Sample records for qtl fine mapping

  1. Robust Indices of Hardy-Weinberg Disequilibrium for QTL Fine Mapping

    Microsoft Academic Search

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

    2003-01-01

    Hardy-Weinberg disequilibrium (HWD) measures have been proposed using dense markers to fine map a quantitative trait locus (QTL) to regions < ? 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.

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

    ERIC Educational Resources Information Center

    Donthu, Ravikiran

    2009-01-01

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

  3. Using haplotypes for the prediction of allelic identity to fine-map QTL: characterization and properties

    PubMed Central

    2014-01-01

    Background Numerous methods have been developed over the last decade to predict allelic identity at unobserved loci between pairs of chromosome segments along the genome. These loci are often unobserved positions tested for the presence of quantitative trait loci (QTL). The main objective of this study was to understand from a theoretical standpoint the relation between linkage disequilibrium (LD) and allelic identity prediction when using haplotypes for fine mapping of QTL. In addition, six allelic identity predictors (AIP) were also compared in this study to determine which one performed best in theory and application. Results A criterion based on a simple measure of matrix distance was used to study the relation between LD and allelic identity prediction when using haplotypes. The consistency of this criterion with the accuracy of QTL localization, another criterion commonly used to compare AIP, was evaluated on a set of real chromosomes. For this set of chromosomes, the criterion was consistent with the mapping accuracy of a simulated QTL with either low or high effect. As measured by the matrix distance, the best AIP for QTL mapping were those that best captured LD between a tested position and a QTL. Moreover the matrix distance between a tested position and a QTL was shown to decrease for some AIP when LD increased. However, the matrix distance for AIP with continuous predictions in the [0,1] interval was algebraically proven to decrease less rapidly up to a lower bound with increasing LD in the simplest situations, than the discrete predictor based on identity by state between haplotypes (IBS hap), for which there was no lower bound. The expected LD between haplotypes at a tested position and alleles at a QTL is a quantity that increases naturally when the tested position gets closer to the QTL. This behavior was demonstrated with pig and unrelated human chromosomes. Conclusions When the density of markers is high, and therefore LD between adjacent loci can be assumed to be high, the discrete predictor IBS hap is recommended since it predicts allele identity correctly when taking LD into account. PMID:25022866

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects.

    PubMed

    Wan, X Y; Wan, J M; Jiang, L; Wang, J K; Zhai, H Q; Weng, J F; Wang, H L; Lei, C L; Wang, J L; Zhang, X; Cheng, Z J; Guo, X P

    2006-05-01

    Grain length in rice plays an important role in determining rice appearance, milling, cooking and eating quality. In this study, the genetic basis of grain length was dissected into six main-effect quantitative trait loci (QTLs) and twelve pairs of epistatic QTLs. The stability of these QTLs was evaluated in four environments using an F7 recombinant inbred line (RIL) population derived from the cross between a Japonica variety, Asominori, and an Indica variety, IR24. Moreover, chromosome segment substitution lines (CSSLs) harboring each of the six main-effect QTLs were used to evaluate gene action of QTLs across eight environments. A major QTL denoted as qGL-3a, was found to express stably not only in the isogenic background of Asominori but also in the recombinant background of Asominori and IR24 under multiple environments. The IR24 allele at qGL-3a has a positive effect on grain length. Based on the test of advanced backcross progenies, qGL-3a was dissected as a single Mendelian factor, i.e., long rice grain was controlled by a recessive gene gl-3. High-resolution genetic and physical maps were further constructed for fine mapping gl-3 by using 11 simple sequence repeat (SSR) markers designed using sequence information from seven BAC/PAC clones and a BC4F2 population consisting of 2,068 individuals. Consequently, the gl-3 gene was narrowed down to a candidate genomic region of 87.5 kb long defined by SSR markers RMw357 and RMw353 on chromosome 3, which provides a basis for map-based cloning of this gene and for marker-aided QTL pyramiding in rice quality breeding. PMID:16477428

  6. Complex microcolinearity among wheat, rice, and barley revealed by fine mapping of the genomic region harboring a major QTL for resistance to Fusarium head blight in wheat

    Microsoft Academic Search

    Sixin Liu; Xiuling Zhang; Michael O. Pumphrey; Robert W. Stack; Bikram S. Gill; James A. Anderson

    2006-01-01

    A major quantitative trait locus (QTL), Qfhs.ndsu-3BS, for resistance to Fusarium head blight (FHB) in wheat has been identified and verified by several research groups. The objectives\\u000a of this study were to construct a fine genetic map of this QTL region and to examine microcolinearity in the QTL region among\\u000a wheat, rice, and barley. Two simple sequence repeat (SSR) markers

  7. Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice.

    PubMed

    Andaya, V C; Tai, T H

    2006-08-01

    The temperate japonica rice cultivar M202 is the predominant variety grown in California due to its tolerance to low temperature stress, good grain quality and high yield. Earlier analysis of a recombinant inbred line mapping population derived from a cross between M202 and IR50, an indica cultivar that is highly sensitive to cold stress, resulted in the identification of a number of QTL conferring tolerance to cold-induced wilting and necrosis. A major QTL, qCTS12, located on the short arm of chromosome 12, contributes over 40% of the phenotypic variance. To identify the gene(s) underlying qCTS12, we have undertaken the fine mapping of this locus. Saturating the short arm of chromosome 12 with microsatellite markers revealed that qCTS12 is closest to RM7003. Using RM5746 and RM3103, which are immediately outside of RM7003, we screened 1,954 F(5)-F(10) lines to find recombinants in the qCTS12 region. Additional microsatellite markers were identified from publicly available genomic sequence and used to fine map qCTS12 to a region of approximately 87 kb located on the BAC clone OSJNBb0071I17. This region contains ten open reading frames (ORFs) consisting of five hypothetical and expressed proteins of unknown function, a transposon protein, a putative NBS-LRR disease resistance protein, two zeta class glutathione S-transferases (OsGSTZ1 and OsGSTZ2), and a DAHP synthetase. Further fine mapping with markers developed from the ORFs delimited the QTL to a region of about 55 kb. The most likely candidates for the gene(s) underlying qCTS12 are OsGSTZ1 and OsGSTZ2. PMID:16741739

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

    PubMed

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

    2010-11-01

    The identification and utilization of a high-level of host plant resistance is the most effective and economical approach 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 RNR Upland cotton line (Gossypium hirsutum L.) of the Auburn 623 RNR source. The QTL is located in a 12.9-cM interval flanked by the two SSR markers CIR069 and CIR316 on the distal segment of chromosome 11. To construct a fine map around the target region, a bulked segregation analysis was performed using two DNA pools consisting of five individuals, with each being homozygous for the two parental alleles. From a survey of 1,152 AFLP primer combinations, 9 AFLP markers closely linked to the target region were identified. By screening an additional 1,221 F(2) individuals developed from the initial mapping population, the Mi-C11 locus was delimited to a 3.6-cM interval flanked by the SSR marker CIR069 and the AFLP marker E14M27-375. These results further elucidate the genetic fine structure of the Mi-C11 locus and provide the basis for map-based isolation of the nematode resistance gene in M-120 RNR. PMID:20680610

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

    PubMed Central

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

    2014-01-01

    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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  11. QTL Fine Mapping by Measuring and Testing for Hardy-Weinberg and Linkage Disequilibrium at a Series of Linked Marker Loci in Extreme Samples of Populations

    Microsoft Academic Search

    Hong-Wen Deng; Wei-Min Chen; Robert R. Recker

    2000-01-01

    It has recently been demonstrated that fine-scale mapping of a susceptibility locus for a complex disease can be accomplished on the basis of deviations from Hardy-Weinberg (HW) equilibrium at closely linked marker loci among affected individuals. We extend this theory to fine-scale localization of a quantitative-trait locus (QTL) from extreme individuals in populations, by means of HW and linkage-disequilibrium (LD)

  12. Quantitative Trait Loci (QTL) Analysis For Rice Grain Width and Fine Mapping of an Identified QTL Allele gw-5 in a Recombination Hotspot Region on Chromosome 5

    PubMed Central

    Wan, Xiangyuan; Weng, Jianfeng; Zhai, Huqu; Wang, Jiankang; Lei, Cailin; Liu, Xiaolu; Guo, Tao; Jiang, Ling; Su, Ning; Wan, Jianmin

    2008-01-01

    Rice grain width and shape play a crucial role in determining grain quality and yield. The genetic basis of rice grain width was dissected into six additive quantitative trait loci (QTL) and 11 pairs of epistatic QTL using an F7 recombinant inbred line (RIL) population derived from a single cross between Asominori (japonica) and IR24 (indica). QTL by environment interactions were evaluated in four environments. Chromosome segment substitution lines (CSSLs) harboring the six additive effect QTL were used to evaluate gene action across eight environments. A major, stable QTL, qGW-5, consistently decreased rice grain width in both the Asominori/IR24 RIL and CSSL populations with the genetic background Asominori. By investigating the distorted segregation of phenotypic values of rice grain width and genotypes of molecular markers in BC4F2 and BC4F3 populations, qGW-5 was dissected into a single recessive gene, gw-5, which controlled both grain width and length–width ratio. gw-5 was narrowed down to a 49.7-kb genomic region with high recombination frequencies on chromosome 5 using 6781 BC4F2 individuals and 10 newly developed simple sequence repeat markers. Our results provide a basis for map-based cloning of the gw-5 gene and for marker-aided gene/QTL pyramiding in rice quality breeding. PMID:18689882

  13. A new finely mapped Oryza australiensis-derived QTL in rice confers resistance to brown planthopper.

    PubMed

    Hu, Jie; Xiao, Cong; Cheng, Ming-Xing; Gao, Guan-Jun; Zhang, Qing-Lu; He, Yu-Qing

    2015-04-25

    Brown planthopper (BPH) is the most destructive pest of rice in Asia. The BPH resistance in the introgression line IR65482-17-511-5-7 (IR65482-17) is derived from the wild rice species Oryza australiensis. An F2:3 population from a cross between Zhenshan 97 (ZS97) and IR65482-17 was used to map three quantitative trait loci (QTLs) for seedling resistance and feeding rate to BPH. The loci were distributed on chromosomes 2, 4 and 12. The QTL qBph4.2 on chromosome 4 had the largest effect, and contributed 36-44% of the phenotypic variance with a LOD score of 19-29. To validate the effect of qBph4.2, two near-isogenic lines (NILs) containing the qBph4.2 locus in the backgrounds of ZS97 and 9311 were developed by marker-assisted backcrossing (MABC). BPH bioassays showed that lines homozygous for the IR65482-17 allele (NIL+) of qBph4.2 tented to have significantly higher seedling resistance to BPH than those homozygous for the ZS97 or 9311 alleles (NIL-). Resistance was associated with a lower feeding rate by the insect. qBph4.2 was delimited to a ~300kb (0.04cM) region flanked by markers RM261 and S1, and co-segregating with XC4-27. This study will facilitate map-based cloning and marker-assisted selection of the gene, and permits further studies of gene function and resistance mechanisms in rice: BPH interaction. PMID:25682936

  14. Validation and fine mapping of a QTL for ovulation rate on swine chromosome 3

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ovulation rate (OR) is an important component of litter size. The causative mutation(s) in gene(s) underlying OR QTLs have yet to be identified in pigs. Markers within an OR QTL on SSC3 were genotyped in three white composite lines selected for 10 generations for increased OR, uterine capacity (UC)...

  15. Fine mapping of a major QTL controlling panicle number in rice

    Microsoft Academic Search

    Jinyan ZhuYong; Yong Zhou; Yanhua Liu; Zhongde Wang; Zaixiang Tang; Chuandeng Yi; Shuzhu Tang; Minghong Gu; Guohua Liang

    2011-01-01

    Rice panicle number per plant is a grain yield component that directly influences rice yield. The identification of the genes\\u000a controlling panicle number will play a vital role in high-yield rice breeding. C3074, a chromosome segment substitution line\\u000a containing an introgression segment of Nipponbare in the genetic background of Guangluai 4, had significantly fewer panicles.\\u000a Quantitative trait locus (QTL) analysis

  16. Human QTL Linkage Mapping

    PubMed Central

    Almasy, Laura; Blangero, John

    2009-01-01

    Human quantitative trait locus (QTL) linkage mapping, although based on classical statistical genetic methods that have been around for many years, has been employed for genome-wide screening for only the last 10-15 years. In this time, there have been many success stories, ranging from QTLs that have been replicated in independent studies to those for which one or more genes underlying the linkage peak have been identified to a few with specific functional variants that have been confirmed in in vitro laboratory assays. Despite these successes, there is a general perception that linkage approaches do not work for complex traits, possibly because many human QTL linkage studies have been limited in sample size and have not employed the family configurations that maximize the power to detect linkage. We predict that human QTL linkage studies will continue to be productive for the next several years, particularly in combination with RNA expression level traits that are showing evidence of regulatory QTLs of large effect sizes and in combination with high-density genome-wide SNP panels. These SNP panels are being used to identify QTLs previously localized by linkage and linkage results are being used to place informative priors on genome-wide association studies. PMID:18668207

  17. 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...

  18. FINE MAPPING OF THE QCTS12 LOCUS, A MAJOR QTL FOR SEEDLING COLD TOLERANCE IN RICE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The temperate japonica rice cultivar M-202 is the predominant variety grown in California due to its tolerance to low temperature stress, good grain quality and high yield. Earlier analysis of a recombinant inbred line mapping population derived from a cross between M-202 and IR50, an indica cultiva...

