gilad, Yoav

6

Fine-Mapping and Selective Sweep Analysis of QTL for Cold Tolerance in Drosophila melanogaster  

PubMed Central

There is a growing interest in investigating the relationship between genes with signatures of natural selection and genes identified in QTL mapping studies using combined population and quantitative genetics approaches. We dissected an X-linked interval of 6.2 Mb, which contains two QTL underlying variation in chill coma recovery time (CCRT) in Drosophila melanogaster from temperate (European) and tropical (African) regions. This resulted in two relatively small regions of 131 kb and 124 kb. The latter one co-localizes with a very strong selective sweep in the European population. We examined the genes within and near the sweep region individually using gene expression analysis and P-element insertion lines. Of the genes overlapping with the sweep, none appears to be related to CCRT. However, we have identified a new candidate gene of CCRT, brinker, which is located just outside the sweep region and is inducible by cold stress. We discuss these results in light of recent population genetics theories on quantitative traits. PMID:24970882

Wilches, Ricardo; Voigt, Susanne; Duchen, Pablo; Laurent, Stefan; Stephan, Wolfgang

2014-01-01

7

FINE MAPPING OF A MALTING-QUALITY QTL COMPLEX NEAR THE CHROMOSOME 4H S TELOMERE IN BARLEY  

Technology Transfer Automated Retrieval System (TEKTRAN)

Malting quality has long been an active objective in barley breeding programs. However it is difficult for breeders to manipulate malting quality traits because of inheritance complexity and difficulty in evaluation of these quantitative traits. Quantitative trait Locus (QTL) mapping provides breede...

8

Fine mapping QMi - C11 a major QTL controlling root-knot nematodes resistance in Upland cotton  

Microsoft Academic Search

The identification and utilization of a high-level of host plant resistance is the most effective and economical approach\\u000a to control root-knot nematode (Meloidogyne incognita). In an earlier study, we identified a major quantitative trait locus (QTL) for resistance to root-knot nematode in the M-120\\u000a RNR Upland cotton line (Gossypium hirsutum L.) of the Auburn 623 RNR source. The QTL is

Xinlian Shen; Yajun He; Edward L. Lubbers; Richard F. Davis; Robert L. Nichols; Peng W. Chee

2010-01-01

9

QTL mapping of resistance to gray leaf spot in maize.  

PubMed

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. PMID:22903692

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

2012-12-01

10

A Grid Portal Implementation for Genetic Mapping of Multiple QTL  

E-print Network

QTL mapping study, genetic data (genotype data) from an experimental population is used as inputA Grid Portal Implementation for Genetic Mapping of Multiple QTL Salman Toor1 , Mahen Jayawardena1 words: QTL analysis, grid computing 1 Genetic mapping of QTL Most traits of medical or economic

Flener, Pierre

11

Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map  

Microsoft Academic Search

A simulation study was carried out on a backcross population in order to determine the effect of marker spacing, gene effect and population size on the power of marker-quantitative trait loci (QTL) linkage experiments and on the standard error of maximum likelihood estimates (MLE) of QTL gene effect and map location. Power of detecting a QTL was virtually the same

A. Darvasi; A. Weinreb; V. Minke; M. Soller; J. I. Weller

1993-01-01

12

qtl.outbred: Interfacing outbred line cross data with the R\\/qtl mapping software  

Microsoft Academic Search

Background  \\u000a qtl.outbred is an extendible interface in the statistical environment, R, for combining quantitative trait loci (QTL) mapping tools.\\u000a It is built as an umbrella package that enables outbred genotype probabilities to be calculated and\\/or imported into the software\\u000a package R\\/qtl.\\u000a \\u000a \\u000a \\u000a \\u000a Findings  Using qtl.outbred, the genotype probabilities from outbred line cross data can be calculated by interfacing with a new and

Ronald M Nelson; Xia Shen; Örjan Carlborg

2011-01-01

13

Linkage, QTL, Mapping Populations and  

E-print Network

· Doubled monoploid cross ­ Segregation in one parent - testcross #12;Mapped disease resistance genes) ·10,000+ AFLP markers (from 381 primer combinations) · ordered on 136 progeny of diploid RH x SH cross heterotic pools of elite germplasm. Introgression of special trait (e.g. disease resistance) from exotic

Douches, David S.

14

Mapping dynamic QTL for plant height in triticale  

PubMed Central

Background Plant height is a prime example of a dynamic trait that changes constantly throughout adult development. In this study we utilised a large triticale mapping population, comprising 647 doubled haploid lines derived from 4 families, to phenotype for plant height by a precision phenotyping platform at multiple time points. Results Using multiple-line cross QTL mapping we identified main effect and epistatic QTL for plant height for each of the time points. Interestingly, some QTL were detected at all time points whereas others were specific to particular developmental stages. Furthermore, the contribution of the QTL to the genotypic variance of plant height also varied with time as exemplified by a major QTL identified on chromosome 6A. Conclusions Taken together, our results in the small grain cereal triticale reveal the importance of considering temporal genetic patterns in the regulation of complex traits such as plant height. PMID:24885543

2014-01-01

15

Epigenetic QTL Mapping in Brassica napus  

PubMed Central

There is increasing evidence that epigenetic marks such as DNA methylation contribute to phenotypic variation by regulating gene transcription, developmental plasticity, and interactions with the environment. However, relatively little is known about the relationship between the stability and distribution of DNA methylation within chromosomes and the ability to detect trait loci. Plant genomes have a distinct range of target sites and more extensive DNA methylation than animals. We analyzed the stability and distribution of epialleles within the complex genome of the oilseed crop plant Brassica napus. For methylation sensitive AFLP (MSAP) and retrotransposon (RT) epimarkers, we found a high degree of stability, with 90% of mapped markers retaining their allelic pattern in contrasting environments and developmental stages. Moreover, for two distinct parental lines 97% of epialleles were transmitted through five meioses and segregated in a mapping population. For the first time we have established the genetic position for 17 of the 19 centromeres within this amphidiploid species. Epiloci and genetic loci were distributed within distinct clusters, indicating differential detection of recombination events. This enabled us to identify additional significant QTL associated with seven important agronomic traits in the centromeric regions of five linkage groups. PMID:21890742

Long, Yan; Xia, Wei; Li, Ruiyuan; Wang, Jing; Shao, Mingqin; Feng, Ji; King, Graham J.; Meng, Jinling

2011-01-01

16

An Introgression Line Population of Lycopersicon pennellii in the Cultivated Tomato Enables the Identification and Fine Mapping of Yield-Associated QTL  

Microsoft Academic Search

Methodologies for mapping of genes underlying quantitative traits have advanced considerably but have not been accompanied by a parallel development of new population structures. We present a novel population consisting of 50 introgression lines (ILs) originating from a cross between the green-fruited species Lycopersicon pennellii and the cultivated tomato (cv M82). Each of the lines contains a single homozygous restriction

Yuval Eshed; Dani Zamir

17

A large QTL for fear and anxiety mapped using an F2 cross can be dissected into multiple smaller QTLs  

PubMed Central

Using chromosome substitution strains (CSS), we previously identified a large quantitative trait locus (QTL) for conditioned fear (CF) on mouse chromosome 10. Here, we used an F2 cross between CSS-10 and C57BL/6J (B6) to localize that QTL to distal chromosome 10. That QTL accounted for all of the difference between CSS-10 and B6. We then produced congenic strains to fine-map that interval. We identified two congenic strains that captured some or all of the QTL. The larger congenic strain (Line 1; 122.387121 – 129.068 Mb; build 37) appeared to account for all of the difference between CSS-10 and B6. The smaller congenic strain (Line 2; 127.277–129.068 Mb) was intermediate between CSS-10 and B6. We used haplotype mapping followed by qPCR to identify one gene that was differentially expressed in both lines relative to B6 (Rnf41) and one that was differentially expressed between only Line 1 and B6 (Shmt2). These cis-eQTLs may cause the behavioral QTLs; however, further studies are required to validate these candidate genes. More generally, our observation that a large QTL mapped using CSS and F2 crosses can be dissected into multiple smaller QTLs demonstrates a weaknesses of two-stage approaches that seek to use coarse mapping to identify large regions followed by fine-mapping. Indeed, additional dissection of these congenic strains might result in further subdivision of these QTL regions. Despite these limitations we have successfully fine mapped two QTLs to small regions and identified putative candidate genes, demonstrating that the congenic approach can be effective for fine mapping QTLs. PMID:23876074

Parker, Clarissa C.; Sokoloff, Greta; Leung, Emily; Kirkpatrick, Stacey L.; Palmer, Abraham A.

2013-01-01

18

Approximate thresholds of interval mapping tests for QTL detection.  

PubMed

A general method is proposed for calculating approximate thresholds of interval mapping tests for quantitative trait loci (QTL) detection. Simulation results show that this method, when applied to backcross and F2 populations, gives good approximations and is useful for any situation. Programs which calculate these thresholds for backcross, recombinant inbreds and F2 for any given level and any chromosome with any given distribution of codominant markers were written in Fortran 77 and are available under request. The approach presented here could be used to obtain, after suitable calculations, thresholds for most segregating populations used in QTL mapping experiments. PMID:8001790

Rebaï, A; Goffinet, B; Mangin, B

1994-09-01

19

Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara.  

PubMed

Advanced backcross QTL (AB-QTL) analysis was carried out in two Oryza nivara-derived BC2F2 populations. For nine traits, we identified 28 QTL in population 1 and 26 QTL in population 2. The two most significant yield-enhancing QTL, yldp9.1 and yldp2.1 showed an additive effect of 16 and 7 g per plant in population 1, while yld2.1 and yld11.1 showed an additive effect of 11 and 10 g per plant in population 2. At least one O. nivara-derived QTL with a phenotypic variance of >15% was detected for seven traits in population 1 and three traits in population 2. The O. nivara-derived QTL ph1.1, nt12.1, nsp1.1, nfg1.1, bm11.1, yld2.1 and yld11.1 were conserved at the same chromosomal locations in both populations. Two major QTL clusters were detected at the marker intervals RM488-RM431 and RM6-RM535 on chromosomes 1 and 2, respectively. The colocation of O. nivara-derived yield QTL with yield meta-QTL on chromosomes 1, 2 and 9 indicates their accuracy and consistency. The major-effect QTL reported in this study are useful for marker-assisted breeding and are also suitable for further fine mapping and candidate gene identification. PMID:25572223

Swamy, B P Mallikarjuna; Kaladhar, K; Reddy, G Ashok; Viraktamath, B C; Sarla, N

2014-12-01

20

Genetic Analysis of Genome-Wide Transcriptional Regulation through eQTL Mapping in Soy  

Technology Transfer Automated Retrieval System (TEKTRAN)

Variation in gene transcript accumulation levels can be measured to map underlying expression Quantitative Trait Loci (eQTL). Coincident genetic locations of eQTL and phenotypic QTL provide the basis for further investigation of the molecular mechanisms involved. Genetic analysis of expression trait...

21

Genetic analysis of genome-wide transcriptional regulation through eQTL mapping in soybean  

Technology Transfer Automated Retrieval System (TEKTRAN)

Gene expression Quantitative Trait Loci (eQTL) mapping is a powerful tool for identifying the genetic basis of gene expression variation. Coincident genetic locations of eQTL and phenotypic QTL provide the basis for further investigation of the molecular mechanisms involved. Genetic analysis of expr...

22

Development and characterization of 96 microsatellite markers suitable for QTL mapping and accession control in an Arabidopsis core collection  

PubMed Central

Background To identify plant genes involved in various key traits, QTL mapping is a powerful approach. This approach is based on the use of mapped molecular markers to identify genomic regions controlling quantitative traits followed by a fine mapping and eventually positional cloning of candidate genes. Mapping technologies using SNP markers are still rather expensive and not feasible in every laboratory. In contrast, microsatellite (also called SSR for Simple Sequence Repeat) markers are technologically less demanding and less costly for any laboratory interested in genetic mapping. Results In this study, we present the development and the characterization of a panel of 96 highly polymorphic SSR markers along the Arabidopsis thaliana genome allowing QTL mapping among accessions of the Versailles 24 core collection that covers a high percentage of the A. thaliana genetic diversity. These markers can be used for any QTL mapping analysis involving any of these accessions. We optimized the use of these markers in order to reveal polymorphism using standard PCR conditions and agarose gel electrophoresis. In addition, we showed that the use of only three of these markers allows differentiating all 24 accessions which makes this set of markers a powerful tool to control accession identity or any cross between any of these accessions. Conclusion The set of SSR markers developed in this study provides a simple and efficient tool for any laboratory focusing on QTL mapping in A. thaliana and a simple means to control seed stock or crosses between accessions. PMID:24447639

2014-01-01

23

Construction of genetic linkage map and mapping of QTL for seed color in Brassica rapa.  

PubMed

A genetic linkage map of Brassica rapa L. was constructed using recombinant inbred lines (RILs) derived from a cross between yellow-seeded cultivar Sampad and a yellowish brown seeded inbred line 3-0026.027. The RILs were evaluated for seed color under three conditions: field plot, greenhouse, and controlled growth chambers. Variation for seed color in the RILs ranged from yellow, like yellow sarson, to dark brown/black even though neither parent had shown brown/black colored seeds. One major QTL (SCA9-2) and one minor QTL (SCA9-1) on linkage group (LG) A9 and two minor QTL (SCA3-1, SCA5-1) on LG A3 and LG A5, respectively, were detected. These collectively explained about 67% of the total phenotypic variance. SCA9-2 mapped in the middle of LG A9, explained about 55% phenotypic variance, and consistently expressed in all environments. The second QTL on LG A9 was ~70 cM away from SCA9-2, suggesting that independent assortment of these QTLs is possible. A digenic epistatic interaction was found between the two main effect QTL on LG A9; and the epistasis × environment interaction was nonsignificant, suggesting stability of the interaction across the environments. The QTL effect on LG A9 was validated using simple sequence repeat (SSR) markers from the two QTL regions of this LG on a B(1)S(1) population (F(1) backcrossed to Sampad followed by self-pollination) segregating for brown and yellow seed color, and on their self-pollinated progenies (B(1)S(2)). The SSR markers from the QTL region SCA9-2 showed a stronger linkage association with seed color as compared with the marker from SCA9-1. This suggests that the QTL SCA9-2 is the major determinant of seed color in the A genome of B. rapa. PMID:23231600

Kebede, Berisso; Cheema, Kuljit; Greenshields, David L; Li, Changxi; Selvaraj, Gopalan; Rahman, Habibur

2012-12-01

24

Body composition and gene expression QTL mapping in mice reveals imprinting and interaction effects  

PubMed Central

Background Shifts in body composition, such as accumulation of body fat, can be a symptom of many chronic human diseases; hence, efforts have been made to investigate the genetic mechanisms that underlie body composition. For example, a few quantitative trait loci (QTL) have been discovered using genome-wide association studies, which will eventually lead to the discovery of causal mutations that are associated with tissue traits. Although some body composition QTL have been identified in mice, limited research has been focused on the imprinting and interaction effects that are involved in these traits. Previously, we found that Myostatin genotype, reciprocal cross, and sex interacted with numerous chromosomal regions to affect growth traits. Results Here, we report on the identification of muscle, adipose, and morphometric phenotypic QTL (pQTL), translation and transcription QTL (tQTL) and expression QTL (eQTL) by applying a QTL model with additive, dominance, imprinting, and interaction effects. Using an F2 population of 1000 mice derived from the Myostatin-null C57BL/6 and M16i mouse lines, six imprinted pQTL were discovered on chromosomes 6, 9, 10, 11, and 18. We also identified two IGF1 and two Atp2a2 eQTL, which could be important trans-regulatory elements. pQTL, tQTL and eQTL that interacted with Myostatin, reciprocal cross, and sex were detected as well. Combining with the additive and dominance effect, these variants accounted for a large amount of phenotypic variation in this study. Conclusions Our study indicates that both imprinting and interaction effects are important components of the genetic model of body composition traits. Furthermore, the integration of eQTL and traditional QTL mapping may help to explain more phenotypic variation than either alone, thereby uncovering more molecular details of how tissue traits are regulated. PMID:24165562

2013-01-01

25

FastMap: Fast eQTL mapping in homozygous populations  

PubMed Central

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

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

2009-01-01

26

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

PubMed

Since the dawn of wheat cytogenetics, chromosome 3B has been known to harbor a gene(s) that, when removed, causes chromosome desynapsis and gametic sterility. The lack of natural genetic diversity for this gene(s) has prevented any attempt to fine map and further characterize it. Here, gamma radiation treatment was used to create artificial diversity for this locus. A total of 696 radiation hybrid lines were genotyped with a custom mini array of 140 DArT markers, selected to evenly span the whole 3B chromosome. The resulting map spanned 2,852 centi Ray with a calculated resolution of 0.384 Mb. Phenotyping for the occurrence of meiotic desynapsis was conducted by measuring the level of gametic sterility as seeds produced per spikelet and pollen viability at booting. Composite interval mapping revealed a single QTL with LOD of 16.2 and r (2) of 25.6 % between markers wmc326 and wPt-8983 on the long arm of chromosome 3B. By independent analysis, the location of the QTL was confirmed to be within the deletion bin 3BL7-0.63-1.00 and to correspond to a single gene located ~1.4 Mb away from wPt-8983. The meiotic behavior of lines lacking this gene was characterized cytogenetically to reveal striking similarities with mutants for the dy locus, located on the syntenic chromosome 3 of maize. This represents the first example to date of employing radiation hybrids for QTL analysis. The success achieved by this approach provides an ideal starting point for the final cloning of this interesting gene involved in meiosis of cereals. PMID:23715938

Bassi, F M; Kumar, A; Zhang, Q; Paux, E; Huttner, E; Kilian, A; Dizon, R; Feuillet, C; Xu, S S; Kianian, S F

2013-08-01

27

Mapping of QTL for Body Conformation and Behavior in Cattle  

Microsoft Academic Search

Genome scans for quantitative trait loci (QTL) in farm animals have concentrated on primary production and health traits, and information on QTL for other important traits is rare. We performed a whole genome scan in a granddaughter design to detect QTL affecting body conformation and behavior in dairy cattle. The analysis included 16 paternal half-sib families of the Holstein breed

S. Hiendleder; H. THOMSEN; N. REINSCH; J. BENNEWITZ; B. LEYHE-HORN; C. LOOFT; N. XU; I. MEDJUGORAC; I. RUSS; C. KUHN; G. A. BROCKMANN; J. BLUMEL; B. BRENIG; F. REINHARDT; R. REENTS; G. AVERDUNK; M. SCHWERIN; E. KALM; G. ERHARDT

2003-01-01

28

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

PubMed

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

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

29

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

PubMed Central

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

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

30

QTL Map Meets Population Genomics: An Application to Rice  

PubMed Central

Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance. PMID:24376738

Takuno, Shohei; Yoshida, Kentaro; Sugino, Ryuichi P.; Kosugi, Shunichi; Natsume, Satoshi; Mitsuoka, Chikako; Uemura, Aiko; Takagi, Hiroki; Abe, Akira; Ishii, Takashige; Terauchi, Ryohei; Innan, Hideki

2013-01-01

31

QTL map meets population genomics: an application to rice.  

PubMed

Genes involved in the transition from wild to cultivated crop species should be of great agronomic importance. Population genomic approaches utilizing genome resequencing data have been recently applied for this purpose, although it only reports a large list of candidate genes with no biological information. Here, by resequencing more than 30 genomes altogether of wild rice Oryza rufipogon and cultivated rice O. sativa, we identified a number of regions with clear footprints of selection during the domestication process. We then focused on identifying candidate domestication genes in these regions by utilizing the wealth of QTL information in rice. We were able to identify a number of interesting candidates such as transcription factors that should control key domestication traits such as shattering, awn length, and seed dormancy. Other candidates include those that might have been related to the improvement of grain quality and those that might have been involved in the local adaptation to dry conditions and colder environments. Our study shows that population genomic approaches and QTL mapping information can be used together to identify genes that might be of agronomic importance. PMID:24376738

Fawcett, Jeffrey A; Kado, Tomoyuki; Sasaki, Eriko; Takuno, Shohei; Yoshida, Kentaro; Sugino, Ryuichi P; Kosugi, Shunichi; Natsume, Satoshi; Mitsuoka, Chikako; Uemura, Aiko; Takagi, Hiroki; Abe, Akira; Ishii, Takashige; Terauchi, Ryohei; Innan, Hideki

2013-01-01

32

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

PubMed Central

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 seven, with QTL in the current study overlapping with two of these. Two QTL from this study did not overlap with previously reported QTL. PMID:24885661

2014-01-01

33

Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene  

PubMed Central

Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian F2 resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this F2 population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the F2 population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. PMID:22420340

2012-01-01

34

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

PubMed

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

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

2014-12-01

35

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

PubMed Central

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

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

2014-01-01

36

High-Resolution Mapping of the Blood Pressure QTL on Chromosome 7 Using Dahl Rat Congenic Strains  

E-print Network

High-Resolution Mapping of the Blood Pressure QTL on Chromosome 7 Using Dahl Rat Congenic Strains-sensitive (S) and salt-resistant (R) rats that a blood pressure quan- titative trait locus (QTL) was present-hydroxy- 11-deoxy corticosterone, is very likely to account for the blood pressure QTL on chromosome 7

Abraham, Nader G.

37

QTL Mapping of Flowering and Fruiting Traits in Olive  

PubMed Central

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. PMID:23690957

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

38

A New Simple Method for Improving QTL Mapping Under Selective Genotyping.  

PubMed

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 genotyping and that using smaller genotyping proportions has difficulties doing so. The R code of our proposed method is available on http://www.stat.sinica.edu.tw/chkao/. PMID:25245793

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

2014-12-01

39

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

PubMed

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. PMID:22491896

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

2012-08-01

40

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

PubMed

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. PMID:25039860

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

2014-09-01

41

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

PubMed Central

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

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

2013-01-01

42

Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep.  

PubMed

An (Awassi x Merino) x Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL) for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine ovine lactation curve characteristics. Derived milk traits for milk, fat, protein and lactose yield, as well as percentage composition and somatic cell score were used for single and two-QTL approaches using maximum likelihood estimation and regression analysis. A total of 15 significant (P < 0.01) and additional 25 suggestive (P < 0.05) QTL were detected across both single QTL methods and all traits. In preparation of a meta-analysis, all QTL results were compared with a meta-assembly of QTL for milk production traits in dairy ewes from various public domain sources and can be found on the ReproGen ovine gbrowser http://crcidp.vetsci.usyd.edu.au/cgi-bin/gbrowse/oaries_genome/. Many of the QTL for milk production traits have been reported on chromosomes 1, 3, 6, 16 and 20. Those on chromosomes 3 and 20 are in strong agreement with the results reported here. In addition, novel QTL were found on chromosomes 7, 8, 9, 14, 22 and 24. In a cross-species comparison, we extended the meta-assembly by comparing QTL regions of sheep and cattle, which provided strong evidence for synteny conservation of QTL regions for milk, fat, protein and somatic cell score data between cattle and sheep. PMID:19849860

Raadsma, Herman W; Jonas, Elisabeth; McGill, David; Hobbs, Matthew; Lam, Mary K; Thomson, Peter C

2009-01-01

43

Consensus mapping of major resistance genes and independent QTL for quantitative resistance to sunflower downy mildew.  

PubMed

Major gene resistance to sunflower downy mildew (Plasmopara halstedii) races 304 and 314 was found to segregate independently from the resistance to races 334, 307 and 304 determined by the gene Pl2, already positioned on Linkage Group (LG) 8 of sunflower molecular maps. Using a consensus SSR-SNP map constructed from the INEDI RIL population and a new RIL population FU × PAZ2, the positions of Pl2 and Pl5 were confirmed and the new gene, denoted Pl21, was mapped on LG13, at 8 cM from Pl5. The two RIL populations were observed for their quantitative resistance to downy mildew in the field and both indicated the existence of a QTL on LG8 at 20-40 cM from the major resistance gene cluster. In addition, for the INEDI population, a strong QTL on LG10, reported previously, was confirmed and a third QTL was mapped on LG7. A growth chamber test methodology, significantly correlated with field results, also revealed the major QTL on LG10, explaining 65 % of variability. This QTL mapped in the same area as a gene involved in stomatal opening and root growth, which may be suggested as a possible candidate to explain the control of this character. These results indicate that it should be possible to combine major genes and other resistance mechanisms, a strategy that could help to improve durability of sunflower resistance to downy mildew. PMID:22576236

Vincourt, Patrick; As-Sadi, Falah; Bordat, Amandine; Langlade, Nicolas B; Gouzy, Jerome; Pouilly, Nicolas; Lippi, Yannick; Serre, Frédéric; Godiard, Laurence; Tourvieille de Labrouhe, Denis; Vear, Felicity

2012-09-01

44

Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle  

PubMed Central

Background Many studies have found segregating quantitative trait loci (QTL) for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the confidence interval for QTL location by linkage analysis spans tens of map units, or hundreds of genes. Combining mapping and arraying has been suggested as an approach to identify candidate genes. Thus, gene expression analysis in the mammary gland of genes positioned in the confidence interval of the QTL can bridge the gap between fine mapping and quantitative trait nucleotide (QTN) determination. Results We hybridized Affymetrix microarray (MG-U74v2), containing 12,488 murine probes, with RNA derived from mammary gland of virgin, pregnant, lactating and involuting C57BL/6J mice in a total of nine biological replicates. We combined microarray data from two additional studies that used the same design in mice with a total of 75 biological replicates. The same filtering and normalization was applied to each microarray data using GeneSpring software. Analysis of variance identified 249 differentially expressed probe sets common to the three experiments along the four developmental stages of puberty, pregnancy, lactation and involution. 212 genes were assigned to their bovine map positions through comparative mapping, and thus form a list of candidate genes for previously identified QTLs for milk production traits. A total of 82 of the genes showed mammary gland-specific expression with at least 3-fold expression over the median representing all tissues tested in GeneAtlas. Conclusion This work presents a web tool for candidate genes for QTL (cgQTL) that allows navigation between the map of bovine milk production QTL, potential candidate genes and their level of expression in mammary gland arrays and in GeneAtlas. Three out of four confirmed genes that affect QTL in livestock (ABCG2, DGAT1, GDF8, IGF2) were over expressed in the target organ. Thus, cgQTL can be used to determine priority of candidate genes for QTN analysis based on differential expression in the target organ. PMID:17584498

Ron, Micha; Israeli, Galit; Seroussi, Eyal; Weller, Joel I; Gregg, Jeffrey P; Shani, Moshe; Medrano, Juan F

2007-01-01

45

Selective Advance for Accelerated Development of Recombinant Inbred QTL Mapping Populations  

Microsoft Academic Search

Quantitative trait locus (QTL) mapping resolu- tion of recombinant inbred lines (RILs) is limited by the amount of recombination they experience during development. Intercrossing during line development can be used to counter this disad- vantage but requires additional generations and is diffi cult in self-pollinated species. It is desir- able to improve mapping resolution for success of marker-assisted selection and

Prashanth Boddhireddy; Jean-Luc Jannink; James C. Nelson

2009-01-01

46

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

PubMed Central

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 ?g/g, highest 661 ?g/g) and ?3-fold variation in females (lowest 222 ?g/g, highest 658 ?g/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

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

47

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

PubMed

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. PMID:19917044

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

2010-04-01

48

QTL mapping reveals the genetic architecture of loci affecting pre- and post-zygotic isolating barriers in Louisiana Iris  

PubMed Central

Background Hybridization among Louisiana Irises has been well established and the genetic architecture of reproductive isolation is known to affect the potential for and the directionality of introgression between taxa. Here we use co-dominant markers to identify regions where QTL are located both within and between backcross maps to compare the genetic architecture of reproductive isolation and fitness traits across treatments and years. Results QTL mapping was used to elucidate the genetic architecture of reproductive isolation between Iris fulva and Iris brevicaulis. Homologous co-dominant EST-SSR markers scored in two backcross populations between I. fulva and I. brevicaulis were used to generate genetic linkage maps. These were used as the framework for mapping QTL associated with variation in 11 phenotypic traits likely responsible for reproductive isolation and fitness. QTL were dispersed throughout the genome, with the exception of one region of a single linkage group (LG) where QTL for flowering time, sterility, and fruit production clustered. In most cases, homologous QTL were not identified in both backcross populations, however, homologous QTL for flowering time, number of growth points per rhizome, number of nodes per inflorescence, and number of flowers per node were identified on several linkage groups. Conclusions Two different traits affecting reproductive isolation, flowering time and sterility, exhibit different genetic architectures, with numerous QTL across the Iris genome controlling flowering time and fewer, less distributed QTL affecting sterility. QTL for traits affecting fitness are largely distributed across the genome with occasional overlap, especially on LG 4, where several QTL increasing fitness and decreasing sterility cluster. Given the distribution and effect direction of QTL affecting reproductive isolation and fitness, we have predicted genomic regions where introgression may be more likely to occur (those regions associated with an increase in fitness and unlinked to loci controlling reproductive isolation) and those that are less likely to exhibit introgression (those regions linked to traits decreasing fitness and reproductive isolation). PMID:22702308

2012-01-01

49

Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep  

Microsoft Academic Search

An (Awassi × Merino) × Merino backcross family of 172 ewes was used to map quantitative trait loci (QTL) for different milk production traits on a framework map of 200 loci across all autosomes. From five previously proposed mathematical models describing lactation curves, the Wood model was considered the most appropriate due to its simplicity and its ability to determine

Herman W Raadsma; Elisabeth Jonas; David McGill; Matthew Hobbs; Mary K Lam; Peter C Thomson

2009-01-01

50

MAPPING AND QTL ANALYSIS OF PLANT ARCHITECTURE AND FRUIT YIELD IN MELON  

Technology Transfer Automated Retrieval System (TEKTRAN)

The inheritance of plant architecture and fruit yield in melon (Cucumis melo L.; 2n = 2x = 24) is poorly understood, and the mapping of quantitative trait loci (QTL) for yield-related traits has not been reported. Therefore, a set of 81 recombinant inbred lines (RIL) was developed from a cross betw...

51

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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...

52

In "silico" QTL mapping of maternal nurturing ability using the mouse divesity panel  

Technology Transfer Automated Retrieval System (TEKTRAN)

Significant variation exists for maternal nurturing ability in inbred mice. Although classical mapping approaches have identified quantitative trait loci (QTL) that may account for this variation, the underlying genes are unknown. In this study, lactation performance data among the mouse diversity p...

53

Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches  

Microsoft Academic Search

A new methodology based on mixed linear models was developed for mapping QTLs with digenic epistasis and QTL?environment (QE)\\u000a interactions. Reliable estimates of QTL main effects (additive and epistasis effects) can be obtained by the maximum-likelihood\\u000a estimation method, while QE interaction effects (additive?environment interaction and epistasis?environment interaction) can\\u000a be predicted by the-best-linear-unbiased-prediction (BLUP) method. Likelihood ratio and t statistics were

D. L. Wang; J. Zhu; Z. K. L. Li; A. H. Paterson

1999-01-01

54

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

PubMed Central

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

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

2014-01-01

55

Fine mapping of the FT1 locus for soybean flowering time using a residual heterozygous line derived from a recombinant inbred line  

Microsoft Academic Search

Fine-mapping of loci related to complex quantitative traits is essential for map-based cloning. A residual heterozygous line (RHL) of soybean ( Glycine max) derived from a recombinant inbred line (RIL) was used for fine-mapping FT1, which is a major quantitative trait locus (QTL) responsible for soybean flowering time. The residual heterozygous line RHL1-156 was selected from the RILs that were

Naoki Yamanaka; Satoshi Watanabe; Kyoko Toda; Masaki Hayashi; Hiroki Fuchigami; Ryoji Takahashi; Kyuya Harada

2005-01-01

56

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

PubMed

The agronomic importance of developing durably resistant cultivars has led to substantial research in the field of quantitative disease resistance (QDR) and, in particular, mapping quantitative trait loci (QTL) for disease resistance. The assessment of QDR is typically conducted by visual estimation of disease severity, which raises concern over the accuracy and precision of visual estimates. Although previous studies have examined the factors affecting the accuracy and precision of visual disease assessment in relation to the true value of disease severity, the impact of this variability on the identification of disease resistance QTL has not been assessed. In this study, the effects of rater variability and rating scales on mapping QTL for northern leaf blight resistance in maize were evaluated in a recombinant inbred line population grown under field conditions. The population of 191 lines was evaluated by 22 different raters using a direct percentage estimate, a 0-to-9 ordinal rating scale, or both. It was found that more experienced raters had higher precision and that using a direct percentage estimation of diseased leaf area produced higher precision than using an ordinal scale. QTL mapping was then conducted using the disease estimates from each rater using stepwise general linear model selection (GLM) and inclusive composite interval mapping (ICIM). For GLM, the same QTL were largely found across raters, though some QTL were only identified by a subset of raters. The magnitudes of estimated allele effects at identified QTL varied drastically, sometimes by as much as threefold. ICIM produced highly consistent results across raters and for the different rating scales in identifying the location of QTL. We conclude that, despite variability between raters, the identification of QTL was largely consistent among raters, particularly when using ICIM. However, care should be taken in estimating QTL allele effects, because this was highly variable and rater dependent. PMID:20955083

Poland, Jesse A; Nelson, Rebecca J

2011-02-01

57

Mapping a Quantitative Trait Locus (QTL) conferring pyrethroid resistance in the African malaria vector Anopheles funestus  

PubMed Central

Background Pyrethroid resistance in Anopheles funestus populations has led to an increase in malaria transmission in southern Africa. Resistance has been attributed to elevated activities of cytochrome P450s but the molecular basis underlying this metabolic resistance is unknown. Microsatellite and SNP markers were used to construct a linkage map and to detect a quantitative trait locus (QTL) associated with pyrethroid resistance in the FUMOZ-R strain of An. funestus from Mozambique. Results By genotyping 349 F2 individuals from 11 independent families, a single major QTL, rp1, at the telomeric end of chromosome 2R was identified. The rp1 QTL appears to present a major effect since it accounts for more than 60% of the variance in susceptibility to permethrin. This QTL has a strong additive genetic effect with respect to susceptibility. Candidate genes associated with pyrethroid resistance in other species were physically mapped to An. funestus polytene chromosomes. This showed that rp1 is genetically linked to a cluster of CYP6 cytochrome P450 genes located on division 9 of chromosome 2R and confirmed earlier reports that pyrethroid resistance in this strain is not associated with target site mutations (knockdown resistance). Conclusion We hypothesize that one or more of these CYP6 P450s clustered on chromosome 2R confers pyrethroid resistance in the FUMOZ-R strain of An. funestus. PMID:17261170

Wondji, Charles S; Morgan, John; Coetzee, Maureen; Hunt, Richard H; Steen, Keith; Black, William C; Hemingway, Janet; Ranson, Hilary

2007-01-01

58

Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar  

PubMed Central

Background The genetic control of important adaptive traits, such as bud set, is still poorly understood in most forest trees species. Poplar is an ideal model tree to study bud set because of its indeterminate shoot growth. Thus, a full-sib family derived from an intraspecific cross of P. nigra with 162 clonally replicated progeny was used to assess the phenotypic plasticity and genetic variation of bud set in two sites of contrasting environmental conditions. Results Six crucial phenological stages of bud set were scored. Night length appeared to be the most important signal triggering the onset of growth cessation. Nevertheless, the effect of other environmental factors, such as temperature, increased during the process. Moreover, a considerable role of genotype × environment (G × E) interaction was found in all phenological stages with the lowest temperature appearing to influence the sensitivity of the most plastic genotypes. Descriptors of growth cessation and bud onset explained the largest part of phenotypic variation of the entire process. Quantitative trait loci (QTL) for these traits were detected. For the four selected traits (the onset of growth cessation (date2.5), the transition from shoot to bud (date1.5), the duration of bud formation (subproc1) and bud maturation (subproc2)) eight and sixteen QTL were mapped on the maternal and paternal map, respectively. The identified QTL, each one characterized by small or modest effect, highlighted the complex nature of traits involved in bud set process. Comparison between map location of QTL and P. trichocarpa genome sequence allowed the identification of 13 gene models, 67 bud set-related expressional and six functional candidate genes (CGs). These CGs are functionally related to relevant biological processes, environmental sensing, signaling, and cell growth and development. Some strong QTL had no obvious CGs, and hold great promise to identify unknown genes that affect bud set. Conclusions This study provides a better understanding of the physiological and genetic dissection of bud set in poplar. The putative QTL identified will be tested for associations in P. nigra natural populations. The identified QTL and CGs will also serve as useful targets for poplar breeding. PMID:22471289

2012-01-01

59

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

PubMed Central

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

2012-01-01

60

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

PubMed Central

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 toward the identification of genes potentially linked to phenotypic variation of growth and stress response in brook charr. The ultimate goal is to provide new tools for developing Molecular Assisted Selection for this species. PMID:22690380

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

2012-01-01

61

QTL and candidate gene mapping for polyphenolic composition in apple fruit  

PubMed Central

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

2012-01-01

62

Graph-regularized dual Lasso for robust eQTL mapping  

PubMed Central

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

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

2014-01-01

63

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

Microsoft Academic Search

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\\u000a 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

Chun Shi; Alireza Navabi; Kangfu Yu

2011-01-01

64

A Set of Lotus japonicus Gifu × Lotus burttii Recombinant Inbred Lines Facilitates Map-based Cloning and QTL Mapping  

PubMed Central

Model legumes such as Lotus japonicus have contributed significantly to the understanding of symbiotic nitrogen fixation. This insight is mainly a result of forward genetic screens followed by map-based cloning to identify causal alleles. The L. japonicus ecotype ‘Gifu’ was used as a common parent for inter-accession crosses to produce F2 mapping populations either with other L. japonicus ecotypes, MG-20 and Funakura, or with the related species L. filicaulis. These populations have all been used for genetic studies but segregation distortion, suppression of recombination, low polymorphism levels, and poor viability have also been observed. More recently, the diploid species L. burttii has been identified as a fertile crossing partner of L. japonicus. To assess its qualities in genetic linkage analysis and to enable quantitative trait locus (QTL) mapping for a wider range of traits in Lotus species, we have generated and genotyped a set of 163 Gifu × L. burttii recombinant inbred lines (RILs). By direct comparisons of RIL and F2 population data, we show that L. burttii is a valid alternative to MG-20 as a Gifu mapping partner. In addition, we demonstrate the utility of the Gifu × L. burttii RILs in QTL mapping by identifying an Nfr1-linked QTL for Sinorhizobium fredii nodulation. PMID:22619310

Sandal, Niels; Jin, Haojie; Rodriguez-Navarro, Dulce Nombre; Temprano, Francisco; Cvitanich, Cristina; Brachmann, Andreas; Sato, Shusei; Kawaguchi, Masayoshi; Tabata, Satoshi; Parniske, Martin; Ruiz-Sainz, Jose E.; Andersen, Stig U.; Stougaard, Jens

2012-01-01

65

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

PubMed Central

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

Everett, Meredith V; Seeb, James E

2014-01-01

66

Multiparental mapping of plant height and flowering time QTL in partially isogenic sorghum families.  

PubMed

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

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

2014-09-01

67

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

PubMed Central

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

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

2014-01-01

68

QTL analysis for disease resistance using F2 and F5 genetic maps in peanut (Arachis hapogaea L.)  

Technology Transfer Automated Retrieval System (TEKTRAN)

One mapping population derived from Tifrunner × GT-C20 has shown great potential in developing a high density genetic map and identifying quantitative trait loci (QTL) for important disease resistance, Tomato spotted wilt virus (TSWV) and leaf spot (LS). Both F2 and F5 generation-based genetic maps ...

69

Brain eQTL Mapping Informs Genetic Studies of Psychiatric Diseases  

PubMed Central

Genome-wide association studies (GWASs) have been used to identify genes that increase risk of psychiatric diseases. However, much of the variation in disease risk is still unexplained, suggesting that there are genes still to be discovered. Functional annotation of genetic variants may increase the power of GWASs to identify disease genes by providing prior information that can be used in Bayesian analysis or in reducing the number of tests. Genetic mapping of expression quantitative trait loci (eQTLs) is helping us to reveal novel functional effects of thousands of single nucleotide polymorphisms (SNPs). The published brain eQTL studies are reviewed here, and major methodological issues and their possible solutions are discussed. We emphasize the frequently-ignored problems of batch effects, covariates, and multiple testing, all of which can lead to false positives and false negatives. The future application of eQTL data to the GWAS analysis is also discussed. PMID:21441974

Liu, Chunyu

2011-01-01

70

Multiple QTL for Horticultural Traits and Quantitative Resistance to Phytophthora infestans Linked on Solanum habrochaites Chromosome 11  

PubMed Central

Previously, a Phytophthora infestans resistance QTL from Solanum habrochaites chromosome 11 was introgressed into cultivated tomato (S. lycopersicum). Fine mapping of this resistance QTL using near-isogenic lines (NILs) revealed some co-located QTL with undesirable effects on plant size, canopy density, and fruit size traits. Subsequently, higher-resolution mapping with sub-NILs detected multiple P. infestans resistance QTL within this 9.4-cM region of chromosome 11. In our present study, these same sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over 2 years. The horticultural trait QTL originally detected by fine mapping each fractionated into two or more QTL at higher resolution. A total of 34 QTL were detected across all traits, with 14% exhibiting significant QTL × environment interactions (QTL × E). QTL for many traits were co-located, suggesting either pleiotropic effects or tight linkage among genes controlling these traits. Recombination in the pericentromeric region of the introgression between markers TG147 and At4g10050 was suppressed to approximately 29.7 Mbp per cM, relative to the genomewide average of 750 kbp per cM. The genetic architecture of many of the horticultural and P. infestans resistance traits that mapped within this chromosome 11 S. habrochaites region is complex. Complicating factors included fractionation of QTL, pleiotropy or tight linkage of QTL for multiple traits, pericentromeric chromosomal location(s), and/or QTL × E. High-resolution mapping of QTL in this region would be needed to determine which specific target QTL could be useful in breeding cultivated tomato. PMID:25504736

Haggard, J. Erron; Johnson, Emily B.; St. Clair, Dina A.

2014-01-01

71

Multiple QTL for Horticultural Traits and Quantitative Resistance to Phytophthora infestans Linked on Solanum habrochaites Chromosome 11.  

PubMed

Previously, a Phytophthora infestans resistance QTL from Solanum habrochaites chromosome 11 was introgressed into cultivated tomato (S. lycopersicum). Fine mapping of this resistance QTL using near-isogenic lines (NILs) revealed some co-located QTL with undesirable effects on plant size, canopy density, and fruit size traits. Subsequently, higher-resolution mapping with sub-NILs detected multiple P. infestans resistance QTL within this 9.4-cM region of chromosome 11. In our present study, these same sub-NILs were also evaluated for 17 horticultural traits, including yield, maturity, fruit size and shape, fruit quality, and plant architecture traits in replicated field experiments over 2 years. The horticultural trait QTL originally detected by fine mapping each fractionated into two or more QTL at higher resolution. A total of 34 QTL were detected across all traits, with 14% exhibiting significant QTL × environment interactions (QTL × E). QTL for many traits were co-located, suggesting either pleiotropic effects or tight linkage among genes controlling these traits. Recombination in the pericentromeric region of the introgression between markers TG147 and At4g10050 was suppressed to approximately 29.7 Mbp per cM, relative to the genomewide average of 750 kbp per cM. The genetic architecture of many of the horticultural and P. infestans resistance traits that mapped within this chromosome 11 S. habrochaites region is complex. Complicating factors included fractionation of QTL, pleiotropy or tight linkage of QTL for multiple traits, pericentromeric chromosomal location(s), and/or QTL × E. High-resolution mapping of QTL in this region would be needed to determine which specific target QTL could be useful in breeding cultivated tomato. PMID:25504736

Haggard, J Erron; Johnson, Emily B; St Clair, Dina A

2014-01-01

72

A novel QTL for Septoria speckled leaf blotch resistance in barley (Hordeum vulgare L.) accession PI 643302 by whole-genome QTL mapping.  

PubMed

Septoria speckled leaf blotch (SSLB), caused by Septoria passerinii, is one of the most important foliar diseases of barley (Hordeum vulgare L.) in North America. The primary problem caused by this disease is substantial yield loss. The objective of this study was to determine the chromosomal location of SSLB resistance genes in the barley accession PI 643302. A recombinant inbred line population was developed from the cross Zhenongda 7/PI 643302. PI 643302 is resistant while Zhenongda 7 is susceptible to SSLB. The population was phenotyped for SSLB resistance in five experiments in the greenhouse. A linkage map comprising 113 molecular markers was constructed and simplified composite interval mapping was performed. Two QTLs, designated QrSp-1H and QrSP-2H, were found. QrSp-1H was found on the short arm of chromosome 1H (1HS) in all five experiments and showed a large effect against SSLB. Based on the location of QrSp-1H, it is likely the SSLB resistance gene Rsp2. The QTL QrSp-2H mapped to the distal region on the long arm of chromosome 2H (2HL), had a smaller effect than QrSp-1H, and was also detected consistently in all five experiments. A QTL for SSLB resistance in the same region on chromosome 2H has not been reported previously in either cultivated or wild barley; thus, QrSp-2H is a new QTL for SSLB resistance in barley. PMID:20725150

Yu, G T; Franckowiak, J D; Lee, S H; Horsley, R D; Neate, S M

2010-08-01

73

QTL mapping of resistance to sorghum downy mildew in maize  

E-print Network

were mapped using both restriction fragment length polymorphisms (RFLPs), and simple sequence repeats (SSRs) in 220 F2 individual maize progeny derived from a cross between two extremes; highly susceptible inbred parent SC-TEP5-19-1-3-1-4-1-1 (white...

Sabry, Ahmed Mohamed-Bashir

2004-09-30

74

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

Microsoft Academic Search

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

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

2007-01-01

75

A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.).  

PubMed

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. PMID:23821949

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

76

An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae  

PubMed Central

Dissecting the molecular basis of quantitative traits is a significant challenge and is essential for understanding complex diseases. Even in model organisms, precisely determining causative genes and their interactions has remained elusive, due in part to difficulty in narrowing intervals to single genes and in detecting epistasis or linked quantitative trait loci. These difficulties are exacerbated by limitations in experimental design, such as low numbers of analyzed individuals or of polymorphisms between parental genomes. We address these challenges by applying three independent high-throughput approaches for QTL mapping to map the genetic variants underlying 11 phenotypes in two genetically distant Saccharomyces cerevisiae strains, namely (1) individual analysis of >700 meiotic segregants, (2) bulk segregant analysis, and (3) reciprocal hemizygosity scanning, a new genome-wide method that we developed. We reveal differences in the performance of each approach and, by combining them, identify eight polymorphic genes that affect eight different phenotypes: colony shape, flocculation, growth on two nonfermentable carbon sources, and resistance to two drugs, salt, and high temperature. Our results demonstrate the power of individual segregant analysis to dissect QTL and address the underestimated contribution of interactions between variants. We also reveal confounding factors like mutations and aneuploidy in pooled approaches, providing valuable lessons for future designs of complex trait mapping studies. PMID:24374355

Wilkening, Stefan; Lin, Gen; Fritsch, Emilie S.; Tekkedil, Manu M.; Anders, Simon; Kuehn, Raquel; Nguyen, Michelle; Aiyar, Raeka S.; Proctor, Michael; Sakhanenko, Nikita A.; Galas, David J.; Gagneur, Julien; Deutschbauer, Adam; Steinmetz, Lars M.

2014-01-01

77

Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex  

PubMed Central

Background The Asteraceae species Cynara cardunculus (2n?=?2x?=?34) includes the two fully cross-compatible domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach. Results A set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5?cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance. Conclusion The newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection. PMID:22621324

2012-01-01

78

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

PubMed Central

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

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

2013-01-01

79

Fine-Mapping, Gene Expression and Splicing Analysis of the Disease Associated LRRK2 Locus  

PubMed Central

Association studies have identified several signals at the LRRK2 locus for Parkinson's disease (PD), Crohn's disease (CD) and leprosy. However, little is known about the molecular mechanisms mediating these effects. To further characterize this locus, we fine-mapped the risk association in 5,802 PD and 5,556 controls using a dense genotyping array (ImmunoChip). Using samples from 134 post-mortem control adult human brains (UK Human Brain Expression Consortium), where up to ten brain regions were available per individual, we studied the regional variation, splicing and regulation of LRRK2. We found convincing evidence for a common variant PD association located outside of the LRRK2 protein coding region (rs117762348, A>G, P?=?2.56×10?8, case/control MAF 0.083/0.074, odds ratio 0.86 for the minor allele with 95% confidence interval [0.80–0.91]). We show that mRNA expression levels are highest in cortical regions and lowest in cerebellum. We find an exon quantitative trait locus (QTL) in brain samples that localizes to exons 32–33 and investigate the molecular basis of this eQTL using RNA-Seq data in n?=?8 brain samples. The genotype underlying this eQTL is in strong linkage disequilibrium with the CD associated non-synonymous SNP rs3761863 (M2397T). We found two additional QTLs in liver and monocyte samples but none of these explained the common variant PD association at rs117762348. Our results characterize the LRRK2 locus, and highlight the importance and difficulties of fine-mapping and integration of multiple datasets to delineate pathogenic variants and thus develop an understanding of disease mechanisms. PMID:23967090

Emmett, Warren; Ramasamy, Adaikalavan; Lackner, Karl J.; Zeller, Tanja; Walker, Robert; Smith, Colin; Lewis, Patrick A.; Mamais, Adamantios; de Silva, Rohan; Vandrovcova, Jana; Hernandez, Dena; Nalls, Michael A.; Sharma, Manu; Garnier, Sophie; Lesage, Suzanne; Simon-Sanchez, Javier; Gasser, Thomas; Heutink, Peter; Brice, Alexis; Singleton, Andrew; Cai, Huaibin; Schadt, Eric; Wood, Nicholas W.; Bandopadhyay, Rina; Weale, Michael E.; Hardy, John; Plagnol, Vincent

2013-01-01

80

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

PubMed

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. PMID:24335788

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

2015-01-01

81

QTL mapping for frond length and width in Laminaria japonica aresch (Laminarales, Phaeophyta) using AFLP and SSR markers.  

PubMed

In Laminaria japonica Aresch breeding practice, two quantitative traits, frond length (FL) and frond width (FW), are the most important phenotypic selection index. In order to increase the breeding efficiency by integrating phenotypic selection and marker-assisted selection, the first set of QTL controlling the two traits were determined in F(2) family using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Two prominent L. japonicas inbred lines, one with "broad and thin blade" characteristics and another with "long and narrow blade" characteristics, were applied in the hybridization to yield the F(2) mapping population with 92 individuals. A total of 287 AFLP markers and 11 SSR markers were used to construct a L. japonica genetic map. The yielded map was consisted of 28 linkage groups (LG) named LG1 to LG28, spanning 1,811.1 cM with an average interval of 6.7 cM and covering the 82.8% of the estimated genome 2,186.7 cM. While three genome-wide significant QTL were detected on LG1 (two QTL) and LG4 for "FL," explaining in total 42.36% of the phenotypic variance, two QTL were identified on LG3 and LG5 for the trait "FW," accounting for the total of 36.39% of the phenotypic variance. The gene action of these QTL was additive and partially dominant. The yielded linkage map and the detected QTL can provide a tool for further genetic analysis of two traits and be potential for maker-assisted selection in L. japonica breeding. PMID:19768507

Liu, Fuli; Shao, Zhanru; Zhang, Haining; Liu, Jidong; Wang, Xiuliang; Duan, Delin

2010-08-01

82

Genetic variation, linkage mapping of QTL and correlation studies for yield, root, and agronomic traits for aerobic adaptation  

PubMed Central

Background Water scarcity and drought have seriously threatened traditional rice cultivation practices in several parts of the world, including India. Aerobic rice that uses significantly less water than traditional flooded systems has emerged as a promising water-saving technology. The identification of QTL conferring improved aerobic adaptation may facilitate the development of high-yielding aerobic rice varieties. In this study, experiments were conducted for mapping QTL for yield, root-related traits, and agronomic traits under aerobic conditions using HKR47 × MAS26 and MASARB25 × Pusa Basmati 1460 F2:3 mapping populations. Results A total of 35 QTL associated with 14 traits were mapped on chromosomes 1, 2, 5, 6, 8, 9, and 11 in MASARB25 x Pusa Basmati 1460 and 14 QTL associated with 9 traits were mapped on chromosomes 1, 2, 8, 9, 10, 11, and 12 in HKR47 × MAS26. Two QTL (qGY8.1 with an R2 value of 34.0% and qGY2.1 with an R2 value of 22.8%) and one QTL (qGY2.2 with an R2 value of 43.2%) were identified for grain yield under aerobic conditions in the mapping populations MASARB25 × Pusa Basmati 1460 and HKR47 × MAS26, respectively. A number of breeding lines with higher yield per plant, root length, dry biomass, length-breadth ratio, and with Pusa Basmati 1460-specific alleles in a homozygous or heterozygous condition at the BAD2 locus were identified that will serve as novel material for the selection of stable aerobic Basmati rice breeding lines. Conclusions Our results identified positive correlation between some of the root traits and yield under aerobic conditions, indicating the role of root traits for improving yield under aerobic situations possibly through improved water and nutrient uptake. Co-localization of QTL for yield, root traits, and yield-related agronomic traits indicates that the identified QTL may be immediately exploited in marker-assisted-breeding to develop novel high-yielding aerobic rice varieties. PMID:24168061

2013-01-01

83

Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis).  

PubMed

The evolution of reproductive isolation in an ecological context may involve multiple facets of species divergence on which divergent selection may operate. These include variation in quantitative phenotypic traits, regulation of gene expression, and differential transmission of particular allelic combinations. Thus, an integrative approach to the speciation process involves identifying the genetic basis of these traits, in order to understand how they are affected by divergent selection in nature and how they ultimately contribute to reproductive isolation. In the Lake Whitefish (Coregonus clupeaformis), dwarf and normal species pairs sympatrically occur in several North American postglacial lakes. The limnetic dwarf whitefish distinguishes from its normal benthic relative by numerous life history, behavioural, morphological and gene expression traits, in relation with the exploitation of distinct ecological niches. Here, we have applied the RAD-Sequencing method to a hybrid backcross family to reconstruct a high-density genetic linkage map and perform QTL mapping in the Lake Whitefish. The 3061 cM map encompassed 3438 segregating RAD markers distributed over 40 linkage groups, for an average resolution of 0.89 cM. We mapped phenotypic and expression QTL underlying ecologically important traits as well as transmission ratio distortion QTL, and identified genomic regions harbouring clusters of such QTL. A narrow genomic region strongly associated with sex determination was also evidenced. Positional and functional information revealed in this study will be useful in ongoing population genomic studies to illuminate our understanding of the genomic architecture of reproductive isolation between whitefish species pairs. PMID:23181719

Gagnaire, Pierre-Alexandre; Normandeau, Eric; Pavey, Scott A; Bernatchez, Louis

2013-06-01

84

LINKAGE MAPPING OF PORCINE DGAT1 TO A REGION OF PORCINE CHROMOSOME 4 THAT CONTAINS QTL FOR GROWTH AND FATNESS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Diacylglycerol acyltransferase (DGAT1) is a microsomal enzyme that catalyzes the formation of triglycerides, and maps to human chromosome 8q24.3. Several QTL for growth and fatness have been identified in swine on porcine chromosome 4 (SSC4). Bi-directional chromosome painting and comparative mappin...

85

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

PubMed Central

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 studies. Conclusions This study demonstrated that association mapping using a reasonable number of markers, distributed across the genome and with application of plant materials that are routinely developed in a plant breeding program can detect significant QTLs for traits of interest. PMID:21435233

2011-01-01

86

Development of Genetic Markers Linked to Straighthead Resistance through Fine Mapping in Rice (Oryza sativa L.)  

PubMed Central

Straighthead, a physiological disorder characterized by sterile florets and distorted spikelets, causes significant yield losses in rice, and occurs in many countries. The current control method of draining paddies early in the season stresses plants, is costly, and wastes water. Development of resistant cultivar is regarded as the most efficient way for its control. We mapped a QTL for straighthead resistance using two recombinant inbred line (RIL) F9 populations that were phenotyped over two years using monosodium methanearsonate (MSMA) to induce the symptoms. One population of 170 RILs was genotyped with 136 SSRs and the other population of 91 RILs was genotyped with 159 SSRs. A major QTL qSH-8 was identified in an overlapping region in both populations, and explained 46% of total variation in one and 67% in another population for straighthead resistance. qSH-8 was fine mapped from 1.0 Mbp to 340 kb using 7 SSR markers and further mapped to 290 kb in a population between RM22573 and InDel 27 using 4 InDel markers. SSR AP3858-1 and InDel 11 were within the fine mapped region, and co-segregated with straighthead resistance in both RIL populations, as well as in a collection of diverse global accessions. These results demonstrate that AP3858-1 and InDel 11 can be used for marker-assisted selection (MAS) for straighthead resistant cultivars, which is especially important because there is no effective way to directly evaluate straighthead resistance. PMID:23285082

Yan, Wengui; Jia, Melissa; Jackson, Aaron; Li, Xiaobai; Jia, Limeng; Huang, Bihu; Xu, Peizhou; Correa-Victoria, Fernando; Li, Shigui

2012-01-01

87

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

PubMed

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. PMID:21184048

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

2011-04-01

88

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

PubMed Central

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

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

2007-01-01

89

Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males.  

PubMed

Whereas detection and positioning of genes that affect quantitative traits (quantitative trait loci (QTL)) using linkage mapping uses only information from recombinants in the genotyped generations, linkage disequilibrium (LD) mapping uses historical recombinants. Thus, whereas linkage mapping requires large family sizes to detect and accurately position QTL, LD mapping is more dependent on the number of families sampled from the population. In commercial Atlantic salmon breeding programmes, only a small number of individuals per family are routinely phenotyped for traits such as disease resistance and meat colour. In this paper, we assess the power and accuracy of combined linkage disequilibrium linkage analysis (LDLA) to detect QTL in the commercial population using simulation. When 15 half-sib sire families (each sire mated to 30 dams, each dam with 10 progeny) were sampled from the population for genotyping, we were able to detect a QTL explaining 10% of the phenotypic variance in 85% of replicates and position this QTL within 3 cM of the true position in 70% of replicates. When recombination was absent in males, a feature of the salmon genome, power to detect QTL increased; however, the accuracy of positioning the QTL was decreased. By increasing the number of sire families sampled from the population to be genotyped to 30, we were able to increase both the proportion of QTL detected and correctly positioned (even with no recombination in males). QTL with much smaller effect could also be detected. The results suggest that even with the existing recording structure in commercial salmon breeding programmes, there is considerable power to detect and accurately position QTL using LDLA. PMID:16685283

Hayes, B J; Gjuvsland, A; Omholt, S

2006-07-01

90

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

PubMed

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. PMID:21344184

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

2011-05-01

91

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

PubMed

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. PMID:12589541

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

2003-02-01

92

QTL mapping for economically important traits of common carp (Cyprinus carpio L.).  

PubMed

Quantitative trait loci (QTL) were analyzed for three economically important traits, i.e., body weight (BW), body length (BL), and body thickness (BT), in an F1 family of common carp holding the 190 progeny. A genetic linkage map spanning 3,301 cM in 50 linkage groups with 627 markers and an average distance of 5.6 cM was utilized for QTL mapping. Sixteen QTLs associated with all three growth-related traits were scattered across ten linkage groups, LG6, LG10, LG17, LG19, LG25, LG27, LG28, LG29, LG30, and LG39. Six QTLs for BW and five each for BL and BT explained phenotypic variance in the range 17.0-32.1 %. All the nearest markers of QTLs were found to be significantly (p???0.05) related with the trait. Among these QTLs, a total of four, two (qBW30 and qBW39) related with BW, one (qBL39) associated with BL, and one (qBT29) related to BT, were found to be the major QTLs with a phenotypic variance of >20 %. qBW30 and qBW39 with the nearest markers HLJ1691 and HLJ1843, respectively, show significant values of 0.0038 and 0.0031, correspondingly. QTLs qBL39 and qBT29 were found to have significant values of 0.0047 and 0.0015, respectively. Three QTLs (qBW27, qBW30, qBW39) of BW, two for BL (qBL19, qBL39), and two for BT (qBT6, qBT25) found in this study were similar to populations with different genetic backgrounds. In this study, the genomic region controlling economically important traits were located. These genomic regions will be the major sources for the discovery of important genes and pathways associated with growth-related traits in common carp. PMID:25078056

Laghari, Muhammad Younis; Lashari, Punhal; Zhang, Xiaofeng; Xu, Peng; Narejo, Naeem Tariq; Xin, Baoping; Zhang, Yan; Sun, Xiaowen

2015-02-01

93

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

PubMed Central

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

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

94

Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress  

PubMed Central

Background Drought is one of the most important abiotic stresses that cause drastic reduction in rice grain yield (GY) in rainfed environments. The identification and introgression of QTL leading to high GY under drought have been advocated to be the preferred breeding strategy to improve drought tolerance of popular rice varieties. Genetic control of GY under reproductive-stage drought stress (RS) was studied in two BC1F4 mapping populations derived from crosses of Kali Aus, a drought-tolerant aus cultivar, with high-yielding popular varieties MTU1010 and IR64. The aim was to identify QTL for GY under RS that show a large and consistent effect for the trait. Bulk segregant analysis (BSA) was used to identify significant markers putatively linked with high GY under drought. Results QTL analysis revealed major-effect GY QTL: qDTY 1.2 , qDTY 2.2 and qDTY 1.3 , qDTY 2.3 (DTY; Drought grain yield) under drought consistently over two seasons in Kali Aus/2*MTU1010 and Kali Aus/2*IR64 populations, respectively. qDTY 1.2 and qDTY 2.2 explained an additive effect of 288 kg ha?1 and 567 kg ha?1 in Kali Aus/2*MTU1010, whereas qDTY 1.3 and qDTY 2.3 explained an additive effect of 198 kg ha?1 and 147 kg ha?1 in Kali Aus/2*IR64 populations, respectively. Epistatic interaction was observed for DTF (days to flowering) between regions on chromosome 2 flanked by markers RM154–RM324 and RM263–RM573 and major epistatic QTL for GY showing interaction between genomic locations on chromosome 1 at marker interval RM488–RM315 and chromosome 2 at RM324–RM263 in 2012 DS and 2013 DS RS in Kali Aus/2*IR64 mapping populations. Conclusion The QTL, qDTY 1.2 , qDTY 1.3 , qDTY 2.2 , and qDTY 2.3, identified in this study can be used to improve GY of mega varieties MTU1010 and IR64 under different degrees of severity of drought stress through marker-aided backcrossing and provide farmers with improved varieties that effectively combine high yield potential with good yield under drought. The observed epistatic interaction for GY and DTF will contribute to our understanding of the genetic basis of agronomically important traits and enhance predictive ability at an individualized level in agriculture. PMID:24885990

2014-01-01

95

Fine mapping and association analysis of a quantitative trait locus for milk production traits on Bos taurus autosome 4.  

PubMed

To fine map a quantitative trait locus (QTL) affecting milk production traits previously associated with microsatellite RM188, we implemented an interval mapping analysis by using microsatellite markers in a large Israeli Holstein half-sib sire family, and linkage disequilibrium (LD) mapping in a large set of US Holstein bulls. Interval mapping located the target QTL to the near vicinity of RM188. For the LD mapping, we identified 42 single nucleotide polymorphisms (SNP) in 15 genes in a 12-Mb region on bovine chromosome 4. A total of 24 tag SNP were genotyped in 882 bulls belonging to the University of California Davis archival collection of Holstein bull DNA samples with predicted transmitted ability phenotypes. Marker-to-marker LD analysis revealed 2 LD blocks, with intrablock r(2) values of 0.10 and 0.46, respectively; outside the blocks, r(2) values ranged from 0.002 to 0.23. A standard additive/dominance model using the generalized linear model procedure of SAS and the regression module of HelixTree software were used to test marker-trait associations. Single nucleotide polymorphism 9 on ARL4A, SNP10 on XR_027435.1, SNP12 on ETV1, SNP21 on SNX13, and SNP24 were significantly associated with milk production traits. We propose the interval encompassing ARL4A and SNX13 genes as a candidate region in bovine chromosome 4 for a concordant QTL related to milk protein traits in dairy cattle. Functional studies are needed to confirm this result. PMID:19164688

Rincón, G; Islas-Trejo, A; Casellas, J; Ronin, Y; Soller, M; Lipkin, E; Medrano, J F

2009-02-01

96

QTL Mapping of Combining Ability and Heterosis of Agronomic Traits in Rice Backcross Recombinant Inbred Lines and Hybrid Crosses  

PubMed Central

Background Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis. Methodology/Principal Findings In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits. Conclusions/Significance The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1–6 in this study) were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability. PMID:22291881

Luo, Junyuan; Wang, Peng; Yu, Sibin; Mou, Tongmin; Zheng, Xingfei; Hu, Zhongli

2012-01-01

97

Improving Maize by QTL Mapping, Agronomic Performance and Breeding to Reduce Aflatoxin in Texas  

E-print Network

performance traits. The goal of this study was to investigate germplasm for traits to reduce preharvest aflatoxin accumulation. The specific objectives of this research were: 1) to validate QTL estimates previously identified in lines per se and estimate new...

Mayfield, Kerry Lucas

2012-07-16

98

Genetic variability and QTL mapping of freezing tolerance and related traits in Medicago truncatula.  

PubMed

Freezing is a major environmental limitation to crop productivity for a number of species including legumes. We investigated the genetic determinism of freezing tolerance in the model legume Medicago truncatula Gaertn (M. truncatula). After having observed a large variation for freezing tolerance among 15 M. truncatula accessions, the progeny of a F6 recombinant inbred line population, derived from a cross between two accessions, was acclimated to low above-freezing temperatures and assessed for: (a) number of leaves (NOL), leaf area (LA), chlorophyll content index (CCI), shoot and root dry weights (SDW and RDW) at the end of the acclimation period and (b) visual freezing damage (FD) during the freezing treatment and 2 weeks after regrowth and foliar electrolyte leakage (EL) 2 weeks after regrowth. Consistent QTL positions with additive effects for FD were found on LG1, LG4 and LG6, the latter being the most explanatory (R (2) ? 40 %). QTL for NOL, QTL for EL, NOL and RDW, and QTL for EL and CCI colocalized with FD QTL on LG1, LG4 and LG6, respectively. Favorable alleles for these additive effects were brought by the same parent suggesting that this accession contributes to superior freezing tolerance by affecting plants' capacity to maintain growth at low above-freezing temperatures. No epistatic effects were found between FD QTL, but for each of the studied traits, 3-6 epistatic effects were detected between loci not detected directly as QTL. These results open the way to the assessment of syntenic relationships between QTL for frost tolerance in M. truncatula and cultivated legume species. PMID:23778689

Avia, Komlan; Pilet-Nayel, Marie-Laure; Bahrman, Nasser; Baranger, Alain; Delbreil, Bruno; Fontaine, Véronique; Hamon, Céline; Hanocq, Eric; Niarquin, Martine; Sellier, Hélène; Vuylsteker, Christophe; Prosperi, Jean-Marie; Lejeune-Hénaut, Isabelle

2013-09-01

99

Meta-analyses of QTL for grain yield and anthesis silking interval in 18 maize populations evaluated under water-stressed and well-watered environments  

PubMed Central

Background Identification of QTL with large phenotypic effects conserved across genetic backgrounds and environments is one of the prerequisites for crop improvement using marker assisted selection (MAS). The objectives of this study were to identify meta-QTL (mQTL) for grain yield (GY) and anthesis silking interval (ASI) across 18 bi-parental maize populations evaluated in the same conditions across 2-4 managed water stressed and 3-4 well watered environments. Results The meta-analyses identified 68 mQTL (9 QTL specific to ASI, 15 specific to GY, and 44 for both GY and ASI). Mean phenotypic variance explained by each mQTL varied from 1.2 to 13.1% and the overall average was 6.5%. Few QTL were detected under both environmental treatments and/or multiple (>4 populations) genetic backgrounds. The number and 95% genetic and physical confidence intervals of the mQTL were highly reduced compared to the QTL identified in the original studies. Each physical interval of the mQTL consisted of 5 to 926 candidate genes. Conclusions Meta-analyses reduced the number of QTL by 68% and narrowed the confidence intervals up to 12-fold. At least the 4 mQTL (mQTL2.2, mQTL6.1, mQTL7.5 and mQTL9.2) associated with GY under both water-stressed and well-watered environments and detected up to 6 populations may be considered for fine mapping and validation to confirm effects in different genetic backgrounds and pyramid them into new drought resistant breeding lines. This is the first extensive report on meta-analysis of data from over 3100 individuals genotyped using the same SNP platform and evaluated in the same conditions across a wide range of managed water-stressed and well-watered environments. PMID:23663209

2013-01-01

100

INVESTIGATION Do Large Effect QTL Fractionate? A Case Study  

E-print Network

, the identified QTL are rarely mapped to the underlying genes and it is usually unclear whether a QTL corresponds trait and these QTL all mapped to tb1. These results indicate that tb1 is the sole gene for plant traits. Overall, these results provide examples for both a major QTL that maps to a single gene, as well

Doebley, John

101

QTL analyses and comparative genetic mapping of frost tolerance, winter survival and drought tolerance in meadow fescue (Festuca pratensis Huds.).  

PubMed

Quantitative trait loci (QTLs) for frost and drought tolerance, and winter survival in the field, were mapped in meadow fescue (Festuca pratensis Huds.) and compared with corresponding traits in Triticeae and rice to study co-location with putatively orthologous QTLs and known abiotic stress tolerance genes. The genomes of grass species are highly macrosyntenic; however, the Festuca/Lolium and Triticeae homoeologous chromosomes 4 and 5 show major structural differences that is especially interesting in comparative genomics of frost tolerance. The locations of two frost tolerance/winter survival QTLs on Festuca chromosome 5F correspond most likely to the Fr-A1 and Fr-A2 loci on wheat homoeologous group 5A chromosomes. A QTL for long-term drought tolerance on chromosome 3F (syntenic with rice 1) support evidence from introgression of Festuca genome segments onto homoeologous Lolium chromosomes (3L) that this genome region is an excellent source of tolerance towards drought stress. The coincident location of several stress tolerance QTL in Festuca with QTL and genes in Triticeae species, notably dehydrins, CBF transcription factors and vernalisation response genes indicate the action of structural or regulatory genes conserved across evolutionarily distant species. PMID:21505831

Alm, Vibeke; Busso, Carlos S; Ergon, Ashild; Rudi, Heidi; Larsen, Arild; Humphreys, Michael W; Rognli, Odd Arne

2011-08-01

102

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

PubMed

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 structural variation in mammary ductal development, and determined if these QTL correlated with genomic intervals conferring BrCa susceptibility in humans. For about half of the traits, developmental variation among the complete set of strains in this study was greater (P < 0.05) than that of previously studied strains, or strains 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 identified 20 mammary development QTL (Mdq). Of these, five were syntenic with previously reported human BrCa loci. The most 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 linked SNP (r(2) > 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 mammary tumorigenesis and normal ductal development are influenced by common genetic factors and that further studies of genetically diverse mice can improve our understanding of BrCa in humans. PMID:25552398

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

2015-02-01

103

Genotyping-by-sequencing based intra-specific genetic map refines a ''QTL-hotspot" region for drought tolerance in chickpea.  

PubMed

To enhance the marker density in the "QTL-hotspot" region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the "QTL-hotspot" region. These efforts have refined the "QTL-hotspot" region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. In addition, 49 SNPs integrated in the "QTL-hotspot" region were converted into cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers which can be used in marker-assisted breeding. PMID:25344290

Jaganathan, Deepa; Thudi, Mahendar; Kale, Sandip; Azam, Sarwar; Roorkiwal, Manish; Gaur, Pooran M; Kishor, P B Kavi; Nguyen, Henry; Sutton, Tim; Varshney, Rajeev K

2014-10-25

104

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

PubMed Central

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

2014-01-01

105

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

PubMed

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. PMID:23921957

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

2013-11-01

106

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

PubMed Central

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

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

2014-01-01

107

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

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. PMID:19531576

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

2009-08-01

108

Genetic Linkage Map Construction and QTL Mapping of Salt Tolerance Traits in Zoysiagrass (Zoysia japonica)  

PubMed Central

Zoysiagrass (Zoysia Willd.) is an important warm season turfgrass that is grown in many parts of the world. Salt tolerance is an important trait in zoysiagrass breeding programs. In this study, a genetic linkage map was constructed using sequence-related amplified polymorphism markers and random amplified polymorphic DNA markers based on an F1 population comprising 120 progeny derived from a cross between Zoysia japonica Z105 (salt-tolerant accession) and Z061 (salt-sensitive accession). The linkage map covered 1211 cM with an average marker distance of 5.0 cM and contained 24 linkage groups with 242 marker loci (217 sequence-related amplified polymorphism markers and 25 random amplified polymorphic DNA markers). Quantitative trait loci affecting the salt tolerance of zoysiagrass were identified using the constructed genetic linkage map. Two significant quantitative trait loci (qLF-1 and qLF-2) for leaf firing percentage were detected; qLF-1 at 36.3 cM on linkage group LG4 with a logarithm of odds value of 3.27, which explained 13.1% of the total variation of leaf firing and qLF-2 at 42.3 cM on LG5 with a logarithm of odds value of 2.88, which explained 29.7% of the total variation of leaf firing. A significant quantitative trait locus (qSCW-1) for reduced percentage of dry shoot clipping weight was detected at 44.1 cM on LG5 with a logarithm of odds value of 4.0, which explained 65.6% of the total variation. This study provides important information for further functional analysis of salt-tolerance genes in zoysiagrass. Molecular markers linked with quantitative trait loci for salt tolerance will be useful in zoysiagrass breeding programs using marker-assisted selection. PMID:25203715

Guo, Hailin; Ding, Wanwen; Chen, Jingbo; Chen, Xuan; Zheng, Yiqi; Wang, Zhiyong; Liu, Jianxiu

2014-01-01

109

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

PubMed

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. PMID:24333858

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

2014-02-15

110

A comprehensive analysis of QTL for abdominal fat and breast muscle weights on chicken chromosome 5 using a multivariate approach.  

PubMed

Quantitative trait loci (QTL) influencing the weight of abdominal fat (AF) and of breast muscle (BM) were detected on chicken chromosome 5 (GGA5) using two successive F(2) crosses between two divergently selected 'Fat' and 'Lean' INRA broiler lines. Based on these results, the aim of the present study was to identify the number, location and effects of these putative QTL by performing multitrait and multi-QTL analyses of the whole available data set. Data concerned 1186 F(2) offspring produced by 10 F(1) sires and 85 F(1) dams. AF and BM traits were measured on F(2) animals at slaughter, at 8 (first cross) or 9 (second cross) weeks of age. The F(0), F(1) and F(2) birds were genotyped for 11 microsatellite markers evenly spaced along GGA5. Before QTL detection, phenotypes were adjusted for the fixed effects of sex, F(2) design, hatching group within the design, and for body weight as a covariable. Univariate analyses confirmed the QTL segregation for AF and BM on GGA5 in male offspring, but not in female offspring. Analyses of male offspring data using multitrait and linked-QTL models led us to conclude the presence of two QTL on the distal part of GGA5, each controlling one trait. Linked QTL models were applied after correction of phenotypic values for the effects of these distal QTL. Several QTL for AF and BM were then discovered in the central region of GGA5, splitting one large QTL region for AF into several distinct QTL. Neither the 'Fat' nor the 'Lean' line appeared to be fixed for any QTL genotype. These results have important implications for prospective fine mapping studies and for the identification of underlying genes and causal mutations. PMID:19243366

Le Mignon, G; Pitel, F; Gilbert, H; Le Bihan-Duval, E; Vignoles, F; Demeure, O; Lagarrigue, S; Simon, J; Cogburn, L A; Aggrey, S E; Douaire, M; Le Roy, P

2009-04-01

111

Genetic complexity of an obesity QTL (Fob3) revealed by detailed genetic mapping  

E-print Network

, these are responsible for only a small proportion of human cases of obesity. By divergent selection for high and low fat of polygenic obesity similar to the situation in human popula- tions. From previous crosses of these lines, four body fat quantitative trait loci (QTL) were identified. We have created congenic lines (Fchr15L

Keightley, Peter

112

Mapping Disease Resistance QTL for Three Foliar Diseases of Maize in a RIL Population  

Technology Transfer Automated Retrieval System (TEKTRAN)

Southern leaf blight (SLB), gray leaf spot (GLS), and northern leaf blight (NLB) are three important foliar diseases impacting maize production. The objectives of this study were to identify quantitative trait loci for disease resistance (dQTL) for resistance to these diseases in a maize recombinan...

113

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

PubMed Central

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

2012-01-01

114

Fine-grained nociceptive maps in primary somatosensory cortex  

PubMed Central

Topographic maps of the receptive surface are a fundamental feature of neural organization in many sensory systems. While touch is finely mapped in the cerebral cortex, it remains controversial how precise any cortical nociceptive map may be. Given that nociceptive innervation density is relatively low on distal skin regions such as the digits, one might conclude that the nociceptive system lacks fine representation of these regions. Indeed, only gross spatial organization of nociceptive maps has been reported so far. However, here we reveal the existence of fine-grained somatotopy for nociceptive inputs to the digits in human primary somatosensory cortex (SI). Using painful nociceptive-selective laser stimuli to the hand, and phase-encoded fMRI analysis methods, we observed somatotopic maps of the digits in contralateral SI. These nociceptive maps were highly aligned with maps of non-painful tactile stimuli, suggesting comparable cortical representations for, and possible interactions between, mechanoreceptive and nociceptive signals. Our findings may also be valuable for future studies tracking the timecourse and the spatial pattern of plastic changes in cortical organization involved in chronic pain. PMID:23197708

Mancini, Flavia; Haggard, Patrick; Iannetti, Gian Domenico; Longo, Matthew R.; Sereno, Martin I.

2012-01-01

115

Fine-mapping natural alleles: quantitative complementation to the rescue  

PubMed Central

Mapping the genes responsible for natural variation and divergence is a challenging task. Many studies have mapped genes to genomic regions, or generated lists of candidates, but few studies have implicated specific genes with a high standard of evidence. I propose that combining recent advances in genomic engineering with a modified version of the quantitative complementation test will help turn candidate genes into causal genes. By creating loss-of-function mutations in natural strains, and using these mutations to quantitatively fail-to-complement natural alleles, fine mapping should be greatly facilitated. As an example, I propose that the CRISPR/Cas9 system could be combined with the FLP/FRT system to fine-map genes in the numerous systems where inversions have frustrated these efforts. PMID:24628660

Turner, Thomas L.

2014-01-01

116

QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red.  

PubMed

Wide adoption of direct-seeded rice practices has been hindered by poorly leveled fields, heavy rainfall and poor drainage, which cause accumulation of water in the fields shortly after sowing, leading to poor crop establishment. This is due to the inability of most rice varieties to germinate and reach the water surface under complete submergence. Hence, tolerance of anaerobic conditions during germination is an essential trait for direct-seeded rice cultivation in both rainfed and irrigated ecosystems. A QTL study was conducted to unravel the genetic basis of tolerance of anaerobic conditions during germination using a population derived from a cross between IR42, a susceptible variety, and Ma-Zhan Red, a tolerant landrace from China. Phenotypic data was collected based on the survival rates of the seedlings at 21 days after sowing of dry seeds under 10 cm of water. QTL analysis of the mapping population consisting of 175 F2:3 families genotyped with 118 SSR markers identified six significant QTLs on chromosomes 2, 5, 6, and 7, and in all cases the tolerant alleles were contributed by Ma-Zhan Red. The largest QTL on chromosome 7, having a LOD score of 14.5 and an R (2) of 31.7 %, was confirmed using a BC2F3 population. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to rapidly develop varieties with improved tolerance to anaerobic condition during germination. Ultimately, this trait can be combined with other abiotic stress tolerance QTLs to provide resilient varieties for direct-seeded systems. PMID:23417074

Septiningsih, Endang M; Ignacio, John Carlos I; Sendon, Pamella M D; Sanchez, Darlene L; Ismail, Abdelbagi M; Mackill, David J

2013-05-01

117

Mapping quantitative trait loci (QTL) in sheep. I. A new male framework linkage map and QTL for growth rate and body weight  

Microsoft Academic Search

A male sheep linkage map comprising 191 microsatellites was generated from a single family of 510 Awassi-Merino backcross progeny. Except for ovine chromosomes 1, 2, 10 and 17, all other chromosomes yielded a LOD score difference greater than 3.0 between the best and second-best map order. The map is on average 11% longer than the Sheep Linkage Map v4.7 male-specific

Herman W Raadsma; Peter C Thomson; Kyall R Zenger; Colin Cavanagh; Mary K Lam; Elisabeth Jonas; Marilyn Jones; Gina Attard; David Palmer; Frank W Nicholas

2009-01-01

118

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

PubMed

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. PMID:19050847

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

2009-02-01

119

Saturation and comparative mapping of a major Fusarium head blight resistance QTL in tetraploid wheat  

Microsoft Academic Search

Fusarium head blight (FHB) is a devastating disease of cultivated wheat worldwide. Partial resistance to FHB has been identified\\u000a in common wheat (Triticum aestivum L.). However, sources of effective FHB resistance have not been found in durum wheat (T. turgidum L. var. durum). A major FHB resistance quantitative trait loci (QTL), Qfhs.ndsu-3AS, was identified on chromosome 3A of T.\\u000a dicoccoides,

Xunfen Chen; Justin D. Faris; Jinguo Hu; Robert W. Stack; Tika Adhikari; Elias M. Elias; Shahryar F. Kianian; Xiwen Cai

2007-01-01

120

Modeling and mapping QTL for senescence-related traits in winter wheat under high temperature  

Microsoft Academic Search

Senescence is a genetically programmed and environmentally influenced process resulting in the destruction of chlorophyll\\u000a and remobilization of nutrients to younger or reproductive parts of plants. Delayed senescence, or stay-green, contributes\\u000a to a long grain-filling period and stable yield under stress. To model senescence and identify quantitative trait loci (QTL)\\u000a for the trait, a population of recombinant inbred lines (RIL)

Kolluru VijayalakshmiAllan; Allan K. Fritz; Gary M. Paulsen; Guihua Bai; Satchidanand Pandravada; Bikram S. Gill

2010-01-01

121

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

PubMed Central

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 and highlight the importance of considering growth as a composite trait (such as yields for annual plants) for a better understanding of its genetic bases. PMID:23978279

2013-01-01

122

Integrating QTL mapping and genome scans towards the characterization of candidate loci under parallel selection in the lake whitefish (Coregonus clupeaformis).  

PubMed

As natural selection must act on underlying genetic variation, discovering the number and location of loci under the influence of selection is imperative towards understanding adaptive divergence in evolving populations. Studies employing genome scans have hypothesized that the action of divergent selection should reduce gene flow at the genomic locations implicated in adaptation and speciation among natural populations, yet once 'outlier' patterns of variation have been identified the function and role of such loci needs to be confirmed. We integrated adaptive QTL mapping and genomic scans among diverging sympatric pairs of the lake whitefish (Coregonus clupeaformis) species complex in order to test the hypothesis that differentiation between dwarf and normal ecotypes at growth-associated QTL was maintained by directional selection. We found evidence of significantly high levels of molecular divergence among eight growth QTL where two of the strongest candidate loci under the influence of directional selection exhibited parallel reductions of gene flow over multiple populations. PMID:15660930

Rogers, S M; Bernatchez, L

2005-02-01

123

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

PubMed

The mule duck, an interspecific hybrid obtained by crossing common duck (Anas platyrhynchos) females with Muscovy (Cairina moschata) drakes, is widely used for fatty liver production. The purpose of the present study was to detect and map single and pleiotropic QTL that segregate in the common duck species, and influence the expression of traits in their overfed mule duck offspring. To this end, we generated a common duck backcross (BC) population by crossing Kaiya and heavy Pekin experimental lines, which differ notably in regard to the BW and overfeeding ability of their mule progeny. The BC females were mated to Muscovy drakes and, on average, 4 male mule ducks hatched per BC female (1600 in total) and were measured for growth, metabolism during growth and the overfeeding period, overfeeding ability, and the quality of their breast meat and fatty liver. The phenotypic value of BC females was estimated for each trait by assigning to each female the mean value of the phenotypes of her offspring. Estimations allowed for variance, which depended on the number of male offspring per BC and the heritability of the trait considered. The genetic map used for QTL detection consisted of 91 microsatellite markers aggregated into 16 linkage groups (LG) covering a total of 778 cM. Twenty-two QTL were found to be significant at the 1% chromosome-wide threshold level using the single-trait detection option of the QTLMap software. Most of the QTL detected were related to the quality of breast meat and fatty liver: QTL for meat pH 20 min post mortem were mapped to LG4 (at the 1% genome-wide significance level), and QTL for meat lipid content and cooking losses were mapped to LG2a. The QTL related to fatty liver weight and liver protein and lipid content were for the most part detected on LG2c and LG9. Multitrait analysis highlighted the pleiotropic effects of QTL in these chromosome regions. Apart from the strong QTL for plasma triglyceride content at the end of the overfeeding period mapped to chromosome Z using single-trait analysis, all metabolic trait QTL were detected with the multitrait approach: the QTL mapped to LG14 and LG21 affected the plasma cholesterol and triglyceride contents, whereas the QTL mapped to LG2a seemed to impact glycemia and the basal plasma corticosterone content. A greater density genetic map will be needed to further fine map the QTL. PMID:23148259

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

2013-02-01

124

Genetic Map Construction and Quantitative Trait Locus (QTL) Detection of Growth-Related Traits in Litopenaeus vannamei for Selective Breeding Applications  

PubMed Central

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. PMID:24086466

Andriantahina, Farafidy; Liu, Xiaolin; Huang, Hao

2013-01-01

125

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

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 linkage group 2. The two clusters represent marker-trait associations that might be useful for marker-assisted plant breeding applications. In silico comparative analysis indicated conservation of the genetic loci controlling Rubisco concentration in perennial ryegrass and rice. PMID:23505311

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

2013-03-01

126

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

PubMed Central

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

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

127

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

PubMed

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

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

128

QTL affecting stress response to crowding in a rainbow trout broodstock population  

PubMed Central

Background Genomic analyses have the potential to impact selective breeding programs by identifying markers that serve as proxies for traits which are expensive or difficult to measure. Also, identifying genes affecting traits of interest enhances our understanding of their underlying biochemical pathways. To this end we conducted genome scans of seven rainbow trout families from a single broodstock population to identify quantitative trait loci (QTL) having an effect on stress response to crowding as measured by plasma cortisol concentration. Our goal was to estimate the number of major genes having large effects on this trait in our broodstock population through the identification of QTL. Results A genome scan including 380 microsatellite markers representing 29 chromosomes resulted in the de novo construction of genetic maps which were in good agreement with the NCCCWA genetic map. Unique sets of QTL were detected for two traits which were defined after observing a low correlation between repeated measurements of plasma cortisol concentration in response to stress. A highly significant QTL was detected in three independent analyses on Omy16, many additional suggestive and significant QTL were also identified. With linkage-based methods of QTL analysis such as half-sib regression interval mapping and a variance component method, we determined that the significant and suggestive QTL explain about 40-43% and 13-27% of the phenotypic trait variation, respectively. Conclusions The cortisol response to crowding stress is a complex trait controlled in a sub-sample of our broodstock population by multiple QTL on at least 8 chromosomes. These QTL are largely different from others previously identified for a similar trait, documenting that population specific genetic variants independently affect cortisol response in ways that may result in different impacts on growth. Also, mapping QTL for multiple traits associated with stress response detected trait specific QTL which indicate the significance of the first plasma cortisol measurement in defining the trait. Fine mapping these QTL can lead towards the identification of genes affecting stress response and may influence approaches to selection for this economically important stress response trait. PMID:23134666

2012-01-01

129

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

PubMed Central

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

2013-01-01

130

Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L.).  

PubMed

A major quantitative trait loci (QTL) conditioning common bacterial blight (CBB) resistance in common bean (Phaseolus vulgaris L.) lines HR45 and HR67 was derived from XAN159, a resistant line obtained from an interspecific cross between common bean lines and the tepary bean (P. acutifolius L.) line PI319443. This source of CBB resistance is widely used in bean breeding. Several other CBB resistance QTL have been identified but none of them have been physically mapped. Four molecular markers tightly linked to this QTL have been identified suitable for marker assisted selection and physical mapping of the resistance gene. A bacterial artificial chromosome (BAC) library was constructed from high molecular weight DNA of HR45 and is composed of 33,024 clones. The size of individual BAC clone inserts ranges from 30 kb to 280 kb with an average size of 107 kb. The library is estimated to represent approximately sixfold genome coverage. The BAC library was screened as BAC pools using four PCR-based molecular markers. Two to seven BAC clones were identified by each marker. Two clones were found to have both markers PV-tttc001 and STS183. One preliminary contig was assembled based on DNA finger printing of those positive BAC clones. The minimum tiling path of the contig contains 6 BAC clones spanning an estimated size of 750 kb covering the QTL region. PMID:20419470

Liu, S Y; Yu, K; Huffner, M; Park, S J; Banik, M; Pauls, K P; Crosby, W

2010-07-01

131

Genetic mapping and QTL analysis for body weight in Jian carp (Cyprinus carpio var. Jian) compared with mirror carp (Cyprinus carpio L.)  

NASA Astrophysics Data System (ADS)

We report the genetic linkage map of Jian carp (Cyprinus carpio var. Jian). An F1 population comprising 94 Jian carp individuals was mapped using 254 microsatellite markers. The genetic map spanned 1 381.592 cM and comprised 44 linkage groups, with an average marker distance of 6.58 cM. We identified eight quantitative trait loci (QTLs) for body weight (BW) in seven linkage groups, explaining 12.6% to 17.3% of the phenotypic variance. Comparative mapping was performed between Jian carp and mirror carp (Cyprinus carpio L.), which both have 50 chromosomes. One hundred and ninety-eight Jian carp marker loci were found in common with the mirror carp map, with 186 (93.94%) showing synteny. All 44 Jian carp linkage groups could be one-to-one aligned to the 44 mirror carp linkage groups, mostly sharing two or more common loci. Three QTLs for BW in Jian carp were conserved in mirror carp. QTL comparison suggested that the QTL confidence interval in mirror carp was more precise than the homologous interval in Jian carp, which was contained within the QTL interval in Jian carp. The syntenic relationship and consensus QTLs between the two varieties provide a foundation for genomic research and genetic breeding in common carp.

Gu, Ying; Lu, Cuiyun; Zhang, Xiaofeng; Li, Chao; Yu, Juhua; Sun, Xiaowen

2015-01-01

132

Whole genome scanning and association mapping identified a significant association between growth and a SNP in the IFABP-a gene of the Asian seabass  

PubMed Central

Background Aquaculture is the quickest growing sector in agriculture. However, QTL for important traits have been only identified in a few aquaculture species. We conducted QTL mapping for growth traits in an Asian seabass F2 family with 359 individuals using 123 microsatellites and 22 SNPs, and performed association mapping in four populations with 881 individuals. Results Twelve and nine significant QTL, as well as 14 and 10 suggestive QTL were detected for growth traits at six and nine months post hatch, respectively. These QTL explained 0.9-12.0% of the phenotypic variance. For body weight, two QTL intervals at two stages were overlapped while the others were mapped onto different positions. The IFABP-a gene located in a significant QTL interval for growth on LG5 was cloned and characterized. A SNP in exon 3 of the gene was significantly associated with growth traits in different populations. Conclusions The results of QTL mapping for growth traits suggest that growth at different stages was controlled by some common QTL and some different QTL. Positional candidate genes and association mapping suggest that the IFABP-a is a strong candidate gene for growth. Our data supply a basis for fine mapping QTL, marker-assisted selection and further detailed analysis of the functions of the IFABP-a gene in fish growth. PMID:23634810

2013-01-01

133

Matrix eQTL: Ultra fast eQTL analysis via large matrix operations  

Microsoft Academic Search

Expression quantitative trait loci (eQTL) mapping aims to determine genomic regions that regulate gene transcription. Expression QTL is used to study the regulatory structure of normal tissues and to search for genetic factors in complex diseases such as cancer, diabetes, and cystic fibrosis. A modern eQTL dataset contains millions of SNPs and thousands of transcripts measured for hundreds of samples.

Andrey A. Shabalin

2011-01-01

134

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

PubMed Central

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

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

2012-01-01

135

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

PubMed

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, PMID:12897862

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

2003-08-01

136

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

PubMed Central

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

Li, Hongjun; Liu, Xiao; Zhang, Guofan

2012-01-01

137

Limitation of Number of Strains and Persistence of False Positive Loci in QTL Mapping Using Recombinant Inbred Strains  

PubMed Central

While the identification of causal genes of quantitative trait loci (QTL) remains a difficult problem in the post-genome era, the number of QTL continues to accumulate, mainly identified using the recombinant inbred (RI) strains. Over the last decade, hundreds of publications have reported nearly a thousand QTL identified from RI strains. We hypothesized that the inaccuracy of most of these QTL makes it difficult to identify causal genes. Using data from RI strains derived from C57BL/6J (B6) X DBA/2J (D2), we tested the possibility of detection of reliable QTL with different numbers of strains in the same trait in five different traits. Our results indicated that studies using RI strains of less than 30 in general have a higher probability of failing to detect reliable QTL. Errors in many studies could include false positive loci, switches between QTL with small and major effects, and missing the real major loci. The similar data was obtained from a RI strain population derived from a different pair of parents and a RI strain population of rat. Thus, thousands of reported QTL from studies of RI strains may need to be double-checked for accuracy before proceeding to causal gene identification. PMID:25032693

Wang, Lishi; Jiao, Yan; Cao, Yanhong; Liu, Gaifen; Wang, Yongjun; Gu, Weikuan

2014-01-01

138

QTL mapping of growth-related traits in a full-sib family of rubber tree (Hevea brasiliensis) evaluated in a sub-tropical climate.  