  19. Quantitative Trait Loci (QTL) Analysis For Rice Grain Width and Fine Mapping of an Identified QTL Allele gw-5 in a Recombination Hotspot Region on Chromosome 5

    Microsoft Academic Search

    Xiangyuan Wan; Jianfeng Weng; Huqu Zhai; Jiankang Wang; Cailin Lei; Xiaolu Liu; Tao Guo; Ling Jiang; Ning Su; Jianmin Wan

    2008-01-01

    Rice grain width and shape play a crucial role in determining grain quality and yield. The genetic basis of rice grain width was dissected into six additive quantitative trait loci (QTL) and 11 pairs of epistatic QTL using an F7 recombinant inbred line (RIL) population derived from a single cross between Asominori (japonica) and IR24 (indica). QTL by environment interactions

  20. Fine Mapping QTL for Drought Resistance Traits in Rice ( Oryza sativa L.) Using Bulk Segregant Analysis

    Microsoft Academic Search

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

    2011-01-01

    Drought stress is a major limitation to rice (Oryza sativa L.) yields and its stability, especially in rainfed conditions. Developing rice cultivars with inherent capacity to withstand\\u000a drought stress would improve rainfed rice production. Mapping quantitative trait loci (QTLs) linked to drought resistance\\u000a traits will help to develop rice cultivars suitable for water-limited environments through molecular marker-assisted selection\\u000a (MAS) strategy.

  1. Identification and fine-mapping of a QTL, qMrdd1, that confers recessive resistance to maize rough dwarf disease

    PubMed Central

    2013-01-01

    Background Maize rough dwarf disease (MRDD) is a devastating viral disease that results in considerable yield losses worldwide. Three major strains of virus cause MRDD, including maize rough dwarf virus in Europe, Mal de Río Cuarto virus in South America, and rice black-streaked dwarf virus in East Asia. These viral pathogens belong to the genus fijivirus in the family Reoviridae. Resistance against MRDD is a complex trait that involves a number of quantitative trait loci (QTL). The primary approach used to minimize yield losses from these viruses is to breed and deploy resistant maize hybrids. Results Of the 50 heterogeneous inbred families (HIFs), 24 showed consistent responses to MRDD across different years and locations, in which 9 were resistant and 15 were susceptible. We performed trait-marker association analysis on the 24 HIFs and found six chromosomal regions which were putatively associated with MRDD resistance. We then conducted QTL analysis and detected a major resistance QTL, qMrdd1, on chromosome 8. By applying recombinant-derived progeny testing to self-pollinated backcrossed families, we fine-mapped the qMrdd1 locus into a 1.2-Mb region flanked by markers M103-4 and M105-3. The qMrdd1 locus acted in a recessive manner to reduce the disease-severity index (DSI) by 24.2–39.3%. The genetic effect of qMrdd1 was validated using another F6 recombinant inbred line (RIL) population in which MRDD resistance was segregating and two genotypes at the qMrdd1 locus differed significantly in DSI values. Conclusions The qMrdd1 locus is a major resistance QTL, acting in a recessive manner to increase maize resistance to MRDD. We mapped qMrdd1 to a 1.2-Mb region, which will enable the introgression of qMrdd1-based resistance into elite maize hybrids and reduce MRDD-related crop losses. PMID:24079304

  2. Fine-mapping of candidate region in Amish and Ashkenazi families confirms linkage of refractive error to a QTL on 1p34-p36

    PubMed Central

    Bailey-Wilson, Joan E.; Stambolian, Dwight

    2009-01-01

    Purpose A previous genome-wide study in Orthodox Ashkenazi Jewish pedigrees showed significant linkage of ocular refraction to a Quantitative Trait Locus (QTL) on 1p34-36.1. We carried out a fine-mapping study of this region in Orthodox Ashkenazi Jewish (ASHK) and Old Order Amish (OOA) families to confirm linkage and narrow the candidate region. Methods Families were recruited from ASHK and OOA American communities. The samples included: 402 individuals in 53 OOA families; and 596 members in 68 ASHK families. Families were ascertained to contain multiple myopic individuals. Genotyping of 1,367 SNPs was carried out within a 35cM (~23.9 Mb) candidate QTL region on 1p34-36. Multipoint variance components (VC) and regression-based (REG) linkage analyses were carried out separately in OOA and ASHK groups, and in a combined analysis that included all families. Results Evidence of linkage of refractive error was found in both OOA (VC LOD=3.45, REG LOD=3.38 at ~59 cM) and ASHK families (VC LOD=3.12, REG LOD=4.263 at ~66 cM). Combined analyses showed three highly significant linkage peaks, separated by ~11cM (or 10 Mb), within the candidate region. Conclusion In a fine-mapping linkage study of OOA and ASHK families, we have confirmed linkage of refractive error to a QTL on 1p. The area of linkage has been narrowed down to a gene-rich region at 1p34.2-35.1 containing ~124 genes. PMID:19626131

  3. Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis: A Method for High-Resolution Mapping of QTL Within a Single Population

    PubMed Central

    Peleman, Johan D.; Wye, Crispin; Zethof, Jan; Sørensen, Anker P.; Verbakel, Henk; van Oeveren, Jan; Gerats, Tom; van der Voort, Jeroen Rouppe

    2005-01-01

    In the quest for fine mapping quantitative trait loci (QTL) at a subcentimorgan scale, several methods that involve the construction of inbred lines and the generation of large progenies of such inbred lines have been developed (Complex Trait Consortium 2003). Here we present an alternative method that significantly speeds up QTL fine mapping by using one segregating population. As a first step, a rough mapping analysis is performed on a small part of the population. Once the QTL have been mapped to a chromosomal interval by standard procedures, a large population of 1000 plants or more is analyzed with markers flanking the defined QTL to select QTL isogenic recombinants (QIRs). QIRs bear a recombination event in the QTL interval of interest, while other QTL have the same homozygous genotype. Only these QIRs are subsequently phenotyped to fine map the QTL. By focusing at an early stage on the informative individuals in the population only, the efforts in population genotyping and phenotyping are significantly reduced as compared to prior methods. The principles of this approach are demonstrated by fine mapping an erucic acid QTL of rapeseed at a subcentimorgan scale. PMID:16085696

  4. Fine mapping of a strong QTL of field resistance against rice blast, Pikahei-1(t), from upland rice Kahei, utilizing a novel resistance evaluation system in the greenhouse.

    PubMed

    Xu, Xin; Chen, H; Fujimura, T; Kawasaki, S

    2008-10-01

    Field resistances (FR) against rice blast are highly evaluated by breeders for their durability, in contrast to the conspicuous but often less durable true resistances. However, lack of efficient systems for evaluation of resistance has delayed their practical application. Kahei, an upland domestic cv., is known for its very high FR against rice blast. We fine-mapped its highest quantitative trait loci (QTL), qBFR4-1, using residual heterozygosity of recombinant inbred lines (RILs) and our semi-natural rice blast inoculation/evaluation system in the greenhouse, with comparable accuracy to the true resistance genes. This system enabled reproducible high-density infection, and consequently allowed quantification of the resistance level in individual plants. The target region was first narrowed down to about 1 Mb around at 32 Mb from the top of chromosome 4 in the Nipponbare genome, with the upland evaluation system assessing the F7 generation of Koshihikari (lowland, FR: very weak) x Kahei (upland, FR: very strong) RILs. Then, F9 plants (4,404)--siblings of hetero F8 plants at the region--were inoculated with rice blast in a greenhouse using the novel inoculation system, and individual resistance levels were diagnosed for fine QTL analysis and graphical genotyping. Thus, the resistance gene was fine-mapped within 300 kb at 31.2-31.5 Mb on chromosome 4, and designated Pikahei-1(t). By annotation analysis, seven resistance gene analog (RGA) ORFs of nucleotide-binding-site and leucine-rich-repeat (NBS-LRR)-type were found in the center of the region as the most likely candidate counterparts of the resistance gene. This is similar in structure to the recently reported Pik cluster region, suggesting that most of the other dominant QTLs of the FRs may have similar RGA structures. PMID:18758744

  5. Fine-mapping of qRfg2, a QTL for resistance to Gibberella stalk rot in maize.

    PubMed

    Zhang, Dongfeng; Liu, Yongjie; Guo, Yanling; Yang, Qin; Ye, Jianrong; Chen, Shaojiang; Xu, Mingliang

    2012-02-01

    Stalk rot is one of the most devastating diseases in maize worldwide. In our previous study, two QTLs, a major qRfg1 and a minor qRfg2, were identified in the resistant inbred line '1145' to confer resistance to Gibberella stalk rot. In the present study, we report on fine-mapping of the minor qRfg2 that is located on chromosome 1 and account for ~8.9% of the total phenotypic variation. A total of 22 markers were developed in the qRfg2 region to resolve recombinants. The progeny-test mapping strategy was developed to accurately determine the phenotypes of all recombinants for fine-mapping of the qRfg2 locus. This fine-mapping process was performed from BC(4)F(1) to BC(8)F(1) generations to narrow down the qRfg2 locus into ~300 kb, flanked by the markers SSRZ319 and CAPSZ459. A predicted gene in the mapped region, coding for an auxin-regulated protein, is believed to be a candidate for qRfg2. The qRfg2 locus could steadily increase the resistance percentage by ~12% across different backcross generations, suggesting its usefulness in enhancing maize resistance against Gibberella stalk rot. PMID:22048640

  6. A population of ‘TeQing’-into-‘Lemont’ chromosome segment substitution lines supports QTL discovery, fine-mapping, and determination of breeding values

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic maps and populations are important tools for gene/QTL mapping, and for functional genomics research. One of the most phenotypically characterized rice mapping populations is a set of 280 ‘Lemont’/‘TeQing’ recombinant inbred lines (LT-RILs) in which more than 250 agronomically important loci...

  7. QTL mapping in outbred populations: successes and challenges

    PubMed Central

    2013-01-01

    Quantitative trait locus (QTL) mapping in animal populations has been a successful strategy for identifying genomic regions that play a role in complex diseases and traits. When conducted in an F2 intercross or backcross population, the resulting QTL is frequently large, often encompassing 30 Mb or more and containing hundreds of genes. To narrow the locus and identify candidate genes, additional strategies are needed. Congenic strains have proven useful but work less well when there are multiple tightly linked loci, frequently resulting in loss of phenotype. As an alternative, we discuss the use of highly recombinant outbred models for directly fine-mapping QTL to only a few megabases. We discuss the use of several currently available models such as the advanced intercross (AI), heterogeneous stocks (HS), the diversity outbred (DO), and commercially available outbred stocks (CO). Once a QTL has been fine-mapped, founder sequence and expression QTL mapping can be used to identify candidate genes. In this regard, the large number of alleles found in outbred stocks can be leveraged to identify causative genes and variants. We end this review by discussing some important statistical considerations when analyzing outbred populations. Fine-resolution mapping in outbred models, coupled with full genome sequence, has already led to the identification of several underlying causative genes for many complex traits and diseases. These resources will likely lead to additional successes in the coming years. PMID:24326347

  8. QTL mapping in rice

    Microsoft Academic Search

    Susan R. McCough; Rebecca W. Doerge

    1995-01-01

    In the past 10 years, interest in applying the tools of molecular genetics to the problem of increasing world rice production has resulted in the generation of two highly saturated, molecular linkage maps of rice, and the localization of numerous genes and quantitative trait loci (QTLs). Primary studies have identified QTLs associated with disease resistance, abiotic stress tolerance and yield

  9. Fine mapping and identification of candidate rice genes associated with qSTV11(SG), a major QTL for rice stripe disease resistance.

    PubMed

    Kwon, Tackmin; Lee, Jong-Hee; Park, Soo-Kwon; Hwang, Un-Ha; Cho, Jun-Hyun; Kwak, Do-Yeon; Youn, Yeong-Nam; Yeo, Un-Sang; Song, You-Chun; Nam, Jaesung; Kang, Hang-Won; Nam, Min-Hee; Park, Dong-Soo

    2012-09-01

    Rice stripe disease, caused by rice stripe virus (RSV) is a serious constraint to rice production in subtropical regions of East Asia. We performed fine mapping of a RSV resistance QTL on chromosome 11, qSTV11 ( SG ), using near-isogenic lines (NILs, BC(6)F(4)) derived from a cross between the highly resistant variety, Shingwang, and the highly susceptible variety, Ilpum, using 11 insertion and deletion (InDel) markers. qSTV11 ( SG ) was localized to a 150-kb region between InDel 11 (17.86 Mbp) and InDel 5 (18.01 Mbp). Among the two markers in this region, InDel 7 is diagnostic of RSV resistance in 55 Korean japonica and indica rice varieties. InDel 7 could also distinguish the allele type of Nagdong, Shingwang, Mudgo, and Pe-bi-hun from Zenith harboring the Stv-b ( i ) allele. As a result, qSTV11 ( SG ) is likely to be the Stv-b ( i ) allele. There were 21 genes in the 150-kb region harboring the qSTV11 ( SG ) locus. Three of these genes, LOC_Os11g31430, LOC_Os11g31450, and LOC_Os11g31470, were exclusively expressed in the susceptible variety. These expression profiles were consistent with the quantitative nature along with incomplete dominance of RSV resistance. Sequencing of these genes showed that there were several amino acid substitutions between susceptible and resistant varieties. Putative functions of these candidate genes for qSTV11 (SG) are discussed. PMID:22751999

  10. Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice

    Microsoft Academic Search

    V. C. Andaya; T. H. Tai

    2006-01-01

    The temperate japonica rice cultivar M202 is the predominant variety grown in California due to its tolerance to low temperature stress, good grain quality and high yield. Earlier analysis of a recombinant inbred line mapping population derived from a cross between M202 and IR50, an indica cultivar that is highly sensitive to cold stress, resulted in the identification of a

  11. The power of QTL mapping with RILs.

    PubMed

    Takuno, Shohei; Terauchi, Ryohei; Innan, Hideki

    2012-01-01

    QTL (quantitative trait loci) mapping is commonly used to identify genetic regions responsible to important phenotype variation. A common strategy of QTL mapping is to use recombinant inbred lines (RILs), which are usually established by several generations of inbreeding of an F1 population (usually up to F6 or F7 populations). As this inbreeding process involves a large amount of labor, we are particularly interested in the effect of the number of inbreeding generations on the power of QTL mapping; a part of the labor could be saved if a smaller number of inbreeding provides sufficient power. By using simulations, we investigated the performance of QTL mapping with recombinant inbred lines (RILs). As expected, we found that the power of F4 population could be almost comparable to that of F6 and F7 populations. A potential problem in using F4 population is that a large proportion of RILs are heterozygotes. We here introduced a new method to partly relax this problem. The performance of this method was verified by simulations with a wide range of parameters including the size of the segregation population, recombination rate, genome size and the density of markers. We found our method works better than the commonly used standard method especially when there are a number of heterozygous markers. Our results imply that in most cases, QTL mapping does not necessarily require RILs at F6 or F7 generations; rather, F4 (or even F3) populations would be almost as useful as F6 or F7 populations. Because the cost to establish a number of RILs for many generations is enormous, this finding will cause a reduction in the cost of QTL mapping, thereby accelerating gene mapping in many species. PMID:23056339

  12. QTL MAPPING FOR BIRTH WEIGHT ON BOVINE CHROMOSOME 14

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative Trait Loci (QTL) mapping in livestock allows the identification of genes that determine the genetic variation affecting traits of economic interest. Diverse QTL for growth traits are described in literature, indicating the possibility of QTL mapping for these traits through the scan of...