PubMed

The rubber tree (Hevea spp.), cultivated in equatorial and tropical countries, is the primary plant used in natural rubber production. Due to genetic and physiological constraints, inbred lines of this species are not available. Therefore, alternative approaches are required for the characterization of this species, such as the genetic mapping of full-sib crosses derived from outbred parents. In the present study, an integrated genetic map was obtained for a full-sib cross family with simple sequence repeats (SSRs) and expressed sequence tag (EST-SSR) markers, which can display different segregation patterns. To study the genetic architecture of the traits related to growth in two different conditions (winter and summer), quantitative trait loci (QTL) mapping was also performed using the integrated map. Traits evaluated were height and girth growth, and the statistical model was based in an extension of composite interval mapping. The obtained molecular genetic map has 284 markers distributed among 23 linkage groups with a total length of 2688.8 cM. A total of 18 QTLs for growth traits during the summer and winter seasons were detected. A comparison between the different seasons was also conducted. For height, QTLs detected during the summer season were different from the ones detected during winter season. This type of difference was also observed for girth. Integrated maps are important for genetics studies in outbred species because they represent more accurately the polymorphisms observed in the genitors. QTL mapping revealed several interesting findings, such as a dominance effect and unique segregation patterns that each QTL could exhibit, which were independent of the flanking markers. The QTLs identified in this study, especially those related to phenotypic variation associated with winter could help studies of marker-assisted selection that are particularly important when the objective of a breeding program is to obtain phenotypes that are adapted to sub-optimal regions. PMID:23620732

Souza, Livia Moura; Gazaffi, Rodrigo; Mantello, Camila Campos; Silva, Carla Cristina; Garcia, Dominique; Le Guen, Vincent; Cardoso, Saulo Emilio Almeida; Garcia, Antonio Augusto Franco; Souza, Anete Pereira

2013-01-01

139

Large-Scale East-Asian eQTL Mapping Reveals Novel Candidate Genes for LD Mapping and the Genomic Landscape of Transcriptional Effects of Sequence Variants  

PubMed Central

Profiles of sequence variants that influence gene transcription are very important for understanding mechanisms that affect phenotypic variation and disease susceptibility. Using genotypes at 1.4 million SNPs and a comprehensive transcriptional profile of 15,454 coding genes and 6,113 lincRNA genes obtained from peripheral blood cells of 298 Japanese individuals, we mapped expression quantitative trait loci (eQTLs). We identified 3,804 cis-eQTLs (within 500 kb from target genes) and 165 trans-eQTLs (>500 kb away or on different chromosomes). Cis-eQTLs were often located in transcribed or adjacent regions of genes; among these regions, 5? untranslated regions and 5? flanking regions had the largest effects. Epigenetic evidence for regulatory potential accumulated in public databases explained the magnitude of the effects of our eQTLs. Cis-eQTLs were often located near the respective target genes, if not within genes. Large effect sizes were observed with eQTLs near target genes, and effect sizes were obviously attenuated as the eQTL distance from the gene increased. Using a very stringent significance threshold, we identified 165 large-effect trans-eQTLs. We used our eQTL map to assess 8,069 disease-associated SNPs identified in 1,436 genome-wide association studies (GWAS). We identified genes that might be truly causative, but GWAS might have failed to identify for 148 out of the GWAS-identified SNPs; for example, TUFM (P?=?3.3E-48) was identified for inflammatory bowel disease (early onset); ZFP90 (P?=?4.4E-34) for ulcerative colitis; and IDUA (P?=?2.2E-11) for Parkinson's disease. We identified four genes (P<2.0E-14) that might be related to three diseases and two hematological traits; each expression is regulated by trans-eQTLs on a different chromosome than the gene. PMID:24956270

Narahara, Maiko; Higasa, Koichiro; Nakamura, Seiji; Tabara, Yasuharu; Kawaguchi, Takahisa; Ishii, Miho; Matsubara, Kenichi; Matsuda, Fumihiko; Yamada, Ryo

2014-01-01

140

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

PubMed

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. PMID:15067400

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

141

Fine-scale mapping using Hardy-Weinberg disequilibrium.  

PubMed

Hardy-Weinberg disequilibrium (HWD) among affected individuals has recently been proposed for fine-scale mapping of disease susceptibility genes. We investigate the statistical properties of several available HWD measures and develop a new HWD measure J for fine-scale mapping. It is shown both theoretically and through simulations that the available HWD measures depend not only on the genetic distance between the marker locus of interest and the disease susceptibility locus, but also on the allele frequencies at the marker locus. On the contrary, the new measure is not affected by the allele frequencies at the marker locus under the following assumptions: (a) there is initial complete linkage disequilibrium between the marker and the disease loci, (b) there are no new mutations at the marker and the disease loci, and (c) the population under study is large. We develop a novel method to estimate the location of the disease susceptibility gene based on the HWD measure J. The estimator is robust to low mutation rates at the marker and the disease loci. We compare the standard error of the estimated disease gene loci using P excess for case-control studies with the standard error using J for case-only studies under various disease models. The newly developed method is successfully applied to a data set on hereditary haemochromatosis (HH). PMID:11427179

Jiang, R; Dong, J; Wang, D; Sun, F Z

2001-03-01

142

QTL mapping of the production of wine aroma compounds by yeast  

PubMed Central

Background 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. Results 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. Conclusions 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. PMID:23110365

2012-01-01

143

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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...

144

Genetic and epigenetic fine mapping of causal autoimmune disease variants.  

PubMed

Genome-wide association studies have identified loci underlying human diseases, but the causal nucleotide changes and mechanisms remain largely unknown. Here we developed a fine-mapping algorithm to identify candidate causal variants for 21 autoimmune diseases from genotyping data. We integrated these predictions with transcription and cis-regulatory element annotations, derived by mapping RNA and chromatin in primary immune cells, including resting and stimulated CD4(+) T-cell subsets, regulatory T cells, CD8(+) T cells, B cells, and monocytes. We find that ?90% of causal variants are non-coding, with ?60% mapping to immune-cell enhancers, many of which gain histone acetylation and transcribe enhancer-associated RNA upon immune stimulation. Causal variants tend to occur near binding sites for master regulators of immune differentiation and stimulus-dependent gene activation, but only 10-20% directly alter recognizable transcription factor binding motifs. Rather, most non-coding risk variants, including those that alter gene expression, affect non-canonical sequence determinants not well-explained by current gene regulatory models. PMID:25363779

Farh, Kyle Kai-How; Marson, Alexander; Zhu, Jiang; Kleinewietfeld, Markus; Housley, William J; Beik, Samantha; Shoresh, Noam; Whitton, Holly; Ryan, Russell J H; Shishkin, Alexander A; Hatan, Meital; Carrasco-Alfonso, Marlene J; Mayer, Dita; Luckey, C John; Patsopoulos, Nikolaos A; De Jager, Philip L; Kuchroo, Vijay K; Epstein, Charles B; Daly, Mark J; Hafler, David A; Bernstein, Bradley E

2015-02-19

145

Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat-Triticum militinae introgression line.  

PubMed

Introgression of several genomic loci from tetraploid Triticum militinae into bread wheat cv. Tähti has increased resistance of introgression line 8.1 to powdery mildew in seedlings and adult plants. In our previous work, only a major quantitative trait locus (QTL) on chromosome 4AL of the line 8.1 contributed significantly to resistance, whereas QTL on chromosomes 1A, 1B, 2A, 5A and 5B were detected merely on a suggestive level. To verify and characterize all QTLs in the line 8.1, a mapping population of double haploid lines was established. Testing for seedling resistance to 16 different races/mixtures of Blumeria graminis f. sp. tritici revealed four highly significant non-race-specific resistance QTL including the main QTL on chromosome 4AL, and a race-specific QTL on chromosome 5B. The major QTL on chromosome 4AL (QPm.tut-4A) as well as QTL on chromosome 5AL and a newly detected QTL on 7AL were highly effective at the adult stage. The QPm.tut-4A QTL accounts on average for 33-49 % of the variation in resistance in the double haploid population. Interactions between the main QTL QPm.tut-4A and the minor QTL were evaluated and discussed. A population of 98 F(2) plants from a cross of susceptible cv. Chinese Spring and the line 8.1 was created that allowed mapping the QPm.tut-4A locus to the proximal 2.5-cM region of the introgressed segment on chromosome 4AL. The results obtained in this work make it feasible to use QPm.tut-4A in resistance breeding and provide a solid basis for positional cloning of the major QTL. PMID:22534789

Jakobson, Irena; Reis, Diana; Tiidema, Anu; Peusha, Hilma; Timofejeva, Ljudmilla; Valárik, Miroslav; Kladivová, Monika; Simková, Hana; Doležel, Jaroslav; Järve, Kadri

2012-08-01

146

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

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 associated with resistance to Stewart's wilt and common rust, while qNLB1.06Tx303 conferred resistance to Stewart's wilt. The non-specific resistance may be attributed to pleiotropy or linkage. Conclusions Our research has led to successful identification of two reliably-expressed QTL that can potentially be utilized to protect maize from S. turcica in different environments. This approach to identifying and dissecting quantitative resistance in plants will facilitate the application of quantitative resistance in crop protection. PMID:20529319

2010-01-01

147

SRAP-based mapping and QTL detection for inflorescence-related traits in chrysanthemum ( Dendranthema morifolium )  

Microsoft Academic Search

Chrysanthemum (Dendranthema morifolium) is an economically important ornamental species and comprises a large proportion of the flower industry in south-east Asian\\u000a and European countries. In this study, a segregating population of 142 F1 progeny of the cross between the two chrysanthemum cultivars ‘Yuhualuoying’ and ‘Aoyunhanxiao’ was used to construct two\\u000a separate genetic linkage maps via a double pseudo-testcross mapping strategy.

Fei Zhang; Sumei Chen; Fadi Chen; Weimin Fang; Yu Chen; Fengtong Li

2011-01-01

148

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

PubMed Central

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 lymphocyte specific protein tyrosine kinase. Conclusions A panel of markers has been identified that will be validated for use with both genomic and marker-assisted selection to improve resistance of L. rohita to A. hydrophila. PMID:24984705

2014-01-01

149

Insight into the genetic components of community genetics: QTL mapping of insect association in a fast-growing forest tree.  

PubMed

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. PMID:24260320

DeWoody, Jennifer; Viger, Maud; Lakatos, Ferenc; Tuba, Katalin; Taylor, Gail; Smulders, Marinus J M

2013-01-01

150

Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree  

PubMed Central

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. PMID:24260320

DeWoody, Jennifer; Viger, Maud; Lakatos, Ferenc; Tuba, Katalin; Taylor, Gail; Smulders, Marinus J. M.

2013-01-01

151

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

PubMed Central

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

2014-01-01

152

Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip  

PubMed Central

Background The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP) and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses. Results Three generations (F3, Backcross 1 and Backcross 2) of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes. Conclusions The use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine genome annotation. PMID:22607048

2012-01-01

153

Use of AFLP Markers for Gene Mapping and QTL Detection in the Rat  

Microsoft Academic Search

The AFLP technique is a new DNA marker technology based on the selective amplification of restriction fragments. Multiple polymorphic markers are simultaneously produced and can be tested in one PCR. No prior information on genomic DNA sequences is needed. In the current study, we contribute 18 AFLP markers to the linkage map of the rat. Seven AFLP markers were assigned

Myrthe Otsen; Maria den Bieman; Martin T. R. Kuiper; Michal Pravenec; Vladimir Kren; Theodore W. Kurtz; Howard J. Jacob; Ægidius Lankhorst; Bert F. M. van Zutphen

1996-01-01

154

Mapping minor QTL for increased stearic acid content in sunflower seed oil  

Microsoft Academic Search

Increased stearic acid (C18:0) content in the seed oil of sunflower would improve the oil quality for some edible uses. The sunflower line CAS-20 (C18:0 genotype Es1Es1es2es2), developed from the high C18:0 mutant line CAS-3 (C18:0 genotype es1es1es2es2; 25% C18:0), shows increased C18:0 levels in its seed oil (8.6%). The objective of this research was to map quantitative trait loci

Begoña Pérez-Vich; Steven J. Knapp; Alberto J. Leon; José M. Fernández-Martínez; Simon T. Berry

2004-01-01

155

Comparative mapping reveals similar linkage of functional genes to QTL of yield-related traits between Brassica napus and Oryza sativa.  

PubMed

Oryza sativa and Brassica napus-two important crops for food and oil, respectively-share high seed yield as a common breeding goal. As a model plant, O. sativa genomics have been intensively investigated and its agronomic traits have been advanced. In the present study, we used the available information on O. sativa to conduct comparative mapping between O. sativa and B. napus, with the aim of advancing research on seed-yield and yield-related traits in B. napus. Firstly, functional markers (from 55 differentially expressed genes between a hybrid and its parents) were used to detect B. napus genes that co-localized with yield-related traits in an F(2:3) population. Referring to publicly available sequences of 55 B. napus genes, 53 homologous O. sativa genes were subsequently detected by screening, and their chromosomal locations were determined using silico mapping. Comparative location of yield-related QTL between the two species showed that a total of 37 O. sativa and B. napus homologues were located in similar yield-related QTL between species. Our results indicate that homologous genes between O. sativa and B. napus may have consistent function and control similar traits, which may be helpful for agronomic gene characterization in B. napus based on what is known in O. sativa. PMID:22942086

Li, Fupeng; Ma, Chaozhi; Chen, Qingfang; Liu, Touming; Shen, Jinxiong; Tu, Jinxing; Xing, Yongzhong; Fu, Tingdong

2012-08-01

156

Fine mapping and characterization of linked quantitative trait loci involved in the transition of the maize apical meristem from vegetative to generative structures.  

PubMed Central

Quantitative trait locus (QTL) mapping has detected two linked QTL in the 8L chromosome arm segment introgressed from Gaspé Flint (a Northern Flint open-pollinated population) into the background of N28 (a Corn Belt Dent inbred line). Homozygous recombinant lines, with a variable length of the introgressed segment, confirmed the presence of the two previously identified, linked QTL. In the N28 background, Gaspé Flint QTL alleles at both loci induce a reduction in node number, height, and days to anthesis (pollen shed). Given the determinate growth pattern of maize, the phenotypic effects indicate that the two QTL are involved in the transition of the apical meristem from vegetative to generative structures. Relative to the effects of the two QTL in the background of N28, we distinguish two general developmental factors affecting the timing of pollen shed. The primary factor is the timing of the transition of the apical meristem. The second, derivative factor is the global extent of internode elongation. Having separated the two linked QTL, we have laid the foundation for the positional cloning of the QTL with a larger effect. PMID:10511573

Vl?du?u, C; McLaughlin, J; Phillips, R L

1999-01-01

157

hi2-1, A QTL which improves harvest index, earliness and alters metabolite accumulation of processing tomatoes  

PubMed Central

Harvest index, defined as the ratio of reproductive yield to total plant biomass, and early ripening are traits with important agronomic value in processing tomatoes. The Solanum pennellii introgression-line (IL) population shows variation for harvest index and earliness. Most of the QTL mapped for these traits display negative agronomic effects; however, hi2-1 is a unique QTL displaying improved harvest index and earliness. This introgression was tested over several years and under different genetic backgrounds. Thirty-one nearly isogenic sub-lines segregating for the 18 cM TG33–TG276 interval were used for fine mapping of this multi-phenotypic QTL. Based on this analysis the phenotypic effects for plant weight, Brix, total yield and earliness were co-mapped to the same region. In a different mapping experiment these sub-lines were tested as heterozygotes in order to map the harvest index QTL which were only expressed in the heterozygous state. These QTL mapped to the same candidate region, suggesting that hi2-1 is either a single gene with pleiotropic effects or represents linked genes independently affecting these traits. Metabolite profiling of the fruit pericarp revealed that a number of metabolic QTL co-segregate with the harvest index trait including those for important transport assimilates such as sugars and amino acids. Analysis of the flowering pattern of these lines revealed induced flowering at IL2-1 plants, suggest that hi2-1 may also affect harvest index and early ripening by changing plant architecture and flowering rate. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1412-8) contains supplementary material, which is available to authorized users. PMID:20680612

Gur, Amit; Osorio, Sonia; Fridman, Eyal; Zamir, Dani

2010-01-01

158

hi2-1, a QTL which improves harvest index, earliness and alters metabolite accumulation of processing tomatoes.  

PubMed

Harvest index, defined as the ratio of reproductive yield to total plant biomass, and early ripening are traits with important agronomic value in processing tomatoes. The Solanum pennellii introgression-line (IL) population shows variation for harvest index and earliness. Most of the QTL mapped for these traits display negative agronomic effects; however, hi2-1 is a unique QTL displaying improved harvest index and earliness. This introgression was tested over several years and under different genetic backgrounds. Thirty-one nearly isogenic sub-lines segregating for the 18 cM TG33-TG276 interval were used for fine mapping of this multi-phenotypic QTL. Based on this analysis the phenotypic effects for plant weight, Brix, total yield and earliness were co-mapped to the same region. In a different mapping experiment these sub-lines were tested as heterozygotes in order to map the harvest index QTL which were only expressed in the heterozygous state. These QTL mapped to the same candidate region, suggesting that hi2-1 is either a single gene with pleiotropic effects or represents linked genes independently affecting these traits. Metabolite profiling of the fruit pericarp revealed that a number of metabolic QTL co-segregate with the harvest index trait including those for important transport assimilates such as sugars and amino acids. Analysis of the flowering pattern of these lines revealed induced flowering at IL2-1 plants, suggest that hi2-1 may also affect harvest index and early ripening by changing plant architecture and flowering rate. PMID:20680612

Gur, Amit; Osorio, Sonia; Fridman, Eyal; Fernie, Alisdair R; Zamir, Dani

2010-11-01

159

An entropy-based index for fine-scale mapping of disease genes.  

PubMed

By comparing the entropy and the conditional entropy in a marker, an entropy-based index has been presented for fine-scale linkage disequilibrium gene mapping using high-density marker maps for human disease genes. The index can quantify the level of linkage disequilibrium (LD) between the marker and the disease susceptibility locus (DSL) of genes. The advantage of using the index is attributed to the fact that it does not depend on marker allele frequencies across loci. Moreover, it is parallel to Hardy-Weinberg disequilibrium (HWD) measure for DSL fine mapping. Through various simulations, the fine mapping performances of the proposed entropy-based index was extensively investigated under various genetic parameters. The results show that the index presented is both robust and powerful for DSL mapping in genes. PMID:17643952

Li, Yumei; Xiang, Yang; Deng, Hongwen; Sun, Zhenqiu

2007-07-01

160

Construction of a first genetic map of distylous Turnera and a fine-scale map of the S -locus region  

Microsoft Academic Search

As a prelude to discovery of genes involved in floral dimorphism and incompatibility, a genetic map of disty- lous Turnera was constructed along with a fine-scale map of the S-locus region. The genetic map consists of 79 PCR- based molecular markers (48 AFLP, 18 RAPD, 9 ISSR, 4 RAMP), 5 isozyme loci, one additional gene, and the S-locus, spanning a

J. D. J. Labonne; A. Vaisman; J. S. Shore

2008-01-01

161

Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation inter-cross population.  

PubMed

Animals in nature are frequently challenged by toxic compounds, from those that occur naturally in plants as a defense against herbivory, to pesticides used to protect crops. On exposure to such xenobiotic substances, animals mount a transcriptional response, generating detoxification enzymes and transporters that metabolize and remove the toxin. Genetic variation in this response can lead to variation in the susceptibility of different genotypes to the toxic effects of a given xenobiotic. Here we use Drosophila melanogaster to dissect the genetic basis of larval resistance to nicotine, a common plant defense chemical and widely used addictive drug in humans. We identified quantitative trait loci (QTL) for the trait using the DSPR (Drosophila Synthetic Population Resource), a panel of multiparental advanced intercross lines. Mapped QTL collectively explain 68.4% of the broad-sense heritability for nicotine resistance. The two largest-effect loci-contributing 50.3 and 8.5% to the genetic variation-map to short regions encompassing members of classic detoxification gene families. The largest QTL resides over a cluster of ten UDP-glucuronosyltransferase (UGT) genes, while the next largest QTL harbors a pair of cytochrome P450 genes. Using RNAseq we measured gene expression in a pair of DSPR founders predicted to harbor different alleles at both QTL and showed that Ugt86Dd, Cyp28d1, and Cyp28d2 had significantly higher expression in the founder carrying the allele conferring greater resistance. These genes are very strong candidates to harbor causative, regulatory polymorphisms that explain a large fraction of the genetic variation in larval nicotine resistance in the DSPR. PMID:25236448

Marriage, Tara N; King, Elizabeth G; Long, Anthony D; Macdonald, Stuart J

2014-09-01

162

Joint QTL analyses for partial resistance to Phytophthora sojae using six nested inbred populations with heterogeneous conditions  

Technology Transfer Automated Retrieval System (TEKTRAN)

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...

163

A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content  

Technology Transfer Automated Retrieval System (TEKTRAN)

Background: The availability of a high-density SNP chip and a reference genome sequence of the pig have enabled the construction of a high-density linkage map. A high density linkage map is an essential tool for the further fine-mapping of QTL for a variety of traits in the pig and for a better und...

164

Genetic architecture of sensory exploitation: QTL mapping of female and male receiver traits in an acoustic moth.  

PubMed

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. PMID:24118224

Alem, S; Streiff, R; Courtois, B; Zenboudji, S; Limousin, D; Greenfield, M D

2013-12-01

165

The age related markers lipofuscin and apoptosis show different genetic architecture by QTL mapping in short-lived Nothobranchius fish  

PubMed Central

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

Ng'oma, Enoch; Reichwald, Kathrin; Dorn, Alexander; Wittig, Michael; Balschun, Tobias; Franke, Andre; Platzer, Matthias; Cellerino, Allesandro

2014-01-01

166

Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses  

PubMed Central

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 ?-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 ?-decalactone production in ripening fruit. The FaFAD1 gene is specifically expressed in ripe fruits and its expression fully correlates with the presence of ?-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 ?-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 ?-decalactone is naturally controlled in strawberry, and proposes enzymatic activities necessary for the formation of this VOC in plants. PMID:24742100

2014-01-01

167

Applying QTL analysis to conservation genetics  

Microsoft Academic Search

Both analytical and molecular tools currently exist that can be used to prolifically apply quantitative trait loci (QTL) analysis\\u000a to the study of natural populations. In this communication, we review and exemplify the use of QTL mapping tools and genetic\\u000a modeling for conservation geneticists. We simulate populations inspired by relevant cases that can be encountered in the field\\u000a and analyze

François Besnier; Arnaud Le Rouzic; José M. Álvarez-Castro

2010-01-01

168

Microarray assisted fine mapping of quantitative trait loci on Chromosome 15 for susceptibility to seizure-induced cell death in mice  

PubMed Central

Prior studies with crosses of the FVB/NJ (FVB; seizure-induced cell death susceptible) mouse and the seizure-induced cell death resistant mouse, C57BL/6J (B6), revealed the presence of a quantitative trait locus (QTL) on chromosome 15 (Chr. 15) that influenced susceptibility to kainic acid-induced cell death (Sicd2). In an earlier study, we confirmed that the Sicd2 interval harbors gene(s) conferring strong protection against seizure-induced cell death through the creation of the FVB.B6-Sicd2 congenic strain and created three interval-specific congenic lines (ISCLs) that encompass Sicd2 on Chr. 15 to fine-map this locus. To further localize this Sicd2 QTL, an additional congenic line carrying overlapping intervals of the B6 segment was created (ISCL-4) and compared to previously created ISCLs-1-3 and assessed for seizure-induced cell death phenotype. While all of the ISCLs exhibited reduced cell death associated with the B6 phenotype, the most dramatic of these, ISCL-4 showed the most extensive reduction in seizure-induced cell death throughout all hippocampal subfields. In order to characterize the susceptibility loci on Sicd2 using this ISCL and identify compelling candidate genes, we have undertaken an integrative genomic strategy of comparing exon transcript abundance in the hippocampus of this newly developed Chr. 15 subcongenic line (ISCL-4) and FVB-like littermates. We identified ten putative candidate genes that are alternatively spliced between the strains and may govern strain-dependent differences in susceptibility to seizure-induced excitotoxic cell death. These results illustrate the importance of identifying transcriptomics variants in expression studies, and implicate novel candidate genes conferring susceptibility to seizure-induced cell death. PMID:24001120

Schauwecker, P. Elyse

2013-01-01

169

Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine mapping by selective sweep analysis  

PubMed Central

Drosophila melanogaster is a cosmopolitan species that colonizes a great variety of environments. One trait that shows abundant evidence for naturally segregating genetic variance in different populations of D. melanogaster is cold tolerance. Previous work has found quantitative trait loci (QTL) exclusively on the second and the third chromosomes. To gain insight into the genetic architecture of cold tolerance on the X chromosome and to compare the results with our analyses of selective sweeps, a mapping population was derived from a cross between substitution lines that solely differed in the origin of their X chromosome: one originates from a European inbred line and the other one from an African inbred line. We found a total of six QTL for cold tolerance factors on the X chromosome of D. melanogaster. Although the composite interval mapping revealed slightly different QTL profiles between sexes, a coherent model suggests that most QTL overlapped between sexes, and each explained around 5–14% of the genetic variance (which may be slightly overestimated). The allelic effects were largely additive, but we also detected two significant interactions. Taken together, this provides evidence for multiple QTL that are spread along the entire X chromosome and whose effects range from low to intermediate. One detected transgressive QTL influences cold tolerance in different ways for the two sexes. While females benefit from the European allele increasing their cold tolerance, males tend to do better with the African allele. Finally, using selective sweep mapping, the candidate gene CG16700 for cold tolerance colocalizing with a QTL was identified. PMID:21199023

SVETEC, NICOLAS; WERZNER, ANNEGRET; WILCHES, RICARDO; PAVLIDIS, PAVLOS; ÁLVAREZ-CASTRO, JOSÉ M.; BROMAN, KARL W.; METZLER, DIRK; STEPHAN, WOLFGANG

2013-01-01

170

Genome-wide interval mapping using SNPs identifies new QTL for growth, body composition and several physiological variables in an F2 intercross between fat and lean chicken lines  

PubMed Central

Background For decades, genetic improvement based on measuring growth and body composition traits has been successfully applied in the production of meat-type chickens. However, this conventional approach is hindered by antagonistic genetic correlations between some traits and the high cost of measuring body composition traits. Marker-assisted selection should overcome these problems by selecting loci that have effects on either one trait only or on more than one trait but with a favorable genetic correlation. In the present study, identification of such loci was done by genotyping an F2 intercross between fat and lean lines divergently selected for abdominal fatness genotyped with a medium-density genetic map (120 microsatellites and 1302 single nucleotide polymorphisms). Genome scan linkage analyses were performed for growth (body weight at 1, 3, 5, and 7 weeks, and shank length and diameter at 9 weeks), body composition at 9 weeks (abdominal fat weight and percentage, breast muscle weight and percentage, and thigh weight and percentage), and for several physiological measurements at 7 weeks in the fasting state, i.e. body temperature and plasma levels of IGF-I, NEFA and glucose. Interval mapping analyses were performed with the QTLMap software, including single-trait analyses with single and multiple QTL on the same chromosome. Results Sixty-seven QTL were detected, most of which had never been described before. Of these 67 QTL, 47 were detected by single-QTL analyses and 20 by multiple-QTL analyses, which underlines the importance of using different statistical models. Close analysis of the genes located in the defined intervals identified several relevant functional candidates, such as ACACA for abdominal fatness, GHSR and GAS1 for breast muscle weight, DCRX and ASPSCR1 for plasma glucose content, and ChEBP for shank diameter. Conclusions The medium-density genetic map enabled us to genotype new regions of the chicken genome (including micro-chromosomes) that influenced the traits investigated. With this marker density, confidence intervals were sufficiently small (14 cM on average) to search for candidate genes. Altogether, this new information provides a valuable starting point for the identification of causative genes responsible for important QTL controlling growth, body composition and metabolic traits in the broiler chicken. PMID:24079476

2013-01-01

171

Fine mapping of canine parvovirus B cell epitopes.  

PubMed

In this report we describe the topological mapping of neutralizing domains of canine parvovirus (CPV). We obtained 11 CPV-specific monoclonal antibodies (MAbs), six of which are neutralizing. The reactivities were as determined by ELISA and Western blot (immunoblot) analysis. VP2, the most abundant protein of the CPV capsid, seemed to contain all the neutralization sites. Also, an almost full-length genomic clone of CPV was constructed in the bacterial plasmid pUC18 to enable expression of CPV proteins. All the neutralizing MAbs recognized recombinant VP2 when it was expressed as a free protein in Escherichia coli but not when expressed as a fusion protein with glutathione-S-transferase. When two large fragments containing about 85% and 67% of the C terminus of VP2 were expressed, no neutralization sites were detected. When fusion proteins containing the N terminus were expressed, two linear determinants were mapped, one between residues 1 to 10 of VP2, and the other between amino acids 11 and 23. The peptide 11 GQPAVRNERATGS 23, recognized by MAb 3C9, was synthesized chemically and checked for immunogenicity, not being able to induce neutralizing activity. Although the antibody response in rabbits to all the fusion proteins was uniformly high, the anti-CPV response was very variable. Protein from pCPVEx11, which contains a T cell epitope (peptide PKIFINLAKKKKAG) present in the VP1-specific region as well as the B cell epitopes, seemed to be the most effective in inducing virus neutralization. PMID:1919526

López de Turiso, J A; Cortés, E; Ranz, A; García, J; Sanz, A; Vela, C; Casal, J I

1991-10-01

172

A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content  

Microsoft Academic Search

We have developed a new DH mapping population for oilseed rape, named TNDH, using genetically and phenotypically diverse parental lines. We used the population in the construction of a high stringency genetic linkage map, consisting of 277 loci, for use in quantitative genetic analysis. A proportion of the markers had been used previously in the construction of linkage maps for

D. Qiu; C. Morgan; J. Shi; Y. Long; J. Liu; R. Li; X. Zhuang; Y. Wang; X. Tan; E. Dietrich; T. Weihmann; C. Everett; S. Vanstraelen; P. Beckett; F. Fraser; M. Trick; S. Barnes; J. Wilmer; R. Schmidt; J. Li; D. Li; J. Meng; I. Bancroft

2006-01-01

173

Characterization and Mapping of Very Fine Particles in an Engine Machining and Assembly Facility  

Microsoft Academic Search

Very fine particle number and mass concentrations were mapped in an engine machining and assembly facility in the winter and summer. A condensation particle counter (CPC) was used to measure particle number concentrations in the 0.01 ? m to 1 ? m range, and an optical particle counter (OPC) was used to measure particle number concentrations in 15 channels between

William A. Heitbrink; Douglas E. Evans; Thomas M. Peters; Thomas J. Slavin

2007-01-01

174

ORIGINAL PAPER Fine mapping of fw3.2 controlling fruit weight in tomato  

E-print Network

ORIGINAL PAPER Fine mapping of fw3.2 controlling fruit weight in tomato Na Zhang · Marin Talbot in the Solanaceae family. One of the key traits selected during domestication is fruit mass which is con- trolled by many quantitative trait loci. The fruit weight locus fw3.2 is one of the major loci responsible

van der Knaap, Esther

175

Searching QTL by gene expression: analysis of diabesity  

Microsoft Academic Search

BACKGROUND: Recent developments in sequence databases provide the opportunity to relate the expression pattern of genes to their genomic position, thus creating a transcriptome map. Quantitative trait loci (QTL) are phenotypically-defined chromosomal regions that contribute to allelically variant biological traits, and by overlaying QTL on the transcriptome, the search for candidate genes becomes extremely focused. RESULTS: We used our novel

Aaron C Brown; William I Olver; Charles J Donnelly; Marjorie E May; Jürgen K Naggert; Daniel J Shaffer; Derry C Roopenian

2005-01-01

176

Saturation of an Intra-Gene Pool Linkage Map: Towards a Unified Consensus Linkage Map for Fine Mapping and Synteny Analysis in Common Bean  

PubMed Central

Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364×BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364×G19833 (DG) and BAT93×JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning. PMID:22174773

Galeano, Carlos H.; Fernandez, Andrea C.; Franco-Herrera, Natalia; Cichy, Karen A.; McClean, Phillip E.; Vanderleyden, Jos; Blair, Matthew W.

2011-01-01

177

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

Microsoft Academic Search

We constructed a linkage map for the population QDH, which was derived from a cross between an oilseed rape cultivar and a\\u000a 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.

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

2011-01-01

178

Functional screening of willow alleles in Arabidopsis combined with QTL mapping in willow (Salix) identifies SxMAX4 as a coppicing response gene.  

PubMed

Willows (Salix spp.) are important biomass crops due to their ability to grow rapidly with low fertilizer inputs and ease of cultivation in short-rotation coppice cycles. They are relatively undomesticated and highly diverse, but functional testing to identify useful allelic variation is time-consuming in trees and transformation is not yet possible in willow. Arabidopsis is heralded as a model plant from which knowledge can be transferred to advance the improvement of less tractable species. Here, knowledge and methodologies from Arabidopsis were successfully used to identify a gene influencing stem number in coppiced willows, a complex trait of key biological and industrial relevance. The strigolactone-related More AXillary growth (MAX) genes were considered candidates due to their role in shoot branching. We previously demonstrated that willow and Arabidopsis show similar response to strigolactone and that transformation rescue of Arabidopsis max mutants with willow genes could be used to detect allelic differences. Here, this approach was used to screen 45 SxMAX1, SxMAX2, SxMAX3 and SxMAX4 alleles cloned from 15 parents of 11 mapping populations varying in shoot-branching traits. Single-nucleotide polymorphism (SNP) frequencies were locus dependent, ranging from 29.2 to 74.3 polymorphic sites per kb. SxMAX alleles were 98%-99% conserved at the amino acid level, but different protein products varying in their ability to rescue Arabidopsis max mutants were identified. One poor rescuing allele, SxMAX4D, segregated in a willow mapping population where its presence was associated with increased shoot resprouting after coppicing and colocated with a QTL for this trait. PMID:24393130

Salmon, Jemma; Ward, Sally P; Hanley, Steven J; Leyser, Ottoline; Karp, Angela

2014-05-01

179

Fatness QTL on chicken chromosome 5 and interaction with sex  

PubMed Central

Quantitative trait loci (QTL) affecting fatness in male chickens were previously identified on chromosome 5 (GGA5) in a three-generation design derived from two experimental chicken lines divergently selected for abdominal fat weight. A new design, established from the same pure lines, produced 407 F2 progenies (males and females) from 4 F1-sire families. Body weight and abdominal fat were measured on the F2 at 9 wk of age. In each sire family, selective genotyping was carried out for 48 extreme individuals for abdominal fat using seven microsatellite markers from GGA5. QTL analyses confirmed the presence of QTL for fatness on GGA5 and identified a QTL by sex interaction. By crossing one F1 sire heterozygous at the QTL with lean line dams, three recombinant backcross 1 (BC1) males were produced and their QTL genotypes were assessed in backcross 2 (BC2) progenies. These results confirmed the QTL by sex interaction identified in the F2 generation and they allow mapping of the female QTL to less than 8 Mb at the distal part of the GGA5. They also indicate that fat QTL alleles were segregating in both fat and lean lines. PMID:16635451

Abasht, Behnam; Pitel, Frédérique; Lagarrigue, Sandrine; Le Bihan-Duval, Elisabeth; Le Roy, Pascale; Demeure, Olivier; Vignoles, Florence; Simon, Jean; Cogburn, Larry; Aggrey, Sammy; Vignal, Alain; Douaire, Madeleine

2006-01-01

180

Genetic linkage map of melon ( Cucumis melo L.) and localization of a major QTL for powdery mildew resistance  

Microsoft Academic Search

Powdery mildew caused by Podosphaera xanthii has become a major problem in melon since it occurs all year round irrespective of the growing system. The TGR-1551 melon\\u000a genotype was found to be resistant to several melon diseases, among them powdery mildew. However, the corresponding resistance\\u000a genes have been never mapped. We constructed an integrated genetic linkage map using an F2

Fernando J. Yuste-LisbonaCarmen; Carmen Capel; Emilio Sarria; Rocío Torreblanca; María L. Gómez-Guillamón; Juan Capel; Rafael Lozano; Ana I. López-Sesé

2011-01-01

181

SNPs detection in DHPS-WDR83 overlapping genes mapping on porcine chromosome 2 in a QTL region for meat pH  

PubMed Central

Background The pH is an important parameter influencing technological quality of pig meat, a trait affected by environmental and genetic factors. Several quantitative trait loci associated to meat pH are described on PigQTL database but only two genes influencing this parameter have been so far detected: Ryanodine receptor 1 and Protein kinase, AMP-activated, gamma 3 non-catalytic subunit. To search for genes influencing meat pH we analyzed genomic regions with quantitative effect on this trait in order to detect SNPs to use for an association study. Results The expressed sequences mapping on porcine chromosomes 1, 2, 3 in regions associated to pork pH were searched in silico to find SNPs. 356 out of 617 detected SNPs were used to genotype Italian Large White pigs and to perform an association analysis with meat pH values recorded in semimembranosus muscle at about 1 hour (pH1) and 24 hours (pHu) post mortem. The results of the analysis showed that 5 markers mapping on chromosomes 1 or 3 were associated with pH1 and 10 markers mapping on chromosomes 1 or 2 were associated with pHu. After False Discovery Rate correction only one SNP mapping on chromosome 2 was confirmed to be associated to pHu. This polymorphism was located in the 3’UTR of two partly overlapping genes, Deoxyhypusine synthase (DHPS) and WD repeat domain 83 (WDR83). The overlapping of the 3’UTRs allows the co-regulation of mRNAs stability by a cis-natural antisense transcript method of regulation. DHPS catalyzes the first step in hypusine formation, a unique amino acid formed by the posttranslational modification of the protein eukaryotic translation initiation factor 5A in a specific lysine residue. WDR83 has an important role in the modulation of a cascade of genes involved in cellular hypoxia defense by intensifying the glycolytic pathway and, theoretically, the meat pH value. Conclusions The involvement of the SNP detected in the DHPS/WDR83 genes on meat pH phenotypic variability and their functional role are suggestive of molecular and biological processes related to glycolysis increase during post-mortem phase. This finding, after validation, can be applied to identify new biomarkers to be used to improve pig meat quality. PMID:24103193

2013-01-01

182

Mapping QTL for resistance to frosty pod and black pod diseases, and for horticultural traits in Theobroma cacao L.  

Technology Transfer Automated Retrieval System (TEKTRAN)

An F1 heterozygous mapping population of cacao (Theobroma cacao L.) was created and evaluated for resistance to frosty pod (Moniliophthora roreri [Cif. and Par.]), black pod (Phytophtora palmivora [Butl.] Butl.) and for five horticultural traits at CATIE in Turrialba, Costa Rica. The population cons...

183

Genetic mapping and QTL analysis of horticultural traits in cucumber ( Cucumis sativus L.) using recombinant inbred lines  

Microsoft Academic Search

A set of 171 recombinant inbred lines (RIL) were developed from a narrow cross in cucumber ( Cucumis sativus L.; 2n = 2 x = 14) using the determinate ( de), gynoecious ( F), standard-sized leaf line G421 and the indeterminate, monoecious, little-leaf ( ll) line H-19. A 131-point genetic map was constructed using these RILs and 216 F 2

G. Fazio; J. E. Staub; M. R. Stevens

2003-01-01

184

Identification of QTL for drought tolerance and characterization of extreme phenotypes in the Buster x Roza mapping population  

Technology Transfer Automated Retrieval System (TEKTRAN)

Terminal and intermittent drought limits dry bean production worldwide.The Buster/Roza mapping population (140 F7:9 RILs) has been screened for drought tolerance across multiple years/locations. In 2011 and 2012 the RILs were tested for terminal drought response at two locations: Othello, WA and Sco...

185

Genome-wide protein QTL mapping identifies human plasma kallikrein as a post-translational regulator of serum uPAR levels  

PubMed Central

The soluble cleaved urokinase plasminogen activator receptor (scuPAR) is a circulating protein detected in multiple diseases, including various cancers, cardiovascular disease, and kidney disease, where elevated levels of scuPAR have been associated with worsening prognosis and increased disease aggressiveness. We aimed to identify novel genetic and biomolecular mechanisms regulating scuPAR levels. Elevated serum scuPAR levels were identified in asthma (n=514) and chronic obstructive pulmonary disease (COPD; n=219) cohorts when compared to controls (n=96). In these cohorts, a genome-wide association study of serum scuPAR levels identified a human plasma kallikrein gene (KLKB1) promoter polymorphism (rs4253238) associated with serum scuPAR levels in a control/asthma population (P=1.17×10?7), which was also observed in a COPD population (combined P=5.04×10?12). Using a fluorescent assay, we demonstrated that serum KLKB1 enzymatic activity was driven by rs4253238 and is inverse to scuPAR levels. Biochemical analysis identified that KLKB1 cleaves scuPAR and negates scuPAR's effects on primary human bronchial epithelial cells (HBECs) in vitro. Chymotrypsin was used as a proproteolytic control, while basal HBECs were used as a control to define scuPAR-driven effects. In summary, we reveal a novel post-translational regulatory mechanism for scuPAR using a hypothesis-free approach with implications for multiple human diseases.—Portelli, M. A., Siedlinski, M., Stewart, C. E., Postma, D. S., Nieuwenhuis, M. A., Vonk, J. M., Nurnberg, P., Altmuller, J., Moffatt, M. F., Wardlaw, A. J., Parker, S. G., Connolly, M. J., Koppelman, G. H., Sayers, I. Genome-wide protein QTL mapping identifies human plasma kallikrein as a post-translational regulator of serum uPAR levels. PMID:24249636

Portelli, Michael A.; Siedlinski, Mateusz; Stewart, Ceri E.; Postma, Dirkje S.; Nieuwenhuis, Maartje A.; Vonk, Judith M.; Nurnberg, Peter; Altmuller, Janine; Moffatt, Miriam F.; Wardlaw, Andrew J.; Parker, Stuart G.; Connolly, Martin J.; Koppelman, Gerard H.; Sayers, Ian

2014-01-01

186

Genetic mapping and QTL analysis for disease resistance using F2 and F5 mapping population derived from the same cross in peanut (Arachis hypogaea L.)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Achieving a high dense genetic map in peanut is very challenging due to availability of limited genomic resources, low polymorphism and large genome. Realizing the importance of dense genetic maps in several genetic and breeding applications, a mapping population derived from Tifrunner × GT-C20 (T p...

187

Informative markers identification and multivariate analysis of selected DxP for the purpose of QTL mapping  

NASA Astrophysics Data System (ADS)

A study was carried out to generate a linkage map of oil palm dura x pisifera (DXP) population. A subset of sample from a DXP mapping family was screened using 325 SSR primers, of which 221 were informative. To date, 150 SSRs have been genotyped across the entire DxP population via capillary sequencer, where 73 SSRs had 1:1 segregation ratio, 64 had 1:1:1:1, 3 had 3:1 and ten had 1:2:1 segregation ratios. Kolmogorov-Smirnov tests by SPSS revealed that most of the bunch quality components had normal distribution which fulfilled one of the pre-requisites to carry out phenotype-genotype correlation association.

Hazirah S., Z.; Maizura, I.; Rajinder, S.; Mohd Isa Z., A.; Ismanizan, I.

2014-09-01

188

Favorable QTL Alleles for Yield and Its Components Identified by Association Mapping in Chinese Upland Cotton Cultivars  

PubMed Central

Linkage disequilibrium based association mapping is a powerful tool for dissecting the genetic basis underlying complex traits. In this study, an association mapping panel consisting of 356 representative Upland cotton cultivars was constructed, evaluated in three environments and genotyped using 381 SSRs to detect molecular markers associated with lint yield and its components. The results showed that abundant phenotypic and moderate genetic diversities existed within this germplasm panel. The population could be divided into two subpopulations, and weak relatedness was detected between pair-wise accessions. LD decayed to the background (r2?=?0.1182, P?0.01), r2?=?0.1 and r2?=?0.2 level within 12–13 cM, 17–18 cM and 3–4 cM, respectively, providing the potential for association mapping of agronomically important traits in Chinese Upland cotton. A total of 55 marker-trait associations were detected between 26 SSRs and seven lint yield traits, based on a mixed linear model (MLM) and Bonferroni correction (P?0.05/145, ?log10P?3.46). Of which 41 could be detected in more than one environment and 17 markers were simultaneously associated with two or more traits. Many associations were consistent with QTLs identified by linkage mapping in previous reports. Phenotypic values of alleles of each loci in 41 stably detected associations were compared, and 23 favorable alleles were identified. Population frequency of each favorable allele in historically released cultivar groups was also evaluated. The QTLs detected in this study will be helpful in further understanding the genetic basis of lint yield and its components, and the favorable alleles may facilitate future high-yield breeding by genomic selection in Upland cotton. PMID:24386089

Mei, Hongxian; Zhu, Xiefei; Zhang, Tianzhen

2013-01-01

189

Fine mapping, physical mapping and development of diagnostic markers for the Rrs2 scald resistance gene in barley.  

PubMed

The Rrs2 gene confers resistance to the fungal pathogen Rhynchosporium secalis which causes leaf scald, a major barley disease. The Rrs2 gene was fine mapped to an interval of 0.08 cM between markers 693M6_6 and P1D23R on the distal end of barley chromosome 7HS using an Atlas (resistant) x Steffi (susceptible) mapping population of 9,179 F(2)-plants. The establishment of a physical map of the Rrs2 locus led to the discovery that Rrs2 is located in an area of suppressed recombination within this mapping population. The analysis of 58 barley genotypes revealed a large linkage block at the Rrs2 locus extending over several hundred kb which is present only in Rrs2 carrying cultivars. Due to the lack of recombination in the mapping population and the presence of a Rrs2-specific linkage block, we assume a local chromosomal rearrangement (alien introgression or inversion) in Rrs2 carrying varieties. The variety analysis led to the discovery of eight SNPs which were diagnostic for the Rrs2 phenotype. Based on these SNPs diagnostic molecular markers (CAPS and pyrosequencing markers) were developed which are highly useful for marker-assisted selection in resistance gene pyramiding programmes for Rhynchosporium secalis resistance in barley. PMID:19789848

Hanemann, Anja; Schweizer, Günther F; Cossu, Roberto; Wicker, Thomas; Röder, Marion S

2009-11-01

190

Conditional QTL underlying resistance to late blight in a diploid potato population.  

PubMed

A large number of quantitative trait loci (QTL) for resistance to late blight of potato have been reported with a "conventional" method in which each phenotypic trait reflects the cumulative genetic effects for the duration of the disease process. However, as genes controlling response to disease may have unique contributions with specific temporal features, it is important to consider the phenotype as dynamic. Here, using the net genetic effects evidenced at consecutive time points during disease development, we report the first conditional mapping of QTL underlying late blight resistance in potato under five environments in Peru. Six conditional QTL were mapped, one each on chromosome 2, 7 and 12 and three on chromosome 9. These QTL represent distinct contributions to the phenotypic variation at different stages of disease development. By comparison, when conventional mapping was conducted, only one QTL was detected on chromosome 9. This QTL was the same as one of the conditional QTL. The results imply that conditional QTL reflect genes that function at particular stages during the host-pathogen interaction. The dynamics revealed by conditional QTL mapping could contribute to the understanding of the molecular mechanism of late blight resistance and these QTL could be used to target genes for marker development or manipulation to improve resistance. PMID:22274766

Li, Jingcai; Lindqvist-Kreuze, Hannele; Tian, Zhendong; Liu, Jun; Song, Botao; Landeo, Juan; Portal, Leticia; Gastelo, Manuel; Frisancho, Julio; Sanchez, Laura; Meijer, Dennis; Xie, Conghua; Bonierbale, Merideth

2012-05-01

191

Fine Mapping of qRC10-2, a Quantitative Trait Locus for Cold Tolerance of Rice Roots at Seedling and Mature Stages  

PubMed Central

Cold stress causes various injuries to rice seedlings in low-temperature and high-altitude areas and is therefore an important factor affecting rice production in such areas. In this study, root conductivity (RC) was used as an indicator to map quantitative trait loci (QTLs) of cold tolerance in Oryza rufipogon Griff., Dongxiang wild rice (DX), at its two-leaf stage. The correlation coefficients between RC and the plant survival rate (PSR) at the seedling and maturity stages were –0.85 and –0.9 (P?=?0.01), respectively, indicating that RC is a reliable index for evaluating cold tolerance of rice. A preliminary mapping group was constructed from 151 BC2F1 plants using DX as a cold-tolerant donor and the indica variety Nanjing 11 (NJ) as a recurrent parent. A total of 113 codominant simple-sequence repeat (SSR) markers were developed, with a parental polymorphism of 17.3%. Two cold-tolerant QTLs, named qRC10-1 and qRC10-2 were detected on chromosome 10 by composite interval mapping. qRC10-1 (LOD?=?3.1, RM171-RM1108) was mapped at 148.3 cM, and qRC10-2 (LOD?=?6.1, RM25570-RM304) was mapped at 163.3 cM, which accounted for 9.4% and 32.1% of phenotypic variances, respectively. To fine map the major locus qRC10-2, NJ was crossed with a BC4F2 plant (L188-3), which only carried the QTL qRC10-2, to construct a large BC5F2 fine-mapping population with 13,324 progenies. Forty-five molecular markers were designed to evenly cover qRC10-2, and 10 markers showed polymorphisms between DX and NJ. As a result, qRC10-2 was delimited to a 48.5-kb region between markers qc45 and qc48. In this region, Os10g0489500 and Os10g0490100 exhibited different expression patterns between DX and NJ. Our results provide a basis for identifying the gene(s) underlying qRC10-2, and the markers developed here may be used to improve low-temperature tolerance of rice seedling and maturity stages via marker-assisted selection (MAS). Key Message With root electrical conductivity used as a cold-tolerance index, the quantitative trait locus qRC10-2 was fine mapped to a 48.5-kb candidate region, and Os10g0489500 and Os10g0490100 were identified as differently expressed genes for qRC10-2. PMID:24788204

Zhang, Xiao-xiang; Gao, Yong; Li, Ai-hong; Dai, Yi; Yu, Ling; Liu, Guang-qing; Pan, Cun-hong; Li, Yu-hong; Dai, Zheng-yuan; Chen, Jian-min

2014-01-01

192

Characterization and mapping of very fine particles in an engine machining and assembly facility.  