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

    Microsoft Academic Search

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

    1993-01-01

    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

  14. QTL Mapping of Chlorophyll Contents in Rice

    Microsoft Academic Search

    Bo SHEN; Jie-yun ZHUANG; Ke-qin ZHANG; Wei-min DAI; Ye LU; Li-qing FU; Jia-ming DING; Kang-le ZHENG

    2007-01-01

    The objectives of this study were to investigate the genetic factors controlling the chlorophyll content of rice leaf using QTL analysis. A linkage map consisting of 207 DNA markers was constructed by using 247 recombinant inbred lines (RILs) derived from an indica-indica rice cross of Zhenshan97B×Milyang 46. In 2002 and 2003, the contents of chlorophyll a and b of the

  15. Fine mapping of a strong QTL of field resistance against rice blast, Pikahei-1 (t), from upland rice Kahei, utilizing a novel resistance evaluation system in the greenhouse

    Microsoft Academic Search

    Xin Xu; H. Chen; T. Fujimura; S. Kawasaki

    2008-01-01

    Field resistances (FR) against rice blast are highly evaluated by breeders for their durability, in contrast to the conspicuous\\u000a but often less durable true resistances. However, lack of efficient systems for evaluation of resistance has delayed their\\u000a practical application. Kahei, an upland domestic cv., is known for its very high FR against rice blast. We fine-mapped its\\u000a highest quantitative trait

  16. Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line

    Microsoft Academic Search

    Lei Zhou; Yawen Zeng; Weiwei Zheng; Bo Tang; Shuming Yang; Hongliang Zhang; Jinjie Li; Zichao Li

    2010-01-01

    Low temperature at the booting stage is a serious abiotic stress in rice, and cold tolerance is a complex trait controlled\\u000a by many quantitative trait loci (QTL). A QTL for cold tolerance at the booting stage in cold-tolerant near-isogenic rice line\\u000a ZL1929-4 was analyzed. A total of 647 simple sequence repeat (SSR) markers distributed across 12 chromosomes were used to

  17. Genome Assembly Anchored QTL Map of Bovine Chromosome 14

    PubMed Central

    Wibowo, Tito A.; Gaskins, Charles T.; Newberry, Ruth C.; Thorgaard, Gary H.; Michal, Jennifer J.; Jiang, Zhihua

    2008-01-01

    Bovine chromosome 14 (BTA14) has been widely explored for quantitative trait loci (QTL) and genes related to economically important traits in both dairy and beef cattle. We reviewed more than 40 investigations and anchored 126 QTL to the current genome assembly (Btau 4_0). Using this anchored QTL map, we observed that, in dairy cattle, the region spanning 0 – 10 Mb on BTA14 has the highest density QTL map with a total of 56 QTL, mainly for milk production traits. It is very likely that both somatic cell score (SCS) and clinical mastitis share some common QTL in two regions: 61.48 Mb - 73.84 Mb and 7.86 Mb – 39.55 Mb, respectively. As well, both ovulation rate and twinning rate might share a common QTL region from 34.16 Mb to 65.38 Mb. However, there are no common QTL locations in three pregnancy related phenotypes: non-return rate, pregnancy rate and daughter pregnancy rate. In beef cattle, the majority of QTL are located in a broad region of 15 Mb – 45 Mb on the chromosome. Functional genes, such as CRH, CYP11B1, DGAT1, FABP4 and TG, as potential candidates for some of these QTL, were also reviewed. Therefore, our review provides a standardized QTL map anchored within the current genome assembly, which would enhance the process of selecting positional and physiological candidate genes for many important traits in cattle. PMID:19043607

  18. Meta-analysis of QTL mapping experiments.

    PubMed

    Wu, Xiao-Lin; Hu, Zhi-Liang

    2012-01-01

    Meta-analysis is an important tool for integrating information from multiple quantitative trait loci (QTLs) studies. Pooling of results from several studies allows greater statistical power for QTL detection and more precise estimation of their genetic effects. Hence, a meta-analysis can yield conclusions that are stronger than those of individual studies and can give greater insight into the genetic architecture of complex traits. In this chapter, we present basic theories and methods for meta-analysis of QTL mapping experiments. The meta-analytic procedures are described in a general context. The statistical methods cover both parametric and nonparametric statistical models. Finally, we illustrate the features of these statistical methods using simulated and real datasets. PMID:22565836

  19. Educational Software for Mapping Quantitative Trait Loci (QTL)

    ERIC Educational Resources Information Center

    Helms, T. C.; Doetkott, C.

    2007-01-01

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

  20. Mapping dynamic QTL for plant height in triticale

    PubMed Central

    2014-01-01

    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

  1. Using TeQing-into-Lemont introgression lines (TILs) to dissect sheath blight resistance QTLs and fine-map a spreading culm gene

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have been using a set of TeQing-into-Lemont introgression lines to fine-map sheath blight resistance QTL. In the course of dissection a QTL region previously mapped on chromosome 9, we discovered a gene for spreading culms (or open plant-type) residing in one half of the QTL region, while the she...

  2. Epigenetic QTL Mapping in Brassica napus

    PubMed Central

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

    2011-01-01

    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

  3. Mapping Isoflavone QTL with Main, Epistatic and QTL × Environment Effects in Recombinant Inbred Lines of Soybean.

    PubMed

    Wang, Yan; Han, Yingpeng; Zhao, Xue; Li, Yongguang; Teng, Weili; Li, Dongmei; Zhan, Yong; Li, Wenbin

    2015-01-01

    Soybean (Glycine max (L.) Merr.) isoflavone is important for human health and plant defense system. To identify novel quantitative trait loci (QTL) and epistatic QTL underlying isoflavone content in soybean, F5:6, F5:7 and F5:8 populations of 130 recombinant inbred (RI) lines, derived from the cross of soybean cultivar 'Zhong Dou 27' (high isoflavone) and 'Jiu Nong 20' (low isoflavone), were analyzed with 95 new SSR markers. A new linkage map including 194 SSR markers and covering 2,312 cM with mean distance of about 12 cM between markers was constructed. Thirty four QTL for both individual and total seed isoflavone contents of soybean were identified. Six, seven, ten and eleven QTL were associated with daidzein (DZ), glycitein (GC), genistein (GT) and total isoflavone (TI), respectively. Of them 23 QTL were newly identified. The qTIF_1 between Satt423 and Satt569 shared the same marker Satt569 with qDZF_2, qGTF_1 and qTIF_2. The qGTD2_1 between Satt186 and Satt226 was detected in four environments and explained 3.41%-10.98% of the phenotypic variation. The qGTA2_1, overlapped with qGCA2_1 and detected in four environments, was close to the previously identified major QTL for GT, which were responsible for large a effects. QTL (qDZF_2, qGTF_1 and qTIF_2) between Satt144-Satt569 were either clustered or pleiotropic. The qGCM_1, qGTM_1 and qTIM_1 between Satt540-Sat_244 explained 2.02%-9.12% of the phenotypic variation over six environments. Moreover, the qGCE_1 overlapped with qGTE_1 and qTIE_1, the qTIH_2 overlapped with qGTH_1, qGCI_1 overlapped with qDZI_1, qTIL_1 overlapped with qGTL_1, and qTIO_1 overlapped with qGTO_1. In this study, some of unstable QTL were detected in different environments, which were due to weak expression of QTL, QTL by environment interaction in the opposite direction to a effects, and/or epistasis. The markers identified in multi-environments in this study could be applied in the selection of soybean cultivars for higher isoflavone content and in the map-based gene cloning. PMID:25738957

  4. Mapping Isoflavone QTL with Main, Epistatic and QTL × Environment Effects in Recombinant Inbred Lines of Soybean

    PubMed Central

    Wang, Yan; Han, Yingpeng; Zhao, Xue; Li, Yongguang; Teng, Weili; Li, Dongmei; Zhan, Yong; Li, Wenbin

    2015-01-01

    Soybean (Glycine max (L.) Merr.) isoflavone is important for human health and plant defense system. To identify novel quantitative trait loci (QTL) and epistatic QTL underlying isoflavone content in soybean, F5:6, F5:7 and F5:8 populations of 130 recombinant inbred (RI) lines, derived from the cross of soybean cultivar ‘Zhong Dou 27? (high isoflavone) and ‘Jiu Nong 20? (low isoflavone), were analyzed with 95 new SSR markers. A new linkage map including 194 SSR markers and covering 2,312 cM with mean distance of about 12 cM between markers was constructed. Thirty four QTL for both individual and total seed isoflavone contents of soybean were identified. Six, seven, ten and eleven QTL were associated with daidzein (DZ), glycitein (GC), genistein (GT) and total isoflavone (TI), respectively. Of them 23 QTL were newly identified. The qTIF_1 between Satt423 and Satt569 shared the same marker Satt569 with qDZF_2, qGTF_1 and qTIF_2. The qGTD2_1 between Satt186 and Satt226 was detected in four environments and explained 3.41%-10.98% of the phenotypic variation. The qGTA2_1, overlapped with qGCA2_1 and detected in four environments, was close to the previously identified major QTL for GT, which were responsible for large a effects. QTL (qDZF_2, qGTF_1 and qTIF_2) between Satt144-Satt569 were either clustered or pleiotropic. The qGCM_1, qGTM_1 and qTIM_1 between Satt540-Sat_244 explained 2.02%–9.12% of the phenotypic variation over six environments. Moreover, the qGCE_1 overlapped with qGTE_1 and qTIE_1, the qTIH_2 overlapped with qGTH_1, qGCI_1 overlapped with qDZI_1, qTIL_1 overlapped with qGTL_1, and qTIO_1 overlapped with qGTO_1. In this study, some of unstable QTL were detected in different environments, which were due to weak expression of QTL, QTL by environment interaction in the opposite direction to a effects, and/or epistasis. The markers identified in multi-environments in this study could be applied in the selection of soybean cultivars for higher isoflavone content and in the map-based gene cloning. PMID:25738957

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

    PubMed Central

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

    2013-01-01

    Using chromosome substitution strains (CSS), we previously identified a large quantitative trait locus (QTL) for conditioned fear (CF) on mouse chromosome 10. Here, we used an F2 cross between CSS-10 and C57BL/6J (B6) to localize that QTL to distal chromosome 10. That QTL accounted for all 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

  6. Mapping of QTL for Embryo Size in Rice

    Microsoft Academic Search

    Yanjun Dong; Eiji Tsuzuki; Hiroshi Kamiunten; Hiroyuki Terao; Dongzhi Lin

    2003-01-01

    size. Thus, an understanding the genetic basis underly- ing the inheritance of embryo size in rice has significant The development of molecular genetic maps has accelerated the implications for quality improvement. identification and mapping of genomic regions controlling quantitative trait loci (QTL) in rice (Oryza sativa L.). Minimizing embryo size in The recent advances in high-density marker linkage rice would

  7. 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

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

    2014-12-01

    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

  8. Confidence intervals in QTL mapping by bootstrapping

    Microsoft Academic Search

    Peter M. Visscher; Robin Thompson; Chris S. Haley

    1996-01-01

    The determination of empirical confidence intervals for the location of quantitative trait loci (QTLs) was investigated using simulation. Empirical confidence intervals were calculated using a bootstrap resampling method for a backcross population derived from inbred lines. Sample sizes were either 200 or 500 individuals, and the QTL explained 1, 5, or 10% of the phenotypic variance. The method worked well

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. GENE LINKAGE MAPPING OF THE PORCINE CHROMOSOME X REGION HARBOURING QTL FOR FAT DEPOSITION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The QTL for backfat thickness and intramuscular fat content on SSCX is well documented in Meishan x Western breed pedigrees. The QTL has been mapped to the chromosome region between microsatellites SW2456 and SW1943. In the French pedigree with more than 1,100 F2 animals the QTL mapped at position 7...