PubMed

Very fine particle number and mass concentrations were mapped in an engine machining and assembly facility in the winter and summer. A condensation particle counter (CPC) was used to measure particle number concentrations in the 0.01 microm to 1 microm range, and an optical particle counter (OPC) was used to measure particle number concentrations in 15 channels between 0.3 microm and 20 microm. The OPC measurements were used to estimate the respirable mass concentration. Very fine particle number concentrations were estimated by subtracting the OPC particle number concentrations from 0.3 microm to 1 microm from the CPC number concentrations. At specific locations during the summer visit, an electrical low pressure impactor was used to measure particle size distribution from 0.07 microm to 10 microm in 12 channels. The geometric mean ratio of respirable mass concentration estimated from the OPC to the gravimetrically measured mass concentration was 0.66 with a geometric standard deviation of 1.5. Very fine particle number concentrations in winter were substantially greater where direct-fire natural gas heaters were operated (7.5 x 10(5) particles/cm(3)) than where steam was used for heat (3 x 10(5) particles/cm(3)). During summer when heaters were off, the very fine particle number concentrations were below 10(5) particles/cm(3), regardless of location. Elevated very fine particle number concentrations were associated with machining operations with poor enclosures. Whereas respirable mass concentrations did not vary noticeably with season, they were greater in areas with poorly fitting enclosures (0.12 mg/m(3)) than in areas where state-of-the-art enclosures were used (0.03 mg/m(3)). These differences were attributed to metalworking fluid mist that escaped from poorly fitting enclosures. Particles generated from direct-fire natural gas heater operation were very small, with a number size distribution modal diameter of less than 0.023 microm. Aerosols generated by machining operations had number size distributions modes in the 0.023 microm to 0.1 microm range. However, multiple modes in the mass size distributions estimated from OPC measurements occurred in the 2-20 microm range. Although elevated, very fine particle concentrations and respirable mass concentrations were both associated with poorly enclosed machining operations; the operation of the direct-fire natural gas heaters resulted in the greatest very fine particle concentrations without elevating the respirable mass concentration. These results suggest that respirable mass concentration may not be an adequate indicator for very fine particle exposure. PMID:17454502

Heitbrink, William A; Evans, Douglas E; Peters, Thomas M; Slavin, Thomas J

2007-05-01

193

Identification and mapping QTL for high-temperature adult-plant resistance to stripe rust in winter wheat (Triticum aestivum L.) cultivar ‘Stephens’  

Technology Transfer Automated Retrieval System (TEKTRAN)

High-temperature adult-plant (HTAP) resistance from the winter wheat (Triticum aestivum) cultivar ‘Stephens’ has protected wheat crops from stripe rust caused by Puccinia striiformis f. sp. tritici for 30 years. The objectives of this study were to identify major quantitative trait loci (QTL) for H...

194

Fine-mapping using the weighted average method for a case-control study.  

PubMed

We present a new method for fine-mapping a disease susceptibility locus using a case-control design. The new method, termed the weighted average (WA) statistic, averages the Cochran-Armitage (CA) trend test statistic and the difference between the Hardy-Weinberg disequilibrium test statistic for cases and controls (the HWD trend). The main characteristics of the WA statistic are that it improves on the weaknesses, and maintains the strengths, of both the CA trend test and the HWD trend test. Data from three different populations in the Genetic Analysis Workshop 14 (GAW14) simulated dataset (Aipotu, Karangar, and Danacaa) were first subjected to model-free linkage analysis to find regions exhibiting linkage. Then, for fine-scale mapping, 140 SNPs within the significant linkage regions were analyzed with the WA test statistic on replicates of the three populations, both separately and combined. The regions that were significant in the multipoint linkage analysis were also significant in this fine-scale mapping. The most significant regions that were obtained using the WA statistic were regions in chromosome 3 (B03T3056-B03T3058, p-value < 1 x 10(-10)) and chromosome 9 (B09T8332-B09T8334, p-value 1 x 10(-6)). Based on the results of the simulated GAW14 data, the WA test statistic showed good performance and could narrow down the region containing the susceptibility locus. However, the strength of the signal depends on both the strength of the linkage disequilibrium and the heterozygosity of the linked marker. PMID:16451680

Song, Kijoung; Orloff, Mohammed S; Lu, Qing; Elston, Robert C

2005-01-01

195

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

PubMed

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

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

2014-04-01

196

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

PubMed Central

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

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

2014-01-01

197

Molecular mapping across three populations reveals a QTL hotspot region on chromosome 3 for secondary traits associated with drought tolerance in tropical maize.  

PubMed

Identifying quantitative trait loci (QTL) of sizeable effects that are expressed in diverse genetic backgrounds across contrasting water regimes particularly for secondary traits can significantly complement the conventional drought tolerance breeding efforts. We evaluated three tropical maize biparental populations under water-stressed and well-watered regimes for drought-related morpho-physiological traits, such as anthesis-silking interval (ASI), ears per plant (EPP), stay-green (SG) and plant-to-ear height ratio (PEH). In general, drought stress reduced the genetic variance of grain yield (GY), while that of morpho-physiological traits remained stable or even increased under drought conditions. We detected consistent genomic regions across different genetic backgrounds that could be target regions for marker-assisted introgression for drought tolerance in maize. A total of 203 QTL for ASI, EPP, SG and PEH were identified under both the water regimes. Meta-QTL analysis across the three populations identified six constitutive genomic regions with a minimum of two overlapping traits. Clusters of QTL were observed on chromosomes 1.06, 3.06, 4.09, 5.05, 7.03 and 10.04/06. Interestingly, a ~8-Mb region delimited in 3.06 harboured QTL for most of the morpho-physiological traits considered in the current study. This region contained two important candidate genes viz., zmm16 (MADS-domain transcription factor) and psbs1 (photosystem II unit) that are responsible for reproductive organ development and photosynthate accumulation, respectively. The genomic regions identified in this study partially explained the association of secondary traits with GY. Flanking single nucleotide polymorphism markers reported herein may be useful in marker-assisted introgression of drought tolerance in tropical maize. PMID:25076840

Almeida, Gustavo Dias; Nair, Sudha; Borém, Aluízio; Cairns, Jill; Trachsel, Samuel; Ribaut, Jean-Marcel; Bänziger, Marianne; Prasanna, Boddupalli M; Crossa, Jose; Babu, Raman

2014-01-01

198

MROrchestrator: A Fine-Grained Resource Orchestration Framework for MapReduce Clusters  

SciTech Connect

Efficient resource management in data centers and clouds running large distributed data processing frameworks like MapReduce is crucial for enhancing the performance of hosted applications and boosting resource utilization. However, existing resource scheduling schemes in Hadoop MapReduce allocate resources at the granularity of fixed-size, static portions of nodes, called slots. In this work, we show that MapReduce jobs have widely varying demands for multiple resources, making the static and fixed-size slot-level resource allocation a poor choice both from the performance and resource utilization standpoints. Furthermore, lack of co-ordination in the management of mul- tiple resources across nodes prevents dynamic slot reconfigura- tion, and leads to resource contention. Motivated by this, we propose MROrchestrator, a MapReduce resource Orchestrator framework, which can dynamically identify resource bottlenecks, and resolve them through fine-grained, co-ordinated, and on- demand resource allocations. We have implemented MROrches- trator on two 24-node native and virtualized Hadoop clusters. Experimental results with a suite of representative MapReduce benchmarks demonstrate up to 38% reduction in job completion times, and up to 25% increase in resource utilization. We further show how popular resource managers like NGM and Mesos when augmented with MROrchestrator can hike up their performance.

Sharma, Bikash [Pennsylvania State University, University Park, PA; Prabhakar, Ramya [Pennsylvania State University, University Park, PA; Kandemir, Mahmut [Pennsylvania State University; Das, Chita [Pennsylvania State University, University Park, PA; Lim, Seung-Hwan [ORNL

2012-01-01

199

An eQTL mapping approach reveals that rare variants in the SEMA5A regulatory network impact autism risk  

PubMed Central

To date, genome-wide single nucleotide polymorphism (SNP) and copy number variant (CNV) association studies of autism spectrum disorders (ASDs) have led to promising signals but not to easily interpretable or translatable results. Our own genome-wide association study (GWAS) showed significant association to an intergenic SNP near Semaphorin 5A (SEMA5A) and provided evidence for reduced expression of the same gene. In a novel GWAS follow-up approach, we map an expression regulatory pathway for a GWAS candidate gene, SEMA5A, in silico by using population expression and genotype data sets. We find that the SEMA5A regulatory network significantly overlaps rare autism-specific CNVs. The SEMA5A regulatory network includes previous autism candidate genes and regions, including MACROD2, A2BP1, MCPH1, MAST4, CDH8, CADM1, FOXP1, AUTS2, MBD5, 7q21, 20p, USH2A, KIRREL3, DBF4B and RELN, among others. Our results provide: (i) a novel data-derived network implicated in autism, (ii) evidence that the same pathway seeded by an initial SNP association shows association with rare genetic variation in ASDs, (iii) a potential mechanism of action and interpretation for the previous autism candidate genes and genetic variants that fall in this network, and (iv) a novel approach that can be applied to other candidate genes for complex genetic disorders. We take a step towards better understanding of the significance of SEMA5A pathways in autism that can guide interpretation of many other genetic results in ASDs. PMID:23575222

Cheng, Ye; Quinn, Jeffrey Francis; Weiss, Lauren Anne

2013-01-01

200

Coalescent-based association mapping and fine mapping of complex trait loci.  

PubMed

We outline a general coalescent framework for using genotype data in linkage disequilibrium-based mapping studies. Our approach unifies two main goals of gene mapping that have generally been treated separately in the past: detecting association (i.e., significance testing) and estimating the location of the causative variation. To tackle the problem, we separate the inference into two stages. First, we use Markov chain Monte Carlo to sample from the posterior distribution of coalescent genealogies of all the sampled chromosomes without regard to phenotype. Then, averaging across genealogies, we estimate the likelihood of the phenotype data under various models for mutation and penetrance at an unobserved disease locus. The essential signal that these models look for is that in the presence of disease susceptibility variants in a region, there is nonrandom clustering of the chromosomes on the tree according to phenotype. The extent of nonrandom clustering is captured by the likelihood and can be used to construct significance tests or Bayesian posterior distributions for location. A novelty of our framework is that it can naturally accommodate quantitative data. We describe applications of the method to simulated data and to data from a Mendelian locus (CFTR, responsible for cystic fibrosis) and from a proposed complex trait locus (calpain-10, implicated in type 2 diabetes). PMID:15489534

Zöllner, Sebastian; Pritchard, Jonathan K

2005-02-01

201

QTL detection for a medium density SNP panel: comparison of different LD and LA methods  

PubMed Central

Background New molecular technologies allow high throughput genotyping for QTL mapping with dense genetic maps. Therefore, the interest of linkage analysis models against linkage disequilibrium could be questioned. As these two strategies are very sensitive to marker density, experimental design structures, linkage disequilibrium extent and QTL effect, we propose to investigate these parameters effects on QTL detection. Methods The XIIIth QTLMAS workshop simulated dataset was analysed using three linkage disequilibrium models and a linkage analysis model. Interval mapping, multivariate and interaction between QTL analyses were performed using QTLMAP. Results The linkage analysis models identified 13 QTL, from which 10 mapped close of the 18 which were simulated and three other positions being falsely mapped as containing a QTL. Most of the QTLs identified by interval mapping analysis are not clearly detected by any linkage disequilibrium model. In addition, QTL effects are evolving during the time which was not observed using the linkage disequilibrium models. Conclusions Our results show that for such a marker density the interval mapping strategy is still better than using the linkage disequilibrium only. While the experimental design structure gives a lot of power to both approaches, the marker density and informativity clearly affect linkage disequilibrium efficiency for QTL detection. PMID:20380753

Filangi, Olivier; Le Roy, Pascale

2010-01-01

202

Construction of a first genetic map of distylous Turnera and a fine-scale map of the S-locus region.  

PubMed

As a prelude to discovery of genes involved in floral dimorphism and incompatibility, a genetic map of distylous Turnera was constructed along with a fine-scale map of the S-locus region. The genetic map consists of 79 PCR-based molecular markers (48 AFLP, 18 RAPD, 9 ISSR, 4 RAMP), 5 isozyme loci, one additional gene, and the S-locus, spanning a total distance of 683.3 cM. The 86 markers are distributed in 5 linkage groups, corresponding to the haploid chromosome number. Molecular markers tightly linked or co-segregating with the S-locus in an initial mapping population of 94 individuals were used to assay an additional 642 progeny to construct a map of the S-locus region. The fine-scale map consists of 2 markers (IS864a and RP45E9) flanking the S-locus at distances of 0.41 and 0.54 cM, respectively, and 3 additional markers (OPK14c, RP45G18, and RP81E18) co-segregating with the S-locus in the total mapping population of 736 individuals. The genetic map constructed will serve as a framework for localization of genes outside the S-locus affecting distyly, while molecular markers of the fine-scale map will be used to initiate chromosome walking to find the genes residing at the S-locus. PMID:18545271

Labonne, J D J; Vaisman, A; Shore, J S

2008-07-01

203

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

Microsoft Academic Search

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\\u000a source of the most commercial valuable maize inbred lines in temperate zones, while the intermated B73 × Mo17 (IBM) population\\u000a is an invaluable source for QTL identification. However, no or few

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

2009-01-01

204

Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana  

PubMed Central

Flowering time (FT) is the developmental transition coupling an internal genetic program with external local and seasonal climate cues. The genetic loci sensitive to predictable environmental signals underlie local adaptation. We dissected natural variation in FT across a new global diversity set of 473 unique accessions, with >12,000 plants across two seasonal plantings in each of two simulated local climates, Spain and Sweden. Genome-wide association mapping was carried out with 213,497 SNPs. A total of 12 FT candidate quantitative trait loci (QTL) were fine-mapped in two independent studies, including 4 located within ±10 kb of previously cloned FT alleles and 8 novel loci. All QTL show sensitivity to planting season and/or simulated location in a multi-QTL mixed model. Alleles at four QTL were significantly correlated with latitude of origin, implying past selection for faster flowering in southern locations. Finally, maximum seed yield was observed at an optimal FT unique to each season and location, with four FT QTL directly controlling yield. Our results suggest that these major, environmentally sensitive FT QTL play an important role in spatial and temporal adaptation. PMID:21078970

Huang, Yu; Bergelson, Joy; Nordborg, Magnus; Borevitz, Justin O.

2010-01-01

205

Identification of putative QTL that underlie yield in interspecific soybean backcross populations.  

PubMed

Glycine soja, the wild progenitor of soybean, is a potential source of useful genetic variation in soybean improvement. The objective of our study was to map quantitative trait loci (QTL) from G. soja that could improve the crop. Five populations of BC(2)F(4)-derived lines were developed using the Glycine max cultivar IA2008 as a recurrent parent and the G. soja plant introduction (PI) 468916 as a donor parent. There were between 57 and 112 BC(2)F(4)-derived lines in each population and a total of 468 lines for the five populations. The lines were evaluated with simple sequence repeat markers and in field tests for yield, maturity, plant height, and lodging. The field testing was done over 2 years and at two locations each year. Marker data were analyzed for linkage and combined with field data to identify QTL. Using an experimentwise significance threshold of P=0.05, four yield QTL were identified across environments on linkage groups C2, E, K, and M. For these yield QTL, the IA2008 marker allele was associated with significantly greater yield than the marker allele from G. soja. In addition, one lodging QTL, four maturity QTL, and five QTL for plant height were identified across environments. Of the 14 QTL identified, eight mapped to regions where QTL with similar effects were previously mapped. Many regions carrying the yield QTL were also significant for other traits, such as plant height and lodging. When the significance threshold was reduced and the data were analyzed with simple linear regression, four QTL with a positive allele for yield from G. soja were mapped. One epistatic interaction between two genetic regions was identified for yield using an experimentwise significance threshold of P=0.05. Additional research is needed to establish whether multiple trait associations are the result of pleiotropy or genetic linkage and to retest QTL with a positive effect from G. soja. PMID:14504749

Wang, D; Graef, G L; Procopiuk, A M; Diers, B W

2004-02-01

206

Meta-eQTL: a tool set for flexible eQTL meta-analysis.  

PubMed

BackgroundIncreasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue types to improve statistical power especially in trans-eQTL mapping. Meta-analysis framework is also necessary for ChrX eQTL discovery.ResultsWe developed a novel tool, meta-eqtl , for fast eQTL meta-analysis of arbitrary sample size and arbitrary number of datasets. Further, this tool accommodates versatile modeling, eg. non-parametric model and mixed effect models. In addition, meta-eqtl readily handles calculation of chrX eQTLs.ConclusionsWe demonstrated and validated meta-eqtl as fast and comprehensive tool to meta-analyze multiple datasets and ChrX eQTL discovery. Meta-eqtl is a set of command line utilities written in R, with some computationally intensive parts written in C. The software runs on Linux platforms and is designed to intelligently adapt to high performance computing (HPC) cluster. We applied the novel tool to liver and adipose tissue data, and revealed eSNPs underlying diabetes GWAS loci. PMID:25431350

Di Narzo, Antonio; Cheng, Haoxiang; Lu, Jianwei; Hao, Ke

2014-11-28

207

Remote sensing and object-based techniques for mapping fine-scale industrial disturbances  

NASA Astrophysics Data System (ADS)

Remote sensing provides an important data source for the detection and monitoring of disturbances; however, using this data to recognize fine-spatial resolution industrial disturbances dispersed across extensive areas presents unique challenges (e.g., accurate delineation and identification) and deserves further investigation. In this study, we present and assess a geographic object-based image analysis (GEOBIA) approach with high-spatial resolution imagery (SPOT 5) to map industrial disturbances using the oil sands region of Alberta's northeastern boreal forest as a case study. Key components of this study were (i) the development of additional spectral, texture, and geometrical descriptors for characterizing image-objects (groups of alike pixels) and their contextual properties, and (ii) the introduction of decision trees with boosting to perform the object-based land cover classification. Results indicate that the approach achieved an overall accuracy of 88%, and that all descriptor groups provided relevant information for the classification. Despite challenges remaining (e.g., distinguishing between spectrally similar classes, or placing discrete boundaries), the approach was able to effectively delineate and classify fine-spatial resolution industrial disturbances.

Powers, Ryan P.; Hermosilla, Txomin; Coops, Nicholas C.; Chen, Gang

2015-02-01

208

Developing Methods for Mapping Soil Moisture in Nash Draw, NM Using RADARSAT 1 SAR Fine Imagery  

NASA Astrophysics Data System (ADS)

Nash Draw, in southeastern NM, is a karst valley that developed in response to subsurface dissolution of evaporites, including halite and sulfate rocks. The hydrologic system within Nash Draw is poorly understood. This study focuses on identifying the distribution and amount of recharge in Nash Draw to assist in understanding the existing processes modifying Nash Draw by solution. We hypothesize that 1) soil moisture contents will be higher in the areas where potential recharge occurs and 2) these areas can be identified using remote sensing. To test the second part of this hypothesis, this study has been designed to determine the spatial and temporal distribution of soil moisture in the study site using microwave data. An area of 225 sq. km in Nash Draw has been selected as the study site. Imagery was acquired from the Alaska SAR Facility (ASF) for 8 scenes of RADARDSAT 1 SAR Fine Beam imagery with different incidence angles (40° and 48°) and imaging modes (ascending and descending). We use RADARDSAT 1 SAR Fine Beam imagery acquired on August 1, 2006 and August 2, 2006 and near real-time ground truth data to develop suitable model to map the spatial distribution of soil moisture in the study site. During the image acquisitions on August 1 and 2, 80 soil samples were collected to determine the near real- time volumetric soil moisture in the study site. Soil samples were collected using a stratified sampling method, and locations of the samples were recorded using GPS. Soil water is compared, using linear regression, to radar backscatter to develop an empirical model of the relationship. The radar backscatter used in this model was acquired at different incidence angles. This study also provides an opportunity to investigate the impact of variable incidence angles on the potential of space-borne active microwave data for soil moisture mapping in semi-arid region like Nash Draw.

Hossain, A. A.; Easson, G.; Powers, D. W.; Holt, R. M.

2006-12-01

209

Fine mapping major histocompatibility complex associations in psoriasis and its clinical subtypes.  

PubMed

Psoriasis vulgaris (PsV) risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but its genetic architecture has yet to be fully elucidated. Here, we conducted a large-scale fine-mapping study of PsV risk in the MHC region in 9,247 PsV-affected individuals and 13,589 controls of European descent by imputing class I and II human leukocyte antigen (HLA) genes from SNP genotype data. In addition, we imputed sequence variants for MICA, an MHC HLA-like gene that has been associated with PsV, to evaluate association at that locus as well. We observed that HLA-C(?)06:02 demonstrated the lowest p value for overall PsV risk (p = 1.7 × 10(-364)). Stepwise analysis revealed multiple HLA-C(?)06:02-independent risk variants in both class I and class II HLA genes for PsV susceptibility (HLA-C(?)12:03, HLA-B amino acid positions 67 and 9, HLA-A amino acid position 95, and HLA-DQ?1 amino acid position 53; p < 5.0 × 10(-8)), but no apparent risk conferred by MICA. We further evaluated risk of two major clinical subtypes of PsV, psoriatic arthritis (PsA; n = 3,038) and cutaneous psoriasis (PsC; n = 3,098). We found that risk heterogeneity between PsA and PsC might be driven by HLA-B amino acid position 45 (Pomnibus = 2.2 × 10(-11)), indicating that different genetic factors underlie the overall risk of PsV and the risk of specific PsV subphenotypes. Our study illustrates the value of high-resolution HLA and MICA imputation for fine mapping causal variants in the MHC. PMID:25087609

Okada, Yukinori; Han, Buhm; Tsoi, Lam C; Stuart, Philip E; Ellinghaus, Eva; Tejasvi, Trilokraj; Chandran, Vinod; Pellett, Fawnda; Pollock, Remy; Bowcock, Anne M; Krueger, Gerald G; Weichenthal, Michael; Voorhees, John J; Rahman, Proton; Gregersen, Peter K; Franke, Andre; Nair, Rajan P; Abecasis, Gonçalo R; Gladman, Dafna D; Elder, James T; de Bakker, Paul I W; Raychaudhuri, Soumya

2014-08-01

210

Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies  

PubMed Central

Standard statistical approaches for prioritization of variants for functional testing in fine-mapping studies either use marginal association statistics or estimate posterior probabilities for variants to be causal under simplifying assumptions. Here, we present a probabilistic framework that integrates association strength with functional genomic annotation data to improve accuracy in selecting plausible causal variants for functional validation. A key feature of our approach is that it empirically estimates the contribution of each functional annotation to the trait of interest directly from summary association statistics while allowing for multiple causal variants at any risk locus. We devise efficient algorithms that estimate the parameters of our model across all risk loci to further increase performance. Using simulations starting from the 1000 Genomes data, we find that our framework consistently outperforms the current state-of-the-art fine-mapping methods, reducing the number of variants that need to be selected to capture 90% of the causal variants from an average of 13.3 to 10.4 SNPs per locus (as compared to the next-best performing strategy). Furthermore, we introduce a cost-to-benefit optimization framework for determining the number of variants to be followed up in functional assays and assess its performance using real and simulation data. We validate our findings using a large scale meta-analysis of four blood lipids traits and find that the relative probability for causality is increased for variants in exons and transcription start sites and decreased in repressed genomic regions at the risk loci of these traits. Using these highly predictive, trait-specific functional annotations, we estimate causality probabilities across all traits and variants, reducing the size of the 90% confidence set from an average of 17.5 to 13.5 variants per locus in this data. PMID:25357204

Kichaev, Gleb; Yang, Wen-Yun; Lindstrom, Sara; Hormozdiari, Farhad; Eskin, Eleazar; Price, Alkes L.; Kraft, Peter; Pasaniuc, Bogdan

2014-01-01

211

Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus  

PubMed Central

Background In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics backgrounds is essential for their successful use in Marker-assisted Selection. In this study, an attempt was made to locate consistent QTL regions associated with yield increase under drought by applying a genome-wide QTL meta-analysis approach. Results The integration of 15 maps resulted in a consensus map with 531 markers and a total map length of 1821 cM. Fifty-three yield QTL reported in 15 studies were projected on a consensus map and meta-analysis was performed. Fourteen meta-QTL were obtained on seven chromosomes. MQTL1.2, MQTL1.3, MQTL1.4, and MQTL12.1 were around 700 kb and corresponded to a reasonably small genetic distance of 1.8 to 5 cM and they are suitable for use in marker-assisted selection (MAS). The meta-QTL for grain yield under drought coincided with at least one of the meta-QTL identified for root and leaf morphology traits under drought in earlier reports. Validation of major-effect QTL on a panel of random drought-tolerant lines revealed the presence of at least one major QTL in each line. DTY12.1 was present in 85% of the lines, followed by DTY4.1 in 79% and DTY1.1 in 64% of the lines. Comparative genomics of meta-QTL with other cereals revealed that the homologous regions of MQTL1.4 and MQTL3.2 had QTL for grain yield under drought in maize, wheat, and barley respectively. The genes in the meta-QTL regions were analyzed by a comparative genomics approach and candidate genes were deduced for grain yield under drought. Three groups of genes such as stress-inducible genes, growth and development-related genes, and sugar transport-related genes were found in clusters in most of the meta-QTL. Conclusions Meta-QTL with small genetic and physical intervals could be useful in Marker-assisted selection individually and in combinations. Validation and comparative genomics of the major-effect QTL confirmed their consistency within and across the species. The shortlisted candidate genes can be cloned to unravel the molecular mechanism regulating grain yield under drought. PMID:21679437

2011-01-01

212

Fine Mapping of 14q24.1 Breast Cancer Susceptibility Locus  

PubMed Central

In the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGEMS) genome-wide association study of breast cancer, a single nucleotide polymorphism (SNP) marker, rs999737, in the 14q24.1 interval, was associated with breast cancer risk. In order to fine map this region, we imputed a 3.93MB region flanking rs999737 for Stages 1 and 2 of the CGEMS study (5,692 cases, 5,576 controls) using the combined reference panels of the HapMap 3 and the 1000 Genomes Project. Single-marker association testing and variable-sized sliding-window haplotype analysis were performed, and for both analyses the initial tagging SNP rs999737 retained the strongest association with breast cancer risk. Investigation of contiguous regions did not reveal evidence for an additional independent signal. Therefore, we conclude that rs999737 is an optimal tag SNP for common variants in the 14q24.1 region and thus narrow the candidate variants that should be investigated in follow-up laboratory evaluation. PMID:21959381

Lee, Phoebe; Fu, Yi-Ping; Figueroa, Jonine D.; Prokunina-Olsson, Ludmila; Gonzalez-Bosquet, Jesus; Kraft, Peter; Wang, Zhaoming; Jacobs, Kevin B.; Yeager, Meredith; Horner, Marie-Josèphe; Hankinson, Susan E.; Hutchinson, Amy; Chatterjee, Nilanjan; Garcia-Closas, Montserrat; Ziegler, Regina G.; Berg, Christine D.; Buys, Saundra S.; McCarty, Catherine A.; Feigelson, Heather Spencer; Thun, Michael J.; Diver, Ryan; Prentice, Ross; Jackson, Rebecca; Kooperberg, Charles; Chlebowski, Rowan; Lissowska, Jolanta; Peplonska, Beata; Brinton, Louise A.; Tucker, Margaret; Fraumeni, Joseph F.; Hoover, Robert N.; Thomas, Gilles; Hunter, David J.; Chanock, Stephen J.

2014-01-01

213

Admixture Fine-Mapping in African Americans Implicates XAF1 as a Possible Sarcoidosis Risk Gene  

PubMed Central

Sarcoidosis is a complex, multi-organ granulomatous disease with a likely genetic component. West African ancestry confers a higher risk for sarcoidosis than European ancestry. Admixture mapping provides the most direct method to locate genes that underlie such ethnic variation in disease risk. We sought to identify genetic risk variants within four previously-identified ancestry-associated regions—6p24.3–p12.1, 17p13.3–13.1, 2p13.3–q12.1, and 6q23.3–q25.2—in a sample of 2,727 African Americans. We used logistic regression fit by generalized estimating equations and the MIX score statistic to determine which variants within ancestry-associated regions were associated with risk and responsible for the admixture signal. Fine mapping was performed by imputation, based on a previous genome-wide association study; significant variants were validated by direct genotyping. Within the 6p24.3–p12.1 locus, the most significant ancestry-adjusted SNP was rs74318745 (p?=?9.4*10?11), an intronic SNP within the HLA-DRA gene that did not solely explain the admixture signal, indicating the presence of more than a single risk variant within this well-established sarcoidosis risk region. The locus on chromosome 17p13.3–13.1 revealed a novel sarcoidosis risk SNP, rs6502976 (p?=?9.5*10?6), within intron 5 of the gene X-linked Inhibitor of Apoptosis Associated Factor 1 (XAF1) that accounted for the majority of the admixture linkage signal. Immunohistochemical expression studies demonstrated lack of expression of XAF1 and a corresponding high level of expression of its downstream target, X-linked Inhibitor of Apoptosis (XIAP) in sarcoidosis granulomas. In conclusion, ancestry and association fine mapping revealed a novel sarcoidosis susceptibility gene, XAF1, which has not been identified by previous genome-wide association studies. Based on the known biology of the XIAP/XAF1 apoptosis pathway and the differential expression patterns of XAF1 and XIAP in sarcoidosis granulomas, we suggest that this pathway may play a role in the maintenance of sarcoidosis granulomas. PMID:24663488

Levin, Albert M.; Iannuzzi, Michael C.; Montgomery, Courtney G.; Trudeau, Sheri; Datta, Indrani; Adrianto, Indra; Chitale, Dhananjay A.; McKeigue, Paul; Rybicki, Benjamin A.

2014-01-01

214

QTLS associated with resistance to soybean cyst nematode: Meta-analysis of QTL locations  

Technology Transfer Automated Retrieval System (TEKTRAN)

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is the most important pest of soybean (Glycine max (L.) Merr) in the world. A total of 17 quantitative trait locus (QTL) mapping papers and 62 marker-QTL associations have been reported for resistance to soybean cyst nematode in soybean. C...

215

Mapping Fine-Scale Fire Effects After Wildfires in Alaska's Boreal Forest  

NASA Astrophysics Data System (ADS)

In recent years, large, severe wildfires have burned in Alaska, which stands to continue as global climate trends continue to be warmer and drier. In 2004, 26,700 km2 (6.6 million acres) burned, and 19,000 km2 (4.7 million acres) in 2005. By these numbers, nearly 10% of Alaska's boreal forest burned in these two years. The boreal forest biome contains a significant percentage of the world's carbon stored as moss and in the highly organic soils. Thus, the extent and severity of fires in the boreal forests is important on a global scale due to the level of carbon emissions from a high amount of organic consumption. To investigate fine-scale fire effects on vegetation and soils, we collected airborne hyperspectral imagery on three interior Alaska wildfires in 2004. The interior area of Alaska is dominated by black spruce forests with dense mats of feather moss on the ground. We applied a five-endmember spectral unmixing model representing green feather moss, a green shrub species, charred feather moss, ash and rock to calibrated reflectance data. The result was fractional cover maps of each input cover type. Significant correlations between the field and remotely sensed data indicated the map was representative of the burned area. The pixel size of the hyperspectral data was 3 m on the ground, meaning the percent of charred and uncharred vegetation and exposed soil or rock was discernable at this scale. The ability to accurately map these biophysical cover fractions, especially fire effects on surface moss and organic soils, may indicate the degree or amount of consumption which can be related to carbon emissions.

Lewis, S. A.; Hudak, A. T.; Lentile, L. B.; Robichaud, P. R.; Morgan, P.

2007-12-01

216

High-density fine-mapping of a chromosome 10q26 linkage peak suggests association between  

E-print Network

endometriosis and variants close to CYP2C19 Jodie N. Painter, Ph.D.,a Dale R. Nyholt, Ph.D.,a Andrew Morris, Ph peak for endometriosis on chromosome 10q26, and conduct follow-up analyses and a fine-mapping association study across the region to identify new candidate genes for endometriosis. Design: Case

Nyholt, Dale R.

217

Pathotype-specific QTL for stem rust resistance in Lolium perenne.  

PubMed

A genetic map populated with RAD and SSR markers was created from F1 progeny of a stem rust-susceptible and stem rust-resistant parent of perennial ryegrass (Lolium perenne). The map supplements a previous map of this population by having markers in common with several other Lolium spp. maps including EST-SSR anchor markers from a consensus map published by other researchers. A QTL analysis was conducted with disease severity and infection type data obtained by controlled inoculation of the population with each of two previously characterized pathotypes of Puccinia graminis subsp. graminicola that differ in virulence to different host plant genotypes in the F1 population. Each pathotype activated a specific QTL on one linkage group (LG): qLpPg1 on LG7 for pathotype 101, or qLpPg2 on LG1 for pathotype 106. Both pathotypes also activated a third QTL in common, qLpPg3 on LG6. Anchor markers, present on a consensus map, were located in proximity to each of the three QTL. These QTL had been detected also in previous experiments in which a genetically heterogeneous inoculum of the stem rust pathogen activated all three QTL together. The results of this and a previous study are consistent with the involvement of the pathotype-specific QTL in pathogen recognition and the pathotype-nonspecific QTL in a generalized resistance response. By aligning the markers common to other published reports, it appears that two and possibly all three of the stem rust QTL reported here are in the same general genomic regions containing some of the L. perenne QTL reported to be activated in response to the crown rust pathogen (P. coronata). PMID:23361523

Pfender, W F; Slabaugh, M E

2013-05-01

218

Mapping epistatic quantitative trait loci.  

PubMed

BackgroundHow to map quantitative trait loci (QTL) with epistasis efficiently and reliably has been a persistent problem for QTL mapping analysis. There are a number of difficulties for studying epistatic QTL. Linkage can impose a significant challenge for finding epistatic QTL reliably. If multiple QTL are in linkage and have interactions, searching for QTL can become a very delicate issue. A commonly used strategy that performs a two-dimensional genome scan to search for a pair of QTL with epistasis can suffer from low statistical power and also may lead to false identification due to complex linkage disequilibrium and interaction patterns.ResultsTo tackle the problem of complex interaction of multiple QTL with linkage, we developed a three-stage search strategy. In the first stage, main effect QTL are searched and mapped. In the second stage, epistatic QTL that interact significantly with other identified QTL are searched. In the third stage, new epistatic QTL are searched in pairs. This strategy is based on the consideration that most genetic variance is due to the main effects of QTL. Thus by first mapping those main-effect QTL, the statistical power for the second and third stages of analysis for mapping epistatic QTL can be maximized. The search for main effect QTL is robust and does not bias the search for epistatic QTL due to a genetic property associated with the orthogonal genetic model that the additive and additive by additive variances are independent despite of linkage. The model search criterion is empirically and dynamically evaluated by using a score-statistic based resampling procedure. We demonstrate through simulations that the method has good power and low false positive in the identification of QTL and epistasis.ConclusionThis method provides an effective and powerful solution to map multiple QTL with complex epistatic pattern. The method has been implemented in the user-friendly computer software Windows QTL Cartographer. This will greatly facilitate the application of the method for QTL mapping data analysis. PMID:25367219

Laurie, Cecelia; Wang, Shengchu; Carlini-Garcia, Luciana; Zeng, Zhao-Bang

2014-11-01

219

Fractionation, Stability, and Isolate-Specificity of QTL for Resistance to Phytophthora infestans in Cultivated Tomato (Solanum lycopersicum)  

PubMed Central

Cultivated tomato (Solanum lycopersicum) is susceptible to late blight, a major disease caused by Phytophthora infestans, but quantitative resistance exists in the wild tomato species S. habrochaites. Previously, we mapped several quantitative trait loci (QTL) from S. habrochaites and then introgressed each individually into S. lycopersicum. Near-isogenic lines (NILs) were developed, each containing a single introgressed QTL on chromosome 5 or 11. NILs were used to create two recombinant sub-NIL populations, one for each target chromosome region, for higher-resolution mapping. The sub-NIL populations were evaluated for foliar and stem resistance to P. infestans in replicated field experiments over two years, and in replicated growth chamber experiments for resistance to three California isolates. Each of the original single QTL on chromosomes 5 and 11 fractionated into between two and six QTL for both foliar and stem resistance, indicating a complex genetic architecture. The majority of QTL from the field experiments were detected in multiple locations or years, and two of the seven QTL detected in growth chambers were co-located with QTL detected in field experiments, indicating stability of some QTL across environments. QTL that confer foliar and stem resistance frequently co-localized, suggesting that pleiotropy and/or tightly linked genes control the trait phenotypes. Other QTL exhibited isolate-specificity and QTL × environment interactions. Map-based comparisons between QTL mapped in this study and Solanaceae resistance genes/QTL detected in other published studies revealed multiple cases of co-location, suggesting conservation of gene function. PMID:23050225

Johnson, Emily B.; Haggard, J. Erron; St.Clair, Dina A.

2012-01-01

220

Genetic fine-mapping of DIPLOSPOROUS in Taraxacum (dandelion; Asteraceae) indicates a duplicated DIP-gene  

PubMed Central

Background DIPLOSPOROUS (DIP) is the locus for diplospory in Taraxacum, associated to unreduced female gamete formation in apomicts. Apomicts reproduce clonally through seeds, including apomeiosis, parthenogenesis, and autonomous or pseudogamous endosperm formation. In Taraxacum, diplospory results in first division restitution (FDR) nuclei, and inherits as a dominant, monogenic trait, independent from the other apomixis elements. A preliminary genetic linkage map indicated that the DIP-locus lacks suppression of recombination, which is unique among all other map-based cloning efforts of apomeiosis to date. FDR as well as apomixis as a whole are of interest in plant breeding, allowing for polyploidization and fixation of hybrid vigor, respectively. No dominant FDR or apomixis genes have yet been isolated. Here, we zoom-in to the DIP-locus by largely extending our initial mapping population, and by analyzing (local) suppression of recombination and allele sequence divergence (ASD). Results We identified 24 recombinants between two most closely linked molecular markers to DIP in an F1-population of 2227 plants that segregates for diplospory and lacks parthenogenesis. Both markers segregated c. 1:1 in the entire population, indicating a 1:1 segregation rate of diplospory. Fine-mapping showed three amplified fragment length polymorphisms (AFLPs) closest to DIP at 0.2 cM at one flank and a single AFLP at 0.4 cM at the other flank. Our data lacked strong evidence for ASD at marker regions close to DIP. An unexpected bias towards diplosporous plants among the recombinants (20 out of 24) was found. One third of these diplosporous recombinants showed incomplete penetrance of 50-85% diplospory. Conclusions Our data give interesting new insights into the structure of the diplospory locus in Taraxacum. We postulate a locus with a minimum of two DIP-genes and possibly including one or two enhancers or cis-regulatory elements on the basis of the bias towards diplosporous recombinants and incomplete penetrance of diplospory in some of them. We define the DIP-locus to 0.6 cM, which is estimated to cover ~200-300 Kb, with the closest marker at 0.2 cM. Our results confirm the minor role of suppression of recombination and ASD around DIP, making it an excellent candidate to isolate via a chromosome-walking approach. PMID:20659311

2010-01-01

221

Novel Distal eQTL Analysis Demonstrates Effect of Population Genetic Architecture on Detecting and Interpreting Associations  

PubMed Central

Mapping expression quantitative trait loci (eQTL) has identified genetic variants associated with transcription rates and has provided insight into genotype–phenotype associations obtained from genome-wide association studies (GWAS). Traditional eQTL mapping methods present significant challenges for the multiple-testing burden, resulting in a limited ability to detect eQTL that reside distal to the affected gene. To overcome this, we developed a novel eQTL testing approach, “network-based, large-scale identification of distal eQTL” (NetLIFT), which performs eQTL testing based on the pairwise conditional dependencies between genes’ expression levels. When applied to existing data from yeast segregants, NetLIFT replicated most previously identified distal eQTL and identified 46% more genes with distal effects compared to local effects. In liver data from mouse lines derived through the Collaborative Cross project, NetLIFT detected 5744 genes with local eQTL while 3322 genes had distal eQTL. This analysis revealed founder-of-origin effects for a subset of local eQTL that may contribute to previously described phenotypic differences in metabolic traits. In human lymphoblastoid cell lines, NetLIFT was able to detect 1274 transcripts with distal eQTL that had not been reported in previous studies, while 2483 transcripts with local eQTL were identified. In all species, we found no enrichment for transcription factors facilitating eQTL associations; instead, we found that most trans-acting factors were annotated for metabolic function, suggesting that genetic variation may indirectly regulate multigene pathways by targeting key components of feedback processes within regulatory networks. Furthermore, the unique genetic history of each population appears to influence the detection of genes with local and distal eQTL. PMID:25230953

Weiser, Matthew; Mukherjee, Sayan; Furey, Terrence S.

2014-01-01

222

Lineage-specific mapping of quantitative trait loci  

PubMed Central

We present an approach for quantitative trait locus (QTL) mapping, termed as ‘lineage-specific QTL mapping', for inferring allelic changes of QTL evolution along with branches in a phylogeny. We describe and analyze the simplest case: by adding a third taxon into the normal procedure of QTL mapping between pairs of taxa, such inferences can be made along lineages to a presumed common ancestor. Although comparisons of QTL maps among species can identify homology of QTLs by apparent co-location, lineage-specific mapping of QTL can classify homology into (1) orthology (shared origin of QTL) versus (2) paralogy (independent origin of QTL within resolution of map distance). In this light, we present a graphical method that identifies six modes of QTL evolution in a three taxon comparison. We then apply our model to map lineage-specific QTLs for inbreeding among three taxa of yellow monkey-flower: Mimulus guttatus and two inbreeders M. platycalyx and M. micranthus, but critically assuming outcrossing was the ancestral state. The two most common modes of homology across traits were orthologous (shared ancestry of mutation for QTL alleles). The outbreeder M. guttatus had the fewest lineage-specific QTL, in accordance with the presumed ancestry of outbreeding. Extensions of lineage-specific QTL mapping to other types of data and crosses, and to inference of ancestral QTL state, are discussed. PMID:23612690

Chen, C; Ritland, K

2013-01-01

223

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

PubMed Central

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

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

2013-01-01

224

A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12  

PubMed Central

A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping. PMID:25014030

Talukder, Zahirul I.; Gong, Li; Hulke, Brent S.; Pegadaraju, Venkatramana; Song, Qijian; Schultz, Quentin; Qi, Lili

2014-01-01

225

Fine-grained mapping of mouse brain functional connectivity with resting-state fMRI.  

PubMed

Understanding the intrinsic circuit-level functional organization of the brain has benefited tremendously from the advent of resting-state fMRI (rsfMRI). In humans, resting-state functional network has been consistently mapped and its alterations have been shown to correlate with symptomatology of various neurological or psychiatric disorders. To date, deciphering the mouse brain functional connectivity (MBFC) with rsfMRI remains a largely underexplored research area, despite the plethora of human brain disorders that can be modeled in this specie. To pave the way from pre-clinical to clinical investigations we characterized here the intrinsic architecture of mouse brain functional circuitry, based on rsfMRI data acquired at 7T using the Cryoprobe technology. High-dimensional spatial group independent component analysis demonstrated fine-grained segregation of cortical and subcortical networks into functional clusters, overlapping with high specificity onto anatomical structures, down to single gray matter nuclei. These clusters, showing a high level of stability and reliability in their patterning, formed the input elements for computing the MBFC network using partial correlation and graph theory. Its topological architecture conserved the fundamental characteristics described for the human and rat brain, such as small-worldness and partitioning into functional modules. Our results additionally showed inter-modular interactions via "network hubs". Each major functional system (motor, somatosensory, limbic, visual, autonomic) was found to have representative hubs that might play an important input/output role and form a functional core for information integration. Moreover, the rostro-dorsal hippocampus formed the highest number of relevant connections with other brain areas, highlighting its importance as core structure for MBFC. PMID:24718287

Mechling, Anna E; Hübner, Neele S; Lee, Hsu-Lei; Hennig, Jürgen; von Elverfeldt, Dominik; Harsan, Laura-Adela

2014-08-01

226

SNP fine mapping of chromosome 8q24 in bipolar disorder.  

PubMed

We previously reported linkage to chromosome 8q24 in bipolar disorder (BP) with a LOD of 3.32. We fine mapped the locus with SNPs and tested for association with BP in families with evidence of linkage to the region. We genotyped 249 informative SNPs over 3.4 Mb in an initial sample of 155 nuclear families (352 affected offsprings), and followed up the best findings by genotyping six of the most significantly associated SNPs in a replication sample of 103 nuclear families (231 affected offsprings). We used FBAT and GIST for association tests. Two clusters of SNPs emerged with the strongest evidence of association. The first consisted of three SNPs, approximately 3 kb 5' from the gene ST3GAL1. These SNPs were associated with BP in the initial sample by FBAT (best P = 0.001) and GIST (best P = 0.05) and associated in the replication sample by FBAT (best P = 0.04). The second cluster consisted of four SNPs (one of which was not genotyped in the replication sample), approximately 480 kb 5' of ST3GAL1 in a relative gene desert. These SNPs were associated with BP in the initial sample by FBAT (best P = 0.007) and GIST (best P = 0.03), and marginally associated in the replication sample by FBAT (best P = 0.07) and GIST (P = 0.04). ST3GAL1 belongs to a family of glycosyltransferase proteins, several members of which are highly expressed in the brain and involved in neurogenesis. Several other interesting candidate genes are also located nearby. The congruence of findings across methods and samples suggests further investigation is warranted in these two targeted regions. PMID:17357146

Zandi, Peter P; Avramopoulos, Dimitrios; Willour, Virginia L; Huo, Yuqing; Miao, Kuangyi; Mackinnon, Dean F; McInnis, Melvin G; Potash, James B; Depaulo, J Raymond

2007-07-01

227

Clustering by neurocognition for fine mapping of the schizophrenia susceptibility loci on chromosome 6p.  