  11. Fine-Mapping of Quantitative Trait Loci by Identity by Descent in Outbred Populations: Application to Milk Production in Dairy Cattle

    Microsoft Academic Search

    Juliette Riquet; Wouter Coppieters; Nadine Cambisano; Juan-Jose Arranz; Paulette Berzi; Scott K. Davis; Bernard Grisart; Frederick Farnir; Latifa Karim; Myriam Mni; Patricia Simon; Jeremy F. Taylor; Pascal Vanmanshoven; Danny Wagenaar; James E. Womack; Michel Georges

    1999-01-01

    We previously mapped a quantitative trait locus (QTL) affecting milk production to bovine chromosome 14. To refine the map position of this QTL, we have increased the density of the genetic map of BTA14q11-16 by addition of nine microsatellites and three single nucleotide polymorphisms. Fine-mapping of the QTL was accomplished by a two-tiered approach. In the first phase, we identified

  12. Mapping QTL Contributing to SCMV Resistance in Tropical Maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  13. A Grid Portal Implementation for Genetic Mapping of Multiple QTL

    E-print Network

    Flener, Pierre

    A Grid Portal Implementation for Genetic Mapping of Multiple QTL Salman Toor1 , Mahen Jayawardena1 Technology, Uppsala University, Sweden (salman.toor,sverker.holmgren)@it.uu.se 2 University of Colombo School fit (the inner problem). #12;2 Salman Toor, Mahen Jayawardena, Jonas Lindemann and Sverker Holmgren

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

    PubMed

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

    2013-09-15

    A recombinant inbred line (RIL) population bred from a cross between a javanica type (cv. D50) and an indica type (cv. HB277) rice was used to map seven quantitative trait loci (QTLs) for thousand grain weight (TGW). The loci were distributed on chromosomes 2, 3, 5, 6, 8 and 10. The chromosome 3 QTL qTGW3.2 was stably expressed over two years, and contributed 9-10% of the phenotypic variance. A residual heterozygous line (RHL) was selected from the RIL population and its selfed progeny was used to fine map qTGW3.2. In this "F2" population, the QTL explained about 23% of the variance, rising to nearly 33% in the subsequent "F2:3" generation. The physical location of qTGW3.2 was confined to a ~556 kb region flanked by the microsatellite loci RM16162 and RM16194. The region also contains other factors influencing certain yield-related traits, although it is also possible that qTGW3.2 affects these in a pleiotropic fashion. PMID:23769924

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

    PubMed Central

    2014-01-01

    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

  16. 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...

  17. Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci.

    PubMed Central

    Meuwissen, T H; Goddard, M E

    2000-01-01

    A multimarker linkage disequilibrium mapping method was developed for the fine mapping of quantitative trait loci (QTL) using a dense marker map. The method compares the expected covariances between haplotype effects given a postulated QTL position to the covariances that are found in the data. The expected covariances between the haplotype effects are proportional to the probability that the QTL position is identical by descent (IBD) given the marker haplotype information, which is calculated using the genedropping method. Simulation results showed that a QTL was correctly positioned within a region of 3, 1.5, or 0.75 cM in 70, 62, and 68%, respectively, of the replicates using markers spaced at intervals of 1, 0.5, and 0.25 cM, respectively. These results were rather insensitive to the number of generations since the QTL occurred and to the effective population size, except that 10 generations yielded rather poor estimates of the QTL position. The position estimates of this multimarker disequilibrium mapping method were more accurate than those from a single marker transmission disequilibrium test. A general approach for identifying QTL is suggested, where several stages of disequilibrium mapping are used with increasingly dense marker spacing. PMID:10790414

  18. A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana

    PubMed Central

    Kover, Paula X.; Valdar, William; Trakalo, Joseph; Scarcelli, Nora; Ehrenreich, Ian M.; Purugganan, Michael D.; Durrant, Caroline; Mott, Richard

    2009-01-01

    Identifying natural allelic variation that underlies quantitative trait variation remains a fundamental problem in genetics. Most studies have employed either simple synthetic populations with restricted allelic variation or performed association mapping on a sample of naturally occurring haplotypes. Both of these approaches have some limitations, therefore alternative resources for the genetic dissection of complex traits continue to be sought. Here we describe one such alternative, the Multiparent Advanced Generation Inter-Cross (MAGIC). This approach is expected to improve the precision with which QTL can be mapped, improving the outlook for QTL cloning. Here, we present the first panel of MAGIC lines developed: a set of 527 recombinant inbred lines (RILs) descended from a heterogeneous stock of 19 intermated accessions of the plant Arabidopsis thaliana. These lines and the 19 founders were genotyped with 1,260 single nucleotide polymorphisms and phenotyped for development-related traits. Analytical methods were developed to fine-map quantitative trait loci (QTL) in the MAGIC lines by reconstructing the genome of each line as a mosaic of the founders. We show by simulation that QTL explaining 10% of the phenotypic variance will be detected in most situations with an average mapping error of about 300 kb, and that if the number of lines were doubled the mapping error would be under 200 kb. We also show how the power to detect a QTL and the mapping accuracy vary, depending on QTL location. We demonstrate the utility of this new mapping population by mapping several known QTL with high precision and by finding novel QTL for germination data and bolting time. Our results provide strong support for similar ongoing efforts to produce MAGIC lines in other organisms. PMID:19593375

  19. QTL mapping in outbred half-sib families using Bayesian model selection

    PubMed Central

    Fang, M; Liu, J; Sun, D; Zhang, Y; Zhang, Q; Zhang, Y; Zhang, S

    2011-01-01

    In this article, we propose a model selection method, the Bayesian composite model space approach, to map quantitative trait loci (QTL) in a half-sib population for continuous and binary traits. In our method, the identity-by-descent-based variance component model is used. To demonstrate the performance of this model, the method was applied to map QTL underlying production traits on BTA6 in a Chinese half-sib dairy cattle population. A total of four QTLs were detected, whereas only one QTL was identified using the traditional least square (LS) method. We also conducted two simulation experiments to validate the efficiency of our method. The results suggest that the proposed method based on a multiple-QTL model is efficient in mapping multiple QTL for an outbred half-sib population and is more powerful than the LS method based on a single-QTL model. PMID:21487433

  20. Linkage mapping and QTL analysis of agronomic traits in tetraploid potato (Solanum tuberosum subsp. tuberosum)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potato (Solanum tuberosum L) is one of the world’s most important food crops. Using a tetraploid population, we developed a linkage map using AFLP and SSR markers, and searched for QTL via interval mapping and single-marker ANOVA. QTL were detected for flower color, foliage maturity, tuber skin te...

  1. Fine Mapping of Gene Regions Regulating Neurodegeneration

    PubMed Central

    Swanberg, Maria; Diez, Margarita; Lidman, Olle; Piehl, Fredrik

    2009-01-01

    Background Damage to nerve cells and axons leading to neurodegeneration is a characteristic feature of many neurological diseases. The degree of genetic influence on susceptibility to axotomy-induced neuronal death has so far been unknown. We have examined two gene regions, Vra1 and Vra2, previously linked to nerve cell loss after ventral root avulsion in a rat F2 intercross between the DA and PVG inbred rat strains. Methodology/Principal Findings In this study, we use two generations (G8 and G10 cohorts) of an advanced intercross line between DA and PVGav1 to reproduce linkage to Vra1 and to fine-map this region. By isolating the effect from Vra1 in congenic strains, we demonstrate that Vra1 significantly regulates the loss of motoneurons after avulsion. The regulatory effect mediated by Vra1 thus resides in a congenic fragment of 9 megabases. Furthermore, we have used the advanced intercross lines to give more support to Vra2, originally detected as a suggestive QTL. Conclusions/Significance The results demonstrated here show that naturally occurring allelic variations affect susceptibility to axotomy-induced nerve cell death. Vra1 and Vra2 represent the first quantitative trait loci regulating this phenotype that are characterized and fine mapped in an advanced intercross line. In addition, congenic strains provide experimental evidence for the Vra1 effect on the extent of injury-induced neurodegeneration. Identification of the underlying genetic variations will increase our understanding of the regulation and mechanisms of neurodegeneration. PMID:19526058

  2. Mapping QTL Associated with Photoperiod Sensitivity and Assessing the Importance of QTL×Environment Interaction for Flowering Time in Maize

    PubMed Central

    Wang, Cuiling; Chen, Yanhui; Ku, Lixia; Wang, Tiegu; Sun, Zhaohui; Cheng, Fangfang; Wu, Liancheng

    2010-01-01

    Background An understanding of the genetic determinism of photoperiod response of flowering is a prerequisite for the successful exchange of germplasm across different latitudes. In order to contribute to resolve the genetic basis of photoperiod sensitivity in maize, a set of 201 recombinant inbred lines (RIL), derived from a temperate and tropical inbred line cross were evaluated in 5 field trials spread in short- and long-day environments. Methodology/Principal Findings Firstly, QTL analyses for flowering time and photoperiod sensitivity in maize were conducted in individual photoperiod environments separately, and then, the total genetic effect was partitioned into additive effect (A) and additive-by-environment interaction effect (AE) by using a mixed-model-based composite interval mapping (MCIM) method. Conclusions/Significance Seven putative QTL were found associated with DPS thermal time based on the data estimated in individual environments. Nine putative QTL were found associated with DPS thermal time across environments and six of them showed significant QTL×enviroment (QE) interactions. Three QTL for photoperiod sensitivity were identified on chromosome 4, 9 and 10, which had the similar position to QTL for DPS thermal time in the two long-day environment. The major photoperiod sensitive loci qDPS10 responded to both short and long-day photoperiod environments and had opposite effects in different photoperiod environment. The QTL qDPS3, which had the greatest additive effect exclusively in the short-day environment, were photoperiod independent and should be classified in autonomous promotion pathway. PMID:21124912

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

    PubMed Central

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

    2015-01-01

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

  4. Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4+ concentrations in hydroponic conditions

    PubMed Central

    Tamura, Wataru; Ebitani, Takeshi; Yano, Masahiro; Sato, Tadashi; Yamaya, Tomoyuki

    2010-01-01

    Root system development is an important target for improving yield in cereal crops. Active root systems that can take up nutrients more efficiently are essential for enhancing grain yield. In this study, we attempted to identify quantitative trait loci (QTL) involved in root system development by measuring root length of rice seedlings grown in hydroponic culture. Reliable growth conditions for estimating the root length were first established to renew nutrient solutions daily and supply NH4+ as a single nitrogen source. Thirty-eight chromosome segment substitution lines derived from a cross between ‘Koshihikari’, a japonica variety, and ‘Kasalath’, an indica variety, were used to detect QTL for seminal root length of seedlings grown in 5 or 500 ?M NH4+. Eight chromosomal regions were found to be involved in root elongation. Among them, the most effective QTL was detected on a ‘Kasalath’ segment of SL-218, which was localized to the long-arm of chromosome 6. The ‘Kasalath’ allele at this QTL, qRL6.1, greatly promoted root elongation under all NH4+ concentrations tested. The genetic effect of this QTL was confirmed by analysis of the near-isogenic line (NIL) qRL6.1. The seminal root length of the NIL was 13.5–21.1% longer than that of ‘Koshihikari’ under different NH4+ concentrations. Toward our goal of applying qRL6.1 in a molecular breeding program to enhance rice yield, a candidate genomic region of qRL6.1 was delimited within a 337 kb region in the ‘Nipponbare’ genome by means of progeny testing of F2 plants/F3 lines derived from a cross between SL-218 and ‘Koshihikari’. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1328-3) contains supplementary material, which is available to authorized users. PMID:20390245

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

    PubMed Central

    2014-01-01

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

  6. Fine-mapping of qRL6.1 , a major QTL for root length of rice seedlings grown under a wide range of NH 4 + concentrations in hydroponic conditions

    Microsoft Academic Search

    Mitsuhiro Obara; Wataru Tamura; Takeshi Ebitani; Masahiro Yano; Tadashi Sato; Tomoyuki Yamaya

    2010-01-01

    Root system development is an important target for improving yield in cereal crops. Active root systems that can take up nutrients\\u000a more efficiently are essential for enhancing grain yield. In this study, we attempted to identify quantitative trait loci\\u000a (QTL) involved in root system development by measuring root length of rice seedlings grown in hydroponic culture. Reliable\\u000a growth conditions for

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

    PubMed Central

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

    2014-01-01

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

  8. Joint Analysis of Near Isogenic and Recombinant Inbred Line Populations Yields Precise Positional Estimates for QTL

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Near isogenic lines (NILs) are typically constructed to fine-map quantitative trait loci (QTL). The data generated for the initial QTL mapping are usually ignored for fine-mapping purposes. However, combining already-available data from initial recombinant inbred line (RIL) studies with new data fro...