PubMed

Chromosome 6p is one of the most commonly implicated regions in the genome-wide linkage scans of schizophrenia, whereas further association studies for markers in this region were inconsistent likely due to heterogeneity. This study aimed to identify more homogeneous subgroups of families for fine mapping on regions around markers D6S296 and D6S309 (both in 6p24.3) as well as D6S274 (in 6p22.3) by means of similarity in neurocognitive functioning. A total of 160 families of patients with schizophrenia comprising at least two affected siblings who had data for eight neurocognitive test variables of the continuous performance test (CPT) and the Wisconsin card sorting test (WCST) were subjected to cluster analysis with data visualization using the test scores of both affected siblings. Family clusters derived were then used separately in family-based association tests for 64 single nucleotide polymorphisms (SNPs) covering the region of 6p24.3 and 6p22.3. Three clusters were derived from the family-based clustering, with deficit cluster 1 representing deficit on the CPT, deficit cluster 2 representing deficit on both the CPT and the WCST, and a third cluster of nondeficit. After adjustment using false discovery rate for multiple testing, SNP rs13873 and haplotype rs1225934-rs13873 on BMP6-TXNDC5 genes were significantly associated with schizophrenia for the deficit cluster 1 but not for the deficit cluster 2 or nondeficit cluster. Our results provide further evidence that the BMP6-TXNDC5 locus on 6p24.3 may play a role in the selective impairments on sustained attention of schizophrenia. PMID:19694819

Lin, S-H; Liu, C-M; Liu, Y-L; Shen-Jang Fann, C; Hsiao, P-C; Wu, J-Y; Hung, S-I; Chen, C-H; Wu, H-M; Jou, Y-S; Liu, S K; Hwang, T J; Hsieh, M H; Chang, C-C; Yang, W-C; Lin, J-J; Chou, F H-C; Faraone, S V; Tsuang, M T; Hwu, H-G; Chen, W J

2009-11-01

228

Clustering by neurocognition for fine-mapping of the schizophrenia susceptibility loci on chromosome 6p  

PubMed Central

Chromosome 6p is one of the most commonly implicated regions in the genome-wide linkage scans of schizophrenia, whereas further association studies for markers in this region were inconsistent likely due to heterogeneity. This study aimed to identify more homogeneous subgroups of families for fine mapping on regions around markers D6S296 and D6S309 (both in 6p24.3) as well as D6S274 (in 6p22.3) by means of similarity in neurocognitive functioning. A total of 160 families of patients with schizophrenia comprising at least two affected siblings who had data for 8 neurocognitive test variables of the Continuous Performance Test (CPT) and the Wisconsin Card Sorting Test (WCST) were subjected to cluster analysis with data visualization using the test scores of both affected siblings. Family clusters derived were then used separately in family-based association tests for 64 single nucleotide polymorphisms covering the region of 6p24.3 and 6p22.3. Three clusters were derived from the family-based clustering, with deficit cluster 1 representing deficit on the CPT, deficit cluster 2 representing deficit on both the CPT and the WCST, and a third cluster of non-deficit. After adjustment using false discovery rate for multiple testing, SNP rs13873 and haplotype rs1225934-rs13873 on BMP6-TXNDC5 genes were significantly associated with schizophrenia for the deficit cluster 1 but not for the deficit cluster 2 or non-deficit cluster. Our results provide further evidence that the BMP6-TXNDC5 locus on 6p24.3 may play a role in the selective impairments on sustained attention of schizophrenia. PMID:19694819

Lin, Sheng-Hsiang; Liu, Chih-Min; Liu, Yu-Li; Fann, Cathy Shen-Jang; Hsiao, Po-Chang; Wu, Jer-Yuarn; Hung, Shuen-Iu; Chen, Chun-Houh; Wu, Han-Ming; Jou, Yuh-Shan; Liu, Shi K.; Hwang, Tzung J.; Hsieh, Ming H.; Chang, Chien-Ching; Yang, Wei-Chih; Lin, Jin-Jia; Chou, Frank Huang-Chih; Faraone, Stephen V.; Tsuang, Ming T.; Hwu, Hai-Gwo; Chen, Wei J.

2009-01-01

229

Fine-Grained, Local Maps and Coarse, Global Representations Support Human Spatial Working Memory  

PubMed Central

While sensory processes are tuned to particular features, such as an object's specific location, color or orientation, visual working memory (vWM) is assumed to store information using representations, which generalize over a feature dimension. Additionally, current vWM models presume that different features or objects are stored independently. On the other hand, configurational effects, when observed, are supposed to mainly reflect encoding strategies. We show that the location of the target, relative to the display center and boundaries, and overall memory load influenced recall precision, indicating that, like sensory processes, capacity limited vWM resources are spatially tuned. When recalling one of three memory items the target distance from the display center was overestimated, similar to the error when only one item was memorized, but its distance from the memory items' average position was underestimated, showing that not only individual memory items' position, but also the global configuration of the memory array may be stored. Finally, presenting the non-target items at recall, consequently providing landmarks and configurational information, improved precision and accuracy of target recall. Similarly, when the non-target items were translated at recall, relative to their position in the initial display, a parallel displacement of the recalled target was observed. These findings suggest that fine-grained spatial information in vWM is represented in local maps whose resolution varies with distance from landmarks, such as the display center, while coarse representations are used to store the memory array configuration. Both these representations are updated at the time of recall. PMID:25259601

Katshu, Mohammad Zia Ul Haq; d'Avossa, Giovanni

2014-01-01

230

A note on the efficiencies of sampling strategies in two-stage Bayesian regional fine mapping of a quantitative trait.  

PubMed

In focused studies designed to follow up associations detected in a genome-wide association study (GWAS), investigators can proceed to fine-map a genomic region by targeted sequencing or dense genotyping of all variants in the region, aiming to identify a functional sequence variant. For the analysis of a quantitative trait, we consider a Bayesian approach to fine-mapping study design that incorporates stratification according to a promising GWAS tag SNP in the same region. Improved cost-efficiency can be achieved when the fine-mapping phase incorporates a two-stage design, with identification of a smaller set of more promising variants in a subsample taken in stage 1, followed by their evaluation in an independent stage 2 subsample. To avoid the potential negative impact of genetic model misspecification on inference we incorporate genetic model selection based on posterior probabilities for each competing model. Our simulation study shows that, compared to simple random sampling that ignores genetic information from GWAS, tag-SNP-based stratified sample allocation methods reduce the number of variants continuing to stage 2 and are more likely to promote the functional sequence variant into confirmation studies. PMID:25132153

Chen, Zhijian; Craiu, Radu V; Bull, Shelley B

2014-11-01

231

Characterization of fs10.1 , a major QTL controlling fruit elongation in Capsicum  

Microsoft Academic Search

We previously identified fs10.1 as a major QTL controlling fruit shape (index of length to width) in an interspecific F2 cross of Capsicum annuum (round fruit) × C. chinense (elongated fruit) in pepper. To more precisely map and characterize the QTL, we constructed near-isogenic lines for fs10.1 and mapped it in a BC4F2 population. In this population, fs10.1 segregated as a Mendelian

Yelena Borovsky; Ilan Paran

232

Analysis of digenic epistatic effects and QE interaction effects QTL controlling grain weight in rice  

Microsoft Academic Search

Immortalized F2 population of rice (Oryza sativa L.) was developed by randomly mating F1 among recombinant inbred (RI) lines derived from (Zhenshan 97B × Minghui 63), which allowed replications within and across environments. QTL (quantitative trait loci) mapping analysis on kilo-grain weight of immortalized F2 population was performed by using newly developed software for QTL mapping, QTLMapper 2.0. Eleven distinctly

GAO Yong-ming; ZHU Jun; SONG You-shen; SHI Chun-hai; XING Yong-zhong

233

Epistatic association mapping for alkaline and salinity tolerance traits in the soybean germination stage.  

PubMed

Soil salinity and alkalinity are important abiotic components that frequently have critical effects on crop growth, productivity and quality. Developing soybean cultivars with high salt tolerance is recognized as an efficient way to maintain sustainable soybean production in a salt stress environment. However, the genetic mechanism of the tolerance must first be elucidated. In this study, 257 soybean cultivars with 135 SSR markers were used to perform epistatic association mapping for salt tolerance. Tolerance was evaluated by assessing the main root length (RL), the fresh and dry weights of roots (FWR and DWR), the biomass of seedlings (BS) and the length of hypocotyls (LH) of healthy seedlings after treatments with control, 100 mM NaCl or 10 mM Na2CO3 solutions for approximately one week under greenhouse conditions. A total of 83 QTL-by-environment (QE) interactions for salt tolerance index were detected: 24 for LR, 12 for FWR, 11 for DWR, 15 for LH and 21 for BS, as well as one epistatic QTL for FWR. Furthermore, 86 QE interactions for alkaline tolerance index were found: 17 for LR, 16 for FWR, 17 for DWR, 18 for LH and 18 for BS. A total of 77 QE interactions for the original trait indicator were detected: 17 for LR, 14 for FWR, 4 for DWR, 21 for LH and 21 for BS, as well as 3 epistatic QTL for BS. Small-effect QTL were frequently observed. Several soybean genes with homology to Arabidopsis thaliana and soybean salt tolerance genes were found in close proximity to the above QTL. Using the novel alleles of the QTL detected above, some elite parental combinations were designed, although these QTL need to be further confirmed. The above results provide a valuable foundation for fine mapping, cloning and molecular breeding by design for soybean alkaline and salt tolerance. PMID:24416275

Zhang, Wen-Jie; Niu, Yuan; Bu, Su-Hong; Li, Meng; Feng, Jian-Ying; Zhang, Jin; Yang, Sheng-Xian; Odinga, Medrine Mmayi; Wei, Shi-Ping; Liu, Xiao-Feng; Zhang, Yuan-Ming

2014-01-01

234

Epistatic Association Mapping for Alkaline and Salinity Tolerance Traits in the Soybean Germination Stage  

PubMed Central

Soil salinity and alkalinity are important abiotic components that frequently have critical effects on crop growth, productivity and quality. Developing soybean cultivars with high salt tolerance is recognized as an efficient way to maintain sustainable soybean production in a salt stress environment. However, the genetic mechanism of the tolerance must first be elucidated. In this study, 257 soybean cultivars with 135 SSR markers were used to perform epistatic association mapping for salt tolerance. Tolerance was evaluated by assessing the main root length (RL), the fresh and dry weights of roots (FWR and DWR), the biomass of seedlings (BS) and the length of hypocotyls (LH) of healthy seedlings after treatments with control, 100 mM NaCl or 10 mM Na2CO3 solutions for approximately one week under greenhouse conditions. A total of 83 QTL-by-environment (QE) interactions for salt tolerance index were detected: 24 for LR, 12 for FWR, 11 for DWR, 15 for LH and 21 for BS, as well as one epistatic QTL for FWR. Furthermore, 86 QE interactions for alkaline tolerance index were found: 17 for LR, 16 for FWR, 17 for DWR, 18 for LH and 18 for BS. A total of 77 QE interactions for the original trait indicator were detected: 17 for LR, 14 for FWR, 4 for DWR, 21 for LH and 21 for BS, as well as 3 epistatic QTL for BS. Small-effect QTL were frequently observed. Several soybean genes with homology to Arabidopsis thaliana and soybean salt tolerance genes were found in close proximity to the above QTL. Using the novel alleles of the QTL detected above, some elite parental combinations were designed, although these QTL need to be further confirmed. The above results provide a valuable foundation for fine mapping, cloning and molecular breeding by design for soybean alkaline and salt tolerance. PMID:24416275

Feng, Jian-Ying; Zhang, Jin; Yang, Sheng-Xian; Odinga, Medrine Mmayi; Wei, Shi-Ping; Liu, Xiao-Feng; Zhang, Yuan-Ming

2014-01-01

235

Molecular tagging of erucic acid trait in oilseed mustard ( Brassica juncea ) by QTL mapping and single nucleotide polymorphisms in FAE1 gene  

Microsoft Academic Search

Molecular mapping and tagging of the erucic acid trait (C22:1) in Brassica juncea was done by a candidate gene approach. Two QTLs underlying the variation of seed erucic acid content were assigned to two linkage groups of a B. juncea map using a doubled haploid (DH) mapping population derived from high × low erucic acid F 1 hybrid. Two consensus

V. Gupta; A. Mukhopadhyay; N. Arumugam; Y. S. Sodhi; D. Pental; A. K. Pradhan

2004-01-01

236

High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.  

PubMed

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus. PMID:22685170

Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

2012-08-01

237

High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus1[W][OA  

PubMed Central

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Firs.p.QTL2.1 to Firs.p.QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Firs.p.QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Firs.p.QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus. PMID:22685170

Chapman, Natalie H.; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G.; Poole, Mervin; Causse, Mathilde; King, Graham J.; Baxter, Charles; Seymour, Graham B.

2012-01-01

238

Fourteen Years of R/qtl: Just Barely Sustainable.  

PubMed

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

Broman, Karl W

2014-07-01

239

QTL Controlling Masculinization of Ear Tips in a Maize (Zea mays L.) Intraspecific Cross  

PubMed Central

Maize is unique among cereal grasses because of its monoecious flowering habit. Male flowers are normally restricted to the tassel that terminates the primary shoot, whereas female flowers occur as ears at the terminal nodes of lateral branches. We observed Ki14, a tropical maize inbred that produces an ear tipped by a staminate (male) spike under certain environmental conditions, such as long daylengths. Recombinant inbred lines derived from the cross between temperate line B97, which was never observed to produce a staminate ear tip, and Ki14 segregated for the trait under long daylengths. Some progeny lines that had even longer staminate tips than Ki14 were male fertile. We mapped three QTL controlling staminate ear tip using a two-part (binomial plus normal) model. A major QTL on chromosome 3 had a large effect on penetrance of the trait (whether a line would produce staminate ear tips or not) as well as its severity (the length of the staminate tip). This QTL seems to be linked to, but at a distinct position from, a previously mapped QTL controlling the proportion of staminate florets in ears in progeny from crosses between maize and teosinte. Two additional QTL affecting staminate ear tip severity overlapped with QTL controlling photoperiod response previously mapped in this population. Alleles conferring photoperiod sensitivity for delayed flowering at these QTL seem to enhance the production of staminate ear tips under long daylengths. PMID:22384344

Holland, James B.; Coles, Nathan D.

2011-01-01

240

A comprehensive meta QTL analysis for fiber quality, yield, yield related and morphological traits, drought tolerance, and disease resistance in tetraploid cotton  

PubMed Central

Background The study of quantitative trait loci (QTL) in cotton (Gossypium spp.) is focused on traits of agricultural significance. Previous studies have identified a plethora of QTL attributed to fiber quality, disease and pest resistance, branch number, seed quality and yield and yield related traits, drought tolerance, and morphological traits. However, results among these studies differed due to the use of different genetic populations, markers and marker densities, and testing environments. Since two previous meta-QTL analyses were performed on fiber traits, a number of papers on QTL mapping of fiber quality, yield traits, morphological traits, and disease resistance have been published. To obtain a better insight into the genome-wide distribution of QTL and to identify consistent QTL for marker assisted breeding in cotton, an updated comparative QTL analysis is needed. Results In this study, a total of 1,223 QTL from 42 different QTL studies in Gossypium were surveyed and mapped using Biomercator V3 based on the Gossypium consensus map from the Cotton Marker Database. A meta-analysis was first performed using manual inference and confirmed by Biomercator V3 to identify possible QTL clusters and hotspots. QTL clusters are composed of QTL of various traits which are concentrated in a specific region on a chromosome, whereas hotspots are composed of only one trait type. QTL were not evenly distributed along the cotton genome and were concentrated in specific regions on each chromosome. QTL hotspots for fiber quality traits were found in the same regions as the clusters, indicating that clusters may also form hotspots. Conclusions Putative QTL clusters were identified via meta-analysis and will be useful for breeding programs and future studies involving Gossypium QTL. The presence of QTL clusters and hotspots indicates consensus regions across cultivated tetraploid Gossypium species, environments, and populations which contain large numbers of QTL, and in some cases multiple QTL associated with the same trait termed a hotspot. This study combines two previous meta-analysis studies and adds all other currently available QTL studies, making it the most comprehensive meta-analysis study in cotton to date. PMID:24215677

2013-01-01

241

Fine mapping of chromosome 15q25.1 lung cancer susceptibility in African-Americans  

PubMed Central

Several genome-wide association studies identified the chr15q25.1 region, which includes three nicotinic cholinergic receptor genes (CHRNA5-B4) and the cell proliferation gene (PSMA4), for its association with lung cancer risk in Caucasians. A haplotype and its tagging single nucleotide polymorphisms (SNPs) encompassing six genes from IREB2 to CHRNB4 were most strongly associated with lung cancer risk (OR = 1.3; P < 10?20). In order to narrow the region of association and identify potential causal variations, we performed a fine-mapping study using 77 SNPs in a 194 kb segment of the 15q25.1 region in a sample of 448 African-American lung cancer cases and 611 controls. Four regions, two SNPs and two distinct haplotypes from sliding window analyses, were associated with lung cancer. CHRNA5 rs17486278 G had OR = 1.28, 95% CI 1.07–1.54 and P = 0.008, whereas CHRNB4 rs7178270 G had OR = 0.78, 95% CI 0.66–0.94 and P = 0.008 for lung cancer risk. Lung cancer associations remained significant after pack-year adjustment. Rs7178270 decreased lung cancer risk in women but not in men; gender interaction P = 0.009. For two SNPs (rs7168796 A/G and rs7164594 A/G) upstream of PSMA4, lung cancer risks for people with haplotypes GG and AA were reduced compared with those with AG (OR = 0.56, 95% CI 0.38–0.82; P = 0.003 and OR = 0.73, 95% CI 0.59–0.90, P = 0.004, respectively). A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) and CHRNA3 (rs578776 G) was associated with increased lung cancer risk (P = 0.002). The identified regions contain SNPs predicted to affect gene regulation. There are multiple lung cancer risk loci in the 15q25.1 region in African-Americans. PMID:20587604

Hansen, Helen M.; Xiao, Yuanyuan; Rice, Terri; Bracci, Paige M.; Wrensch, Margaret R.; Sison, Jennette D.; Chang, Jeffery S.; Smirnov, Ivan V.; Patoka, Joseph; Seldin, Michael F.; Quesenberry, Charles P.; Kelsey, Karl T.; Wiencke, John K.

2010-01-01

242

Using transcriptome profiling to characterize QTL regions on chicken chromosome 5  

PubMed Central

Background Although many QTL for various traits have been mapped in livestock, location confidence intervals remain wide that makes difficult the identification of causative mutations. The aim of this study was to test the contribution of microarray data to QTL detection in livestock species. Three different but complementary approaches are proposed to improve characterization of a chicken QTL region for abdominal fatness (AF) previously detected on chromosome 5 (GGA5). Results Hepatic transcriptome profiles for 45 offspring of a sire known to be heterozygous for the distal GGA5 AF QTL were obtained using a 20 K chicken oligochip. mRNA levels of 660 genes were correlated with the AF trait. The first approach was to dissect the AF phenotype by identifying animal subgroups according to their 660 transcript profiles. Linkage analysis using some of these subgroups revealed another QTL in the middle of GGA5 and increased the significance of the distal GGA5 AF QTL, thereby refining its localization. The second approach targeted the genes correlated with the AF trait and regulated by the GGA5 AF QTL region. Five of the 660 genes were considered as being controlled either by the AF QTL mutation itself or by a mutation close to it; one having a function related to lipid metabolism (HMGCS1). In addition, a QTL analysis with a multiple trait model combining this 5 gene-set and AF allowed us to refine the QTL region. The third approach was to use these 5 transcriptome profiles to predict the paternal Q versus q AF QTL mutation for each recombinant offspring and then refine the localization of the QTL from 31 cM (100 genes) at a most probable location confidence interval of 7 cM (12 genes) after determining the recombination breakpoints, an interval consistent with the reductions obtained by the two other approaches. Conclusion The results showed the feasibility and efficacy of the three strategies used, the first revealing a QTL undetected using the whole population, the second providing functional information about a QTL region through genes related to the trait and controlled by this region (HMGCS1), the third could drastically refine a QTL region. PMID:19954542

2009-01-01

243

Yeast growth plasticity is regulated by environment-specific multi-QTL interactions.  

PubMed

For a unicellular, nonmotile organism like Saccharomyces cerevisiae, carbon sources act as nutrients and as signaling molecules; consequently, these sources affect various fitness parameters, including growth. It is therefore advantageous for yeast strains to adapt their growth to carbon source variation. The ability of a given genotype to manifest different phenotypes in varying environments is known as phenotypic plasticity. To identify quantitative trait loci (QTL) that drive plasticity in growth, two growth parameters (growth rate and biomass) were measured for a set of meiotic recombinants of two genetically divergent yeast strains grown in different carbon sources. To identify QTL contributing to plasticity across pairs of environments, gene-environment interaction mapping was performed, which identified several QTL that have a differential effect across environments, some of which act antagonistically across pairs of environments. Multi-QTL analysis identified loci interacting with previously known growth affecting QTL as well as novel two-QTL interactions that affect growth. A QTL that had no significant independent effect was found to alter growth rate and biomass for several carbon sources through two-QTL interactions. Our study demonstrates that environment-specific epistatic interactions contribute to the growth plasticity in yeast. We propose that a targeted scan for epistatic interactions, such as the one described here, can help unravel mechanisms regulating phenotypic plasticity. PMID:24474169

Bhatia, Aatish; Yadav, Anupama; Zhu, Chenchen; Gagneur, Julien; Radhakrishnan, Aparna; Steinmetz, Lars M; Bhanot, Gyan; Sinha, Himanshu

2014-05-01

244

Yeast Growth Plasticity Is Regulated by Environment-Specific Multi-QTL Interactions  

PubMed Central

For a unicellular, non-motile organism like Saccharomyces cerevisiae, carbon sources act both as nutrients and as signaling molecules and consequently affect various fitness parameters including growth. It is therefore advantageous for yeast strains to adapt their growth to carbon source variation. The ability of a given genotype to manifest different phenotypes in varying environments is known as phenotypic plasticity. To identify quantitative trait loci (QTL) that drive plasticity in growth, two growth parameters (growth rate and biomass) were measured in a published dataset from meiotic recombinants of two genetically divergent yeast strains grown in different carbon sources. To identify QTL contributing to plasticity across pairs of environments, gene–environment interaction mapping was performed, which identified several QTL that have a differential effect across environments, some of which act antagonistically across pairs of environments. Multi-QTL analysis identified loci interacting with previously known growth affecting QTL as well as novel two-QTL interactions that affect growth. A QTL that had no significant independent effect was found to alter growth rate and biomass for several carbon sources through two-QTL interactions. Our study demonstrates that environment-specific epistatic interactions contribute to the growth plasticity in yeast. We propose that a targeted scan for epistatic interactions, such as the one described here, can help unravel mechanisms regulating phenotypic plasticity. PMID:24474169

Bhatia, Aatish; Yadav, Anupama; Zhu, Chenchen; Gagneur, Julien; Radhakrishnan, Aparna; Steinmetz, Lars M.; Bhanot, Gyan; Sinha, Himanshu

2014-01-01

245

Fine Mapping Links the FTa1 Flowering Time Regulator to the Dominant Spring1 Locus in Medicago  

PubMed Central

To extend our understanding of flowering time control in eudicots, we screened for mutants in the model legume Medicago truncatula (Medicago). We identified an early flowering mutant, spring1, in a T-DNA mutant screen, but spring1 was not tagged and was deemed a somaclonal mutant. We backcrossed the mutant to wild type R108. The F1 plants and the majority of F2 plants were early flowering like spring1, strongly indicating that spring1 conferred monogenic, dominant early flowering. We hypothesized that the spring1 phenotype resulted from over expression of an activator of flowering. Previously, a major QTL for flowering time in different Medicago accessions was located to an interval on chromosome 7 with six candidate flowering- time activators, including a CONSTANS gene, MtCO, and three FLOWERING LOCUS T (FT) genes. Hence we embarked upon linkage mapping using 29 markers from the MtCO/FT region on chromosome 7 on two populations developed by crossing spring1 with Jester. Spring1 mapped to an interval of ?0.5 Mb on chromosome 7 that excluded MtCO, but contained 78 genes, including the three FT genes. Of these FT genes, only FTa1 was up-regulated in spring1 plants. We then investigated global gene expression in spring1 and R108 by microarray analysis. Overall, they had highly similar gene expression and apart from FTa1, no genes in the mapping interval were differentially expressed. Two MADS transcription factor genes, FRUITFULLb (FULb) and SUPPRESSOR OF OVER EXPRESSION OF CONSTANS1a (SOC1a), that were up-regulated in spring1, were also up-regulated in transgenic Medicago over-expressing FTa1. This suggested that their differential expression in spring1 resulted from the increased abundance of FTa1. A 6255 bp genomic FTa1 fragment, including the complete 5? region, was sequenced, but no changes were observed indicating that the spring1 mutation is not a DNA sequence difference in the FTa1 promoter or introns. PMID:23308229

Yeoh, Chin Chin; Balcerowicz, Martin; Zhang, Lulu; Jaudal, Mauren; Brocard, Lysiane; Ratet, Pascal; Putterill, Joanna

2013-01-01

246

Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation.  

PubMed

Zinc (Zn) hyperaccumulation seems to be a constitutive species-level trait in Thlaspi caerulescens. When compared under conditions of equal Zn availability, considerable variation in the degree of hyperaccumulation is observed among accessions originating from different soil types. This variation offers an excellent opportunity for further dissection of the genetics of this trait. A T. caerulescens intraspecific cross was made between a plant from a nonmetallicolous accession [Lellingen (LE)], characterized by relatively high Zn accumulation, and a plant from a calamine accession [La Calamine (LC)], characterized by relatively low Zn accumulation. Zinc accumulation in roots and shoots segregated in the F3 population. This population was used to construct an LE/LC amplified fragment length polymorphism (AFLP)-based genetic linkage map and to map quantitative trait loci (QTL) for Zn accumulation. Two QTL were identified for root Zn accumulation, with the trait-enhancing alleles being derived from each of the parents, and explaining 21.7 and 16.6% of the phenotypic variation observed in the mapping population. Future development of more markers, based on Arabidopsis orthologous genes localized in the QTL regions, will allow fine-mapping and map-based cloning of the genes underlying the QTL. PMID:16539600

Assunção, Ana G L; Pieper, Bjorn; Vromans, Jaap; Lindhout, Pim; Aarts, Mark G M; Schat, Henk

2006-01-01

247

TAGGING AND MAPPING OF GENES AND QTL AND MOLECULAR MARKER-ASSISTED SELECTION FOR TRAITS OF ECONOMIC IMPORTANCE IN BEAN AND COWPEA  

Technology Transfer Automated Retrieval System (TEKTRAN)

Bean/Cowpea Collaborative Research Support Program (B/C CRSP) scientists have successfully integrated consensus maps of the 11 linkage groups in both bean (Phaseolus vulgaris L.) and cowpea (Vigna unguiculata). The bean map is approximately 1200 cM with some 500 markers and an additional 500 marker...

248

Long-Range Regulatory Polymorphisms Affecting a GABA Receptor Constitute a Quantitative Trait Locus (QTL) for Social Behavior in Caenorhabditis elegans  

PubMed Central

Aggregation is a social behavior that varies between and within species, providing a model to study the genetic basis of behavioral diversity. In the nematode Caenorhabditis elegans, aggregation is regulated by environmental context and by two neuromodulatory pathways, one dependent on the neuropeptide receptor NPR-1 and one dependent on the TGF-? family protein DAF-7. To gain further insight into the genetic regulation of aggregation, we characterize natural variation underlying behavioral differences between two wild-type C. elegans strains, N2 and CB4856. Using quantitative genetic techniques, including a survey of chromosome substitution strains and QTL analysis of recombinant inbred lines, we identify three new QTLs affecting aggregation in addition to the two known N2 mutations in npr-1 and glb-5. Fine-mapping with near-isogenic lines localized one QTL, accounting for 5%–8% of the behavioral variance between N2 and CB4856, 3? to the transcript of the GABA neurotransmitter receptor gene exp-1. Quantitative complementation tests demonstrated that this QTL affects exp-1, identifying exp-1 and GABA signaling as new regulators of aggregation. exp-1 interacts genetically with the daf-7 TGF-? pathway, which integrates food availability and population density, and exp-1 mutations affect the level of daf-7 expression. Our results add to growing evidence that genetic variation affecting neurotransmitter receptor genes is a source of natural behavioral variation. PMID:23284308

Bendesky, Andres; Pitts, Jason; Rockman, Matthew V.; Chen, William C.; Tan, Man-Wah; Kruglyak, Leonid; Bargmann, Cornelia I.

2012-01-01

249

Gene Set Enrichment in eQTL Data Identifies Novel Annotations and Pathway Regulators  

PubMed Central

Genome-wide gene expression profiling has been extensively used to generate biological hypotheses based on differential expression. Recently, many studies have used microarrays to measure gene expression levels across genetic mapping populations. These gene expression phenotypes have been used for genome-wide association analyses, an analysis referred to as expression QTL (eQTL) mapping. Here, eQTL analysis was performed in adipose tissue from 28 inbred strains of mice. We focused our analysis on “trans-eQTL bands”, defined as instances in which the expression patterns of many genes were all associated to a common genetic locus. Genes comprising trans-eQTL bands were screened for enrichments in functional gene sets representing known biological pathways, and genes located at associated trans-eQTL band loci were considered candidate transcriptional modulators. We demonstrate that these patterns were enriched for previously characterized relationships between known upstream transcriptional regulators and their downstream target genes. Moreover, we used this strategy to identify both novel regulators and novel members of known pathways. Finally, based on a putative regulatory relationship identified in our analysis, we identified and validated a previously uncharacterized role for cyclin H in the regulation of oxidative phosphorylation. We believe that the specific molecular hypotheses generated in this study will reveal many additional pathway members and regulators, and that the analysis approaches described herein will be broadly applicable to other eQTL data sets. PMID:18464898

Wu, Chunlei; Delano, David L.; Mitro, Nico; Su, Stephen V.; Janes, Jeff; McClurg, Phillip; Batalov, Serge; Welch, Genevieve L.; Zhang, Jie; Orth, Anthony P.; Walker, John R.; Glynne, Richard J.; Cooke, Michael P.; Takahashi, Joseph S.; Shimomura, Kazuhiro; Kohsaka, Akira; Bass, Joseph; Saez, Enrique; Wiltshire, Tim; Su, Andrew I.

2008-01-01

250

Second-Generation Genetic Linkage Map of Catfish and Its Integration with the BAC-Based Physical Map  

PubMed Central

Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus, the dominant aquaculture species in the United States. Here we added 2030 BAC end sequence (BES)-derived microsatellites from 1481 physical map contigs, as well as markers from singleton BES, ESTs, anonymous microsatellites, and SNPs, to construct a second-generation linkage map. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. This work effectively anchored 44.8% of the catfish BAC physical map contigs, covering ?52.8% of the genome. The genome size was estimated to be 2546 cM on the linkage map, and the calculated physical distance per centimorgan was 393 Kb. This integrated map should enable comparative studies with teleost model species as well as provide a framework for ordering and assembling whole-genome scaffolds. PMID:23050234

Ninwichian, Parichart; Peatman, Eric; Liu, Hong; Kucuktas, Huseyin; Somridhivej, Benjaporn; Liu, Shikai; Li, Ping; Jiang, Yanliang; Sha, Zhenxia; Kaltenboeck, Ludmilla; Abernathy, Jason W.; Wang, Wenqi; Chen, Fei; Lee, Yoona; Wong, Lilian; Wang, Shaolin; Lu, Jianguo; Liu, Zhanjiang

2012-01-01

251

Second-generation genetic linkage map of catfish and its integration with the BAC-based physical map.  

PubMed

Construction of high-density genetic linkage maps is crucially important for quantitative trait loci (QTL) studies, and they are more useful when integrated with physical maps. Such integrated maps are valuable genome resources for fine mapping of QTL, comparative genomics, and accurate and efficient whole-genome assembly. Previously, we established both linkage maps and a physical map for channel catfish, Ictalurus punctatus, the dominant aquaculture species in the United States. Here we added 2030 BAC end sequence (BES)-derived microsatellites from 1481 physical map contigs, as well as markers from singleton BES, ESTs, anonymous microsatellites, and SNPs, to construct a second-generation linkage map. Average marker density across the 29 linkage groups reached 1.4 cM/marker. The increased marker density highlighted variations in recombination rates within and among catfish chromosomes. This work effectively anchored 44.8% of the catfish BAC physical map contigs, covering ~52.8% of the genome. The genome size was estimated to be 2546 cM on the linkage map, and the calculated physical distance per centimorgan was 393 Kb. This integrated map should enable comparative studies with teleost model species as well as provide a framework for ordering and assembling whole-genome scaffolds. PMID:23050234

Ninwichian, Parichart; Peatman, Eric; Liu, Hong; Kucuktas, Huseyin; Somridhivej, Benjaporn; Liu, Shikai; Li, Ping; Jiang, Yanliang; Sha, Zhenxia; Kaltenboeck, Ludmilla; Abernathy, Jason W; Wang, Wenqi; Chen, Fei; Lee, Yoona; Wong, Lilian; Wang, Shaolin; Lu, Jianguo; Liu, Zhanjiang

2012-10-01

252

Mapping and QTL analysis of horticultural traits in a narrow cross in cucumber ( Cucumis sativus L.) using random-amplified polymorphic DNA markers  

Microsoft Academic Search

An 80-point genetic map [77 random-amplified polymorphic DNAs (RAPD), F (female sex expression), de (determinate), and ll (little leaf)] was constructed from a narrow cross in cucumber using the determinate, gynoecious, standard-sized leaf line G421 and the indeterminate, monoecious, little leaf line H-19. The map defined nine linkage groups and spanned ca. 600 cM with an average distance between markers

Felix C. Serquen; J Bacher; JE Staub

1997-01-01

253

Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley  

PubMed Central

Background The barley-Puccinia hordei (barley leaf rust) pathosystem is a model for investigating partial disease resistance in crop plants and genetic mapping of phenotypic resistance has identified several quantitative trait loci (QTL) for partial resistance. Reciprocal QTL-specific near-isogenic lines (QTL-NILs) have been developed that combine two QTL, Rphq2 and Rphq3, the largest effects detected in a recombinant-inbred-line (RIL) population derived from a cross between the super-susceptible line L94 and partially-resistant line Vada. The molecular mechanism underpinning partial resistance in these QTL-NILs is unknown. Results An Agilent custom microarray consisting of 15,000 probes derived from barley consensus EST sequences was used to investigate genome-wide and QTL-specific differential expression of genes 18 hours post-inoculation (hpi) with Puccinia hordei. A total of 1,410 genes were identified as being significantly differentially expressed across the genome, of which 55 were accounted for by the genetic differences defined by QTL-NILs at Rphq2 and Rphq3. These genes were predominantly located at the QTL regions and are, therefore, positional candidates. One gene, encoding the transcriptional repressor Ethylene-Responsive Element Binding Factor 4 (HvERF4) was located outside the QTL at 71 cM on chromosome 1H, within a previously detected eQTL hotspot for defence response. The results indicate that Rphq2 or Rphq3 contains a trans-eQTL that modulates expression of HvERF4. We speculate that HvERF4 functions as an intermediate that conveys the response signal from a gene(s) contained within Rphq2 or Rphq3 to a host of down-stream defense responsive genes. Our results also reveal that barley lines with extreme or intermediate partial resistance phenotypes exhibit a profound similarity in their spectrum of Ph-responsive genes and that hormone-related signalling pathways are actively involved in response to Puccinia hordei. Conclusions Differential gene expression between QTL-NILs identifies genes predominantly located within the target region(s) providing both transcriptional and positional candidate genes for the QTL. Genetically mapping the differentially expressed genes relative to the QTL has the potential to discover trans-eQTL mediated regulatory relays initiated from genes within the QTL regions. PMID:21070652

2010-01-01

254

Fine Resolution Topographic Mapping of the Jovian Moons: A Ka-Band High Resolution Topographic Mapping Interferometric Synthetic Aperture Radar  

NASA Technical Reports Server (NTRS)

The topographic data set obtained by MOLA has provided an unprecedented level of information about Mars' geologic features. The proposed flight of JIMO provides an opportunity to accomplish a similar mapping of and comparable scientific discovery for the Jovian moons through use of an interferometric imaging radar analogous to the Shuttle radar that recently generated a new topographic map of Earth. A Ka-band single pass across-track synthetic aperture radar (SAR) interferometer can provide very high resolution surface elevation maps. The concept would use two antennas mounted at the ends of a deployable boom (similar to the Shuttle Radar Topographic Mapper) extended orthogonal to the direction of flight. Assuming an orbit altitude of approximately 100km and a ground velocity of approximately 1.5 km/sec, horizontal resolutions at the 10 meter level and vertical resolutions at the sub-meter level are possible.

Madsen, S. N.; Carsey, F. D.; Turtle, E. P.

2003-01-01

255

Joint linkage QTL analyses for partial resistance to Phytophthora sojae in soybean using six nested inbred populations with heterogeneous conditions.  

PubMed

Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect such QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred line (RIL) populations provides improved power to detect QTL through increased population size, recombination, and allelic diversity. However, uniform development and phenotyping of multiple RIL populations can prove difficult. In this study, the effectiveness of joint linkage QTL analysis was evaluated on combinations of two to six nested RIL populations differing in inbreeding generation, phenotypic assay method, and/or marker set used in genotyping. In comparison to linkage analysis in a single population, identification of QTL by joint linkage analysis was only minimally affected by different phenotypic methods used among populations once phenotypic data were standardized. In contrast, genotyping of populations with only partially overlapping sets of markers had a marked negative effect on QTL detection by joint linkage analysis. In total, 16 genetic regions with QTL for partial resistance against P. sojae were identified, including four novel QTL on chromosomes 4, 9, 12, and 16, as well as significant genotype-by-isolate interactions. Resistance alleles from PI 427106 or PI 427105B contributed to a major QTL on chromosome 18, explaining 10-45% of the phenotypic variance. This case study provides guidance on the application of joint linkage QTL analysis of data collected from populations with heterogeneous assay conditions and a genetic framework for partial resistance to P. sojae. PMID:24247235

Lee, Sungwoo; Mian, M A Rouf; Sneller, Clay H; Wang, Hehe; Dorrance, Anne E; McHale, Leah K

2014-02-01

256

REVIEW Lab Animal Volume 30 No, 7 J 2001 Review of Statistical Methods for QTl  

E-print Network

REVIEW Lab Animal Volume 30 No, 7 J 2001 Review of Statistical Methods for QTl Mapping of the statistical methods for mapping quantitative trait loci (QTLs, the genes responsible for variation in quan for the identification of drug targets. The author reviews the basic statis tical methods for mapping QTLs in experi

Broman, Karl W.

257

A high-resolution association mapping panel for the dissection of complex traits in mice  

PubMed Central

Systems genetics relies on common genetic variants to elucidate biologic networks contributing to complex disease-related phenotypes. Mice are ideal model organisms for such approaches, but linkage analysis has been only modestly successful due to low mapping resolution. Association analysis in mice has the potential of much better resolution, but it is confounded by population structure and inadequate power to map traits that explain less than 10% of the variance, typical of mouse quantitative trait loci (QTL). We report a novel strategy for association mapping that combines classic inbred strains for mapping resolution and recombinant inbred strains for mapping power. Using a mixed model algorithm to correct for population structure, we validate the approach by mapping over 2500 cis-expression QTL with a resolution an order of magnitude narrower than traditional QTL analysis. We also report the fine mapping of metabolic traits such as plasma lipids. This resource, termed the Hybrid Mouse Diversity Panel, makes possible the integration of multiple data sets and should prove useful for systems-based approaches to complex traits and studies of gene-by-environment interactions. PMID:20054062

Bennett, Brian J.; Farber, Charles R.; Orozco, Luz; Min Kang, Hyun; Ghazalpour, Anatole; Siemers, Nathan; Neubauer, Michael; Neuhaus, Isaac; Yordanova, Roumyana; Guan, Bo; Truong, Amy; Yang, Wen-pin; He, Aiqing; Kayne, Paul; Gargalovic, Peter; Kirchgessner, Todd; Pan, Calvin; Castellani, Lawrence W.; Kostem, Emrah; Furlotte, Nicholas; Drake, Thomas A.; Eskin, Eleazar; Lusis, Aldons J.

2010-01-01

258

A high-resolution association mapping panel for the dissection of complex traits in mice.  

PubMed

Systems genetics relies on common genetic variants to elucidate biologic networks contributing to complex disease-related phenotypes. Mice are ideal model organisms for such approaches, but linkage analysis has been only modestly successful due to low mapping resolution. Association analysis in mice has the potential of much better resolution, but it is confounded by population structure and inadequate power to map traits that explain less than 10% of the variance, typical of mouse quantitative trait loci (QTL). We report a novel strategy for association mapping that combines classic inbred strains for mapping resolution and recombinant inbred strains for mapping power. Using a mixed model algorithm to correct for population structure, we validate the approach by mapping over 2500 cis-expression QTL with a resolution an order of magnitude narrower than traditional QTL analysis. We also report the fine mapping of metabolic traits such as plasma lipids. This resource, termed the Hybrid Mouse Diversity Panel, makes possible the integration of multiple data sets and should prove useful for systems-based approaches to complex traits and studies of gene-by-environment interactions. PMID:20054062

Bennett, Brian J; Farber, Charles R; Orozco, Luz; Kang, Hyun Min; Ghazalpour, Anatole; Siemers, Nathan; Neubauer, Michael; Neuhaus, Isaac; Yordanova, Roumyana; Guan, Bo; Truong, Amy; Yang, Wen-pin; He, Aiqing; Kayne, Paul; Gargalovic, Peter; Kirchgessner, Todd; Pan, Calvin; Castellani, Lawrence W; Kostem, Emrah; Furlotte, Nicholas; Drake, Thomas A; Eskin, Eleazar; Lusis, Aldons J

2010-02-01

259

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

PubMed Central

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

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

2007-01-01

260

Fine genetic mapping of cp: a recessive gene for compact (dwarf) plant architecture in cucumber, Cucumis sativus L.  

PubMed

The compact (dwarf) plant architecture is an important trait in cucumber (Cucumis sativus L.) breeding that has the potential to be used in once-over mechanical harvest of cucumber production. Compact growth habit is controlled by a simply inherited recessive gene cp. With 150 F(2:3) families derived from two inbred cucumber lines, PI 308915 (compact vining) and PI 249561 (regular vining), we conducted genome-wide molecular mapping with microsatellite (simple sequence repeat, SSR) markers. A framework genetic map was constructed consisting of 187 SSR loci in seven linkage groups (chromosomes) covering 527.5 cM. Linkage analysis placed cp at the distal half of the long arm of cucumber Chromosome 4. Molecular markers cosegregating with the cp locus were identified through whole genome scaffold-based chromosome walking. Fine genetic mapping with 1,269 F(2) plants delimited the cp locus to a 220 kb genomic DNA region. Annotation and function prediction of genes in this region identified a homolog of the cytokinin oxidase (CKX) gene, which may be a potential candidate of compact gene. Alignment of the CKX gene homologs from both parental lines revealed a 3-bp deletion in the first exon of PI 308915, which can serve as a marker for marker-assisted selection of the compact phenotype. This work also provides a solid foundation for map-based cloning of the compact gene and understanding the molecular mechanisms of the dwarfing in cucumber. PMID:21735235

Li, Yuhong; Yang, Luming; Pathak, Mamta; Li, Dawei; He, Xiaoming; Weng, Yiqun

2011-10-01

261

A fine structure genomic map of the region of 12q13 containing SAS and CDK4  

SciTech Connect

We have recently adapted a method, originally described by Rackwitz, to the rapid restriction mapping of multiple cosmid DNA samples. Linearization of the cosmids at the lambda cohesive site using lambda terminase is followed by partial digestion with selected restriction enzymes and hybridization to oligonucleotides specific for the right or left hand termini. Partial digestions are performed in a microtiter plate thus allowing up to 12 cosmid clones to be digested with one restriction enzyme. We have applied this rapid restriction mapping method to cosmids derived from a region of chromosome 12q13 that has recently been shown to be amplified in a variety of cancers including malignant fibrous histiocytoma, fibrosarcoma, liposarcoma, osteosarcoma and brain tumors. A small segment of this amplification unit containing three genes, SAS (a membrane protein), CDK4 (a cyclin dependent kinase) and OS-9 (a recently described cDNA) has been analyzed with the system described above. This fine structure genomic map will be useful for completing the expression map of this region as well as characterizing its pattern of amplification in tumor specimens.

Linder, C.Y.; Elkahloun, A.G.; Su, Y.A. [National Center for Human Genome Research, Bethesda, MD (United States)] [and others

1994-09-01

262

Mapping and validation of Yr48 and other QTL conferring partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat  

Technology Transfer Automated Retrieval System (TEKTRAN)

A mapping population of 188 recombinant inbred lines developed from a cross between UC1110, an adapted California spring wheat, and PI610750, a synthetic derivative from CIMMYT's wide-cross program, was evaluated for its response to current California races of stripe rust (Puccinia striiformis f.sp....

263

Construction of a linkage map and QTL analysis of horticultural traits for watermelon [ Citrullus lanatus (THUNB.) MATSUM & NAKAI] using RAPD, RFLP and ISSR markers  

Microsoft Academic Search

We have been constructing linkage maps for watermelon (Citrullus lanatus) on the basis of random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), inter-simple sequence repeats (ISSRs) and isozymes using an F2 population derived from a crossing between a cultivated inbred line (H-7; C. lanatus) and an African wild form (SA-1; C. lanatus). A total of 120 F2 plants

T. Hashizume; I. Shimamoto; M. Hirai

2003-01-01

264

Genomics of a Metamorphic Timing QTL: met1 Maps to a Unique Genomic Position and Regulates Morph and Species-Specific Patterns of Brain Transcription  

PubMed Central

Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect quantitative trait locus (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and determine the effect of met1 on larval growth, metamorphic timing, and gene expression in the brain. We show that met1 maps to the position of a urodele-specific chromosome rearrangement on linkage group 2 that uniquely brought functionally associated genes into linkage. Furthermore, we found that more than 200 genes were differentially expressed during larval development as a function of met1 genotype. This list of differentially expressed genes is enriched for proteins that function in the mitochondria, providing evidence of a link between met1, thyroid hormone signaling, and mitochondrial energetics associated with metamorphosis. Finally, we found that met1 significantly affected metamorphic timing in hybrids, but not early larval growth rate. Collectively, our results show that met1 regulates species and morph-specific patterns of brain transcription and life history variation. PMID:23946331

Page, Robert B.; Boley, Meredith A.; Kump, David K.; Voss, Stephen R.

2013-01-01

265

Fine-scale mapping of the gene responsible for multiple endocrine neoplasia type 1 (MEN 1).  

PubMed Central

We have constructed a high-resolution genetic linkage map in the vicinity of the gene responsible for multiple endocrine neoplasia type 1 (MEN1). The mutation causing this disease, inherited as an autosomal dominant, predisposes carriers to development of neoplastic tumors in the parathyroid, the endocrine pancreas, and the anterior lobe of the pituitary. The 12 markers on the genetic linkage map reported here span nearly 20 cM, and linkage analysis of MEN1 pedigrees has placed the MEN1 locus within the 8-cM region between D11S480 and D11S546. The markers on this map will be useful for prenatal or presymptomatic diagnosis of individuals in families that segregate a mutant allele of the MEN1 gene. PMID:1734719

Fujimori, M; Wells, S A; Nakamura, Y

1992-01-01

266

Fine-scaling mapping of the gene responsible for multiple endocrine neoplasia type I (MEN1)  

SciTech Connect

The authors have constructed a high-resolution genetic linkage map in the vicinity of the gene responsible for multiple endocrine neoplasia type 1 (MEN1). The mutation causing this disease, inherited as an autosomal dominant, predisposes carriers to development of neoplastic tumors in the parathyroid, the endocrine pancreas, and the anterior lobe of the pituitary. The 12 markers on the genetic linkage map reported here span nearly 20 cM, and linkage analysis of MEN1 pedigrees has placed the MEN1 locus within the 8-cM region between D11S480 and D11S546. The markers on this map will be useful for prenatal or presymptomatic diagnosis of individuals in families that segregate a mutant allele of the MEN1 gene.