  9. QTL Mapping of Flowering and Fruiting Traits in Olive

    PubMed Central

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

    2013-01-01

    One of the challenge fruit growers are facing is to balance between tree production and vegetative growth from year to year. To investigate the existence of genetic determinism for reproductive behaviour in olive tree, we studied an olive segregating population derived from a cross between ‘Olivière’ and ‘Arbequina’ cultivars. Our strategy was based on (i) an annual assessment of individual trees yield, and (ii) a decomposition of adult growth units at the crown periphery into quantitative variables related to both flowering and fruiting process in relation to their growth and branching. Genetic models, including the year, genotype effects and their interactions, were built with variance function and correlation structure of residuals when necessary. Among the progeny, trees were either ‘ON’ or ‘OFF’ for a given year and patterns of regular vs. irregular bearing were revealed. Genotype effect was significant on yield but not for flowering traits at growth unit (GU) scale, whereas the interaction between genotype and year was significant for both traits. A strong genetic effect was found for all fruiting traits without interaction with the year. Based on the new constructed genetic map, QTLs with small effects were detected, revealing multigenic control of the studied traits. Many were associated to alleles from ‘Arbequina’. Genetic correlations were found between Yield and Fruit set at GU scale suggesting a common genetic control, even though QTL co-localisations were in spe`cific years only. Most QTL were associated to flowering traits in specific years, even though reproductive traits at GU scale did not capture the bearing status of the trees in a given year. Results were also interpreted with respect to ontogenetic changes of growth and branching, and an alternative sampling strategy was proposed for capturing tree fruiting behaviour. Regular bearing progenies were identified and could constitute innovative material for selection programs. PMID:23690957

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

    PubMed

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

    2014-12-01

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

  11. A genetical genomics approach to genome scans increases power for QTL mapping.

    PubMed

    Sun, Guoying; Schliekelman, Paul

    2011-03-01

    We describe a method for integrating gene expression information into genome scans and show that this can substantially increase the statistical power of QTL mapping. The method has three stages. First, standard clustering methods identify small (size 5-20) groups of genes with similar expression patterns. Second, each gene group is tested for a causative genetic locus shared with the clinical trait of interest. This is done using an EM algorithm approach that treats genotype at the putative causative locus as an unobserved variable and combines expression information from all of the genes in the group to infer genotype information at the locus. Finally, expression QTL (eQTL) are mapped for each gene group that shares a causative locus with the clinical trait. Such eQTL are candidates for the causative locus. Simulation results show that this method has far superior power to standard QTL mapping techniques in many circumstances. We applied this method to existing data on mouse obesity. Our method identified 27 putative body weight QTL, whereas standard QTL mapping produced only one. Furthermore, most gene groups with body weight QTL included cis genes, so candidate genes could be immediately identified. Eleven body weight QTL produced 16 candidate genes that have been previously associated with body weight or body weight-related traits, thus validating our method. In addition, 15 of the 16 other loci produced 32 candidate genes that have not been associated with body weight. Thus, this method shows great promise for finding new causative loci for complex traits. PMID:21196521

  12. INVESTIGATION Coding Gene SNP Mapping Reveals QTL Linked to

    E-print Network

    Bernatchez, Louis

    Charr (Salvelinus fontinalis) Christopher Sauvage,*,,1,2 Marie Vagner,,§,1 Nicolas Derôme,* Céline Audet QTL for 27 phenotypes related to growth and stress responses in brook charr (Salvelinus fontinalis QTL detection single-nucleotide polymorphism growth stress response Salvelinus fontinalis Quantitative

  13. Substitution mapping of Pup1 : a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil

    Microsoft Academic Search

    M. Wissuwa; J. Wegner; N. Ae; M. Yano

    2002-01-01

    A major QTL for P uptake had previously been mapped to a 13-cM marker interval on the long arm of chromosome 12. To map that major QTL with higher precision and certainty, a secondary mapping population was developed by backcrossing a near-isogenic line containing the QTL from the donor parent to the recurrent parent of low P uptake. Two different

  14. The comparative analysis based on maize integrated QTL map and meta-analysis of plant height QTLs

    Microsoft Academic Search

    Yi Wang; Ji Yao; Zhengfeng Zhang; Yonglian Zheng

    2006-01-01

    1201 published maize QTLs conferring for 68 traits were collected and imported into local C Map software to construct an integrated\\u000a QTL map, which can be used for marker-mining, QTL localization, gene cloning and marker-assisted selection. The maize integrated\\u000a QTL map showed that maize QTLs for various traits usually clustered in all chromosomes. 22 plant height QTLs of maize were

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2014-09-01

    Local adaptation, defined as higher fitness of local vs. nonlocal genotypes, is commonly identified in reciprocal transplant experiments. Reciprocally adapted populations display fitness trade-offs across environments, but little is known about the traits and genes underlying fitness trade-offs in reciprocally adapted populations. We investigated the genetic basis and adaptive significance of freezing tolerance using locally adapted populations of Arabidopsis thaliana from Italy and Sweden. Previous reciprocal transplant studies of these populations indicated that subfreezing temperature is a major selective agent in Sweden. We used quantitative trait locus (QTL) mapping to identify the contribution of freezing tolerance to previously demonstrated local adaptation and genetic trade-offs. First, we compared the genomic locations of freezing tolerance QTL to those for previously published QTL for survival in Sweden, and overall fitness in the field. Then, we estimated the contributions to survival and fitness across both field sites of genotypes at locally adaptive freezing tolerance QTL. In growth chamber studies, we found seven QTL for freezing tolerance, and the Swedish genotype increased freezing tolerance for five of these QTL. Three of these colocalized with locally adaptive survival QTL in Sweden and with trade-off QTL for overall fitness. Two freezing tolerance QTL contribute to genetic trade-offs across environments for both survival and overall fitness. A major regulator of freezing tolerance, CBF2, is implicated as a candidate gene for one of the trade-off freezing tolerance QTL. Our study provides some of the first evidence of a trait and gene that mediate a fitness trade-off in nature. PMID:25039860

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

    PubMed Central

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

    2013-01-01

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

  18. Dynamic QTL Analysis and Candidate Gene Mapping for Waterlogging Tolerance at Maize Seedling Stage

    PubMed Central

    Osman, Khalid A.; Tang, Bin; Wang, Yaping; Chen, Juanhua; Yu, Feng; Li, Liu; Han, Xuesong; Zhang, Zuxin; Yan, Jianbin; Zheng, Yonglian; Yue, Bing; Qiu, Fazhan

    2013-01-01

    Soil waterlogging is one of the major abiotic stresses adversely affecting maize growth and yield. To identify dynamic expression of genes or quantitative trait loci (QTL), QTL associated with plant height, root length, root dry weight, shoot dry weight and total dry weight were identified via conditional analysis in a mixed linear model and inclusive composite interval mapping method at three respective periods under waterlogging and control conditions. A total of 13, 19 and 23 QTL were detected at stages 3D|0D (the period during 0–3 d of waterlogging), 6D|3D and 9D|6D, respectively. The effects of each QTL were moderate and distributed over nine chromosomes, singly explaining 4.14–18.88% of the phenotypic variation. Six QTL (ph6-1, rl1-2, sdw4-1, sdw7-1, tdw4-1 and tdw7-1) were identified at two consistent stages of seedling development, which could reflect a continuous expression of genes; the remaining QTL were detected at only one stage. Thus, expression of most QTL was influenced by the developmental status. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags markers and microRNAs were conducted. Seven candidate genes were observed to co-localize with the identified QTL on chromosomes 1, 4, 6, 7 and 9, and may be important candidate genes for waterlogging tolerance. These results are a good starting point for understanding the genetic basis for selectively expressing of QTL in different stress periods and the common genetic control mechanism of the co-localized traits. PMID:24244474

  19. QTLs mapping for fruit size and shape in chromosomes 2 and 4 in pepper and a comparison of the pepper QTL map with that of tomato

    Microsoft Academic Search

    S. Zygier; A. B. Chaim; A. Efrati; G. Kaluzky; Y. Borovsky; I. Paran

    2005-01-01

    Quantitative trait locus (QTL) mapping for fruit weight and shape in pepper (Capsicum spp.) was performed using C. chinense and C. frutescens introgression lines of chromosomes 2 and 4. In chromosome 2, a single major fruit-weight QTL, fw2.1, was detected in both populations that explained 62% of the trait variation. This QTL, as well as a fruit-shape QTL, fs2.1, which had

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

    PubMed

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

    2011-01-01

    Tef is a cereal crop of cultural and economic importance in Ethiopia. It is grown primarily for its grain though it is also an important source of fodder. Tef suffers from lodging that reduces both grain yield and quality. As a first step toward executing a marker-assisted breeding program for lodging resistance and grain yield improvement, a linkage map was constructed using 151 F(9) recombinant inbred lines obtained by single-seed-descent from a cross between Eragrostis tef and its wild relative Eragrostis pilosa. The map was primarily based on microsatellite (SSR) markers that were developed from SSR-enriched genomic libraries. The map consisted of 30 linkage groups and spanned a total length of 1,277.4 cM (78.7% of the genome) with an average distance of 5.7 cM between markers. This is the most saturated map for tef to date, and for the first time, all of the markers are PCR-based. Using agronomic data from 11 environments and marker data, it was possible to map quantitative trait loci (QTL) controlling lodging, grain yield and 15 other related traits. The positive effects of the QTL identified from the wild parent were mainly for earliness, reduced culm length and lodging resistance. In this population, it is now possible to combine lodging resistance and grain yield using a marker-assisted selection program targeting the QTL identified for both traits. The newly developed SSR markers will play a key role in germplasm organization, fingerprinting and monitoring the success of the hybridization process in intra-specific crosses lacking distinctive morphological markers. PMID:20706706

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

    PubMed

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

    2009-01-01

    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

  2. Quantitative Trait Locus (QTL) Mapping Reveals a Role for Unstudied Genes in Aspergillus Virulence

    PubMed Central

    Christians, Julian K.; Cheema, Manjinder S.; Vergara, Ismael A.; Watt, Cortney A.; Pinto, Linda J.; Chen, Nansheng; Moore, Margo M.

    2011-01-01

    Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL) affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91). We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP) spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ?527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7–24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as “hypothetical”. This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation. PMID:21559404

  3. Fine mapping implicates two immunity genes in larval resistance to the honey bee brood fungal disease, Chalkbrood

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chalkbrood infection of honey bee (Apis mellifera) brood by the fungus Ascosphaera apis results in fatal encapsulation of susceptible larvae with a mycelial coat. Recent QTL analysis indicates that some level of physiological resistance exists in individual larvae. We performed a fine mapping anal...

  4. Fine mapping of the region on wheat chromosome 7D controlling grain weight

    Microsoft Academic Search

    Marion S. Röder; Xiu-Qiang Huang; Andreas Börner

    2008-01-01

    We report the fine mapping of the previously described quantitative trait loci (QTL) for grain weight QTgw.ipk-7D associated with microsatellite marker Xgwm1002-7D by using introgression lines (ILs) carrying introgressions of the synthetic wheat W-7984 in the genetic background of the\\u000a German winter wheat variety ‘Prinz’. The BC4F3 ILs had a 10% increased thousand grain weight compared to the control group

  5. Using a Linkage Mapping Approach to Identify QTL for Day-Neutrality in the Octoploid Strawberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A linkage mapping approach was used to identify quantitative trait loci (QTL) associated with day-neutrality in the commercial strawberry, Fragaria ×ananassa (Duch ex Rozier). Amplified Fragment Length Polymorphic (AFLP) markers were used to build a genetic map with a population of 127 lines develo...

  6. [Comparative QTL mapping of resistance to sugarcane mosaic virus in maize based on bioinformatics].

    PubMed

    Lv, Xiang-Ling; Li, Xin-Hai; Xie, Chuan-Xiao; Hao, Zhuan-Fang; Ji, Hai-Lian; Shi, Li-Yu; Zhang, Shi-Huang

    2008-01-01

    The development of genomics and bioinformatics offers new tools for comparative gene mapping. In this paper, an integrated QTL map for Sugarcane mosaic virus (SCMV) resistance in maize was constructed by compiling a total of 81 QTL loci available with the Genetic Map IBM2 2005 Neighbors as reference. These 81 QTL loci were scattered on 7 chromosomes of maize, and most of them was clustered on chromosome 3 and 6. By using meta- analysis method, we identified one and two "consensus QTLs" on chromosomes 3 and 6, respectively. These three QTLs cover the genetic distances of 6.44 cM, 6.16 cM and 27.48 cM on the genetic map IBM2 2005 Neighbors, respectively. Four positional candidate resistant genes were identified within the "consensus QTL" on chromosome 3 via comparative genomics strategy. These results suggested that application of the combined meta-analysis within a species with sequence homologous comparison in a related model plant is an efficient approach to identify the major QTL and its candidate gene(s) for the target traits. The results of this study provided useful information for identifying and cloning of the major gene(s) conferring resistance to SCMV in maize. PMID:18244910

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

    PubMed

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

    2010-01-01

    An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ? 3), 15 significant (LOD ? 2), and 11 suggestive QTL (1.7 ? LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21. PMID:20846385

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

    PubMed Central

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

    2013-01-01

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

  9. 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...

  10. Mapping QTL main and interaction influences on milling quality in elite U.S. rice germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits in recombinant inbred line...

  11. Progress in mapping QTL for Sclerotinia stalk rot tolerance in a sunflower recombinant inbred population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The stalk rot caused by Sclerotinia sclerotiorum (Lib.) de Bary is a serious disease of sunflower (Helianthus annuus L.), and mapping quantitative trait loci (QTL) for resistance to Sclerotinia should facilitate the development of marker-assisted selection strategies for enhancing resistance. In thi...

  12. Mapping of QTL for Resistance against the Crucifer Specialist Herbivore Pieris brassicae in a New

    E-print Network

    Boyer, Edmond

    Mapping of QTL for Resistance against the Crucifer Specialist Herbivore Pieris brassicae in a New crucifer-specialist insect herbivores. Methodology/Principal Findings. We analyzed natural variation for resistance against two crucifer specialist lepidopteran herbivores, Pieris brassicae and Plutella xylostella

  13. Use of hidden Markov models for QTL mapping Karl W Broman

    E-print Network

    Broman, Karl W.

    Use of hidden Markov models for QTL mapping Karl W Broman Department of Biostatistics, Johns of algorithms developed for hidden Markov models (HMMs) to perform the tasks mentioned above and thus deal: Illustration of a hidden Markov model. G's indicate underlying genotypes; O's indicate observed marker

  14. Detection and mapping of QTL for earliness components in a bread wheat recombinant inbred lines population

    Microsoft Academic Search

    E. Hanocq; M. Niarquin; E. Heumez; M. Rousset; J. Le Gouis

    2004-01-01

    Earliness, an adaptative trait and factor of variation for agronomic characters, is a major trait in plant breeding. Its constituent traits, photoperiod sensitivity (PS), vernalization requirement (VR) and intrinsic earliness (IE), are largely under independent genetic controls. Mapping of major genes and quantitative trait loci (QTL) controlling these components is in progress. Most of the studies focusing on earliness considered

  15. Application of the BovineSNP50 assay for QTL mapping and prediction of genetic merit in Holstein cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The previous fifteen years have produced numerous QTL mapping experiments aimed at the identification of causal or linked polymorphisms for use in marker assisted selection programs to increase the rate of genetic gain in livestock species. To date, very few causal mutations for QTL have been ident...

  16. A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments

    PubMed Central

    2014-01-01

    Background Common wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat varieties that maintain yield (YD) under moderate or even intense nitrogen (N) deficiency can adapt to low input management systems. A detailed genetic map is necessary for both wheat molecular breeding and genomics research. In this study, an F6:7 recombinant inbred line population comprising 188 lines was used to construct a novel genetic map and subsequently to detect quantitative trait loci (QTL) for YD and response to N stress. Results A genetic map consisting of 591 loci distributed across 21 wheat chromosomes was constructed. The map spanned 3930.7 cM, with one marker per 6.7 cM on average. Genomic simple sequence repeat (g-SSR), expressed sequence tag-derived microsatellite (e-SSR), diversity arrays technology (DArT), sequence-tagged sites (STS), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeat (ISSR) molecular markers were included in the map. The linear relationships between loci found in the present map and in previously compiled physical maps were presented, which were generally in accordance. Information on the genetic and physical positions and allele sizes (when possible) of 17 DArT, 50 e-SSR, 44 SRAP, five ISSR, and two morphological markers is reported here for the first time. Seven segregation distortion regions (SDR) were identified on chromosomes 1B, 3BL, 4AL, 6AS, 6AL, 6BL, and 7B. A total of 22 and 12 QTLs for YD and yield difference between the value (YDDV) under HN and the value under LN were identified, respectively. Of these, QYd-4B-2 and QYddv-4B, two major stable QTL, shared support interval with alleles from KN9204 increasing YD in LN and decreasing YDDV. We probe into the use of these QTLs in wheat breeding programs. Moreover, factors affecting the SDR and total map length are discussed in depth. Conclusions This novel map may facilitate the use of novel markers in wheat molecular breeding programs and genomics research. Moreover, QTLs for YD and YDDV provide useful markers for wheat molecular breeding programs designed to increase yield potential under N stress. PMID:24885313

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2011-02-01

    Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related traits in recombinant inbred lines (RILs) derived from crosses of common parent Cypress, a high-HR US japonica cultivar, with RT0034, a low-HR indica line (129 RILs) and LaGrue, a low-HR japonica cultivar (298 RILs), grown in two US locations in 2005-2007. Early heading increased HR in the Louisiana (LA) but not the Arkansas (AR) location. Fitting QTL-mapping models to separate QTL main and QTL × environment interaction (QEI) effects and identify epistatic interactions revealed six main-effect HR QTLs in the two crosses, at four of which Cypress contributed the increasing allele. Multi-QTL models accounted for 0.36 of genetic and 0.21 of genetic × environment interaction of HR in MY1, and corresponding proportions of 0.25 and 0.37 in MY2. The greater HR advantage of Cypress in LA than in AR corresponded to a genomewide pattern of opposition of HR-increasing QTL effects by AR-specific effects, suggesting a selection strategy for improving this cultivar for AR. Treating year-location combinations as independent environments resulted in underestimation of QEI effects, evidently owing to lower variation among years within location than between location. Identification of robust HR QTLs in elite long-grain germplasm is suggested to require more detailed attention to the interaction of plant and grain development parameters with environmental conditions than has been given to date. PMID:20857082

  19. QTL mapping of yield and yield components for elite hybrid derived-RILs in upland cotton.

    PubMed

    Wang, Baohua; Guo, Wangzhen; Zhu, Xiefei; Wu, Yaoting; Huang, Naitai; Zhang, Tianzhen

    2007-01-01

    A population of 180 recombinant inbred lines (RILs) was developed by single seed descended from the cross of high yield Upland cotton (Gossypium hirsutum L.) varieties Zhongmiansuo12 (ZMS12) and 8891, the two parents of Xiangzamian2 (XZM2). A genetic linkage map consisting of 132 loci and covering 865.20 cM was constructed using the RIL population chiefly with SSR markers. Yield and yield components were investigated for RILs in three environments in China. The purpose of the present research was to analyze the relationship between yield and its components and to map QTL for yield and yield components in cotton. QTL were tagged with data sets from single environment (separate analysis) and a set of data from means of the three environments (joint analysis). A total of 34 QTL for yield and yield components were independently detected in three environments, whereas fifteen QTL were found in joint analysis. Notably, a stable lint percentage QTL qLP-A10-1 was detected both in joint analysis and in two environments of separate analysis, which might be of special value for marker-assisted selection. The QTL detected in the present study provide new information on improving yield and yield components. Results of path analysis showed that bolls/plant had the largest contribution to lint yield, which is consistent with the mid-parent heterosis value in F(1). Accordingly, in cotton breeding, bolls/plant can be considered first and other yield components measured as a whole to implement variety enhancement and hybrid selection of cotton. PMID:17469776

  20. Interval-specific congenic strains (ISCS): an experimental design for mapping a QTL into a 1-centimorgan interval.

    PubMed

    Darvasi, A

    1997-03-01

    A general experimental design that allows mapping of a quantitative trait locus (QTL) into a 1-cM interval is presented. The design consists of a series of strains, termed "interval-specific congenic strains (ISCS)". Each ISCS is recombinant at a specific 1-cM sub-interval out of an ordered set of sub-intervals, which together comprise a wider interval, to which a QTL was previously mapped. It is shown that a specific and previously detected QTL of moderate or even small effect can be accurately mapped into a 1-cM interval in a program involving a total of no more than 1000 individuals. Consequently, ISCS can serve as the ultimate genetic mapping procedure before the application of physical mapping tools for positional cloning of a QTL. PMID:9069114

  1. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.

    PubMed

    Yu, Huihui; Xie, Weibo; Wang, Jia; Xing, Yongzhong; Xu, Caiguo; Li, Xianghua; Xiao, Jinghua; Zhang, Qifa

    2011-01-01

    Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL) analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs), thus are mostly of low density and not able to provide precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, we constructed an ultra-high density genetic map based on high quality single nucleotide polymorphisms (SNPs) from low-coverage sequences of a recombinant inbred line (RIL) population of rice, generated using new sequencing technology. The quality of the map was assessed by validating the positions of several cloned genes including GS3 and GW5/qSW5, two major QTLs for grain length and grain width respectively, and OsC1, a qualitative trait locus for pigmentation. In all the cases the loci could be precisely resolved to the bins where the genes are located, indicating high quality and accuracy of the map. The SNP map was used to perform QTL analysis for yield and three yield-component traits, number of tillers per plant, number of grains per panicle and grain weight, using data from field trials conducted over years, in comparison to QTL mapping based on RFLPs/SSRs. The SNP map detected more QTLs especially for grain weight, with precise map locations, demonstrating advantages in detecting power and resolution relative to the RFLP/SSR map. Thus this study provided an example for ultra-high density map construction using sequencing technology. Moreover, the results obtained are helpful for understanding the genetic bases of the yield traits and for fine mapping and cloning of QTLs. PMID:21390234

  2. Advanced Intercross Lines, an Experimental Population for Fine Genetic Mapping

    Microsoft Academic Search

    A. Darvasi; M. Soller

    1995-01-01

    An advanced intercrossed line (AIL) is an experimental population that can provide more accurate estimates of quantitative trait loci (QTL) map location than conventional mapping populations. An AIL is produced by randomly and sequentially intercrossing a population that initially originated from a cross between two inbred lines or some variant thereof. This provides increasing probability of recombination between any two

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

    PubMed Central

    Courtney, Sean M.

    2012-01-01

    There are large interindividual differences in exercise capacity. It is well established that there is a genetic basis for these differences. However, the genetic factors underlying this variation are undefined. Therefore, the purpose of this study was to identify novel putative quantitative trait loci (QTL) for exercise capacity by measuring exercise capacity in inbred mice and performing genome-wide association mapping. Exercise capacity, defined as run time and work, was assessed in male mice (n = 6) from 34 strains of classical and wild-derived inbred mice performing a graded treadmill test. Genome-wide association mapping was performed with an efficient mixed-model association (EMMA) algorithm to identify QTL. Exercise capacity was significantly different across strains. Run time varied by 2.7-fold between the highest running strain (C58/J) and the lowest running strain (A/J). These same strains showed a 16.5-fold difference in work. Significant associations were identified for exercise time on chromosomes 1, 2, 7, 11, and 13. The QTL interval on chromosome 2 (?168 Mb) contains one gene, Nfatc2, and overlaps with a suggestive QTL for training responsiveness in humans. These results provide phenotype data on the widest range of inbred strains tested thus far and indicate that genetic background significantly influences exercise capacity. Furthermore, the novel QTLs identified in the current study provide new targets for investigating the underlying mechanisms for variation in exercise capacity. PMID:22911454

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

    PubMed Central

    2012-01-01

    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

  5. High-Density Genetic Linkage Map Construction and QTL Mapping of Grain Shape and Size in the Wheat Population Yanda1817 × Beinong6.

    PubMed

    Wu, Qiu-Hong; Chen, Yong-Xing; Zhou, Sheng-Hui; Fu, Lin; Chen, Jiao-Jiao; Xiao, Yao; Zhang, Dong; Ouyang, Shu-Hong; Zhao, Xiao-Jie; Cui, Yu; Zhang, De-Yun; Liang, Yong; Wang, Zhen-Zhong; Xie, Jing-Zhong; Qin, Jin-Xia; Wang, Guo-Xin; Li, De-Lin; Huang, Yin-Lian; Yu, Mei-Hua; Lu, Ping; Wang, Li-Li; Wang, Ling; Wang, Hao; Dang, Chen; Li, Jie; Zhang, Yan; Peng, Hui-Ru; Yuan, Cheng-Guo; You, Ming-Shan; Sun, Qi-Xin; Wang, Ji-Rui; Wang, Li-Xin; Luo, Ming-Cheng; Han, Jun; Liu, Zhi-Yong

    2015-01-01

    High-density genetic linkage maps are necessary for precisely mapping quantitative trait loci (QTLs) controlling grain shape and size in wheat. By applying the Infinium iSelect 9K SNP assay, we have constructed a high-density genetic linkage map with 269 F 8 recombinant inbred lines (RILs) developed between a Chinese cornerstone wheat breeding parental line Yanda1817 and a high-yielding line Beinong6. The map contains 2431 SNPs and 128 SSR & EST-SSR markers in a total coverage of 3213.2 cM with an average interval of 1.26 cM per marker. Eighty-eight QTLs for thousand-grain weight (TGW), grain length (GL), grain width (GW) and grain thickness (GT) were detected in nine ecological environments (Beijing, Shijiazhuang and Kaifeng) during five years between 2010-2014 by inclusive composite interval mapping (ICIM) (LOD?2.5). Among which, 17 QTLs for TGW were mapped on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 3D, 4A, 4D, 5A, 5B and 6B with phenotypic variations ranging from 2.62% to 12.08%. Four stable QTLs for TGW could be detected in five and seven environments, respectively. Thirty-two QTLs for GL were mapped on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6B, 7A and 7B, with phenotypic variations ranging from 2.62% to 44.39%. QGl.cau-2A.2 can be detected in all the environments with the largest phenotypic variations, indicating that it is a major and stable QTL. For GW, 12 QTLs were identified with phenotypic variations range from 3.69% to 12.30%. We found 27 QTLs for GT with phenotypic variations ranged from 2.55% to 36.42%. In particular, QTL QGt.cau-5A.1 with phenotypic variations of 6.82-23.59% was detected in all the nine environments. Moreover, pleiotropic effects were detected for several QTL loci responsible for grain shape and size that could serve as target regions for fine mapping and marker assisted selection in wheat breeding programs. PMID:25675376

  6. High-Density Genetic Linkage Map Construction and QTL Mapping of Grain Shape and Size in the Wheat Population Yanda1817 × Beinong6

    PubMed Central

    Wu, Qiu-Hong; Chen, Yong-Xing; Zhou, Sheng-Hui; Fu, Lin; Chen, Jiao-Jiao; Xiao, Yao; Zhang, Dong; Ouyang, Shu-Hong; Zhao, Xiao-Jie; Cui, Yu; Zhang, De-Yun; Liang, Yong; Wang, Zhen-Zhong; Xie, Jing-Zhong; Qin, Jin-Xia; Wang, Guo-Xin; Li, De-Lin; Huang, Yin-Lian; Yu, Mei-Hua; Lu, Ping; Wang, Li-Li; Wang, Ling; Wang, Hao; Dang, Chen; Li, Jie; Zhang, Yan; Peng, Hui-Ru; Yuan, Cheng-Guo; You, Ming-Shan; Sun, Qi-Xin; Wang, Ji-Rui; Wang, Li-Xin; Luo, Ming-Cheng; Han, Jun; Liu, Zhi-Yong

    2015-01-01

    High-density genetic linkage maps are necessary for precisely mapping quantitative trait loci (QTLs) controlling grain shape and size in wheat. By applying the Infinium iSelect 9K SNP assay, we have constructed a high-density genetic linkage map with 269 F 8 recombinant inbred lines (RILs) developed between a Chinese cornerstone wheat breeding parental line Yanda1817 and a high-yielding line Beinong6. The map contains 2431 SNPs and 128 SSR & EST-SSR markers in a total coverage of 3213.2 cM with an average interval of 1.26 cM per marker. Eighty-eight QTLs for thousand-grain weight (TGW), grain length (GL), grain width (GW) and grain thickness (GT) were detected in nine ecological environments (Beijing, Shijiazhuang and Kaifeng) during five years between 2010–2014 by inclusive composite interval mapping (ICIM) (LOD?2.5). Among which, 17 QTLs for TGW were mapped on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 3D, 4A, 4D, 5A, 5B and 6B with phenotypic variations ranging from 2.62% to 12.08%. Four stable QTLs for TGW could be detected in five and seven environments, respectively. Thirty-two QTLs for GL were mapped on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6B, 7A and 7B, with phenotypic variations ranging from 2.62% to 44.39%. QGl.cau-2A.2 can be detected in all the environments with the largest phenotypic variations, indicating that it is a major and stable QTL. For GW, 12 QTLs were identified with phenotypic variations range from 3.69% to 12.30%. We found 27 QTLs for GT with phenotypic variations ranged from 2.55% to 36.42%. In particular, QTL QGt.cau-5A.1 with phenotypic variations of 6.82–23.59% was detected in all the nine environments. Moreover, pleiotropic effects were detected for several QTL loci responsible for grain shape and size that could serve as target regions for fine mapping and marker assisted selection in wheat breeding programs. PMID:25675376