Fujimori, Minoru; Nakamura, Yusuke (Cancer Institute, Tokyo (Japan)); Wells, S.A. (Washington University School of Medicine, St. Louis (United States))

1992-02-01

267

Identification and fine mapping of Pi33, the rice resistance gene corresponding to the Magnaporthe grisea avirulence gene ACE1.  

PubMed

Rice blast disease is a major constraint for rice breeding. Nevertheless, the genetic basis of resistance remains poorly understood for most rice varieties, and new resistance genes remain to be identified. We identified the resistance gene corresponding to the cloned avirulence gene ACE1 using pairs of isogenic strains of Magnaporthe grisea differing only by their ACE1 allele. This resistance gene was mapped on the short arm of rice chromosome 8 using progenies from the crosses IR64 (resistant) x Azucena (susceptible) and Azucena x Bala (resistant). The isogenic strains also permitted the detection of this resistance gene in several rice varieties, including the differential isogenic line C101LAC. Allelism tests permitted us to distinguish this gene from two other resistance genes [ Pi11 and Pi-29(t)] that are present on the short arm of chromosome 8. Segregation analysis in F(2) populations was in agreement with the existence of a single dominant gene, designated as Pi33. Finally, Pi33 was finely mapped between two molecular markers of the rice genetic map that are separated by a distance of 1.6 cM. Detection of Pi33 in different semi-dwarf indica varieties indicated that this gene could originate from either one or a few varieties. PMID:12838393

Berruyer, R; Adreit, H; Milazzo, J; Gaillard, S; Berger, A; Dioh, W; Lebrun, M-H; Tharreau, D

2003-10-01

268

QTL analysis of potato tuber dormancy.  

PubMed

The potential loss of chemical sprout inhibitors because of public concern over the use of pesticides underscores the desirability of breeding for long dormancy of potato (Solanum tuberosum L.) tubers. Quantitative trait locus (QTL) analyses were performed in reciprocal backcrosses between S. tuberosum and S. berthaultii toward defining the complexity of dormancy. S. berthaultii is a wild Bolivian species characterized by a short-day requirement for tuberization, long tuber dormancy, and resistance to several insect pests. RFLP alleles segregating from the recurrent parents as well as from the interspecific hybrid were monitored in two segregating progenies. We detected QTLs on nine chromosomes that affected tuber dormancy, either alone or through epistatic interactions. Alleles from the wild parent promoted dormancy, with the largest effect at a QTL on chromosome 2. Long dormancy appeared to be recessive in the backcross to S. berthaultii (BCB). In BCB the additive effects of dormancy QTLs accounted for 48% of the measured phenotypic variance, and adding epistatic effects to the model explained only 4% more. In contrast, additive effects explained only 16% of the variance in the backcross to S. tuberosum (BCT), and an additional 24% was explained by the inclusion of epistatic effects. In BCB variation at all QTLs detected was associated with RFLP alleles segregating from the hybrid parent; in BCT all QTLs except for two found through epistasis were detected through RFLP alleles segregating from the recurrent parent. At least three dormancy QTLs mapped to markers previously found to be associated with tuberization in these crosses. PMID:24162286

van den Berg, J H; Ewing, E E; Plaisted, R L; McMurry, S; Bonierbale, M W

1996-08-01

269

Genetic fine-mapping of DIPLOSPOROUS in Taraxacum (dandelion; Asteraceae) indicates a duplicated DIP-gene  

Microsoft Academic Search

BACKGROUND: DIPLOSPOROUS (DIP) is the locus for diplospory in Taraxacum, associated to unreduced female gamete formation in apomicts. Apomicts reproduce clonally through seeds, including apomeiosis, parthenogenesis, and autonomous or pseudogamous endosperm formation. In Taraxacum, diplospory results in first division restitution (FDR) nuclei, and inherits as a dominant, monogenic trait, independent from the other apomixis elements. A preliminary genetic linkage map

Kitty Vijverberg; Slavica Milanovic-Ivanovic; Tanja Bakx-Schotman; Peter J van Dijk

2010-01-01

270

Fine time course expression analysis identifies cascades of activation and repression and maps a putative regulator of mammalian sex determination.  

PubMed

In vertebrates, primary sex determination refers to the decision within a bipotential organ precursor to differentiate as a testis or ovary. Bifurcation of organ fate begins between embryonic day (E) 11.0-E12.0 in mice and likely involves a dynamic transcription network that is poorly understood. To elucidate the first steps of sexual fate specification, we profiled the XX and XY gonad transcriptomes at fine granularity during this period and resolved cascades of gene activation and repression. C57BL/6J (B6) XY gonads showed a consistent ~5-hour delay in the activation of most male pathway genes and repression of female pathway genes relative to 129S1/SvImJ, which likely explains the sensitivity of the B6 strain to male-to-female sex reversal. Using this fine time course data, we predicted novel regulatory genes underlying expression QTLs (eQTLs) mapped in a previous study. To test predictions, we developed an in vitro gonad primary cell assay and optimized a lentivirus-based shRNA delivery method to silence candidate genes and quantify effects on putative targets. We provide strong evidence that Lmo4 (Lim-domain only 4) is a novel regulator of sex determination upstream of SF1 (Nr5a1), Sox9, Fgf9, and Col9a3. This approach can be readily applied to identify regulatory interactions in other systems. PMID:23874228

Munger, Steven C; Natarajan, Anirudh; Looger, Loren L; Ohler, Uwe; Capel, Blanche

2013-01-01

271

Localization of quantitative trait loci (QTL) for agronomic important characters by the use of a RFLP map in barley (Hordeum vulgare L.).  

PubMed

Two hundred and fifty doubled haploid lines were studied from a cross between two 2-row winter barley varieties. The lines were evaluated for several characters in a field experiment for 3 years on two locations with two replications. From a total of 431 RFLP probes 50 were found to be polymorphic and subsequently used to construct a linkage map. Quantitative trait loci (QTLs) were determined and localized for resistance against Rhynchosporium secalis and Erysiphe graminis, for lodging, stalk breaking and ear breaking tendency, for the physical state before harvest, plant height, heading date, several kernel parameters and kernel yield. The heritability of the traits ranged from 0.56 to 0.89. For each trait except for kernel thickness, QTLs have been localized that explain 5-52% of the genetic variance. Transgressive segregation occurred for all of the traits studied. PMID:24173906

Backes, G; Graner, A; Foroughi-Wehr, B; Fischbeck, G; Wenzel, G; Jahoor, A

1995-02-01

272

Fine-Mapping and Phenotypic Analysis of the Ity3 Salmonella Susceptibility Locus Identify a Complex Genetic Structure  

PubMed Central

Experimental animal models of Salmonella infections have been widely used to identify genes important in the host immune response to infection. Using an F2 cross between the classical inbred strain C57BL/6J and the wild derived strain MOLF/Ei, we have previously identified Ity3 (Immunity to Typhimurium locus 3) as a locus contributing to the early susceptibility of MOLF/Ei mice to infection with Salmonella Typhimurium. We have also established a congenic strain (B6.MOLF-Ity/Ity3) with the MOLF/Ei Ity3 donor segment on a C57BL/6J background. The current study was designed to fine map and characterize functionally the Ity3 locus. We generated 12 recombinant sub-congenic strains that were characterized for susceptibility to infection, bacterial load in target organs, cytokine profile and anti-microbial mechanisms. These analyses showed that the impact of the Ity3 locus on survival and bacterial burden was stronger in male mice compared to female mice. Fine mapping of Ity3 indicated that two subloci contribute collectively to the susceptibility of B6.MOLF-Ity/Ity3 congenic mice to Salmonella infection. The Ity3.1 sublocus controls NADPH oxidase activity and is characterized by decreased ROS production, reduced inflammatory cytokine response and increased bacterial burden, thereby supporting a role for Ncf2 (neutrophil cytosolic factor 2 a subunit of NADPH oxidase) as the gene underlying this sublocus. The Ity3.2 sub-locus is characterized by a hyperresponsive inflammatory cytokine phenotype after exposure to Salmonella. Overall, this research provides support to the combined action of hormonal influences and complex genetic factors within the Ity3 locus in the innate immune response to Salmonella infection in wild-derived MOLF/Ei mice. PMID:24505352

Khan, Rabia T.; Yuki, Kyoko E.; Malo, Danielle

2014-01-01

273

Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids  

PubMed Central

We mapped regulatory loci for nearly all protein-coding genes in mammals using comparative genomic hybridization and expression array measurements from a panel of mouse–hamster radiation hybrid cell lines. The large number of breaks in the mouse chromosomes and the dense genotyping of the panel allowed extremely sharp mapping of loci. As the regulatory loci result from extra gene dosage, we call them copy number expression quantitative trait loci, or ceQTLs. The ?2log10P support interval for the ceQTLs was <150 kb, containing an average of <2–3 genes. We identified 29,769 trans ceQTLs with ?log10P > 4, including 13 hotspots each regulating >100 genes in trans. Further, this work identifies 2,761 trans ceQTLs harboring no known genes, and provides evidence for a mode of gene expression autoregulation specific to the X chromosome. PMID:18362883

Park, Christopher C; Ahn, Sangtae; Bloom, Joshua S; Lin, Andy; Wang, Richard T; Wu, Tongtong; Sekar, Aswin; Khan, Arshad H; Farr, Christine J; Lusis, Aldons J; Leahy, Richard M; Lange, Kenneth; Smith, Desmond J

2010-01-01

274

Identification and fine mapping of AvrPi15 , a novel avirulence gene of Magnaporthe grisea  

Microsoft Academic Search

Avirulence of Magnaporthe grisea isolate CHL346 on rice cultivar GA25 was studied with 242 ascospore progenies derived from the cross CHL346 × CHL42. Segregation analysis of the avirulence in the progeny population was in agreement with the existence of a single avirulence (Avr) gene, designated as AvrPi15. For mapping the Avr gene, we developed a total of 121 microsatellite DNA markers [simple

Jun-Hong Ma; Ling Wang; Shu-Jie Feng; Fei Lin; Yi Xiao; Qing-Hua Pan

2006-01-01

275

Fine mapping of trypanosomiasis resistance loci in murine advanced intercross lines  

Microsoft Academic Search

.   We have previously reported the results of genome-wide searches in two murine F2 populations for QTLs that influence survival following Trypanosoma congolense infection. Three loci, Tir1, Tir2, and Tir3, were identified and mapped to mouse Chromosomes (Chrs) 17, 5, and 1 respectively, with confidence intervals (CIs) in the\\u000a range 10–40 cM. The size of these CIs is to a

Fuad Iraqi; Steven J. Clapcott; Praveen Kumari; Chris S. Haley; Stephen J. Kemp; Alan J. Teale

2000-01-01

276

Fine mapping of the clubroot resistance gene, Crr3 , in Brassica rapa  

Microsoft Academic Search

A linkage map of Chinese cabbage (Brassica rapa) was constructed to localize the clubroot resistance (CR) gene, Crr3. Quantitative trait loci analysis using an F3 population revealed a sharp peak in the logarithm of odds score around the sequence-tagged site (STS) marker, OPC11-2S. Therefore, this region contained Crr3. Nucleotide sequences of OPC11-2S and its proximal markers showed homology to sequences

M. Saito; N. Kubo; S. Matsumoto; K. Suwabe; M. Tsukada; M. Hirai

2006-01-01

277

QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomyces euteiches in four sources of resistance in pea  

PubMed Central

Background Development of durable plant genetic resistance to pathogens through strategies of QTL pyramiding and diversification requires in depth knowledge of polygenic resistance within the available germplasm. Polygenic partial resistance to Aphanomyces root rot, caused by Aphanomyces euteiches, one of the most damaging pathogens of pea worldwide, was previously dissected in individual mapping populations. However, there are no data available regarding the diversity of the resistance QTL across a broader collection of pea germplasm. In this study, we performed a meta-analysis of Aphanomyces root rot resistance QTL in the four main sources of resistance in pea and compared their genomic localization with genes/QTL controlling morphological or phenological traits and with putative candidate genes. Results Meta-analysis, conducted using 244 individual QTL reported previously in three mapping populations (Puget x 90–2079, Baccara x PI180693 and Baccara x 552) and in a fourth mapping population in this study (DSP x 90–2131), resulted in the identification of 27 meta-QTL for resistance to A. euteiches. Confidence intervals of meta-QTL were, on average, reduced four-fold compared to mean confidence intervals of individual QTL. Eleven consistent meta-QTL, which highlight seven highly consistent genomic regions, were identified. Few meta-QTL specificities were observed among mapping populations, suggesting that sources of resistance are not independent. Seven resistance meta-QTL, including six of the highly consistent genomic regions, co-localized with six of the meta-QTL identified in this study for earliness and plant height and with three morphological genes (Af, A, R). Alleles contributing to the resistance were often associated with undesirable alleles for dry pea breeding. Candidate genes underlying six main meta-QTL regions were identified using colinearity between the pea and Medicago truncatula genomes. Conclusions QTL meta-analysis provided an overview of the moderately low diversity of loci controlling partial resistance to A. euteiches in four main sources of resistance in pea. Seven highly consistent genomic regions with potential use in marker-assisted-selection were identified. Confidence intervals at several main QTL regions were reduced and co-segregation among resistance and morphological/phenological alleles was identified. Further work will be required to identify the best combinations of QTL for durably increasing partial resistance to A. euteiches. PMID:23497245

2013-01-01

278

Detection of QTL with effects on osmoregulation capacities in the rainbow trout (Oncorhynchus mykiss)  

PubMed Central

Background There is increasing evidence that the ability to adapt to seawater in teleost fish is modulated by genetic factors. Most studies have involved the comparison of species or strains and little is known about the genetic architecture of the trait. To address this question, we searched for QTL affecting osmoregulation capacities after transfer to saline water in a nonmigratory captive-bred population of rainbow trout. Results A QTL design (5 full-sib families, about 200 F2 progeny each) was produced from a cross between F0 grand-parents previously selected during two generations for a high or a low cortisol response after a standardized confinement stress. When fish were about 18 months old (near 204 g body weight), individual progeny were submitted to two successive hyper-osmotic challenges (30 ppt salinity) 14 days apart. Plasma chloride and sodium concentrations were recorded 24 h after each transfer. After the second challenge, fish were sacrificed and a gill index (weight of total gill arches corrected for body weight) was recorded. The genome scan was performed with 196 microsatellites and 85 SNP markers. Unitrait and multiple-trait QTL analyses were carried out on the whole dataset (5 families) through interval mapping methods with the QTLMap software. For post-challenge plasma ion concentrations, significant QTL (P < 0.05) were found on six different linkage groups and highly suggestive ones (P < 0.10) on two additional linkage groups. Most QTL affected concentrations of both chloride and sodium during both challenges, but some were specific to either chloride (2 QTL) or sodium (1 QTL) concentrations. Six QTL (4 significant, 2 suggestive) affecting gill index were discovered. Two were specific to the trait, while the others were also identified as QTL for post-challenge ion concentrations. Altogether, allelic effects were consistent for QTL affecting chloride and sodium concentrations but inconsistent for QTL affecting ion concentrations and gill morphology. There was no systematic lineage effect (grand-parental origin of QTL alleles) on the recorded traits. Conclusions For the first time, genomic loci associated with effects on major physiological components of osmotic adaptation to seawater in a nonmigratory fish were revealed. The results pave the way for further deciphering of the complex regulatory mechanisms underlying seawater adaptation and genes involved in osmoregulatory physiology in rainbow trout and other euryhaline fishes. PMID:21569550

2011-01-01

279

Linkage Disequilibrium with Linkage Analysis of Multiline Crosses Reveals Different Multiallelic QTL for Hybrid Performance in the Flint and Dent Heterotic Groups of Maize.  

PubMed

Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R(2) = 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R(2) < 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production. PMID:25271305

Giraud, Héloïse; Lehermeier, Christina; Bauer, Eva; Falque, Matthieu; Segura, Vincent; Bauland, Cyril; Camisan, Christian; Campo, Laura; Meyer, Nina; Ranc, Nicolas; Schipprack, Wolfgang; Flament, Pascal; Melchinger, Albrecht E; Menz, Monica; Moreno-González, Jesús; Ouzunova, Milena; Charcosset, Alain; Schön, Chris-Carolin; Moreau, Laurence

2014-12-01

280

Genetic characterization and fine mapping of the novel Phytophthora resistance gene in a Chinese soybean cultivar.  

PubMed

Phytophthora root rot (PRR), caused by Phytophthora sojae Kaufmann & Gerdemann, is one of the most destructive diseases of soybean [Glycine max (L.) Merr.]. Deployment of resistance genes is the most economical and effective way of controlling the disease. The soybean cultivar 'Yudou 29' is resistant to many P. sojae isolates in China. The genetic basis of the resistance in 'Yudou 29' was elucidated through an inheritance study and molecular mapping. In response to 25 P. sojae isolates, 'Yudou 29' displayed a new resistance reaction pattern distinct from those of differentials carrying known Rps genes. A population of 214 F2:3 families from a cross between 'Jikedou 2' (PRR susceptible) and 'Yudou 29' was used for Rps gene mapping. The segregation fit a ratio of 1:2:1 for resistance:segregation:susceptibility within this population, indicating that resistance in 'Yudou 29' is controlled by a single dominant gene. This gene was temporarily named RpsYD29 and mapped on soybean chromosome 03 (molecular linkage group N; MLG N) flanked by SSR markers SattWM82-50 and Satt1k4b at a genetic distance of 0.5 and 0.2 cM, respectively. Two nucleotide binding site-leucine rich repeat (NBS-LRR) type genes were detected in the 204.8 kb region between SattWM82-50 and Satt1k4b. These two genes showed high similarity to Rps1k in amino acid sequence and could be candidate genes for PRR resistance. Based on the phenotype reactions and the physical position on soybean chromosome 03, RpsYD29 might be a novel allele at, or a novel gene tightly linked to, the Rps1 locus. PMID:23467992

Zhang, Jiqing; Xia, Changjian; Wang, Xiaoming; Duan, Canxing; Sun, Suli; Wu, Xiaofei; Zhu, Zhendong

2013-06-01

281

Fine Mapping and Evolution of the Major Sex Determining Region in Turbot (Scophthalmus maximus)  

PubMed Central

Fish sex determination (SD) systems are varied, suggesting evolutionary changes including either multiple evolution origins of genetic SD from nongenetic systems (such as environmental SD) and/or turnover events replacing one genetic system by another. When genetic SD is found, cytological differentiation between the two members of the sex chromosome pair is often minor or undetectable. The turbot (Scophthalmus maximus), a valuable commercial flatfish, has a ZZ/ZW system and a major SD region on linkage group 5 (LG5), but there are also other minor genetic and environmental influences. We here report refined mapping of the turbot SD region, supported by comparative mapping with model fish species, to identify the turbot master SD gene. Six genes were located to the SD region, two of them associated with gonad development (sox2 and dnajc19). All showed a high association with sex within families (P = 0), but not at the population level, so they are probably partially sex-linked genes, but not SD gene itself. Analysis of crossovers in LG5 using two families confirmed a ZZ/ZW system in turbot and suggested a revised map position for the master gene. Genetic diversity and differentiation for 25 LG5 genetic markers showed no differences between males and females sampled from a wild population, suggesting a recent origin of the SD region in turbot. We also analyzed associations with markers of the most relevant sex-related linkage groups in brill (S. rhombus), a closely related species to turbot; the data suggest that an ancient XX/XY system in brill changed to a ZZ/ZW mechanism in turbot. PMID:25106948

Taboada, Xoana; Hermida, Miguel; Pardo, Belén G.; Vera, Manuel; Piferrer, Francesc; Viñas, Ana; Bouza, Carmen; Martínez, Paulino

2014-01-01

282

Quantitative Trait Loci (QTL) that Underlie SCN Resistance in the Soybean [Glycine max (L.) Merr.] ‘PI438489B’ by ‘Hamilton’ Recombinant Inbred Line Population  

Technology Transfer Automated Retrieval System (TEKTRAN)

Soybean cyst nematode caused by Heterodera glycines is the most devastating pest in soybean [Glycine max (L.) Merr.]. Resistance to SCN is complex, polygenic, race-cultivar specific, and controlled by several QTL. Our objective was to identify and map QTL for SCN resistance to races 3 and 5 using a ...

283

Mapping of Mcs30, a new mammary carcinoma susceptibility quantitative trait locus (QTL30) on rat chromosome 12: identification of fry as a candidate Mcs gene.  

PubMed

Rat strains differ dramatically in their susceptibility to mammary carcinogenesis. On the assumption that susceptibility genes are conserved across mammalian species and hence inform human carcinogenesis, numerous investigators have used genetic linkage studies in rats to identify genes responsible for differential susceptibility to carcinogenesis. Using a genetic backcross between the resistant Copenhagen (Cop) and susceptible Fischer 344 (F344) strains, we mapped a novel mammary carcinoma susceptibility (Mcs30) locus to the centromeric region on chromosome 12 (LOD score of ?8.6 at the D12Rat59 marker). The Mcs30 locus comprises approximately 12 Mbp on the long arm of rat RNO12 whose synteny is conserved on human chromosome 13q12 to 13q13. After analyzing numerous genes comprising this locus, we identified Fry, the rat ortholog of the furry gene of Drosophila melanogaster, as a candidate Mcs gene. We cloned and determined the complete nucleotide sequence of the 13 kbp Fry mRNA. Sequence analysis indicated that the Fry gene was highly conserved across evolution, with 90% similarity of the predicted amino acid sequence among eutherian mammals. Comparison of the Fry sequence in the Cop and F344 strains identified two non-synonymous single nucleotide polymorphisms (SNPs), one of which creates a putative, de novo phosphorylation site. Further analysis showed that the expression of the Fry gene is reduced in a majority of rat mammary tumors. Our results also suggested that FRY activity was reduced in human breast carcinoma cell lines as a result of reduced levels or mutation. This study is the first to identify the Fry gene as a candidate Mcs gene. Our data suggest that the SNPs within the Fry gene contribute to the genetic susceptibility of the F344 rat strain to mammary carcinogenesis. These results provide the foundation for analyzing the role of the human FRY gene in cancer susceptibility and progression. PMID:24023717

Ren, Xuefeng; Graham, Jessica C; Jing, Lichen; Mikheev, Andrei M; Gao, Yuan; Lew, Jenny Pan; Xie, Hong; Kim, Andrea S; Shang, Xiuling; Friedman, Cynthia; Vail, Graham; Fang, Ming Zhu; Bromberg, Yana; Zarbl, Helmut

2013-01-01

284

Fine-structure mapping and complementation analysis of nif (nitrogen fixation) genes in Klebsiella pneumoniae.  

PubMed Central

Four hundred and eighty-nine independent Nif- strains containing 260 point, 130 millimicron-induced, and 99 deletion mutations in nif in the Klebsiella pneumoniae chromosome were isolated. Three hundred and ninety insertion and point mutations were mapped with millimicron-induced deletions carried on 44 plasmids derived from pTM4010, a recombinant R factor containing the his-nif region of K. pneumoniae. The 99 chromosomal deletions in the nif region were mapped with 69 derivatives of pTM4010 carrying insertion and point mutations in nif. Complementation analysis between 84 derivatives of pTM4010 carrying nif mutations and Rec- derivatives of the 390 Nif- mutants identified 14 genes. The nif mutations were ordered into 49 deletion groups with a gene order of his...nifQBALFMVSNEKDHJ. Complementation analysis of millimicron-induced, amber, frameshift, and deletion mutations indicates there are five polycistronic and two monocistronic operons: nifQ nifB, nifA nifL, nifF, nifM nifV nifS, nifN nifE, nifK nifD nifH, and nifJ. Transcription is from right to left in all polycistronic operons. PMID:361693

MacNeil, T; MacNeil, D; Roberts, G P; Supiano, M A; Brill, W J

1978-01-01

285

A fine scale phenotype-genotype virulence map of a bacterial pathogen.  

PubMed

A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We describe a high-throughput strategy based on the method Tn-seq that can be applied to any genetically manipulatable microorganism. By screening 17 in vitro and two in vivo (carriage and infection) conditions for the pathogen Streptococcus pneumoniae, we create a resource consisting of >1800 interactions that is rich in new genotype-phenotype relationships. We describe genes that are involved in differential carbon source utilization in the host, as well as genes that are involved both in virulence and in resistance against specific in vitro stresses, thereby revealing selection pressures that the pathogen experiences in vivo. We reveal the secondary response to an antibiotic, including a dual role efflux pump also involved in resistance to pH stress. Through genetic-interaction mapping and gene-expression analysis we define the mechanism of attenuation and the regulatory relationship between a two-component system and a core biosynthetic pathway specific to microorganisms. Thus, we have generated a resource that provides detailed insight into the biology and virulence of S. pneumoniae and provided a road map for similar discovery in other microorganisms. PMID:22826510

van Opijnen, Tim; Camilli, Andrew

2012-12-01

286

Fine mapping of the Ph-3 gene conferring resistance to late blight (Phytophthora infestans) in tomato.  

PubMed

Late blight, caused by the oomycete pathogen Phytophthora infestans (Mont.) de Bary, is a devastating disease for tomato and potato crops. In the past decades, many late blight resistance (R) genes have been characterized in potato. In contrast, less work has been conducted on tomato. The Ph-3 gene from Solanum pimpinellifolium was introgressed into cultivated tomatoes and conferred broad-spectrum resistance to P. infestans. It was previously assigned to the long arm of chromosome 9. In this study, a high-resolution genetic map covering the Ph-3 locus was constructed using an F2 population of a cross between Solanum lycopersicum CLN2037B (containing Ph-3) and S. lycopersicum LA4084. Ph-3 was mapped in a 0.5 cM interval between two markers, Indel_3 and P55. Eight putative genes were found in the corresponding 74 kb region of the tomato Heinz1706 reference genome. Four of these genes are resistance gene analogs (RGAs) with a typical nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 domain. Each RGA showed high homology to the late blight R gene Rpi-vnt1.1 from Solanum venturii. Transient gene silencing indicated that a member of this RGA family is required for Ph-3-mediated resistance to late blight in tomato. Furthermore, this RGA family was also found in the potato genome, but the number of the RGAs was higher than in tomato. PMID:23921955

Zhang, Chunzhi; Liu, Lei; Zheng, Zheng; Sun, Yuyan; Zhou, Longxi; Yang, Yuhong; Cheng, Feng; Zhang, Zhonghua; Wang, Xiaowu; Huang, Sanwen; Xie, Bingyan; Du, Yongchen; Bai, Yuling; Li, Junming

2013-10-01

287

Fine-Mapping of Immunodominant Linear B-Cell Epitopes of the Staphylococcus Aureus SEB Antigen Using Short Overlapping Peptides  

PubMed Central

Staphylococcal enterotoxin B (SEB) is one of the most potent Staphylococcus aureus exotoxins (SEs). Due to its conserved sequence and stable structure, SEB might be a good candidate antigen for MRSA vaccines. Although cellular immune responses to SEB are well-characterized, much less is known regarding SEB-specific humoral immune responses, particularly regarding detailed epitope mapping. In this study, we utilized a recombinant nontoxic mutant of SEB (rSEB) and an AlPO4 adjuvant to immunize BALB/c mice and confirmed that rSEB can induce a high antibody level and effective immune protection against MRSA infection. Next, the antisera of immunized mice were collected, and linear B cell epitopes within SEB were finely mapped using a series of overlapping synthetic peptides. Three immunodominant B cell epitopes of SEB were screened by ELISA, including a novel epitope, SEB205-222, and two known epitopes, SEB97–114 and SEB247-261. Using truncated peptides, an ELISA was performed with peptide-KLH antisera, and the core sequence of the three immunodominant B cell epitopes were verified as SEB97-112, SEB207-222, and SEB247-257. In vitro, all of the immunodominant epitope-specific antisera (anti-SEB97-112, anti-SEB207-222 and anti-SEB247-257) were observed to inhibit SEB-induced T cell mitogenesis and cytokine production from splenic lymphocytes of BALB/c mice. The homology analysis indicated that SEB97–112 and SEB207-222 were well-conserved among different Staphylococcus aureus strains. The 3D crystal structure of SEB indicated that SEB97–112 was in the loop region inside SEB, whereas SEB207-222 and SEB247-257 were in the ?-slice region outside SEB. In summary, the fine-mapping of linear B-cell epitopes of the SEB antigen in this study will be useful to understand anti-SEB immunity against MRSA infection further and will be helpful to optimize MRSA vaccine designs that are based on the SEB antigen. PMID:24599257

Zhao, Zhuo; Li, Bin; Sun, He-Qiang; Zhang, Jin-Yong; Wang, Yi-Lin; Chen, Li; Hu, Jian; He, Ya-Fei; Zeng, Hao; Zou, Quan-Ming; Wu, Chao

2014-01-01

288

Three-dimensional mapping of fine structure in the solar atmosphere  

NASA Astrophysics Data System (ADS)

The effects on image formation through a tilted interference filter in a converging beam are investigated and an adequate compensation procedure is established. A method that compensates for small-scale seeing distortions is also developed with the aim of co-aligning non-simultaneous solar images from different passbands. These techniques are applied to data acquired with a narrow tiltable filter at the Swedish 1-meter Solar Telescope. Tilting provides a way to scan the wing of the Ca II H line. The resulting images are used to map the temperature stratification and vertical temperature gradients in a solar active region containing a sunspot at a resolution approaching 0''10. The data are compared with hydro-dynamical quiet sun models and magneto-hydrodynamic models of plage. The comparison gives credence to the observational techniques, the analysis methods, and the simulations. Vertical temperature gradients are lower in magnetic structures than in non-magnetic. Line-of-sight velocities and magnetic field properties in the penumbra of the same sunspot are estimated using the CRISP imaging spectropolarimeter and straylight compensation adequate for the data. These reveal a pattern of upflows and downflows throughout the entire penumbra including the interior penumbra. A correlation with intensity positively identifies these flows as convective in origin. The vertical convective signatures are observed everywhere, but the horizontal Evershed flow is observed to be confined to areas of nearly horizontal magnetic field. The relation between temperature gradient and total circular polarization in magnetically sensitive lines is investigated in different structures of the penumbra. Penumbral dark cores are prominent in total circular polarization and temperature gradient maps. These become longer and more contiguous with increasing height. Dark fibril structures over bright regions are observed in the Ca II H line core, above both the umbra and penumbra.

Henriques, Vasco M. J.

2013-04-01

289

Fine genetic mapping of the Hyp mutation on mouse chromosome X  

SciTech Connect

The hypophosphatemic (Hyp) mouse is the murine homolog of hypophosphatemic vitamin-D-resistant rickets (HYP) in human. Despite extensive investigations in the Hyp mouse, the pathophysiology of this X-linked dominant disorder remains unclear. As a first step toward cloning the Hyp gene, we have generated a high-resolution linkage map in the vicinity of the Hyp locus using two independent backcross panels segregating the Hyp mutation, one generated from an interspecific mating between C57BL/6J-Hyp/Hyp and Mus spretus and the other from an intrasubspecific mating between C57BL/6J-Hyp/Hyp and Mus musculus castaneus. Linkage analyses in 1101 backcross progeny using a total of 23 DNA markers favor the following gene order from the centromere: DXMit13-(DXMit11, DXMit34)-(DXMit36, Alas2)-(Hyp, DXMit80)-DXMit98-(DXMit28, DXMit33, DXMit70)-Pdhal-DXMit20. This study has localized Hyp to a region of approximately 1 cM flanked by the proximal markers DXMit36 and Alas2 and the distal marker DSMit98. One microsatellite marker, DXMit80, was found to be very tightly linked to Hyp, as it was nonrecombinant with Hyp among all the progeny of both backcrosses corresponding to 1101 meioses. 37 refs., 3 figs., 1 tab.

Du, Lisheng; Desbarats, M.; Cornibert, S.; Malo, D.; Ecarot, B. [McGill Univ., Quebec (Canada)] [McGill Univ., Quebec (Canada)

1996-03-01

290

Fine mapping of sequential neutralization epitopes on the subunit protein VP8 of human rotavirus.  

PubMed Central

The epitopes of the HRV (human rotavirus), especially those involved in virus neutralization, have not been determined in their entirety, and would have significant implications for HRV vaccine development. In the present study, we report on the epitope mapping and identification of sequential neutralization epitopes, on the Wa strain HRV subunit protein VP8, using synthetic overlapping peptides. Polyclonal antibodies against recombinant Wa VP8 were produced previously in chicken, and purified from egg yolk, which showed neutralizing activity against HRV in vitro. Overlapping VP8 peptide fragments were synthesized and probed with the anti-VP8 antibodies, revealing five sequential epitopes on VP8. Further analysis suggested that three of the five epitopes detected, M1-L10, I55-D66 and L223-P234, were involved in virus neutralization, indicating that sequential epitopes may also be important for the HRV neutralization. The interactions of the antibodies with the five epitopes were characterized by an examination of the critical amino acids involved in antibody binding. Epitopes comprised primarily of hydrophobic amino acid residues, followed by polar and charged residues. The more critical amino acids appeared to be located near the centre of the epitopes, with proline, isoleucine, serine, glutamine and arginine playing an important role in the binding of antibody to the VP8 epitopes. PMID:12901721

Kovacs-Nolan, Jennifer; Yoo, Dongwan; Mine, Yoshinori

2003-01-01

291

Fine Mapping of Posttranslational Modifications of the Linker Histone H1 from Drosophila melanogaster  

PubMed Central

The linker histone H1 binds to the DNA in between adjacent nucleosomes and contributes to chromatin organization and transcriptional control. It is known that H1 carries diverse posttranslational modifications (PTMs), including phosphorylation, lysine methylation and ADP-ribosylation. Their biological functions, however, remain largely unclear. This is in part due to the fact that most of the studies have been performed in organisms that have several H1 variants, which complicates the analyses. We have chosen Drosophila melanogaster, a model organism, which has a single H1 variant, to approach the study of the role of H1 PTMs during embryonic development. Mass spectrometry mapping of the entire sequence of the protein showed phosphorylation only in the ten N-terminal amino acids, mostly at S10. For the first time, changes in the PTMs of a linker H1 during the development of a multicellular organism are reported. The abundance of H1 monophosphorylated at S10 decreases as the embryos age, which suggests that this PTM is related to cell cycle progression and/or cell differentiation. Additionally, we have found a polymorphism in the protein sequence that can be mistaken with lysine methylation if the analysis is not rigorous. PMID:18253500

Villar-Garea, Ana; Imhof, Axel

2008-01-01

292

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

PubMed Central

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

2010-01-01

293

Analysis of Cytoplasmic Effects and Fine-Mapping of a Genic Male Sterile Line in Rice  

PubMed Central

Cytoplasm has substantial genetic effects on progeny and is important for yield improvement in rice breeding. Studies on the cytoplasmic effects of cytoplasmic male sterility (CMS) show that most types of CMS have negative effects on yield-related traits and that these negative effects vary among CMS. Some types of genic male sterility (GMS), including photo-thermo sensitive male sterility (PTMS), have been widely used in rice breeding, but the cytoplasmic effects of GMS remain unknown. Here, we identified a GMS mutant line, h2s, which exhibited small, white anthers and failed to produce mature pollen. Unlike CMS, the h2s had significant positive cytoplasmic effects on the seed set rate, weight per panicle, yield, and general combining ability (GCA) for plant height, seed set rate, weight per panicle, and yield. These effects indicated that h2s cytoplasm may show promise for the improvement of rice yield. Genetic analysis suggested that the phenotype of h2s was controlled by a single recessive locus. We mapped h2s to a 152 kb region on chromosome 6, where 22 candidate genes were predicted. None of the 22 genes had previously been reported to be responsible for the phenotypes of h2s. Sequencing analysis showed a 12 bp deletion in the sixth exon of Loc_Os06g40550 in h2s in comparison to wild type, suggesting that Loc_Os06g40550 is the best candidate gene. These results lay a strong foundation for cloning of the H2S gene to elucidate the molecular mechanism of male reproduction. PMID:23613915

Li, Yuanyuan; Ma, Bingtian; Li, Shigui

2013-01-01

294

Fine-mapping of the HNF1B multicancer locus identifies candidate variants that mediate endometrial cancer risk.  

PubMed

Common variants in the hepatocyte nuclear factor 1 homeobox B (HNF1B) gene are associated with the risk of Type II diabetes and multiple cancers. Evidence to date indicates that cancer risk may be mediated via genetic or epigenetic effects on HNF1B gene expression. We previously found single-nucleotide polymorphisms (SNPs) at the HNF1B locus to be associated with endometrial cancer, and now report extensive fine-mapping and in silico and laboratory analyses of this locus. Analysis of 1184 genotyped and imputed SNPs in 6608 Caucasian cases and 37 925 controls, and 895 Asian cases and 1968 controls, revealed the best signal of association for SNP rs11263763 (P = 8.4 × 10(-14), odds ratio = 0.86, 95% confidence interval = 0.82-0.89), located within HNF1B intron 1. Haplotype analysis and conditional analyses provide no evidence of further independent endometrial cancer risk variants at this locus. SNP rs11263763 genotype was associated with HNF1B mRNA expression but not with HNF1B methylation in endometrial tumor samples from The Cancer Genome Atlas. Genetic analyses prioritized rs11263763 and four other SNPs in high-to-moderate linkage disequilibrium as the most likely causal SNPs. Three of these SNPs map to the extended HNF1B promoter based on chromatin marks extending from the minimal promoter region. Reporter assays demonstrated that this extended region reduces activity in combination with the minimal HNF1B promoter, and that the minor alleles of rs11263763 or rs8064454 are associated with decreased HNF1B promoter activity. Our findings provide evidence for a single signal associated with endometrial cancer risk at the HNF1B locus, and that risk is likely mediated via altered HNF1B gene expression. PMID:25378557

Painter, Jodie N; O'Mara, Tracy A; Batra, Jyotsna; Cheng, Timothy; Lose, Felicity A; Dennis, Joe; Michailidou, Kyriaki; Tyrer, Jonathan P; Ahmed, Shahana; Ferguson, Kaltin; Healey, Catherine S; Kaufmann, Susanne; Hillman, Kristine M; Walpole, Carina; Moya, Leire; Pollock, Pamela; Jones, Angela; Howarth, Kimberley; Martin, Lynn; Gorman, Maggie; Hodgson, Shirley; De Polanco, Ma Magdalena Echeverry; Sans, Monica; Carracedo, Angel; Castellvi-Bel, Sergi; Rojas-Martinez, Augusto; Santos, Erika; Teixeira, Manuel R; Carvajal-Carmona, Luis; Shu, Xiao-Ou; Long, Jirong; Zheng, Wei; Xiang, Yong-Bing; Montgomery, Grant W; Webb, Penelope M; Scott, Rodney J; McEvoy, Mark; Attia, John; Holliday, Elizabeth; Martin, Nicholas G; Nyholt, Dale R; Henders, Anjali K; Fasching, Peter A; Hein, Alexander; Beckmann, Matthias W; Renner, Stefan P; Dörk, Thilo; Hillemanns, Peter; Dürst, Matthias; Runnebaum, Ingo; Lambrechts, Diether; Coenegrachts, Lieve; Schrauwen, Stefanie; Amant, Frederic; Winterhoff, Boris; Dowdy, Sean C; Goode, Ellen L; Teoman, Attila; Salvesen, Helga B; Trovik, Jone; Njolstad, Tormund S; Werner, Henrica M J; Ashton, Katie; Proietto, Tony; Otton, Geoffrey; Tzortzatos, Gerasimos; Mints, Miriam; Tham, Emma; Hall, Per; Czene, Kamila; Liu, Jianjun; Li, Jingmei; Hopper, John L; Southey, Melissa C; Ekici, Arif B; Ruebner, Matthias; Johnson, Nicola; Peto, Julian; Burwinkel, Barbara; Marme, Frederik; Brenner, Hermann; Dieffenbach, Aida K; Meindl, Alfons; Brauch, Hiltrud; Lindblom, Annika; Depreeuw, Jeroen; Moisse, Matthieu; Chang-Claude, Jenny; Rudolph, Anja; Couch, Fergus J; Olson, Janet E; Giles, Graham G; Bruinsma, Fiona; Cunningham, Julie M; Fridley, Brooke L; Børresen-Dale, Anne-Lise; Kristensen, Vessela N; Cox, Angela; Swerdlow, Anthony J; Orr, Nicholas; Bolla, Manjeet K; Wang, Qin; Weber, Rachel Palmieri; Chen, Zhihua; Shah, Mitul; French, Juliet D; Pharoah, Paul D P; Dunning, Alison M; Tomlinson, Ian; Easton, Douglas F; Edwards, Stacey L; Thompson, Deborah J; Spurdle, Amanda B

2015-03-01

295

Fine mapping of variants associated with endometriosis in the WNT4 region on chromosome 1p36  

PubMed Central

Genome-wide association studies show strong evidence of association with endometriosis for markers on chromosome 1p36 spanning the potential candidate genes WNT4, CDC42 and LINC00339. WNT4 is involved in development of the uterus, and the expression of CDC42 and LINC00339 are altered in women with endometriosis. We conducted fine mapping to examine the role of coding variants in WNT4 and CDC42 and determine the key SNPs with strongest evidence of association in this region. We identified rare coding variants in WNT4 and CDC42 present only in endometriosis cases. The frequencies were low and cannot account for the common signal associated with increased risk of endometriosis. Genotypes for five common SNPs in the region of chromosome 1p36 show stronger association signals when compared with rs7521902 reported in published genome scans. Of these, three SNPs rs12404660, rs3820282, and rs55938609 were located in DNA sequences with potential functional roles including overlap with transcription factor binding sites for FOXA1, FOXA2, ESR1, and ESR2. Functional studies will be required to identify the gene or genes implicated in endometriosis risk. PMID:24319535

Luong, Hien TT; Painter, Jodie N; Shakhbazov, Konstantin; Chapman, Brett; Henders, Anjali K; Powell, Joseph E; Nyholt, Dale R; Montgomery, Grant W

2013-01-01

296

Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions.  

PubMed

At least 17 genomic regions are established as harboring melanoma susceptibility variants, in most instances with genome-wide levels of significance and replication in independent samples. Based on genome-wide single nucleotide polymorphism (SNP) data augmented by imputation to the 1,000 Genomes reference panel, we have fine mapped these regions in over 5,000 individuals with melanoma (mainly from the GenoMEL consortium) and over 7,000 ethnically matched controls. A penalized regression approach was used to discover those SNP markers that most parsimoniously explain the observed association in each genomic region. For the majority of the regions, the signal is best explained by a single SNP, which sometimes, as in the tyrosinase region, is a known functional variant. However in five regions the explanation is more complex. At the CDKN2A locus, for example, there is strong evidence that not only multiple SNPs but also multiple genes are involved. Our results illustrate the variability in the biology underlying genome-wide susceptibility loci and make steps toward accounting for some of the "missing heritability." PMID:25077817

Barrett, Jennifer H; Taylor, John C; Bright, Chloe; Harland, Mark; Dunning, Alison M; Akslen, Lars A; Andresen, Per A; Avril, Marie-Françoise; Azizi, Esther; Bianchi Scarrà, Giovanna; Brossard, Myriam; Brown, Kevin M; D?bniak, Tadeusz; Elder, David E; Friedman, Eitan; Ghiorzo, Paola; Gillanders, Elizabeth M; Gruis, Nelleke A; Hansson, Johan; Helsing, Per; Ho?evar, Marko; Höiom, Veronica; Ingvar, Christian; Landi, Maria Teresa; Lang, Julie; Lathrop, G Mark; Lubi?ski, Jan; Mackie, Rona M; Molven, Anders; Novakovi?, Srdjan; Olsson, Håkan; Puig, Susana; Puig-Butille, Joan Anton; van der Stoep, Nienke; van Doorn, Remco; van Workum, Wilbert; Goldstein, Alisa M; Kanetsky, Peter A; Pharoah, Paul D P; Demenais, Florence; Hayward, Nicholas K; Newton Bishop, Julia A; Bishop, D Timothy; Iles, Mark M

2015-03-15

297

Fine-Mapping of 5q12.1–13.3 Unveils New Genetic Contributors to Caries  

PubMed Central

Caries is a multifactorial disease and little is still known about the host genetic factors influencing susceptibility. Our previous genome-wide linkage scan has identified the interval 5q12.1–5q13.3 as linked to low caries susceptibility in Filipino families. Here we fine-mapped this region in order to identify genetic contributors to caries susceptibility. Four hundred and seventy-seven subjects from 72 pedigrees with similar cultural and behavioral habits and limited access to dental care living in the Philippines were studied. DMFT scores and genotype data of 75 single-nucleotide polymorphisms were evaluated in the Filipino families with the Family-Based Association Test. For replication purposes, a total 1,467 independent subjects from five different populations were analyzed in a case-control format. In the Filipino cohort, statistically significant and borderline associations were found between low caries experience and four genes spanning 13 million base pairs (PART1, ZSWIM6, CCNB1, and BTF3). We were able to replicate these results in some of the populations studied. We detected PART1 and BTF3 expression in whole saliva, and the expression of BTF3 was associated with caries experience. Our results suggest BTF3 may have a functional role in protecting against caries. PMID:23363935

Shimizu, T.; Deeley, K.; Briseño-Ruiz, J.; Faraco, I.M.; Poletta, F.A.; Brancher, J.A.; Pecharki, G.D.; Küchler, E.C.; Tannure, P.N.; Lips, A.; Vieira, T.C.S.; Patir, A.; Yildirim, M.; Mereb, J.C.; Resick, J.M.; Brandon, C.A.; Cooper, M.E.; Seymen, F.; Costa, M.C.; Granjeiro, J.M.; Trevilatto, P.C.; Orioli, I.M.; Castilla, E.E.; Marazita, M.L.; Vieira, A.R.

2013-01-01

298

Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry  

PubMed Central

Adult height is a classic polygenic trait of high heritability (h2 ?0.8). More than 180 single nucleotide polymorphisms (SNPs), identified mostly in populations of European descent, are associated with height. These variants convey modest effects and explain ?10% of the variance in height. Discovery efforts in other populations, while limited, have revealed loci for height not previously implicated in individuals of European ancestry. Here, we performed a meta-analysis of genome-wide association (GWA) results for adult height in 20,427 individuals of African ancestry with replication in up to 16,436 African Americans. We found two novel height loci (Xp22-rs12393627, P?=?3.4×10?12 and 2p14-rs4315565, P?=?1.2×10?8). As a group, height associations discovered in European-ancestry samples replicate in individuals of African ancestry (P?=?1.7×10?4 for overall replication). Fine-mapping of the European height loci in African-ancestry individuals showed an enrichment of SNPs that are associated with expression of nearby genes when compared to the index European height SNPs (P<0.01). Our results highlight the utility of genetic studies in non-European populations to understand the etiology of complex human diseases and traits. PMID:21998595

Ge, Bing; Tayo, Bamidele; Mathias, Rasika A.; Ding, Jingzhong; Nalls, Michael A.; Adeyemo, Adebowale; Adoue, Véronique; Ambrosone, Christine B.; Atwood, Larry; Bandera, Elisa V.; Becker, Lewis C.; Berndt, Sonja I.; Bernstein, Leslie; Blot, William J.; Boerwinkle, Eric; Britton, Angela; Casey, Graham; Chanock, Stephen J.; Demerath, Ellen; Deming, Sandra L.; Diver, W. Ryan; Fox, Caroline; Harris, Tamara B.; Hernandez, Dena G.; Hu, Jennifer J.; Ingles, Sue A.; John, Esther M.; Johnson, Craig; Keating, Brendan; Kittles, Rick A.; Kolonel, Laurence N.; Kritchevsky, Stephen B.; Le Marchand, Loic; Lohman, Kurt; Liu, Jiankang; Millikan, Robert C.; Murphy, Adam; Musani, Solomon; Neslund-Dudas, Christine; North, Kari E.; Nyante, Sarah; Ogunniyi, Adesola; Ostrander, Elaine A.; Papanicolaou, George; Patel, Sanjay; Pettaway, Curtis A.; Press, Michael F.; Redline, Susan; Rodriguez-Gil, Jorge L.; Rotimi, Charles; Rybicki, Benjamin A.; Salako, Babatunde; Schreiner, Pamela J.; Signorello, Lisa B.; Singleton, Andrew B.; Stanford, Janet L.; Stram, Alex H.; Stram, Daniel O.; Strom, Sara S.; Suktitipat, Bhoom; Thun, Michael J.; Witte, John S.; Yanek, Lisa R.; Ziegler, Regina G.; Zheng, Wei; Zhu, Xiaofeng; Zmuda, Joseph M.; Zonderman, Alan B.; Evans, Michele K.; Liu, Yongmei; Becker, Diane M.; Cooper, Richard S.; Pastinen, Tomi; Henderson, Brian E.; Hirschhorn, Joel N.; Lettre, Guillaume; Haiman, Christopher A.