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

    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

    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

  9. A set of Lotus japonicus Gifu x Lotus burttii recombinant inbred lines facilitates map-based cloning and QTL mapping.

    PubMed

    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

    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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-06-01

    Growth performance and reduced stress response are traits of major interest in fish production. Growth and stress-related quantitative trait loci (QTL) have been already identified in several salmonid species, but little effort has been devoted to charrs (genus Salvelinus). Moreover, most QTL studies to date focused on one or very few traits, and little investigation has been devoted to QTL identification for gene expression. Here, our objective was to identify QTL for 27 phenotypes related to growth and stress responses in brook charr (Salvelinus fontinalis), which is one of the most economically important freshwater aquaculture species in Canada. Phenotypes included 12 growth parameters, six blood and plasma variables, three hepatic variables, and one plasma hormone level as well as the relative expression measurements of five genes of interest linked to growth regulation. QTL analysis relied on a linkage map recently built from S. fontinalis consisting of both single-nucleotide polymorphism (SNP, n = 266) and microsatellite (n =81) markers in an F(2) 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

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

    PubMed Central

    Everett, Meredith V; Seeb, James E

    2014-01-01

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

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

    PubMed

    Everett, Meredith V; Seeb, James E

    2014-04-01

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

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

    Microsoft Academic Search

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

    2011-01-01

    Rice (Oryza sativa L.) head-rice yield (HR) is a key export and domestic quality trait whose genetic control is poorly understood. With the\\u000a goal of identifying genomic regions influencing HR, quantitative-trait-locus (QTL) mapping was carried out for quality-related\\u000a traits in recombinant inbred lines (RILs) derived from crosses of common parent Cypress, a high-HR US japonica cultivar, with RT0034, a low-HR

  15. Graph-regularized dual Lasso for robust eQTL mapping

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Niedziela, A; Bednarek, P T; Labudda, M; Ma?kowski, D R; Anio?, A

    2014-02-01

    Triticale (x Triticosecale Wittmack) is a relatively new cereal crop. In Poland, triticale is grown on 12 % of arable land ( http://www.stat.gov.pl ). There is an increasing interest in its cultivation due to lowered production costs and increased adaptation to adverse environmental conditions. However, it has an insufficient tolerance to the presence of aluminum ions (Al(3+)) in the soil. The number of genes controlling aluminum tolerance in triticale and their chromosomal location is not known. Two F2 mapping biparental populations (MP1 and MP15) segregating for aluminum (Al) tolerance were tested with AFLP, SSR, DArT, and specific PCR markers. Genetic mapping enabled the construction of linkage groups representing chromosomes 7R, 5R and 2B. Obtained linkage groups were common for both mapping populations and mostly included the same markers. Composite interval mapping (CIM) allowed identification of a single QTL that mapped to the 7R chromosome and explained 25 % (MP1) and 36 % (MP15) of phenotypic variation. The B1, B26 and Xscm150 markers were 0.04 cM and 0.02 cM from the maximum of the LOD function in the MP1 and MP15, respectively and were highly associated with aluminum tolerance as indicated by Kruskal-Wallis nonparametric test. Moreover, the molecular markers B1, B26, Xrems1162 and Xscm92, previously associated with the Alt4 locus that encoded an aluminum-activated malate transporter (ScALMT1) that was involved in Al tolerance in rye (Secale cereale) also mapped within QTL. Biochemical analysis of plants represented MP1 and MP15 mapping populations confirmed that the QTL located on 7R chromosome in both mapping populations is responsible for Al tolerance. PMID:24222435

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

    PubMed Central

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

    2014-01-01

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

  18. FINE MAPPING OF QUANTITATIVE TRAIT LOCI AND ASSESSMENT OF POSITIONAL CANDIDATE GENES FOR BACKFAT ON BOVINE CHROMOSOME 14 IN A COMMERCIAL LINE OF BOS TAURUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Backfat thickness is one of the major quantitative traits that affect carcass quality in beef cattle. In this study, we have fine mapped a QTL for backfat EBV on bovine chromosome 14, using an identical-by-descent haplotype-sharing analysis, in a commercial line of Bos taurus. We also examined the...

  19. IDENTIFICATION AND FINE MAPPING OF QUANTITATIVE TRAIT LOCI FOR GROWTH TRAITS ON BOVINE CHROMOSOMES 2, 6, 14, 19, 21, AND 23 WITHIN ONE COMMERCIAL LINE OF BOS TAURUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report the identification and fine mapping of QTL for birth weight (BWT), preweaning ADG (PWADG), and postweaning ADG on feed (ADGF) in a commercial line of Bos taurus using an identical-by-descent haplotype sharing method. One hundred seventy-six calves of 12 bulls (9 to 30 male calves from eac...

  20. IDENTIFICATION AND FINE MAPPING OF QUANTITATIVE TRAIT LOCI FOR BACKFAT ON BOVINE CHROMOSOMES 2, 5, 6, 19, 21, AND 23 IN A COMMERCIAL LINE OF BOS TAURUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Backfat thickness is one of the major quantitative traits that affects carcass quality in beef cattle. In this study, we identified and fine-mapped QTL for backfat EBV on bovine chromosomes 2, 5, 6, 19, 21, and 23 using an identical-by-descent haplotype-sharing analysis in a commercial line of Bos ...

  1. Mapping QTL for the traits associated with heat tolerance in wheat ( Triticum aestivum L.).

    PubMed

    Talukder, Shyamal; Babar, Md; Vijayalakshmi, Kolluru; Poland, Jesse; Prasad, Pagadala; Bowden, Robert; Fritz, Allan

    2014-11-11

    BackgroundHigh temperature (heat) stress during grain filling is a major problem in most of the wheat growing areas. Developing heat tolerant cultivars has become a principal breeding goal in the Southern and Central Great Plain areas of the USA. Traits associated with high temperature tolerance can be used to develop heat tolerant cultivars in wheat. The present study was conducted to identify chromosomal regions associated with thylakoid membrane damage (TMD), plasmamembrane damage (PMD), and SPAD chlorophyll content (SCC), which are indicative of high temperature tolerance.ResultsIn this study we have reported one of the first linkage maps in wheat using genotype by sequencing SNP (GBS-SNP) markers to extreme response to post anthesis heat stress conditions. The linkage map was comprised of 972 molecular markers (538 Bin, 258 AFLPs, 175 SSRs, and an EST). The genotypes of the RIL population showed strong variation for TMD, SCC and PMD in both generations (F10 and F9). Composite interval mapping identified five QTL regions significantly associated with response to heat stress. Associations were identified for PMD on chromosomes 7A, 2B and 1D, SCC on 6A, 7A, 1B and 1D and TMD on 6A, 7A and 1D. The variability (R2) explained by these QTL ranged from 11.9 to 30.6% for TMD, 11.4 to 30.8% for SCC, and 10.5 to 33.5% for PMD. Molecular markers Xbarc113 and AFLP AGCTCG-347 on chromosome 6A, Xbarc121 and Xbarc49 on 7A, gwm18 and Bin1130 on 1B, Bin178 and Bin81 on 2B and Bin747 and Bin1546 on 1D were associated with these QTL.ConclusionThe identified QTL can be used for marker assisted selection in breeding wheat for improved heat tolerance in Ventnor or Karl 92 genetic background. PMID:25384418

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

    PubMed Central

    2011-01-01

    Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and association genetic studies of adaptation and growth in Picea taxa. The putative QTNs identified will be tested for associations in natural populations, with potential applications in molecular breeding and gene conservation programs. QTLs mapping consistently across years and environments could also be the most important targets for breeding, because they represent genomic regions that may be least affected by G × E interactions. PMID:21392393

  3. 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 ...

  4. Brain eQTL Mapping Informs Genetic Studies of Psychiatric Diseases

    PubMed Central

    Liu, Chunyu

    2011-01-01

    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

  5. Genotype×environment interaction QTL mapping in plants: lessons from Arabidopsis.

    PubMed

    El-Soda, Mohamed; Malosetti, Marcos; Zwaan, Bas J; Koornneef, Maarten; Aarts, Mark G M

    2014-06-01

    Plant growth and development are influenced by the genetic composition of the plant (G), the environment (E), and the interaction between them (G×E). To produce suitable genotypes for multiple environments, G×E should be accounted for and assessed in plant-breeding programs. Here, we review the genetic basis of G×E and its consequence for quantitative trait loci (QTL) mapping in biparental and genome-wide association (GWA) mapping populations. We also consider the implications of G×E for understanding plant fitness trade-offs and evolutionary ecology. PMID:24491827

  6. PRELIMINARY QTL MAPPING RESULTS TO FROSTY POD AND HORTICULTURAL TRAITS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A mapping population was made and evaluated for resistance and horticultural traits at CATIE, Turrialba, Costa Rica, consisting of 256 F1 progeny from a cross between ‘Pound 7’ x ‘UF 273’. Progeny were used to form a linkage map using 180 markers. It was discovered that two different types of one pa...

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

    PubMed

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

    2009-09-01

    Verticillium wilt is a destructive disease with international consequences for cotton production. Breeding broad-spectrum resistant cultivars is considered to be one of the most effective means for reducing crop losses. A resistant cotton cultivar, 60182, was crossed with a susceptible cultivar, Junmian 1, to identify markers for Verticillium resistance genes and validate the mode of its inheritance. Genetic segregation analysis for Verticillium wilt resistance was evaluated based upon infected leaf percentage in the seedling stage using major gene-polygene mixed inheritance models and joint analysis of P(1), P(2), F(1), B(1), B(2) and F(2) populations obtained from the cultivar cross. We found that resistance of upland cotton cultivar 60182 to isolates BP2, VD8 and T9, and their isoconcentration mixture was controlled by two major genes with additive-dominance-epistatic effects, and the inheritance of the major gene was dominant. Furthermore, a genetic linkage map was constructed using F(2) segregating population and resistance phenotypic data were obtained using F(2:3) families inoculated with different isolates and detected in different developmental stages. The genetic linkage map with 139 loci was comprised of 31 linkage groups covering 1165 cM, with an average distance of 8.38 cM between two markers, or 25.89% of the cotton genome length. From 60182, we found 4 QTL on chromosome D7 and 4 QTL on D9 for BP2, 5 QTL on D7 and 9 QTL on D9 for VD8, 4 QTL on D7 and 5 QTL on D9 for T9 and 3 QTL on D7 and 7 QTL on D7 for mixed pathogens. The QTL mapping results revealed that QTL clusters with high contribution rates were screened simultaneously on chromosomes D9 and D7 by multiple interval mapping (CIM), whether from resistance phenotypic data from different developmental stages or for different isolates. The result is consistent with the genetic model of two major genes in 60182 and suggests broad-spectrum resistance to both defoliating isolates of V. dahliae and nondefoliating isolates. The markers associated with resistance QTL may facilitate the use of Verticillium wilt resistance genes in improving breeding programs for cotton. PMID:19802747

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

    PubMed Central

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

    2014-01-01

    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

  9. Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL Verification and candidate gene mapping.

    PubMed Central

    Brown, Garth R; Bassoni, Daniel L; Gill, Geoffrey P; Fontana, Joseph R; Wheeler, Nicholas C; Megraw, Robert A; Davis, Mark F; Sewell, Mitchell M; Tuskan, Gerald A; Neale, David B

    2003-01-01

    A long-term series of experiments to map QTL influencing wood property traits in loblolly pine has been completed. These experiments were designed to identify and subsequently verify QTL in multiple genetic backgrounds, environments, and growing seasons. Verification of QTL is necessary to substantiate a biological basis for observed marker-trait associations, to provide precise estimates of the magnitude of QTL effects, and to predict QTL expression at a given age or in a particular environment. Verification was based on the repeated detection of QTL among populations, as well as among multiple growing seasons for each population. Temporal stability of QTL was moderate, with approximately half being detected in multiple seasons. Fewer QTL were common to different populations, but the results are nonetheless encouraging for restricted applications of marker-assisted selection. QTL from larger populations accounted for less phenotypic variation than QTL detected in smaller populations, emphasizing the need for experiments employing much larger families. Additionally, 18 candidate genes related to lignin biosynthesis and cell wall structure were mapped genetically. Several candidate genes colocated with wood property QTL; however, these relationships must be verified in future experiments. PMID:12930758

  10. Systems genetics, bioinformatics and eQTL mapping

    Microsoft Academic Search

    Hong Li; Hongwen Deng

    2010-01-01

    Jansen and Nap (Trends Genet 17(7):388–391, 2001) and Jansen (Nat Rev Genet 4:145–151, 2003) first proposed the concept of\\u000a genetical genomics, or genome-wide genetic analysis of gene expression data, which is also called transcriptome mapping. In\\u000a this approach, microarrays are used for measuring gene expression levels across genetic mapping populations. These gene expression\\u000a patterns have been used for genome-wide association

  11. QTL: Why and How UW-Madison PBPG Yandell 2007 1 Gene Mapping

    E-print Network

    Yandell, Brian S.

    linkage disequilibrium associations linked segregating QTL (after Gary Churchill) QTL: Why and How UW/evolution ­ how is the genome organized? ­ identify units of natural selection ­ additive effects may be most additive, dominant, recessive, general effects of a single QTL (Gary Churchill) #12;QTL: Why and How UW

  12. Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle

    Microsoft Academic Search

    E. E. Connor; M. S. Ashwell; R. Schnabel; J. L. Williams

    2006-01-01

    In the absence of a complete and annotated bovine genome sequence, detailed human-bovine comparative maps are one of the most effective tools for identification of positional candidate genes contributing to quantitative trait loci (QTL) in cattle. In the present study, eight genes from human chromosome 8 were selected for mapping in cattle to improve breakpoint resolution and confirm gene order

  13. Comparative QTL Mapping for Seed Weight Between Ryegrass and Cereals

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seed weight is one of the most important, complex traits in breeding and domestication process for several major food crops (e.g. rice and wheat). Comparative mapping studies provide insight into the evolution of genome organization within species and the understanding important traits conserved dur...