2011-01-01

299

Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression  

PubMed Central

Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease. PMID:23535824

Kote-Jarai, Zsofia; Saunders, Edward J.; Leongamornlert, Daniel A.; Tymrakiewicz, Malgorzata; Dadaev, Tokhir; Jugurnauth-Little, Sarah; Ross-Adams, Helen; Al Olama, Ali Amin; Benlloch, Sara; Halim, Silvia; Russel, Roslin; Dunning, Alison M.; Luccarini, Craig; Dennis, Joe; Neal, David E.; Hamdy, Freddie C.; Donovan, Jenny L.; Muir, Ken; Giles, Graham G.; Severi, Gianluca; Wiklund, Fredrik; Gronberg, Henrik; Haiman, Christopher A.; Schumacher, Fredrick; Henderson, Brian E.; Le Marchand, Loic; Lindstrom, Sara; Kraft, Peter; Hunter, David J.; Gapstur, Susan; Chanock, Stephen; Berndt, Sonja I.; Albanes, Demetrius; Andriole, Gerald; Schleutker, Johanna; Weischer, Maren; Canzian, Federico; Riboli, Elio; Key, Tim J.; Travis, Ruth C.; Campa, Daniele; Ingles, Sue A.; John, Esther M.; Hayes, Richard B.; Pharoah, Paul; Khaw, Kay-Tee; Stanford, Janet L.; Ostrander, Elaine A.; Signorello, Lisa B.; Thibodeau, Stephen N.; Schaid, Dan; Maier, Christiane; Vogel, Walther; Kibel, Adam S.; Cybulski, Cezary; Lubinski, Jan; Cannon-Albright, Lisa; Brenner, Hermann; Park, Jong Y.; Kaneva, Radka; Batra, Jyotsna; Spurdle, Amanda; Clements, Judith A.; Teixeira, Manuel R.; Govindasami, Koveela; Guy, Michelle; Wilkinson, Rosemary A.; Sawyer, Emma J.; Morgan, Angela; Dicks, Ed; Baynes, Caroline; Conroy, Don; Bojesen, Stig E.; Kaaks, Rudolf; Vincent, Daniel; Bacot, François; Tessier, Daniel C.; Easton, Douglas F.; Eeles, Rosalind A.

2013-01-01

300

Guidelines for Common Bean QTL Nomenclature  

Technology Transfer Automated Retrieval System (TEKTRAN)

Quantitative trait locus (QTL) analysis has become an important tool for the characterization and breeding of complex traits in crops plants, such as common bean (Phaseolus vulgaris L.). A standard system for naming QTL in common bean is needed for effective referencing of new and previously identif...

301

Breeding lines and host QTL interaction with bacterial strains  

Technology Transfer Automated Retrieval System (TEKTRAN)

Resistance to common bacterial blight (CBB) is controlled by more than 20 QTL (Miklas and Singh, 2007). A QTL on Pv10 linked to SAP6 SCAR markers is derived from common bean. Higher levels of resistance associated with BC420 QTL on Pv06 (Yu et al., 2000) and SU91-CG11 QTL on Pv08 (Pedraza et al., 20...

302

Fine mapping and identification of a candidate gene for a major locus controlling maturity date in peach  

PubMed Central

Background Maturity date (MD) is a crucial factor for marketing of fresh fruit, especially those with limited shelf-life such as peach (Prunus persica L. Batsch): selection of several cultivars with differing MD would be advantageous to cover and extend the marketing season. Aims of this work were the fine mapping and identification of candidate genes for the major maturity date locus previously identified on peach linkage group 4. To improve genetic resolution of the target locus two F2 populations derived from the crosses Contender x Ambra (CxA, 306 individuals) and PI91459 (NJ Weeping) x Bounty (WxBy, 103 individuals) were genotyped with the Sequenom and 9K Illumina Peach Chip SNP platforms, respectively. Results Recombinant individuals from the WxBy F2 population allowed the localisation of maturity date locus to a 220 kb region of the peach genome. Among the 25 annotated genes within this interval, functional classification identified ppa007577m and ppa008301m as the most likely candidates, both encoding transcription factors of the NAC (NAM/ATAF1, 2/CUC2) family. Re-sequencing of the four parents and comparison with the reference genome sequence uncovered a deletion of 232 bp in the upstream region of ppa007577m that is homozygous in NJ Weeping and heterozygous in Ambra, Bounty and the WxBy F1 parent. However, this variation did not segregate in the CxA F2 population being the CxA F1 parent homozygous for the reference allele. The second gene was thus examined as a candidate for maturity date. Re-sequencing of ppa008301m, showed an in-frame insertion of 9 bp in the last exon that co-segregated with the maturity date locus in both CxA and WxBy F2 populations. Conclusions Using two different segregating populations, the map position of the maturity date locus was refined from 3.56 Mb to 220 kb. A sequence variant in the NAC gene ppa008301m was shown to co-segregate with the maturity date locus, suggesting this gene as a candidate controlling ripening time in peach. If confirmed on other genetic materials, this variant may be used for marker-assisted breeding of new cultivars with differing maturity date. PMID:24148786

2013-01-01

303

Fine mapping of the chromosome 10q11-q21 linkage region in Alzheimer's disease cases and controls  

PubMed Central

We have previously reported strong linkage on chromosome 10q in pedigrees transmitting Alzheimer's disease through the mother, overlapping with many significant linkage reports including the largest reported study. Here, we report the most comprehensive fine mapping of this region to date. In a sample of 638 late-onset Alzheimer's disease (LOAD) cases and controls including 104 maternal LOAD cases, we genotyped 3,884 single nucleotide polymorphisms (SNPs) covering 15.2 Mb. We then used imputations and publicly available data to generate an extended dataset including 4,329 SNPs for 1,209 AD cases and 839 controls in the same region. Further, we screened eight genes in this region for rare alleles in 283 individuals by nucleotide sequencing, and we tested for possible monoallelic expression as it might underlie our maternal parent of origin linkage. We excluded the possibility of multiple rare coding risk variants for these genes and monoallelic expression when we could test for it. One SNP, rs10824310 in the PRKG1 gene, showed study-wide significant association without a parent of origin effect, but the effect size estimate is not of sufficient magnitude to explain the linkage, and no association is observed in an independent genome-wide association studies (GWAS) report. Further, no causative variants were identified though sequencing. Analysis of cases with maternal disease origin pointed to a few regions of interest that included the genes PRKG1 and PCDH15 and an intergenic interval of 200 Kb. It is likely that non-transcribed rare variants or other mechanisms involving these genomic regions underlie the observed linkage and parent of origin effect. Acquiring additional support and clarifying the mechanisms of such involvement is important for AD and other complex disorder genetics research. PMID:20182759

Fallin, Margaret Daniele; Szymanski, Megan; Wang, Ruihua; Gherman, Adrian; Bassett, Susan S.; Avramopoulos, Dimitrios

2010-01-01

304

QTL for traits related to humoral immune response estimated from data of a porcine F2 resource population.  

PubMed

This study aimed to map quantitative trait loci (QTL) for traits related to humoral innate immune defence. Therefore, haemolytic complement activity in the alternative and the classical pathway, serum concentration of C3c and of haptoglobin (HP) were measured in blood samples obtained from F2 piglets (n = 457) of a porcine F2 resource population before and after Mycoplasma hyopneumoniae, Aujeszky's disease virus (Suid herpesvirus I, SuHVI) and porcine reproductive and respiratory syndrome virus (PRRSV) vaccination at 6, 14 and 16 weeks of age. Animals were genotyped at 88 autosomal markers. QTL analysis was performed under the line cross and the half sib. Phenotypic data were adjusted for systematic effects by mixed models with and without repeated measures statement. In total, 46 and 21 estimated QTL positions were detected with genome-wide significance at the 0.05 and 0.01 level, respectively. The proximal region of SSC2 (orthologous to HSA11 0-70 Mb), the distal region of SSC4 (HSA1 95-155 Mb), and the intermediate region of SSC16 (HSA5 0-73 Mb and 150-174 Mb) showed a clustering of estimated QTL positions for complement activity based on the different models. A common genetic background, i.e. a single true QTL, might underlie these QTL positions for related traits. In addition, QTL for antibody titres were detected on SSC1, 2, 6 and 7. With regard to number and magnitude of their impact, QTL for humoral innate immune traits behave like those for other quantitative traits. Discovery of such QTL facilitates the identification of candidate genes for disease resistance and immune competence that are applicable in selective breeding and further research towards improving therapeutic and prophylactic measures. PMID:19490209

Wimmers, K; Murani, E; Schellander, K; Ponsuksili, S

2009-06-01

305

Identification of QTL for Resistance to Sclerotinia Stem Rot (Sclerotinia sclerotiorum) in Soybean Plant Introduction 194639  

Technology Transfer Automated Retrieval System (TEKTRAN)

Sclerotinia stem rot of soybean [Glycine max (L.) Merr.], caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a difficult disease to manage, although some gains have been made through breeding for quantitative resistance. The objective was to map quantitative trait loci (QTL) controlling partial ...

306

The identification of QTL that affect the fatty acid composition of milk on sheep chromosome 11.  

PubMed

In this work, we analysed 11 genetic markers localized on OAR11 in a commercial population of Spanish Churra sheep to detect QTL that underlie milk fatty acid (FA) composition traits. Following a daughter design, we analysed 799 ewes distributed in 15 half-sib families. Eight microsatellite markers and three novel SNPs identified in two genes related to fatty acid metabolism, acetyl-CoA carboxylase alpha (ACACA) and fatty acid synthase (FASN), were genotyped in the whole population under study. The phenotypic traits considered in the study included 22 measurements related to the FA composition of the milk and three other milk production traits (milk protein percentage, milk fat percentage and milk yield). Across-family regression analysis revealed four significant QTL at the 5% chromosome-wise level influencing contents of capric acid (C10:0), lauric acid (C12:0), linoleic conjugated acid (CLA) and polyunsaturated fatty acids (PUFA) respectively. The peaks of the QTL affecting C10:0 and PUFA contents in milk map close to the FASN gene, which has been evaluated as a putative positional candidate for these QTL. The QTL influencing C12:0 content reaches its maximum significance at 58 cM, close to the gene coding for the glucose-dependent insulinotropic polypeptide. We were not able to find any candidate genes related to fat metabolism at the QTL influencing CLA content, which is located at the proximal end of the chromosome. Further research efforts will be needed to confirm and refine the QTL locations reported here. PMID:19968648

García-Fernández, M; Gutiérrez-Gil, B; García-Gámez, E; Sánchez, J P; Arranz, J J

2010-06-01

307

A QTL Study for Regions Contributing to Arabidopsis thaliana Root Skewing on Tilted Surfaces.  

PubMed

Plant root systems must grow in a manner that is dictated by endogenous genetic pathways, yet sensitive to environmental input. This allows them to provide the plant with water and nutrients while navigating a heterogeneous soil environment filled with obstacles, toxins, and pests. Gravity and touch, which constitute important cues for roots growing in soil, have been shown to modulate root architecture by altering growth patterns. This is illustrated by Arabidopsis thaliana roots growing on tilted hard agar surfaces. Under these conditions, the roots are exposed to both gravity and touch stimulation. Consequently, they tend to skew their growth away from the vertical and wave along the surface. This complex growth behavior is believed to help roots avoid obstacles in nature. Interestingly, A. thaliana accessions display distinct growth patterns under these conditions, suggesting the possibility of using this variation as a tool to identify the molecular mechanisms that modulate root behavior in response to their mechanical environment. We have used the Cvi/Ler recombinant inbred line population to identify quantitative trait loci that contribute to root skewing on tilted hard agar surfaces. A combination of fine mapping for one of these QTL and microarray analysis of expression differences between Cvi and Ler root tips identifies a region on chromosome 2 as contributing to root skewing on tilted surfaces, potentially by modulating cell wall composition. PMID:22384323

Vaughn, Laura M; Masson, Patrick H

2011-07-01

308

Comparative genetic analysis of quantitative traits in sunflower ( Helianthus annuus L.) 1. QTL involved in resistance to Sclerotinia sclerotiorum and Diaporthe helianthi.  

PubMed

Sclerotinia sclerotiorum and Diaporthe helianthi are important pathogens of sunflower ( Helianthus annuus L.). Two hundred and twenty F2-F3 families were developed from an intraspecific cross between two inbred sunflower lines XRQ and PSC8. Using this segregating population a genetic map of 19 linkage groups with 290 molecular markers covering 2,318 cM was constructed. Disease resistances were measured in field experiments during 3 years (1998, 1999 and 2000) for phomopsis and 2 years for S. sclerotiorum (1997 and 1999). QTL were detected using the interval mapping method at a LOD threshold of 3. A total of 15 QTL for each pathogen resistance were detected across several linkage groups, confirming the polygenic nature of the resistances. These QTL explained from 7 to 41% of the phenotypic variability. The QTL for phomopsis resistance, in the 3 years of tests, mapped in the same region, and this was also true for some forms of S. sclerotiorum resistance in the 2 years of tests. On linkage group 8, QTL affecting resistance to both S. sclerotiorum and D. helianthi mycelium extension on leaves colocalised, suggesting a common component in the mechanism of resistance for these two pathogens. The colocalisation of QTL and breeding for resistance to S. sclerotiorum and to D. helianthi by pyramiding QTL in sunflower are discussed. PMID:12582925

Bert, P.-F.; Jouan, I.; De Labrouhe, D. Tourvieille; Serre, F.; Nicolas, P.; Vear, F.

2002-11-01

309

Combined expression patterns of QTL-linked candidate genes best predict thermotolerance in Drosophila melanogaster.  

PubMed

Knockdown resistance to high temperature (KRHT) is a thermal adaptation trait in Drosophila melanogaster. Here we used quantitative real-time PCR (qRT-PCR) to test for possible associations between KRHT and the expression of candidate genes within quantitative trait loci (QTL) in eight recombinant inbred lines (RIL). hsp60 and hsc70-3 map within an X-linked QTL, while CG10383, catsup, ddc, trap1, and cyp6a13 are linked in a KRHT-QTL on chromosome 2. hsc70-3 expression increased by heat-hardening. Principal Components analysis revealed that catsup, ddc and trap1 were either co-expressed or combined in their expression levels. This composite expression variable (e-PC1) was positively associated to KRHT in non-hardened RIL. In heat-hardened flies, hsp60 was negatively related to hsc70-3 on e-PC2, with effects on KRHT. These results are consistent with the notion that QTL can be shaped by expression variation in combined candidate loci. We found composite variables of gene expression (e-PCs) that best correlated to KRHT. Network effects with other untested linked loci are apparent because, in spite of their associations with KRHT phenotypes, e-PCs were sometimes uncorrelated with their QTL genotype. PMID:19651134

Norry, Fabian M; Larsen, Peter F; Liu, Yongjie; Loeschcke, Volker

2009-11-01

310

Quantitative trait locus mapping in an F2 Duroc x Pietrain resource population: II. Carcass and meat quality traits.  

PubMed

Pigs from the F(2) generation of a Duroc x Pietrain resource population were evaluated to discover QTL affecting carcass composition and meat quality traits. Carcass composition phenotypes included primal cut weights, skeletal characteristics, backfat thickness, and LM area. Meat quality data included LM pH, temperature, objective and subjective color information, marbling and firmness scores, and drip loss. Additionally, chops were analyzed for moisture, protein, and fat composition as well as cook yield and Warner-Bratzler shear force measurements. Palatability of chops was determined by a trained sensory panel. A total of 510 F(2) animals were genotyped for 124 microsatellite markers evenly spaced across the genome. Data were analyzed with line cross, least squares regression interval, mapping methods using sex and litter as fixed effects and carcass weight or slaughter age as covariates. Significance thresholds of the F-statistic for single QTL with additive, dominance, or imprinted effects were determined on chromosome- and genome-wise levels by permutation tests. A total of 94 QTL for 35 of the 38 traits analyzed were found to be significant at the 5% chromosome-wise level. Of these 94 QTL, 44 were significant at the 1% chromosome-wise, 28 of these 44 were also significant at the 5% genome-wise, and 14 of these 28 were also significant at the 1% genome-wise significance thresholds. Putative QTL were discovered for 45-min pH and pH decline from 45 min to 24 h on SSC 3, marbling score and carcass backfat on SSC 6, carcass length and number of ribs on SSC 7, marbling score on SSC 12, and color measurements and tenderness score on SSC 15. These results will facilitate fine mapping efforts to identify genes controlling carcass composition and meat quality traits that can be incorporated into marker-assisted selection programs to accelerate genetic improvement in pig populations. PMID:17965326

Edwards, D B; Ernst, C W; Raney, N E; Doumit, M E; Hoge, M D; Bates, R O

2008-02-01

311

Transferability and fine-mapping of glucose and insulin quantitative trait loci across populations: CARe, the Candidate Gene Association Resource  

PubMed Central

Aims/hypothesis Hyperglycaemia disproportionately affects African-Americans (AfAs). We tested the transferability of 18 single-nucleotide polymorphisms (SNPs) associated with glycaemic traits identified in European ancestry (EuA) populations in 5,984 non-diabetic AfAs. Methods We meta-analysed SNP associations with fasting glucose (FG) or insulin (FI) in AfAs from five cohorts in the Candidate Gene Association Resource. We: (1) calculated allele frequency differences, variations in linkage disequilibrium (LD), fixation indices (Fsts) and integrated haplotype scores (iHSs); (2) tested EuA SNPs in AfAs; and (3) interrogated within ±250 kb around each EuA SNP in AfAs. Results Allele frequency differences ranged from 0.6% to 54%. Fst exceeded 0.15 at 6/16 loci, indicating modest population differentiation. All iHSs were <2, suggesting no recent positive selection. For 18 SNPs, all directions of effect were the same and 95% CIs of association overlapped when comparing EuA with AfA. For 17 of 18 loci, at least one SNP was nominally associated with FG in AfAs. Four loci were significantly associated with FG (GCK, p=5.8 × 10-8; MTNR1B, p=8.5 × 10-9; and FADS1, p=2.2 × 10-4) or FI (GCKR, p=5.9 × 10-4). At GCK and MTNR1B the EuA and AfA SNPs represented the same signal, while at FADS1, and GCKR, the EuA and best AfA SNPs were weakly correlated (r2<0.2), suggesting allelic heterogeneity for association with FG at these loci. Conclusions/interpretation Few glycaemic SNPs showed strict evidence of transferability from EuA to AfAs. Four loci were significantly associated in both AfAs and those with EuA after accounting for varying LD across ancestral groups, with new signals emerging to aid fine-mapping. PMID:22893027

Liu, C.-T.; Ng, M. C. Y.; Rybin, D.; Adeyemo, A.; Bielinski, S. J.; Boerwinkle, E.; Borecki, I.; Cade, B.; Chen, Y. D. I.; Djousse, L.; Fornage, M.; Goodarzi, M. O.; Grant, S. F. A.; Guo, X.; Harris, T.; Kabagambe, E.; Kizer, J. R.; Liu, Y.; Lunetta, K. L.; Mukamal, K.; Nettleton, J. A.; Pankow, J. S.; Patel, S. R.; Ramos, E.; Rasmussen-Torvik, L.; Rich, S. S.; Rotimi, C. N.; Sarpong, D.; Shriner, D.; Sims, M.; Zmuda, J. M.; Redline, S.; Kao, W. H.; Siscovick, D.; Florez, J. C.; Rotter, J. I.; Dupuis, J.; Wilson, J. G.; Bowden, D. W.; Meigs, J. B.

2013-01-01

312

Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits  

PubMed Central

Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus?×?Brahman cattle crossbreds. We identified 24 POE–QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0–9?cM; genomic region of 5.0–10.8?Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4???5.1% of each trait’s phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits. PMID:22303340

Imumorin, Ikhide G.; Kim, Eun-Hee; Lee, Yun-Mi; De Koning, Dirk-Jan; van Arendonk, Johan A.; De Donato, Marcos; Taylor, Jeremy F.; Kim, Jong-Joo

2011-01-01

313

Mapping multiple disease resistance genes using a barley mapping population evaluated in Peru, Mexico, and the USA  

Technology Transfer Automated Retrieval System (TEKTRAN)

We used a well-characterized barley mapping population to determine if barley stripe rust (BSR) resistance QTL mapped in Mexico and the USA were effective against a reported new race in Peru. Essentially the same resistance QTL were detected using data from each of the three environments, indicating...

314

vol. 159, supplement the american naturalist march 2002 Genetic Mapping in Hybrid Zones  

E-print Network

the wild sunflower species Helianthus annuus and Helianthus petiolaris. Results indicate that mapping, Helianthus, hybrid zones, QTL, repro- ductive isolation, speciation. Great strides have been made over

Rieseberg, Loren

315

QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.)  

PubMed Central

Background Rice is staple food for more than half of the world’s population including two billion Asians, who obtain 60-70% of their energy intake from rice and its derivatives. To meet the growing demand from human population, rice varieties with higher yield potential and greater yield stability need to be developed. The favourable alleles for yield and yield contributing traits are distributed among two subspecies i.e., indica and japonica of cultivated rice (Oryza sativa L.). Identification of novel favourable alleles in indica/japonica will pave way to marker-assisted mobilization of these alleles in to a genetic background to break genetic barriers to yield. Results A new plant type (NPT) based mapping population of 310 recombinant inbred lines (RILs) was used to map novel genomic regions and QTL hotspots influencing yield and eleven yield component traits. We identified major quantitative trait loci (QTLs) for days to 50% flowering (R2?=?25%, LOD?=?14.3), panicles per plant (R2?=?19%, LOD?=?9.74), flag leaf length (R2?=?22%, LOD?=?3.05), flag leaf width (R2?=?53%, LOD?=?46.5), spikelets per panicle (R2?=?16%, LOD?=?13.8), filled grains per panicle (R2?=?22%, LOD?=?15.3), percent spikelet sterility (R2?=?18%, LOD?=?14.24), thousand grain weight (R2?=?25%, LOD?=?12.9) and spikelet setting density (R2?=?23%, LOD?=?15) expressing over two or more locations by using composite interval mapping. The phenotypic variation (R2) ranged from 8 to 53% for eleven QTLs expressing across all three locations. 19 novel QTLs were contributed by the NPT parent, Pusa1266. 15 QTL hotpots on eight chromosomes were identified for the correlated traits. Six epistatic QTLs effecting five traits at two locations were identified. A marker interval (RM3276-RM5709) on chromosome 4 harboring major QTLs for four traits was identified. Conclusions The present study reveals that favourable alleles for yield and yield contributing traits were distributed among two subspecies of rice and QTLs were co-localized in different genomic regions. QTL hotspots will be useful for understanding the common genetic control mechanism of the co-localized traits and selection for beneficial allele at these loci will result in a cumulative increase in yield due to the integrative positive effect of various QTLs. The information generated in the present study will be useful to fine map and to identify the genes underlying major robust QTLs and to transfer all favourable QTLs to one genetic background to break genetic barriers to yield for sustained food security. PMID:22876968

2012-01-01

316

The Use of Multiple Markers in a Bayesian Method for Mapping Quantitative Trait Loci  

PubMed Central

Information on multiple linked genetic markers was used in a Bayesian method for the statistical mapping of quantitative trait loci (QTL). Bayesian parameter estimation and hypothesis testing were implemented via Markov chain Monte Carlo algorithms. Variables sampled were the augmented data (marker-QTL genotypes, polygenic effects), an indicator variable for linkage or nonlinkage, and the parameters. The parameter vector included allele frequencies at the markers and the QTL, map distances of the markers and the QTL, QTL substitution effect, and polygenic and residual variances. The criterion for QTL detection was the marginal posterior probability of a QTL being located on the chromosome carrying the markers. The method was evaluated empirically by analyzing simulated granddaughter designs consisting of 2000 sons, 20 related sires, and their ancestors. PMID:8844168

Uimari, P.; Thaller, G.; Hoeschele, I.

1996-01-01

317

High-throughput phenotyping to detect drought tolerance QTL in wild barley introgression lines.  

PubMed

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

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

2014-01-01

318

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

PubMed Central

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

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

2014-01-01

319

The complex quantitative barley-Rhynchosporium secalis interaction: newly identified QTL may represent already known resistance genes.  

PubMed

Two barley populations, i.e. 135 doubled haploid (DH) lines of the cross 'Igri' (rrs1) x 'Triton' (Rrs1) (I x T) and 76 DH lines of the cross 'Post' x 'Vixen' (both rrs1) (P x V), were analysed to identify QTL for Rhynchosporium secalis resistance independent of the Rrs1 locus by using the single spore R. secalis isolate 271 (Rrs1-virulent). A major QTL with its positive allele derived from cv. 'Triton' was detected in the I x T population on chromosome 2HS explaining almost 80% of the phenotypic variance. Thus, it can be considered as an R-gene corresponding to the already described Rrs15(CI8288) on chromosome 2HS. In addition, two minor QTL were identified, one in the centromeric region of 6H in a highly polymorphic region with already several mapped R-genes and a second one at the end of the short arm of chromosome 7H which may be an allele of Rrs2 because of its chromosomal position. Regarding the DH population P x V different minor QTL were identified on chromosomes 6H and 7H. The first one is corresponding to the genomic region of the Rrs13 gene whereas the QTL on chromosome 7H maps in a genomic region where several R-genes against different pathogens have been localized. A comparison of both QTL analyses reveals no R. secalis isolate 271-specific resistance locus but leads to the hypothesis that two of the identified QTL may be alleles of the R-genes Rrs15(CI8288) and Rrs2. PMID:18806993

Wagner, C; Schweizer, G; Krämer, M; Dehmer-Badani, A G; Ordon, F; Friedt, W

2008-12-01

320

Fine epitope mapping of monoclonal antibodies against hemagglutinin of a highly pathogenic H5N1 influenza virus using yeast surface display.  

PubMed

Highly pathogenic H5N1 avian influenza viruses pose a debilitating pandemic threat. Thus, understanding mechanisms of antibody-mediated viral inhibition and neutralization escape is critical. Here, a robust yeast display system for fine epitope mapping of viral surface hemagglutinin (HA)-specific antibodies is demonstrated. The full-length H5 subtype HA (HA0) was expressed on the yeast surface in a correctly folded conformation, determined by binding of a panel of extensively characterized neutralizing human monoclonal antibodies (mAbs). These mAbs target conformationally-dependent epitopes of influenza A HA, which are highly conserved across H5 clades and group 1 serotypes. By separately displaying HA1 and HA2 subunits on yeast, domain mapping of two anti-H5 mAbs, NR2728 and H5-2A, localized their epitopes to HA1. These anti-H5 mAb epitopes were further fine mapped by using a library of yeast-displayed HA1 mutants and selecting for loss of binding without prior knowledge of potential contact residues. By overlaying key mutant residues that impacted binding onto a crystal structure of HA, the NR2728 mAb was found to interact with a fully surface-exposed contiguous patch of residues at the receptor binding site (RBS), giving insight into the mechanism underlying its potent inhibition of virus binding. The non-neutralizing H5-2A mAb was similarly mapped to a highly conserved H5 strain-specific but poorly accessible location on a loop at the trimer HA interface. These data further augment our toolchest for studying HA antigenicity, epitope diversity and accessibility in response to natural and experimental influenza infection and vaccines. PMID:21569761

Han, Thomas; Sui, Jianhua; Bennett, Andrew S; Liddington, Robert C; Donis, Ruben O; Zhu, Quan; Marasco, Wayne A

2011-06-01

321

Functional screening of an asthma QTL in YAC transgenic mice  

SciTech Connect

While large numbers of quantitative trait loci (QTLs) contributing to genetically complex conditions have been discovered, few causative genes have been identified. This is mainly due to the large size of QTLs and the subtle connection between genotype and quantitative phenotype associated with these conditions. While large numbers of quantitative trait loci (QTLs) contributing to genetically complex conditions have been discovered, few causative genes have been identified. This is mainly due to the large size of QTLs and the subtle connection between genotype and quantitative phenotype associated with these conditions. To screen for genes contributing to an asthma QTL mapped to human chromosome 5q33, the authors characterized a panel of large-insert 5q31 transgenics based on studies demonstrating that altering gene dosage frequently affects quantitative phenotypes normally influenced by that gene. This panel of human YAC transgenics, propagating a one megabase interva2048 chromosome 5q31 containing 23 genes, was screened for quantitative changes in several asthma-associated phenotypes. Multiple independent transgenic lines with altered IgE response to antigen treatment shared a 180 kb region containing 5 genes, including human interleukin 4 (IL4) and interleukin 13 (IL13), which induce IgE class switching in B cells5. Further analysis of these mice and mice transgenic for only murine Il4 and Il13 demonstrated that moderate changes in murine Il4 and Il13 expression affect asthma-associated phenotypes in vivo. This functional screen of large-insert transgenics enabled them to sift through multiple genes in the 5q3 asthma QTL without prior consideration of assumed individual gene function and identify genes that influence the QTL phenotype in vivo.

Symula, Derek J.; Frazer, Kelly A.; Ueda, Yukihiko; Denefle, Patrice; Stevens, Mary E.; Wang, Zhi-En; Locksley, Richard; Rubin, Edward M.

1999-07-02

322

An eQTL Analysis of Partial Resistance to Puccinia hordei in Barley  

PubMed Central

Background Genetic resistance to barley leaf rust caused by Puccinia hordei involves both R genes and quantitative trait loci. The R genes provide higher but less durable resistance than the quantitative trait loci. Consequently, exploring quantitative or partial resistance has become a favorable alternative for controlling disease. Four quantitative trait loci for partial resistance to leaf rust have been identified in the doubled haploid Steptoe (St)/Morex (Mx) mapping population. Further investigations are required to study the molecular mechanisms underpinning partial resistance and ultimately identify the causal genes. Methodology/Principal Findings We explored partial resistance to barley leaf rust using a genetical genomics approach. We recorded RNA transcript abundance corresponding to each probe on a 15K Agilent custom barley microarray in seedlings from St and Mx and 144 doubled haploid lines of the St/Mx population. A total of 1154 and 1037 genes were, respectively, identified as being P. hordei-responsive among the St and Mx and differentially expressed between P. hordei-infected St and Mx. Normalized ratios from 72 distant-pair hybridisations were used to map the genetic determinants of variation in transcript abundance by expression quantitative trait locus (eQTL) mapping generating 15685 eQTL from 9557 genes. Correlation analysis identified 128 genes that were correlated with resistance, of which 89 had eQTL co-locating with the phenotypic quantitative trait loci (pQTL). Transcript abundance in the parents and conservation of synteny with rice allowed us to prioritise six genes as candidates for Rphq11, the pQTL of largest effect, and highlight one, a phospholipid hydroperoxide glutathione peroxidase (HvPHGPx) for detailed analysis. Conclusions/Significance The eQTL approach yielded information that led to the identification of strong candidate genes underlying pQTL for resistance to leaf rust in barley and on the general pathogen response pathway. The dataset will facilitate a systems appraisal of this host-pathogen interaction and, potentially, for other traits measured in this population. PMID:20066049

Chen, Xinwei; Hackett, Christine A.; Niks, Rients E.; Hedley, Peter E.; Booth, Clare; Druka, Arnis; Marcel, Thierry C.; Vels, Anton; Bayer, Micha; Milne, Iain; Morris, Jenny; Ramsay, Luke; Marshall, David; Cardle, Linda; Waugh, Robbie

2010-01-01

323

QTL detection for Aeromonas salmonicida resistance related traits in turbot (Scophthalmus maximus)  

PubMed Central

Background Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new disease pressures. The turbot is one of the most promising European aquaculture species. Furunculosis, caused by the bacterium Aeromonas salmonicida, produces important losses to turbot industry. An appealing solution is to achieve more robust broodstock, which can prevent or diminish the devastating effects of epizooties. Genomics strategies have been developed in turbot to look for candidate genes for resistance to furunculosis and a genetic map with appropriate density to screen for genomic associations has been also constructed. In the present study, a genome scan for QTL affecting resistance and survival to A. salmonicida in four turbot families was carried out. The objectives were to identify consistent QTL using different statistical approaches (linear regression and maximum likelihood) and to locate the tightest associated markers for their application in genetic breeding strategies. Results Significant QTL for resistance were identified by the linear regression method in three linkage groups (LGs 4, 6 and 9) and for survival in two LGs (6 and 9). The maximum likelihood methodology identified QTL in three LGs (5, 6 and 9) for both traits. Significant association between disease traits and genotypes was detected for several markers, some of them explaining up to 17% of the phenotypic variance. We also identified candidate genes located in the detected QTL using data from previously mapped markers. Conclusions Several regions controlling resistance to A. salmonicida in turbot have been detected. The observed concordance between different statistical methods at particular linkage groups gives consistency to our results. The detected associated markers could be useful for genetic breeding strategies. A finer mapping will be necessary at the detected QTL intervals to narrow associations and around the closely associated markers to look for candidate genes through comparative genomics or positional cloning strategies. The identification of associated variants at specific genes will be essential, together with the QTL associations detected in this study, for future marker assisted selection programs. PMID:22047500

2011-01-01

324

Host genetics and immune control of HIV-1 infection: fine mapping for the extended human MHC region in an African cohort.  

PubMed

Multiple major histocompatibility complex (MHC) loci encoding human leukocyte antigens (HLA) have allelic variants unequivocally associated with differential immune control of HIV-1 infection. Fine mapping based on single nucleotide polymorphisms (SNPs) in the extended MHC (xMHC) region is expected to reveal causal or novel factors and to justify a search for functional mechanisms. We have tested the utility of a custom fine-mapping platform (the ImmunoChip) for 172 HIV-1 seroconverters (SCs) and 449 seroprevalent individuals (SPs) from Lusaka, Zambia, with a focus on more than 6400 informative xMHC SNPs. When conditioned on HLA and nongenetic factors previously associated with HIV-1 viral load (VL) in the study cohort, penalized approaches (HyperLasso models) identified an intergenic SNP (rs3094626 between RPP21 and HLA-E) and an intronic SNP (rs3134931 in NOTCH4) as novel correlates of early set-point VL in SCs. The minor allele of rs2857114 (downstream from HLA-DOB) was an unfavorable factor in SPs. Joint models based on demographic features, HLA alleles and the newly identified SNP variants could explain 29% and 15% of VL variance in SCs and SPs, respectively. These findings and bioinformatics strongly suggest that both classic and nonclassic MHC genes deserve further investigation, especially in Africans with relatively short haplotype blocks. PMID:24784026

Prentice, H A; Pajewski, N M; He, D; Zhang, K; Brown, E E; Kilembe, W; Allen, S; Hunter, E; Kaslow, R A; Tang, J

2014-01-01

325

A Dense Genetic Linkage Map for Common Carp and Its Integration with a BAC-Based Physical Map  

PubMed Central

Background Common carp (Cyprinus carpio) is one of the most important aquaculture species with an annual global production of 3.4 million metric tons. It is also an important ornamental species as well as an important model species for aquaculture research. To improve the economically important traits of this fish, a number of genomic resources and genetic tools have been developed, including several genetic maps and a bacterial artificial chromosome (BAC)-based physical map. However, integrated genetic and physical maps are not available to study quantitative trait loci (QTL) and assist with fine mapping, positional cloning and whole genome sequencing and assembly. The objective of this study was to integrate the currently available BAC-based physical and genetic maps. Results The genetic map was updated with 592 novel markers, including 312 BAC-anchored microsatellites and 130 SNP markers, and contained 1,209 genetic markers on 50 linkage groups, spanning 3,565.9 cM in the common carp genome. An integrated genetic and physical map of the common carp genome was then constructed, which was composed of 463 physical map contigs and 88 single BACs. Combined lengths of the contigs and single BACs covered a physical length of 498.75 Mb, or around 30% of the common carp genome. Comparative analysis between common carp and zebrafish genomes was performed based on the integrated map, providing more insights into the common carp specific whole genome duplication and segmental rearrangements in the genome. Conclusion We integrated a BAC-based physical map to a genetic linkage map of common carp by anchoring BAC-associated genetic markers. The density of the genetic linkage map was significantly increased. The integrated map provides a tool for both genetic and genomic studies of common carp, which will help us to understand the genomic architecture of common carp and facilitate fine mapping and positional cloning of economically important traits for genetic improvement and modification. PMID:23704958

Ji, Peifeng; Zhang, Xiaofeng; Zhao, Zixia; Hou, Guangyuan; Huo, Linhe; Liu, Guiming; Li, Chao; Xu, Peng; Sun, Xiaowen

2013-01-01

326

RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapa and their use for genome-wide linkage mapping and specific-region fine mapping  

PubMed Central

Background Brassica rapa (AA) contains very diverse forms which include oleiferous types and many vegetable types. Genome sequence of B. rapa line Chiifu (ssp. pekinensis), a leafy vegetable type, was published in 2011. Using this knowledge, it is important to develop genomic resources for the oleiferous types of B. rapa. This will allow more involved molecular mapping, in-depth study of molecular mechanisms underlying important agronomic traits and introgression of traits from B. rapa to major oilseed crops - B. juncea (AABB) and B. napus (AACC). The study explores the availability of SNPs in RNA-seq generated contigs of three oleiferous lines of B. rapa - Candle (ssp. oleifera, turnip rape), YSPB-24 and Tetra (ssp. trilocularis, Yellow sarson) and their use in genome-wide linkage mapping and specific-region fine mapping using a RIL population between Chiifu and Tetra. Results RNA-seq was carried out on the RNA isolated from young inflorescences containing unopened floral buds, floral axis and small leaves, using Illumina paired-end sequencing technology. Sequence assembly was carried out using the Velvet de-novo programme and the assembled contigs were organised against Chiifu gene models, available in the BRAD-CDS database. RNA-seq confirmed the presence of more than 17,000 single-copy gene models described in the BRAD database. The assembled contigs and the BRAD gene models were analyzed for the presence of SSRs and SNPs. While the number of SSRs was limited, more than 0.2 million SNPs were observed between Chiifu and the three oleiferous lines. Assays for SNPs were designed using KASPar technology and tested on a F7-RIL population derived from a Chiifu x Tetra cross. The design of the SNP assays were based on three considerations - the 50 bp flanking region of the SNPs should be strictly similar, the SNP should have a read-depth of ?7 and no exon/intron junction should be present within the 101 bp target region. Using these criteria, a total of 640 markers (580 for genome-wide mapping and 60 for specific-region mapping) marking as many genes were tested for mapping. Out of 640 markers that were tested, 594 markers could be mapped unambiguously which included 542 markers for genome-wide mapping and 42 markers for fine mapping of the tet-o locus that is involved with the trait tetralocular ovary in the line Tetra. Conclusion A large number of SNPs and PSVs are present in the transcriptome of B. rapa lines for genome-wide linkage mapping and specific-region fine mapping. Criteria used for SNP identification delivered markers, more than 93% of which could be successfully mapped to the F7–RIL population of Chiifu x Tetra cross. PMID:23837684

2013-01-01

327

Mapping  

ERIC Educational Resources Information Center

Geologic mapping in the United States increased by about one-quarter in the past year. Examinations of mapping trends were in the following categories: (1) Mapping at scales of 1:100, 000; (2) Metric-scale base maps; (3) International mapping, and (4) Planetary mapping. (MA)

Kinney, Douglas M.; McIntosh, Willard L.

1978-01-01

328

QTL analysis of genetic loci affecting domestication-related spike characters in common wheat.  

PubMed

Domestication-related changes that govern a spike morphology suitable for seed harvesting in cereals have resulted from mutation and selection of the genes. A synthetic hexaploid wheat (S-6214, genome AABBDD) produced by a cross between durum wheat (AABB) and wild goat grass (DD) showed partial non-domestication-related phenotypes due to genetic effects of the wild goat grass genome. Quantitative trait loci (QTLs) affecting wheat domestication-related spike characters including spike threshability, rachis fragility and spike compactness were investigated in F2 progeny of a cross between Chinese Spring (CS) wheat (AABBDD) and S-6214. Of 15 relevant QTLs identified, eight seemed to be consistent with peaks previously reported in wheat, while four QTL regions were novel. Four QTLs that affected spike threshability were localized to chromosomes 2BS, 2DS, 4D and 5DS. The QTL on 2DS probably represents the tenacious glume gene, Tg-D1. Based on its map position, the QTL located on 2BS coincides with Ppd-B1 and seems to be a homoeolocus of the soft glume gene. Two novel QTLs were detected on 4D and 5DS, and their goat grass alleles increased glume tenacity. Three novel QTLs located on 2DL, 3DL and 4D for rachis fragility were found. Based on the map position, the QTL on 3DL seems different from Br1 and Br2 loci and its CS allele appears to promote the generation of barrel-type diaspores. Three disarticulation types of spikelets were found in F2 individuals: wedge-type, barrel-type and both types. Among eight QTL peaks that governed spike morphology, six, located on 2AS, 2BS, 2DS, 4AL and 5AL, coincided with ones previously reported. A QTL for spike compactness on 5AL was distinct from the Q gene. A novel QTL that controls spike length was detected on 5DL. Complex genetic interactions between genetic background and the action of each gene were suggested. PMID:25475935

Katkout, Mazen; Kishii, Masahiro; Kawaura, Kanako; Mishina, Kouhei; Sakuma, Shun; Umeda, Kazuko; Takumi, Shigeo; Nitta, Miyuki; Nasuda, Shuhei; Ogihara, Yasunari

2014-01-01

329

Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16  

PubMed Central

Apple (Malus×domestica Borkh) is among the main sources of phenolic compounds in the human diet. The genetic basis of the quantitative variations of these potentially beneficial phenolic compounds was investigated. A segregating F1 population was used to map metabolite quantitative trait loci (mQTLs). Untargeted metabolic profiling of peel and flesh tissues of ripe fruits was performed using liquid chromatography–mass spectrometry (LC-MS), resulting in the detection of 418 metabolites in peel and 254 in flesh. In mQTL mapping using MetaNetwork, 669 significant mQTLs were detected: 488 in the peel and 181 in the flesh. Four linkage groups (LGs), LG1, LG8, LG13, and LG16, were found to contain mQTL hotspots, mainly regulating metabolites that belong to the phenylpropanoid pathway. The genetics of annotated metabolites was studied in more detail using MapQTL®. A number of quercetin conjugates had mQTLs on LG1 or LG13. The most important mQTL hotspot with the largest number of metabolites was detected on LG16: mQTLs for 33 peel-related and 17 flesh-related phenolic compounds. Structural genes involved in the phenylpropanoid biosynthetic pathway were located, using the apple genome sequence. The structural gene leucoanthocyanidin reductase (LAR1) was in the mQTL hotspot on LG16, as were seven transcription factor genes. The authors believe that this is the first time that a QTL analysis was performed on such a high number of metabolites in an outbreeding plant species. PMID:22330898

Khan, Sabaz Ali; Chibon, Pierre-Yves; de Vos, Ric C.H.; Schipper, Bert A.; Walraven, Evert; Beekwilder, Jules; van Dijk, Thijs; Finkers, Richard; Visser, Richard G.F.; van de Weg, Eric W.; Bovy, Arnaud; Cestaro, Alessandro; Velasco, Riccardo; Jacobsen, Evert; Schouten, Henk J.

2012-01-01

330

Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16.  

PubMed

Apple (Malus×domestica Borkh) is among the main sources of phenolic compounds in the human diet. The genetic basis of the quantitative variations of these potentially beneficial phenolic compounds was investigated. A segregating F? population was used to map metabolite quantitative trait loci (mQTLs). Untargeted metabolic profiling of peel and flesh tissues of ripe fruits was performed using liquid chromatography-mass spectrometry (LC-MS), resulting in the detection of 418 metabolites in peel and 254 in flesh. In mQTL mapping using MetaNetwork, 669 significant mQTLs were detected: 488 in the peel and 181 in the flesh. Four linkage groups (LGs), LG1, LG8, LG13, and LG16, were found to contain mQTL hotspots, mainly regulating metabolites that belong to the phenylpropanoid pathway. The genetics of annotated metabolites was studied in more detail using MapQTL®. A number of quercetin conjugates had mQTLs on LG1 or LG13. The most important mQTL hotspot with the largest number of metabolites was detected on LG16: mQTLs for 33 peel-related and 17 flesh-related phenolic compounds. Structural genes involved in the phenylpropanoid biosynthetic pathway were located, using the apple genome sequence. The structural gene leucoanthocyanidin reductase (LAR1) was in the mQTL hotspot on LG16, as were seven transcription factor genes. The authors believe that this is the first time that a QTL analysis was performed on such a high number of metabolites in an outbreeding plant species. PMID:22330898

Khan, Sabaz Ali; Chibon, Pierre-Yves; de Vos, Ric C H; Schipper, Bert A; Walraven, Evert; Beekwilder, Jules; van Dijk, Thijs; Finkers, Richard; Visser, Richard G F; van de Weg, Eric W; Bovy, Arnaud; Cestaro, Alessandro; Velasco, Riccardo; Jacobsen, Evert; Schouten, Henk J

2012-05-01

331

Genetic dissection of a major anthocyanin QTL contributing to pollinator-mediated reproductive isolation between sister species of Mimulus.  

PubMed

Prezygotic barriers play a major role in the evolution of reproductive isolation, which is a prerequisite for speciation. However, despite considerable progress in identifying genes and mutations responsible for postzygotic isolation, little is known about the genetic and molecular basis underlying prezygotic barriers. The bumblebee-pollinated Mimulus lewisii and the hummingbird-pollinated M. cardinalis represent a classic example of pollinator-mediated prezygotic isolation between two sister species in sympatry. Flower color differences resulting from both carotenoid and anthocyanin pigments contribute to pollinator discrimination between the two species in nature. Through fine-scale genetic mapping, site-directed mutagenesis, and transgenic experiments, we demonstrate that a single-repeat R3 MYB repressor, ROSE INTENSITY1 (ROI1), is the causal gene underlying a major quantitative trait locus (QTL) with the largest effect on anthocyanin concentration and that cis-regulatory change rather than coding DNA mutations cause the allelic difference between M. lewisii and M. cardinalis. Together with the genomic resources and stable transgenic tools developed here, these results suggest that Mimulus is an excellent platform for studying the genetics of pollinator-mediated reproductive isolation and the molecular basis of morphological evolution at the most fundamental level-gene by gene, mutation by mutation. PMID:23335333

Yuan, Yao-Wu; Sagawa, Janelle M; Young, Riane C; Christensen, Brian J; Bradshaw, Harvey D

2013-05-01

332

Genetic Dissection of a Major Anthocyanin QTL Contributing to Pollinator-Mediated Reproductive Isolation Between Sister Species of Mimulus  

PubMed Central

Prezygotic barriers play a major role in the evolution of reproductive isolation, which is a prerequisite for speciation. However, despite considerable progress in identifying genes and mutations responsible for postzygotic isolation, little is known about the genetic and molecular basis underlying prezygotic barriers. The bumblebee-pollinated Mimulus lewisii and the hummingbird-pollinated M. cardinalis represent a classic example of pollinator-mediated prezygotic isolation between two sister species in sympatry. Flower color differences resulting from both carotenoid and anthocyanin pigments contribute to pollinator discrimination between the two species in nature. Through fine-scale genetic mapping, site-directed mutagenesis, and transgenic experiments, we demonstrate that a single-repeat R3 MYB repressor, ROSE INTENSITY1 (ROI1), is the causal gene underlying a major quantitative trait locus (QTL) with the largest effect on anthocyanin concentration and that cis-regulatory change rather than coding DNA mutations cause the allelic difference between M. lewisii and M. cardinalis. Together with the genomic resources and stable transgenic tools developed here, these results suggest that Mimulus is an excellent platform for studying the genetics of pollinator-mediated reproductive isolation and the molecular basis of morphological evolution at the most fundamental level—gene by gene, mutation by mutation. PMID:23335333

Yuan, Yao-Wu; Sagawa, Janelle M.; Young, Riane C.; Christensen, Brian J.; Bradshaw, Harvey D.

2013-01-01

333

Fine genetic map of mouse chromosome 10 around the polycystic kidney disease gene, jcpk, and ankyrin 3  

SciTech Connect

A chlorambucil (CHL)-induced mutation of the jcpk (juvenile congenital polycystic kidney disease) gene causes a severe early onset polycystic kidney disease. In an intercross involving Mus musculus castaneus, jcpk was precisely mapped 0.2 cM distal to D10Mit115 and 0.8 cM proximal to D10Mit173. In addition, five genes, Cdc2a, Col6al, Col6a2, Bcr, and Ank3 were mapped in both this jcpk intercross and a (BALB/c X CAST/Ei)F{sub 1} x BALB/c backcross. All five genes were eliminated as possible candidates for jcpk based on the mapping data. The jcpk intercross allowed the orientation of the Ank3 gene relative to the centromere to be determined. D10Mit115, D10Mit173, D10Mit199, and D10Mit200 were separated genetically in this cross. The order and genetic distances of all markers and gene loci mapped in the jcpk intercross were consistent with those derived from the BALB/c backcross, indicating that the CHL-induced lesion has not generated any gross chromosomal abnormalities detectable in these studies. 39 refs., 3 figs.

Bryda, E.C.; Ling, H.; Rathbun, D.E. [New York State Department of Health, Albany, NY (United States)] [and others] [New York State Department of Health, Albany, NY (United States); and others

1996-08-01

334

Genetic Architecture of Maize Kernel Quality in the Nested Association Mapping (NAM) Population  

Technology Transfer Automated Retrieval System (TEKTRAN)

Many studies have been conducted to identify genes (quantitative trait loci; QTL) underlying kernel quality traits. However, these studies were limited to analyzing two parents at once and often resulted in low resolution mapping of QTL. The maize nested association mapping (NAM) population is a r...

335

QTL analysis of plant development and fruit traits in pepper and performance of selective phenotyping  

Microsoft Academic Search

A QTL analysis was performed to determine the genetic basis of 13 horticultural traits conditioning yield in pepper (Capsicum annuum). The mapping population was a large population of 297 recombinant inbred lines (RIL) originating from a cross between the\\u000a large-fruited bell pepper cultivar ‘Yolo Wonder’ and the small-fruited chilli pepper ‘Criollo de Morelos 334’. A total of\\u000a 76 QTLs were

Lorenzo Barchi; Véronique Lefebvre; Anne-Marie Sage-Palloix; Sergio Lanteri; Alain Palloix

2009-01-01

336

Fine-Scale Mapping of the FGFR2 Breast Cancer Risk Locus: Putative Functional Variants Differentially Bind FOXA1 and E2F1  

PubMed Central

The 10q26 locus in the second intron of FGFR2 is the locus most strongly associated with estrogen-receptor-positive breast cancer in genome-wide association studies. We conducted fine-scale mapping in case-control studies genotyped with a custom chip (iCOGS), comprising 41 studies (n = 89,050) of European ancestry, 9 Asian ancestry studies (n = 13,983), and 2 African ancestry studies (n = 2,028) from the Breast Cancer Association Consortium. We identified three statistically independent risk signals within the locus. Within risk signals 1 and 3, genetic analysis identified five and two variants, respectively, highly correlated with the most strongly associated SNPs. By using a combination of genetic fine mapping, data on DNase hypersensitivity, and electrophoretic mobility shift assays to study protein-DNA binding, we identified rs35054928, rs2981578, and rs45631563 as putative functional SNPs. Chromatin immunoprecipitation showed that FOXA1 preferentially bound to the risk-associated allele (C) of rs2981578 and was able to recruit ER? to this site in an allele-specific manner, whereas E2F1 preferentially bound the risk variant of rs35054928. The risk alleles were preferentially found in open chromatin and bound by Ser5 phosphorylated RNA polymerase II, suggesting that the risk alleles are associated with changes in transcription. Chromatin conformation capture demonstrated that the risk region was able to interact with the promoter of FGFR2, the likely target gene of this risk region. A role for FOXA1 in mediating breast cancer susceptibility at this locus is consistent with the finding that the FGFR2 risk locus primarily predisposes to estrogen-receptor-positive disease. PMID:24290378

Meyer, Kerstin B.; O’Reilly, Martin; Michailidou, Kyriaki; Carlebur, Saskia; Edwards, Stacey L.; French, Juliet D.; Prathalingham, Radhika; Dennis, Joe; Bolla, Manjeet K.; Wang, Qin; de Santiago, Ines; Hopper, John L.; Tsimiklis, Helen; Apicella, Carmel; Southey, Melissa C.; Schmidt, Marjanka K.; Broeks, Annegien; Van ’t Veer, Laura J.; Hogervorst, Frans B.; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Fasching, Peter A.; Lux, Michael P.; Ekici, Arif B.; Beckmann, Matthias W.; Peto, Julian; dos Santos Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Sawyer, Elinor J.; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Marme, Federick; Schneeweiss, Andreas; Sohn, Christof; Burwinkel, Barbara; Guénel, Pascal; Truong, Thérèse; Laurent-Puig, Pierre; Menegaux, Florence; Bojesen, Stig E.; Nordestgaard, Børge G.; Nielsen, Sune F.; Flyger, Henrik; Milne, Roger L.; Zamora, M. Pilar; Arias, Jose I.; Benitez, Javier; Neuhausen, Susan; Anton-Culver, Hoda; Ziogas, Argyrios; Dur, Christina C.; Brenner, Hermann; Müller, Heiko; Arndt, Volker; Stegmaier, Christa; Meindl, Alfons; Schmutzler, Rita K.; Engel, Christoph; Ditsch, Nina; Brauch, Hiltrud; Brüning, Thomas; Ko, Yon-Dschun; Nevanlinna, Heli; Muranen, Taru A.; Aittomäki, Kristiina; Blomqvist, Carl; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Yatabe, Yasushi; Dörk, Thilo; Helbig, Sonja; Bogdanova, Natalia V.; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Chenevix-Trench, Georgia; Wu, Anna H.; Tseng, Chiu-chen; Van Den Berg, David; Stram, Daniel O.; Lambrechts, Diether; Thienpont, Bernard; Christiaens, Marie-Rose; Smeets, Ann; Chang-Claude, Jenny; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Radice, Paolo; Peterlongo, Paolo; Bonanni, Bernardo; Bernard, Loris; Couch, Fergus J.; Olson, Janet E.; Wang, Xianshu; Purrington, Kristen; Giles, Graham G.; Severi, Gianluca; Baglietto, Laura; McLean, Catriona; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S.; Labrèche, France; Dumont, Martine; Teo, Soo-Hwang; Yip, Cheng-Har; Phuah, Sze-Yee; Kristensen, Vessela; Grenaker Alnæs, Grethe; Børresen-Dale, Anne-Lise; Zheng, Wei; Deming-Halverson, Sandra; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Andrulis, Irene L.; Knight, Julia A.; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robert A.E.M.; Seynaeve, Caroline M.; García-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J.; Lissowska, Jolanta; Czene, Kamila; Darabi, Hartef; Eriksson, Kimael; Hooning, Maartje J.; Martens, John W.M.; van den Ouweland, Ans M.W.; van Deurzen, Carolien H.M.; Hall, Per; Li, Jingmei; Liu, Jianjun; Humphreys, Keith; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Cox, Angela; Reed, Malcolm W.R.; Blot, William; Signorello, Lisa B.; Cai, Qiuyin; Pharoah, Paul D.P.; Ghoussaini, Maya; Harrington, Patricia; Tyrer, Jonathan; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K.; Noh, Dong-Young; Hartman, Mikael; Hui, Miao; Lim, Wei-Yen; Buhari, Shaik A.; Hamann, Ute; Försti, Asta; Rüdiger, Thomas; Ulmer, Hans-Ulrich; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Vachon, Celine; Slager, Susan; Fostira, Florentia; Pilarski, Robert; Shen, Chen-Yang; Hsiung, Chia-Ni; Wu, Pei-Ei; Hou, Ming-Feng; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Schoemaker, Minouk J.; Ponder, Bruce A.J.; Dunning, Alison M.; Easton, Douglas F.

2013-01-01

337

Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1.  

PubMed

The 10q26 locus in the second intron of FGFR2 is the locus most strongly associated with estrogen-receptor-positive breast cancer in genome-wide association studies. We conducted fine-scale mapping in case-control studies genotyped with a custom chip (iCOGS), comprising 41 studies (n = 89,050) of European ancestry, 9 Asian ancestry studies (n = 13,983), and 2 African ancestry studies (n = 2,028) from the Breast Cancer Association Consortium. We identified three statistically independent risk signals within the locus. Within risk signals 1 and 3, genetic analysis identified five and two variants, respectively, highly correlated with the most strongly associated SNPs. By using a combination of genetic fine mapping, data on DNase hypersensitivity, and electrophoretic mobility shift assays to study protein-DNA binding, we identified rs35054928, rs2981578, and rs45631563 as putative functional SNPs. Chromatin immunoprecipitation showed that FOXA1 preferentially bound to the risk-associated allele (C) of rs2981578 and was able to recruit ER? to this site in an allele-specific manner, whereas E2F1 preferentially bound the risk variant of rs35054928. The risk alleles were preferentially found in open chromatin and bound by Ser5 phosphorylated RNA polymerase II, suggesting that the risk alleles are associated with changes in transcription. Chromatin conformation capture demonstrated that the risk region was able to interact with the promoter of FGFR2, the likely target gene of this risk region. A role for FOXA1 in mediating breast cancer susceptibility at this locus is consistent with the finding that the FGFR2 risk locus primarily predisposes to estrogen-receptor-positive disease. PMID:24290378

Meyer, Kerstin B; O'Reilly, Martin; Michailidou, Kyriaki; Carlebur, Saskia; Edwards, Stacey L; French, Juliet D; Prathalingham, Radhika; Dennis, Joe; Bolla, Manjeet K; Wang, Qin; de Santiago, Ines; Hopper, John L; Tsimiklis, Helen; Apicella, Carmel; Southey, Melissa C; Schmidt, Marjanka K; Broeks, Annegien; Van 't Veer, Laura J; Hogervorst, Frans B; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Fasching, Peter A; Lux, Michael P; Ekici, Arif B; Beckmann, Matthias W; Peto, Julian; Dos Santos Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Sawyer, Elinor J; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Marme, Federick; Schneeweiss, Andreas; Sohn, Christof; Burwinkel, Barbara; Guénel, Pascal; Truong, Thérèse; Laurent-Puig, Pierre; Menegaux, Florence; Bojesen, Stig E; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Milne, Roger L; Zamora, M Pilar; Arias, Jose I; Benitez, Javier; Neuhausen, Susan; Anton-Culver, Hoda; Ziogas, Argyrios; Dur, Christina C; Brenner, Hermann; Müller, Heiko; Arndt, Volker; Stegmaier, Christa; Meindl, Alfons; Schmutzler, Rita K; Engel, Christoph; Ditsch, Nina; Brauch, Hiltrud; Brüning, Thomas; Ko, Yon-Dschun; Nevanlinna, Heli; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Yatabe, Yasushi; Dörk, Thilo; Helbig, Sonja; Bogdanova, Natalia V; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Chenevix-Trench, Georgia; Wu, Anna H; Tseng, Chiu-Chen; Van Den Berg, David; Stram, Daniel O; Lambrechts, Diether; Thienpont, Bernard; Christiaens, Marie-Rose; Smeets, Ann; Chang-Claude, Jenny; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Radice, Paolo; Peterlongo, Paolo; Bonanni, Bernardo; Bernard, Loris; Couch, Fergus J; Olson, Janet E; Wang, Xianshu; Purrington, Kristen; Giles, Graham G; Severi, Gianluca; Baglietto, Laura; McLean, Catriona; Haiman, Christopher A; Henderson, Brian E; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S; Labrèche, France; Dumont, Martine; Teo, Soo-Hwang; Yip, Cheng-Har; Phuah, Sze-Yee; Kristensen, Vessela; Grenaker Alnæs, Grethe; Børresen-Dale, Anne-Lise; Zheng, Wei; Deming-Halverson, Sandra; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Andrulis, Irene L; Knight, Julia A; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robert A E M; Seynaeve, Caroline M; García-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J; Lissowska, Jolanta; Czene, Kamila; Darabi, Hartef; Eriksson, Kimael; Hooning, Maartje J; Martens, John W M; van den Ouweland, Ans M W; van Deurzen, Carolien H M; Hall, Per; Li, Jingmei; Liu, Jianjun; Humphreys, Keith; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Cox, Angela; Reed, Malcolm W R; Blot, William; Signorello, Lisa B; Cai, Qiuyin; Pharoah, Paul D P; Ghoussaini, Maya; Harrington, Patricia; Tyrer, Jonathan; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K; Noh, Dong-Young; Hartman, Mikael; Hui, Miao; Lim, Wei-Yen; Buhari, Shaik A; Hamann, Ute; Försti, Asta; Rüdiger, Thomas; Ulmer, Hans-Ulrich; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Vachon, Celine; Slager, Susan; Fostira, Florentia; Pilarski, Robert; Shen, Chen-Yang; Hsiung, Chia-Ni; Wu, Pei-Ei; Hou, Ming-Feng; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Schoemaker, Minouk J; Ponder, Bruce A J; Dunning, Alison M; Easton, Douglas F

2013-12-01

338

A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia.  

PubMed

Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species. PMID:25435025

Liu, Feng; Sun, Fei; Xia, Jun Hong; Li, Jian; Fu, Gui Hong; Lin, Grace; Tu, Rong Jian; Wan, Zi Yi; Quek, Delia; Yue, Gen Hua

2014-01-01

339

A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia  

PubMed Central

Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140?dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species. PMID:25435025

Liu, Feng; Sun, Fei; Xia, Jun Hong; Li, Jian; Fu, Gui Hong; Lin, Grace; Tu, Rong Jian; Wan, Zi Yi; Quek, Delia; Yue, Gen Hua

2014-01-01

340

Sequence Haplotypes Revealed by Sequence-Tagged Site Fine Mapping of the Ror1 Gene in the Centromeric Region of Barley Chromosome 1H1[w  

PubMed Central

We describe the development of polymerase chain reaction-based, sequence-tagged site (STS) markers for fine mapping of the barley (Hordeum vulgare) Ror1 gene required for broad-spectrum resistance to powdery mildew (Blumeria graminis f. sp. hordei). After locating Ror1 to the centromeric region of barley chromosome 1H using a combined amplified fragment length polymorphism/restriction fragment-length polymorphism (RFLP) approach, sequences of RFLP probes from this chromosome region of barley and corresponding genome regions from the related grass species oat (Avena spp.), wheat, and Triticum monococcum were used to develop STS markers. Primers based on the RFLP probe sequences were used to polymerase chain reaction-amplify and directly sequence homologous DNA stretches from each of four parents that were used for mapping. Over 28,000 bp from 22 markers were compared. In addition to one insertion/deletion of at least 2.0 kb, 79 small unique sequence polymorphisms were observed, including 65 single nucleotide substitutions, two dinucleotide substitutions, 11 insertion/deletions, and one 5-bp/10-bp exchange. The frequency of polymorphism between any two barley lines ranged from 0.9 to 3.0 kb, and was greatest for comparisons involving an Ethiopian landrace. Haplotype structure was observed in the marker sequences over distances of several hundred basepairs. Polymorphisms in 16 STSs were used to generate genetic markers, scored by restriction enzyme digestion or by direct sequencing. Over 2,300 segregants from three populations were used in Ror1 linkage analysis, mapping Ror1 to a 0.2- to 0.5-cM marker interval. We discuss the implications of sequence haplotypes and STS markers for the generation of high-density maps in cereals. PMID:11244105

Collins, Nicholas C.; Lahaye, Thomas; Peterhänsel, Christoph; Freialdenhoven, Andreas; Corbitt, Margaret; Schulze-Lefert, Paul

2001-01-01

341

Fine Mapping Reveals That Promotion Susceptibility Locus 1 (Psl1) Is a Compound Locus With Multiple Genes That Modify Susceptibility to Skin Tumor Development  

PubMed Central

Although it is well known that the majority of human cancers occur as the result of exposure to environmental carcinogens, it is clear that not all individuals exposed to a specific environmental carcinogen have the same risk of developing cancer. Considerable evidence indicates that common allelic variants of low-penetrance, tumor susceptibility genes are responsible for this interindividual variation in risk. We previously reported a skin tumor promotion susceptibility locus, Psl1, which maps to the distal portion of chromosome 9, that modified skin tumor promotion susceptibility in the mouse. Furthermore, Psl1 was shown to consist of at least two subloci (i.e., Psl1.1 and Psl1.2) and that glutathione S-transferase alpha 4 (Gsta4), which maps to Psl1.2, is a skin tumor promotion susceptibility gene. Finally, variants of human GSTA4 were found to be associated with risk of nonmelanoma skin cancer. In the current study, a combination of nested and contiguous C57BL/6 congenic mouse strains, each inheriting a different portion of the Psl1 locus from DBA/2, were tested for susceptibility to skin tumor promotion with 12-O-tetradecanoylphorbol-13-acetate. These analyses indicate that Psl1 is a compound locus with at least six genes, including Gsta4, that modify skin tumor promotion susceptibility. More than 550 protein-coding genes map within the Psl1 locus. Fine mapping of the Psl1 locus, along with two-strain haplotype analysis, gene expression analysis, and the identification of genes with amino acid variants, has produced a list of fewer than 25 candidate skin tumor promotion susceptibility genes. PMID:24700353

Angel, Joe M.; Abel, Erika L.; Riggs, Penny K.; McClellan, S. Alex; DiGiovanni, John

2014-01-01

342

Fine Mapping of the Cystinosis Gene Using an Integrated Genetic and Physical Map of a Region within Human Chromosome Band 17p13  

Microsoft Academic Search

The cystinosis gene has been reported to reside in a 3.1 cM region of chromosome 17p13 flanked by markers D17S1828 and D17S1798. We created a yeast artificial chromosome (YAC) contig between these markers and report here an integrated genetic and physical map which will aid in the identification of other genes in this area. Using one pertinent YAC clone, 898A10,

Geraldine McDowell; Takao Isogai; Akira Tanigami; Senator Hazelwood; David Ledbetter; Mihael H. Polymeropoulos; Uta Lichter-Konecki; David Konecki; Margaret M. Town; William Van’t Hoff; Jean Weissenbach; William A. Gahl

1996-01-01

343

QTL Conferring Fusarium Crown Rot Resistance in the Elite Bread Wheat Variety EGA Wylie  

PubMed Central

Fusarium crown rot (FCR) is one of the most damaging cereal diseases in semi-arid regions worldwide. The genetics of FCR resistance in the bread wheat (Triticum eastivum L.) variety EGA Wylie, the most resistant commercial variety available, was studied by QTL mapping. Three populations of recombinant inbred lines were developed with this elite variety as the resistant parent. Four QTL conferring FCR resistance were detected and resistance alleles of all of them were derived from the resistant parent EGA Wylie. One of these loci was located on the short arm of chromosome 5D (designated as Qcrs.cpi-5D). This QTL explains up to 31.1% of the phenotypic variance with an LOD value of 9.6. The second locus was located on the long arm of chromosome 2D (designated as Qcrs.cpi-2D) and explained up to 20.2% of the phenotypic variance with an LOD value of 4.5. Significant effects of both Qcrs.cpi-5D and Qcrs.cpi-2D were detected in each of the three populations assessed. Another two QTL (designated as Qcrs.cpi-4B.1 and Qcrs.cpi-4B.2, respectively) were located on the short arm of chromosome 4B. These two QTL explained up to 16.9% and 18.8% of phenotypic variance, respectively. However, significant effects of Qcrs.cpi-4B.1 and Qcrs.cpi-4B.2 were not detected when the effects of plant height was accounted for by covariance analysis. The elite characteristics of this commercial variety should facilitate the incorporation of the resistance loci it contains into breeding programs. PMID:24776887

Zheng, Zhi; Kilian, Andrzej; Yan, Guijun; Liu, Chunji

2014-01-01

344

Multiple-trait quantitative trait locus mapping with incomplete phenotypic data  

PubMed Central

Background Conventional multiple-trait quantitative trait locus (QTL) mapping methods must discard cases (individuals) with incomplete phenotypic data, thereby sacrificing other phenotypic and genotypic information contained in the discarded cases. Under standard assumptions about the missing-data mechanism, it is possible to exploit these cases. Results We present an expectation-maximization (EM) algorithm, derived for recombinant inbred and F2 genetic models but extensible to any mating design, that supports conventional hypothesis tests for QTL main effect, pleiotropy, and QTL-by-environment interaction in multiple-trait analyses with missing phenotypic data. We evaluate its performance by simulations and illustrate with a real-data example. Conclusion The EM method affords improved QTL detection power and precision of QTL location and effect estimation in comparison with case deletion or imputation methods. It may be incorporated into any least-squares or likelihood-maximization QTL-mapping approach. PMID:19061502

Guo, Zhigang; Nelson, James C

2008-01-01

345

Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1.  

PubMed

Genome-wide association studies (GWASs) have revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, we analyzed 909 genetic variants across 5q11.2 in 103,991 breast cancer individuals and control individuals from 52 studies in the Breast Cancer Association Consortium. Multiple logistic regression analyses identified three independent risk signals: the strongest associations were with 15 correlated variants (iCHAV1), where the minor allele of the best candidate, rs62355902, associated with significantly increased risks of both estrogen-receptor-positive (ER(+): odds ratio [OR] = 1.24, 95% confidence interval [CI] = 1.21-1.27, ptrend = 5.7 × 10(-44)) and estrogen-receptor-negative (ER(-): OR = 1.10, 95% CI = 1.05-1.15, ptrend = 3.0 × 10(-4)) tumors. After adjustment for rs62355902, we found evidence of association of a further 173 variants (iCHAV2) containing three subsets with a range of effects (the strongest was rs113317823 [pcond = 1.61 × 10(-5)]) and five variants composing iCHAV3 (lead rs11949391; ER(+): OR = 0.90, 95% CI = 0.87-0.93, pcond = 1.4 × 10(-4)). Twenty-six percent of the prioritized candidate variants coincided with four putative regulatory elements that interact with the MAP3K1 promoter through chromatin looping and affect MAP3K1 promoter activity. Functional analysis indicated that the cancer risk alleles of four candidates (rs74345699 and rs62355900 [iCHAV1], rs16886397 [iCHAV2a], and rs17432750 [iCHAV3]) increased MAP3K1 transcriptional activity. Chromatin immunoprecipitation analysis revealed diminished GATA3 binding to the minor (cancer-protective) allele of rs17432750, indicating a mechanism for its action. We propose that the cancer risk alleles act to increase MAP3K1 expression in vivo and might promote breast cancer cell survival. PMID:25529635

Glubb, Dylan M; Maranian, Mel J; Michailidou, Kyriaki; Pooley, Karen A; Meyer, Kerstin B; Kar, Siddhartha; Carlebur, Saskia; O'Reilly, Martin; Betts, Joshua A; Hillman, Kristine M; Kaufmann, Susanne; Beesley, Jonathan; Canisius, Sander; Hopper, John L; Southey, Melissa C; Tsimiklis, Helen; Apicella, Carmel; Schmidt, Marjanka K; Broeks, Annegien; Hogervorst, Frans B; van der Schoot, C Ellen; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Fasching, Peter A; Ruebner, Matthias; Ekici, Arif B; Beckmann, Matthias W; Peto, Julian; Dos-Santos-Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Pharoah, Paul D P; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Sawyer, Elinor J; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Burwinkel, Barbara; Marme, Frederik; Yang, Rongxi; Surowy, Harald; Guénel, Pascal; Truong, Thérèse; Menegaux, Florence; Sanchez, Marie; Bojesen, Stig E; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; González-Neira, Anna; Benitez, Javier; Zamora, M Pilar; Arias Perez, Jose Ignacio; Anton-Culver, Hoda; Neuhausen, Susan L; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Meindl, Alfons; Schmutzler, Rita K; Brauch, Hiltrud; Ko, Yon-Dschun; Brüning, Thomas; Nevanlinna, Heli; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Tanaka, Hideo; Dörk, Thilo; Bogdanova, Natalia V; Helbig, Sonja; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Wu, Anna H; Tseng, Chiu-Chen; Van Den Berg, David; Stram, Daniel O; Lambrechts, Diether; Zhao, Hui; Weltens, Caroline; van Limbergen, Erik; Chang-Claude, Jenny; Flesch-Janys, Dieter; Rudolph, Anja; Seibold, Petra; Radice, Paolo; Peterlongo, Paolo; Barile, Monica; Capra, Fabio; Couch, Fergus J; Olson, Janet E; Hallberg, Emily; Vachon, Celine; Giles, Graham G; Milne, Roger L; McLean, Catriona; Haiman, Christopher A; Henderson, Brian E; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S; Labrèche, France; Dumont, Martine; Teo, Soo Hwang; Yip, Cheng Har; See, Mee-Hoong; Cornes, Belinda; Cheng, Ching-Yu; Ikram, M Kamran; Kristensen, Vessela; Zheng, Wei; Halverson, Sandra L; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Andrulis, Irene L; Knight, Julia A; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robert A E M; Seynaeve, Caroline; Van Asperen, Christi J; García-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J; Lissowska, Jolanta; Czene, Kamila; Klevebring, Daniel; Darabi, Hatef; Eriksson, Mikael; Hooning, Maartje J; Hollestelle, Antoinette; Martens, John W M; Collée, J Margriet; Hall, Per; Li, Jingmei; Humphreys, Keith; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Cox, Angela; Cross, Simon S; Reed, Malcolm W R; Blot, William; Signorello, Lisa B; Cai, Qiuyin; Shah, Mitul; Ghoussaini, Maya; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K; Noh, Dong-Young; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Tang, Anthony; Hamann, Ute; Torres, Diana; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Olswold, Curtis; Slager, Susan; Toland, Amanda E; Yannoukakos, Drakoulis; Shen, Chen-Yang; Wu, Pei-Ei; Yu, Jyh-Cherng; Hou, Ming-Feng; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Pita, Guillermo; Alonso, M Rosario; Álvarez, Nuria; Herrero, Daniel; Tessier, Daniel C; Vincent, Daniel; Bacot, Francois; Luccarini, Craig; Baynes, Caroline; Ahmed, Shahana; Healey, Catherine S; Brown, Melissa A; Ponder, Bruce A J; Chenevix-Trench, Georgia; Thompson, Deborah J; Edwards, Stacey L; Easton, Douglas F; Dunning, Alison M; French, Juliet D

2015-01-01

346

Fine mapping of foxglove aphid (Aulacorthum solani) resistance gene Raso1 in soybean and its effect on tolerance to Soybean dwarf virus transmitted by foxglove aphid  

PubMed Central

Soybean dwarf virus (SbDV) causes serious dwarfing, yellowing and sterility in soybean (Glycine max). The soybean cv. Adams is tolerant to SbDV infection in the field and exhibits antibiosis to foxglove aphid (Aulacorthum solani), which transmits SbDV. This antibiosis (termed “aphid resistance”) is required for tolerance to SbDV in the field in segregated progenies of Adams. A major quantitative trait locus, Raso1, is reported for foxglove aphid resistance. Our objectives were to fine map Raso1 and to reveal whether Raso1 alone is sufficient to confer both aphid resistance and SbDV tolerance. We introduced Raso1 into cv. Toyomusume by backcrossing and investigated the degree of aphid antibiosis to foxglove aphid and the degree of tolerance to SbDV in the field. All Raso1-introduced backcross lines showed aphid resistance. Interestingly, only one Raso1-introduced backcross line (TM-1386) showed tolerance to SbDV in the field. The results demonstrated Raso1 alone is sufficient to confer aphid resistance but insufficient for SbDV tolerance. Tolerance to SbDV was indicated to require additional gene(s) to Raso1. Additionally, Raso1 was mapped to a 63-kb interval on chromosome 3 of the Williams 82 sequence assembly (Glyma1). This interval includes a nucleotide-binding site–leucine-rich repeat encoding gene and two other genes in the Williams 82 soybean genome sequence. PMID:23136500

Ohnishi, Shizen; Miyake, Noriyuki; Takeuchi, Toru; Kousaka, Fumiko; Hiura, Satoshi; Kanehira, Osamu; Saito, Miki; Sayama, Takashi; Higashi, Ayako; Ishimoto, Masao; Tanaka, Yoshinori; Fujita, Shohei

2012-01-01

347

Fine mapping of the sunflower resistance locus Pl(ARG) introduced from the wild species Helianthus argophyllus.  

PubMed

Downy mildew, caused by Plasmopara halstedii, is one of the most destructive diseases in cultivated sunflower (Helianthus annuus L.). The dominant resistance locus Pl(ARG) originates from silverleaf sunflower (H. argophyllus Torrey and Gray) and confers resistance to all known races of P. halstedii. We mapped Pl(ARG) on linkage group (LG) 1 of (cms)HA342 × ARG1575-2, a population consisting of 2,145 F(2) individuals. Further, we identified resistance gene candidates (RGCs) that cosegregated with Pl(ARG) as well as closely linked flanking markers. Markers from the target region were mapped with higher resolution in NDBLOS(sel) × KWS04, a population consisting of 2,780 F(2) individuals that does not segregate for Pl(ARG). A large-insert sunflower bacterial artificial chromosome (BAC) library was screened with overgo probes designed for markers RGC52 and RGC151, which cosegregated with Pl(ARG). Two RGC-containing BAC contigs were anchored to the Pl(ARG) region on LG 1. PMID:20700574

Wieckhorst, S; Bachlava, E; Dussle, C M; Tang, S; Gao, W; Saski, C; Knapp, S J; Schön, C-C; Hahn, V; Bauer, E

2010-11-01

348

Fine mapping of the sunflower resistance locus PlARG introduced from the wild species Helianthus argophyllus  

PubMed Central

Downy mildew, caused by Plasmopara halstedii, is one of the most destructive diseases in cultivated sunflower (Helianthus annuus L.). The dominant resistance locus PlARG originates from silverleaf sunflower (H. argophyllus Torrey and Gray) and confers resistance to all known races of P. halstedii. We mapped PlARG on linkage group (LG) 1 of (cms)HA342 × ARG1575-2, a population consisting of 2,145 F2 individuals. Further, we identified resistance gene candidates (RGCs) that cosegregated with PlARG as well as closely linked flanking markers. Markers from the target region were mapped with higher resolution in NDBLOSsel × KWS04, a population consisting of 2,780 F2 individuals that does not segregate for PlARG. A large-insert sunflower bacterial artificial chromosome (BAC) library was screened with overgo probes designed for markers RGC52 and RGC151, which cosegregated with PlARG. Two RGC-containing BAC contigs were anchored to the PlARG region on LG 1. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1416-4) contains supplementary material, which is available to authorized users. PMID:20700574

Wieckhorst, S.; Bachlava, E.; Dußle, C. M.; Tang, S.; Gao, W.; Saski, C.; Knapp, S. J.; Schön, C.-C.; Hahn, V.

2010-01-01

349

Fine genetic mapping of the genomic region controlling leaflet shape and number of seeds per pod in the soybean.  

PubMed

Narrow leaflet cultivars tend to have more seeds per pod than broad leaflet cultivars in soybean [Glycine max (L.) Merr.], which suggests that the leaflet-shape trait locus is tightly linked to or cosegregates with the trait locus controlling the number of seeds per pod (NSPP). Here, we attempted to further elucidate the relationship between leaflet shape and NSPP. A BC(3)F(2) population from a cross between the 'Sowon' (narrow leaflets and high NSPP) and 'V94-5152' (broad leaflets and low NSPP) variants was used. The results of the molecular genetic analyses indicated that, although the NSPP characteristic, in particular, the occurrence of 4-seeded pods, is governed by additional modifying genes that are likely present in Sowon, the two traits cosegregate in the BC(3)F(2) population. The mapping results generated using public markers demonstrated that the narrow leaflet-determining gene in Sowon is an allele of the previously highly studied ln gene on chromosome 20. A high-resolution map delimited the genomic region controlling both the leaflet shape and NSPP traits to a sequence length of 66 kb, corresponding to 0.7 cM. Among the three genes annotated in this 66 kb region, Glyma20g25000.1 appeared to be a good candidate for the Ln-encoding gene, owing to its 47.8% homology with the protein encoding for the JAGGED gene that regulates lateral organ development in Arabidopsis. Taken together, our results suggested that phenotypic variations for narrow leaflet and NSPP are predominantly from the pleiotropic effects of the ln gene. Thus, our results should provide a molecular framework for soybean breeding programs with the objective of improving soybean yield. PMID:21104397

Jeong, Namhee; Moon, Jung-Kyung; Kim, Hong Sig; Kim, Chang-Gi; Jeong, Soon-Chun

2011-03-01

350

Fine Epitope Mapping of the Central Immunodominant Region of Nucleoprotein from Crimean-Congo Hemorrhagic Fever Virus (CCHFV)  

PubMed Central

Crimean-Congo hemorrhagic fever (CCHF), a severe viral disease known to have occurred in over 30 countries and distinct regions, is caused by the tick-borne CCHF virus (CCHFV). Nucleocapsid protein (NP), which is encoded by the S gene, is the primary antigen detectable in infected cells. The goal of the present study was to map the minimal motifs of B-cell epitopes (BCEs) on NP. Five precise BCEs (E1, 247FDEAKK252; E2a, 254VEAL257; E2b, 258NGYLNKH264; E3, 267EVDKA271; and E4, 274DSMITN279) identified through the use of rabbit antiserum, and one BCE (E5, 258NGYL261) recognized using a mouse monoclonal antibody, were confirmed to be within the central region of NP and were partially represented among the predicted epitopes. Notably, the five BCEs identified using the rabbit sera were able to react with positive serum mixtures from five sheep which had been infected naturally with CCHFV. The multiple sequence alignment (MSA) revealed high conservation of the identified BCEs among ten CCHFV strains from different areas. Interestingly, the identified BCEs with only one residue variation can apparently be recognized by the positive sera of sheep naturally infected with CCHFV. Computer-generated three-dimensional structural models indicated that all the antigenic motifs are located on the surface of the NP stalk domain. This report represents the first identification and mapping of the minimal BCEs of CCHFV-NP along with an analysis of their primary and structural properties. Our identification of the minimal linear BCEs of CCHFV-NP may provide fundamental data for developing rapid diagnostic reagents and illuminating the pathogenic mechanism of CCHFV. PMID:25365026

Liu, Dongliang; Li, Yang; Zhao, Jing; Deng, Fei; Duan, Xiaomei; Kou, Chun; Wu, Ting; Li, Yijie; Wang, Yongxing; Ma, Ji; Yang, Jianhua; Hu, Zhihong; Zhang, Fuchun; Zhang, Yujiang; Sun, Surong

2014-01-01

351

AB-QTL analysis in spring barley. I. Detection of resistance genes against powdery mildew, leaf rust and scald introgressed from wild barley.  

PubMed

The objective of this study was to map new resistance genes against powdery mildew (Blumeria graminis f. sp. hordei L.), leaf rust (Puccinia hordei L.) and scald [Rhynchosporium secalis (Oud.) J. Davis] in the advanced backcross doubled haploid (BC2DH) population S42 derived from a cross between the spring barley cultivar 'Scarlett' and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). Using field data of disease severity recorded in eight environments under natural infestation and genotype data of 98 SSR loci, we detected nine QTL for powdery mildew, six QTL for leaf rust resistance and three QTL for scald resistance. The presence of the exotic QTL alleles reduced disease symptoms by a maximum of 51.5, 37.6 and 16.5% for powdery mildew, leaf rust and scald, respectively. Some of the detected QTL may correspond to previously identified qualitative (i.e. Mla) and to quantitative resistance genes. Others may be newly identified resistance genes. For the majority of resistance QTL (61.0%) the wild barley contributed the favourable allele demonstrating the usefulness of wild barley in the quest for resistant cultivars. PMID:15902395

von Korff, M; Wang, H; Léon, J; Pillen, K

2005-08-01

352

Combined analysis of data from two granddaughter designs: A simple strategy for QTL confirmation and increasing experimental power in dairy cattle  

PubMed Central

A joint analysis of five paternal half-sib Holstein families that were part of two different granddaughter designs (ADR- or Inra-design) was carried out for five milk production traits and somatic cell score in order to conduct a QTL confirmation study and to increase the experimental power. Data were exchanged in a coded and standardised form. The combined data set (JOINT-design) consisted of on average 231 sires per grandsire. Genetic maps were calculated for 133 markers distributed over nine chromosomes. QTL analyses were performed separately for each design and each trait. The results revealed QTL for milk production on chromosome 14, for milk yield on chromosome 5, and for fat content on chromosome 19 in both the ADR- and the Inra-design (confirmed within this study). Some QTL could only be mapped in either the ADR- or in the Inra-design (not confirmed within this study). Additional QTL previously undetected in the single designs were mapped in the JOINT-design for fat yield (chromosome 19 and 26), protein yield (chromosome 26), protein content (chromosome 5), and somatic cell score (chromosome 2 and 19) with genomewide significance. This study demonstrated the potential benefits of a combined analysis of data from different granddaughter designs. PMID:12729552

Bennewitz, Jörn; Reinsch, Norbert; Grohs, Cécile; Levéziel, Hubert; Malafosse, Alain; Thomsen, Hauke; Xu, Ningying; Looft, Christian; Kühn, Christa; Brockmann, Gudrun A; Schwerin, Manfred; Weimann, Christina; Hiendleder, Stefan; Erhardt, Georg; Medjugorac, Ivica; Russ, Ingolf; Förster, Martin; Brenig, Bertram; Reinhardt, Fritz; Reents, Reinhard; Averdunk, Gottfried; Blümel, Jürgen; Boichard, Didier; Kalm, Ernst

2003-01-01

353

Efficient QTL detection for nonhost resistance in wild lettuce: backcross inbred lines versus F2 population  

PubMed Central

In plants, several population types [F2, recombinant inbred lines, backcross inbred lines (BILs), etc.] are used for quantitative trait locus (QTL) analyses. However, dissection of the trait of interest and subsequent confirmation by introgression of QTLs for breeding purposes has not been as successful as that predicted from theoretical calculations. More practical knowledge of different QTL mapping approaches is needed. In this recent study, we describe the detection and mapping of quantitative resistances to downy mildew in a set of 29 BILs of cultivated lettuce (L. sativa) containing genome segments introgressed from wild lettuce (L. saligna). Introgression regions that are associated with quantitative resistance are considered to harbor a QTL. Furthermore, we compare this with results from an already existing F2 population derived from the same parents. We identified six QTLs in our BIL approach compared to only three in the F2 approach, while there were two QTLs in common. We performed a simulation study based on our actual data to help us interpret them. This revealed that two newly detected QTLs in the BILs had gone unnoticed in the F2, due to a combination of recessiveness of the trait and skewed segregation, causing a deficit of the wild species alleles. This study clearly illustrates the added value of extended genetic studies on two different population types (BILs and F2) to dissect complex genetic traits. PMID:18251002

Pelgrom, K.; Stam, P.; Lindhout, P.

2008-01-01

354

QTL analysis of plant development and fruit traits in pepper and performance of selective phenotyping.  

PubMed

A QTL analysis was performed to determine the genetic basis of 13 horticultural traits conditioning yield in pepper (Capsicum annuum). The mapping population was a large population of 297 recombinant inbred lines (RIL) originating from a cross between the large-fruited bell pepper cultivar 'Yolo Wonder' and the small-fruited chilli pepper 'Criollo de Morelos 334'. A total of 76 QTLs were detected for 13 fruit and plant traits, grouped in 28 chromosome regions. These QTLs explained together between 7% (internode growth time) and 91% (fruit diameter) of the phenotypic variation. The QTL analysis was also performed on two subsets of 141 and 93 RILs sampled using the MapPop software. The smaller populations allowed for the detection of a reduced set of QTLs and reduced the overall percentage of trait variation explained by QTLs. The frequency of false positives as well as the individual effect of QTLs increased in reduced population sets as a result of reduced sampling. The results from the QTL analysis permitted an overall glance over the genetic architecture of traits considered by breeders for selection. Colinearities between clusters of QTLs controlling fruit traits and/or plant development in distinct pepper species and in related solanaceous crop species (tomato and eggplant) suggests that shared mechanisms control the shape and growth of different organs throughout these species. PMID:19219599

Barchi, Lorenzo; Lefebvre, Véronique; Sage-Palloix, Anne-Marie; Lanteri, Sergio; Palloix, Alain

2009-04-01

355

Fine mapping of ZNF804A and genome wide significant evidence for its involvement in schizophrenia and bipolar disorder  

PubMed Central

A recent genome wide association study reported evidence for association between rs1344706 within ZNF804A (encoding zinc finger protein 804A) and schizophrenia (P=1.61 ×10?7), and stronger evidence when the phenotype was broadened to include bipolar disorder (P=9.96 ×10?9). Here we provide additional evidence for association through meta-analysis of a larger dataset (schizophrenia/schizoaffective disorder N = 18945, schizophrenia plus bipolar disorder N =21274, controls N =38675). We also sought to better localize the association signal using a combination of de novo polymorphism discovery in exons, pooled de novo polymorphism discovery spanning the genomic sequence of the locus and high density LD mapping. Meta-analysis provided evidence for association between rs1344706 that surpasses widely accepted benchmarks of significance by several orders of magnitude for both schizophrenia (P=2.5 ×10?11, OR=1.10, 95% CI 1.07–1.14) and schizophrenia and bipolar disorder combined (P=4.1 ×10?13, OR=1.11, 95% CI 1.07–1.14). After de novo polymorphism discovery and detailed association analysis, rs1344706 remained the most strongly associated marker in the gene. The allelic association at the ZNF804A locus is now one of the most compelling in schizophrenia to date, and supports the accumulating data suggesting overlapping genetic risk between schizophrenia and bipolar disorder. PMID:20368704

Williams, Hywel J; Norton, Nadine; Dwyer, Sarah; Moskvina, Valentina; Nikolov, Ivan; Carroll, Liam; Georgieva, Lyudmila; Williams, Nigel M; Morris, Derek W; Quinn, Emma M; Giegling, Ina; Ikeda, Masashi; Wood, Joel; Lencz, Todd; Hultman, Christina; Lichtenstein, Paul; Thiselton, Dawn; Maher, Brion S; Malhotra, Anil K; Riley, Brien; Kendler, Kenneth S; Gill, Michael; Sullivan, Patrick; Sklar, Pamela; Purcell, Shaun; Nimgaonkar, Vishwajit L; Kirov, George; Holmans, Peter; Corvin, Aiden; Rujescu, Dan; Craddock, Nicholas; Owen, Michael J; O’Donovan, Michael C

2013-01-01

356

Fine mapping of a gene responsible for regulating dietary cholesterol absorption; founder effects underlie cases of phytosterolaemia in multiple communities  

PubMed Central

Sitosterolaemia (also known as phytosterolaemia, MIM 210250) is a rare recessive autosomal inherited disorder, characterised by the presence of tendon and tuberous xanthomas, accelerated atherosclerosis and premature coronary artery disease. The defective gene is hypothesised to play an important role in regulating dietary sterol absorption and biliary secretion, thus defining a molecular mechanism whereby this physiological process is carried out. The disease locus was localised previously to chromosome 2p21, in a 15 cM interval between microsatellite markers D2S1788 and D2S1352 (based upon 10 families, maximum lodscore 4.49). In this study, we have extended these studies to include 30 families assembled from around the world. A maximum multipoint lodscore of 11.49 was obtained for marker D2S2998. Homozygosity and haplotype sharing was identified in probands from non-consanguineous marriages from a number of families, strongly supporting the existence of a founder effect among various populations. Additionally, based upon both genealogies, as well as genotyping, two Amish/Mennonite families, that were previously thought not to be related, appear to indicate a founder effect in this population as well. Using both homozygosity mapping, as well as informative recombination events, the sitosterolaemia gene is located at a region defined by markers D2S2294 and Afm210xe9, a distance of less than 2 cM. PMID:11378826

Lee, Mi-Hye; Gordon, Derek; Ott, Jurg; Lu, Kangmo; Ose, Leiv; Miettinen, Tatu; Gylling, Helena; Stalenhoef, Anton F; Pandya, Arti; Hidaka, Hideki; Brewer, Bryan; Kojima, Hideto; Sakuma, Nagahiko; Pegoraro, Rosemary; Salen, Gerald; Patel, Shailendra B

2005-01-01

357

Fine deletion mapping of chromosome 2q21-37 shows three preferentially deleted regions in oral cancer.  

PubMed

We analysed the loss of heterozygosity (LOH) of long arm of chromosome 2 by using 16 polymorphic microsatellite markers in 39 matched oral normal and cancer tissues, and defined the deletional mapping of the region with putative tumor suppressor genes. LOH was detected at least one location in 33 of 39 (85%) tumor tissues. Frequent deletions were detected at the locations of microsatellite markers, D2S2304 (35%), D2S111 (40%), D2S155 (35%), D2S1327 (29%), D2S164 (29%), D2S125 (68%) and D2S140 (32%). Three preferentially deleted regions at 2q21-24, 2q33-35 and 2q37.3 were observed. Several candidate tumor suppressor genes in these regions such as LRP1B, CASP8, CASP10, BARD1, ILKAP, PPP1R7, and ING5, are located. Further molecular analysis of each gene should be performed to clarify their roles in oral carcinogenesis. PMID:16857411

Cengiz, Beyhan; Gunduz, Mehmet; Nagatsuka, Hitoshi; Beder, Levent; Gunduz, Esra; Tamamura, Ryo; Mahmut, Naila; Fukushima, Kunihiro; Ali, Mahmoud Al Sheikh; Naomoto, Yoshio; Shimizu, Kenji; Nagai, Noriyuki

2007-03-01

358

Mapping and Functional Characterization of Candidate Genes  

E-print Network

Mapping and Functional Characterization of Candidate Genes and Mutations for Chicken Growth: GeneticAssociation) #12;Mapping and Functional Characterization of Candidate Genes and Mutations Karyotype 17! 2.4! Gene Mapping and Association Studies 19! 2.4.1! QTL Analysis 19! 2.4.2! Genome

359

MAPS  

... MAPS Data and Information Measurement of Air Pollution from Satellites (MAPS) data were collected during Space Shuttle ... NASA Facts Correlative Data  - CDIAC - Spring & Fall 1994 - Field and Aircraft Campaigns SCAR-B Block:  ...

2014-07-03

360

A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq)  

PubMed Central

High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers. PMID:25610449

Xu, Xuewen; Xu, Ruixue; Zhu, Biyun; Yu, Ting; Qu, Wenqin; Lu, Lu; Xu, Qiang; Qi, Xiaohua; Chen, Xuehao

2015-01-01