  14. QTL consistency and meta-analysis for grain yield components in three generations in maize.

    PubMed

    Li, J Z; Zhang, Z W; Li, Y L; Wang, Q L; Zhou, Y G

    2011-03-01

    Grain yield is the most important and complex trait in maize. In this study, a total of 258 F(9) recombinant inbred lines (RIL), derived from a cross between dent corn inbred Dan232 and popcorn inbred N04, were evaluated for eight grain yield components under four environments. Quantitative trait loci (QTL) and their epistatic interactions were detected for all traits under each environment and in combined analysis. Meta-analysis was used to integrate genetic maps and detected QTL across three generations (RIL, F(2:3) and BC(2)F(2)) derived from the same cross. In total, 103 QTL, 42 pairs of epistatic interactions and 16 meta-QTL (mQTL) were detected. Twelve out of 13 QTL with contributions (R(2)) over 15% were consistently detected in 3-4 environments (or in combined analysis) and integrated in mQTL. Only q100GW-7-1 was detected in all four environments and in combined analysis. 100qGW-1-1 had the largest R(2) (19.3-24.6%) in three environments and in combined analysis. In contrast, 35 QTL for 6 grain yield components were detected in the BC(2)F(2) and F(2:3) generations, no common QTL across three generations were located in the same marker intervals. Only 100 grain weight (100GW) QTL on chromosome 5 were located in adjacent marker intervals. Four common QTL were detected across the RIL and F(2:3) generations, and two between the RIL and BC(2)F(2) generations. Each of five important mQTL (mQTL7-1, mQTL10-2, mQTL4-1, mQTL5-1 and mQTL1-3) included 7-12 QTL associated with 2-6 traits. In conclusion, we found evidence of strong influence of genetic structure and environment on QTL detection, high consistency of major QTL across environments and generations, and remarkable QTL co-location for grain yield components. Fine mapping for five major QTL (q100GW-1-1, q100GW-7-1, qGWP-4-1, qERN-4-1 and qKR-4-1) and construction of single chromosome segment lines for genetic regions of five mQTL merit further studies and could be put into use in marker-assisted breeding. PMID:21063866

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

    PubMed Central

    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

    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

  16. XVIth QTLMAS: simulated dataset and comparative analysis of submitted results for QTL mapping and genomic evaluation

    PubMed Central

    2014-01-01

    Background A common dataset was simulated and made available to participants of the XVIth QTL-MAS workshop. Tasks for the participants were to detect QTLs affecting three traits, to assess their possible pleiotropic effects, and to evaluate the breeding values in a candidate population without phenotypes using genomic information. Methods Four generations consisting of 20 males and 1000 females were generated by mating each male with 50 females. The genome consisted of 5 chromosomes, each of 100 Mb size and carrying 2,000 equally distributed SNPs. Three traits were simulated in order to mimic milk yield, fat yield and fat content. Genetic (co)variances were generated from 50 QTLs with pleiotropic effects. Phenotypes for all traits were expressed only in females, and were provided for the first 3 generations. Fourteen methods for detecting single-trait QTL and 3 methods for investigating their pleiotropic nature were proposed. QTL mapping results were compared according to the following criteria: number of true QTL detected; number of false positives; and the proportion of the true genetic variance explained by submitted positions. Eleven methods for estimating direct genomic values of the candidate population were proposed. Accuracies and bias of predictions were assessed by comparing estimated direct genomic values with true breeding values. Results The number of true detections ranged from 0 to 8 across methods and traits, false positives from 0 to 15, and the proportion of genetic variance captured from 0 to 0.82, respectively. The accuracy and bias of genomic predictions varied from 0.74 to 0.85 and from 0.86 to 1.34 across traits and methods, respectively. Conclusions The best results in terms of detection power were obtained by ridge regression that, however, led to a large number of false positives. Good results both in terms of true detections and false positives were obtained by the approaches that fit polygenic effects in the model. The investigation of the pleiotropic nature of the QTL permitted the identification of few additional markers compared to the single-trait analyses. Bayesian and grouped regularized regression methods performed similarly for genomic prediction while GBLUP produced the poorest results. PMID:25519515

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

    PubMed Central

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

    2013-01-01

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

  18. Combined QTL and Selective Sweep Mappings with Coding SNP Annotation and cis-eQTL Analysis Revealed PARK2 and JAG2 as New Candidate Genes for Adiposity Regulation

    PubMed Central

    Roux, Pierre-François; Boitard, Simon; Blum, Yuna; Parks, Brian; Montagner, Alexandra; Mouisel, Etienne; Djari, Anis; Esquerré, Diane; Désert, Colette; Boutin, Morgane; Leroux, Sophie; Lecerf, Frédéric; Le Bihan-Duval, Elisabeth; Klopp, Christophe; Servin, Bertrand; Pitel, Frédérique; Duclos, Michel Jean; Guillou, Hervé; Lusis, Aldons J.; Demeure, Olivier; Lagarrigue, Sandrine

    2015-01-01

    Very few causal genes have been identified by quantitative trait loci (QTL) mapping because of the large size of QTL, and most of them were identified thanks to functional links already known with the targeted phenotype. Here, we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTL identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for only one trait, the abdominal fat weight, in which several QTL were previously mapped. Using new haplotype-based statistics exploiting the very high SNP density generated through whole-genome resequencing, we found 129 significant selective sweeps. Most of the QTL colocalized with at least one sweep, which markedly narrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strong positional causal candidates with no presupposed function. We then focused on two of these QTL/sweeps. The absence of nonsynonymous SNPs in their coding regions strongly suggests the existence of causal mutations acting in cis on their expression, confirmed by cis-eQTL identification using either allele-specific expression or genetic mapping analyses. Additional expression analyses of those two genes in the chicken and mice contrasted for adiposity reinforces their link with this phenotype. This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. Moreover, it highlights two genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken and mice. PMID:25653314

  19. QTL mapping for photoperiod insensitivity of a Japanese soybean landrace Sakamotowase.

    PubMed

    Liu, Baohui; Abe, Jun

    2010-01-01

    The insensitivity of flowering to long daylength is an important characteristic which soybeans have used to adapt to environments at higher latitude. The objective of this study was to map the novel gene(s) for photoperiod insensitivity in the Japanese soybean landrace Sakamotowase. A previous study suggested that Sakamotowase possessed the genotype e1e1e3e3E4E4. The progeny of testcrosses with the Harosoy isoline for e3 (L62-667) produced the roughly expected segregation pattern for the monogenic inheritance, suggesting the major involvement of a single gene in photoperiod insensitivity of Sakamotowase. By mapping analysis for 6 linkage groups (LGs) harboring the known major genes and quantitative trait loci (QTLs) for flowering, we detected a major QTL for the insensitivity near an simple sequence repeat marker (Satt577) in LG C2 and a minor QTL in LG L. Our results therefore suggest that a novel gene for photoperiod insensitivity of Sakamotowase was located in LG C2. It was estimated from the position of the tagging marker that the novel gene may be an allele at the E1 or E7 loci or a novel gene tightly linked to the E1 locus. PMID:19959597

  20. Mapping of QTL for seed dormancy in a winter oilseed rape doubled haploid population.

    PubMed

    Schatzki, Jörg; Schoo, Burkhard; Ecke, Wolfgang; Herrfurth, Cornelia; Feussner, Ivo; Becker, Heiko C; Möllers, Christian

    2013-09-01

    Following winter oilseed rape cultivation, considerable numbers of volunteer oilseed rape plants may occur in subsequent years in following crops. The appearance of volunteer oilseed rape plants is based on the capability of the seeds to become secondary dormant and to survive in this stage for many years in the soil. Genetic reduction of secondary seed dormancy in oilseed rape could provide a means to reduce the frequency of volunteer plants and especially the dispersal of transgenic oilseed rape. The objective of the present study was to analyse the inheritance of primary and secondary seed dormancy in a winter oilseed rape doubled haploid population derived from the cross Express 617 × R53 and to study correlations to other seed traits. Field experiments were performed in Germany for 2 years at two locations with two replicates. Seeds harvested from open pollinated plants were used for all analyses, including a laboratory test for seed dormancy. A previously developed molecular marker map of the doubled haploid population was used to map QTL of the relevant traits. For primary, secondary and total seed dormancy, the results showed significant effects of the genotypes and their interactions, with years and locations. Two, four and five QTL were detected for primary, secondary and total seed dormancy which explained 19, 35 and 42 % of the phenotypic variance, respectively. Results show that secondary seed dormancy is a heritable trait and that selection for low secondary seed dormancy is possible. PMID:23783224

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

    PubMed Central

    2013-01-01

    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

  2. Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

    PubMed Central

    Yi, Can; Wen, Jia; Jinxing, Tu; Zhang, Yuan Ming

    2015-01-01

    The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F1 crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F1 hybrids, and all these F1 phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F1 hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study. PMID:25822501

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

    PubMed

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

    2013-06-01

    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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 estimatio...

  5. LINKAGE AND RH MAPPING OF 10 GENES TO A QTL REGION FOR FATNESS AND MUSCLING TRAITS ON PIG CHROMOSOME X

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study 10 genes located on human chromosome region Xq13.1 - Xq24 homologous to a QTL region for fatness and body conformation traits were linkage and RH mapped in the pig. PCR primers for amplification of porcine genomic DNAs were designed from orthologous human or porcine (HTR2C) sequences. ...

  6. 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...

  7. MAPPING, EXPRESSION, AND MOLECULAR VARIATION OF POTENTIAL CANDIDATE GENES UNDERLYING A MAJOR EMBRYONIC DEVELOPMENT RATE QTL IN RAINBOW TROUT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A major embryonic development rate QTL has been identified in several crosses of rainbow trout, but potential candidate genes underlying this locus have not been previously identified. From candidate gene mapping efforts, we have identified two genes, a negative growth regulation and differentiation...

  8. Mapping of QTL for Fusarium head blight resistance and morphological and developmental traits in three backcross populations derived from Triticum dicoccum × Triticum durum.

    PubMed

    Buerstmayr, Maria; Huber, Karin; Heckmann, Johannes; Steiner, Barbara; Nelson, James C; Buerstmayr, Hermann

    2012-12-01

    Breeding for resistance to Fusarium head blight (FHB) in durum wheat continues to be hindered by the lack of effective resistance sources. Only limited information is available on resistance QTL for FHB in tetraploid wheat. In this study, resistance to FHB of a Triticum dicoccum line in the background of three Austrian T. durum cultivars was genetically characterized. Three populations of BC(1)F(4)-derived RILs were developed from crosses between the resistant donor line T. dicoccum-161 and the Austrian T. durum recipient varieties DS-131621, Floradur and Helidur. About 130 BC(1)F(4)-derived lines per population were evaluated for FHB response using artificial spray inoculation in four field experiments during two seasons. Lines were genetically fingerprinted using SSR and AFLP markers. Genomic regions on chromosomes 3B, 4B, 6A, 6B and 7B were significantly associated with FHB severity. FHB resistance QTL on 6B and 7B were identified in two populations and a resistance QTL on 4B appeared in three populations. The alleles that enhanced FHB resistance were derived from the T. dicoccum parent, except for the QTL on chromosome 3B. All QTL except the QTL on 6A mapped to genomic regions where QTL for FHB have previously been reported in hexaploid wheat. QTL on 3B and 6B coincided with Fhb1 and Fhb2, respectively. This implies that tetraploid and hexaploid wheat share common genomic regions associated with FHB resistance. QTL for FHB resistance on 4B co-located with a major QTL for plant height and mapped at the position of the Rht-B1 gene, while QTL on 7B overlapped with QTL for flowering time. PMID:22926291

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

    PubMed Central

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

    2014-01-01

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

  10. Genetic mapping and QTL analysis of growth-related traits in Pinctada fucata using restriction-site associated DNA sequencing.

    PubMed

    Li, Yaoguo; He, Maoxian

    2014-01-01

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

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

    PubMed Central

    Li, Yaoguo; He, Maoxian

    2014-01-01

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

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

    PubMed Central

    2011-01-01

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

  13. High-Resolution Genotyping of Wild Barley Introgression Lines and Fine-Mapping of the Threshability Locus thresh-1 Using the Illumina GoldenGate Assay

    PubMed Central

    Schmalenbach, Inga; March, Timothy J.; Bringezu, Thomas; Waugh, Robbie; Pillen, Klaus

    2011-01-01

    Genetically well-characterized mapping populations are a key tool for rapid and precise localization of quantitative trait loci (QTL) and subsequent identification of the underlying genes. In this study, a set of 73 introgression lines (S42ILs) originating from a cross between the spring barley cultivar Scarlett (Hordeum vulgare ssp. vulgare) and the wild barley accession ISR42-8 (H. v. ssp. spontaneum) was subjected to high-resolution genotyping with an Illumina 1536-SNP array. The array enabled a precise localization of the wild barley introgressions in the elite barley background. Based on 636 informative SNPs, the S42IL set represents 87.3% of the wild barley genome, where each line contains on average 3.3% of the donor genome. Furthermore, segregating high-resolution mapping populations (S42IL-HRs) were developed for 70 S42ILs in order to facilitate QTL fine-mapping and cloning. As a case study, we used the developed genetic resources to rapidly identify and fine-map the novel locus thresh-1 on chromosome 1H that controls grain threshability. Here, the recessive wild barley allele confers a difficult to thresh phenotype, suggesting that thresh-1 played an important role during barley domestication. Using a S42IL-HR population, thresh-1 was fine-mapped within a 4.3cM interval that was predicted to contain candidate genes involved in regulation of plant cell wall composition. The set of wild barley introgression lines and derived high-resolution populations are ideal tools to speed up the process of mapping and further dissecting QTL, which ultimately clears the way for isolating the genes behind QTL effects. PMID:22384330

  14. Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle.

    PubMed

    Connor, E E; Ashwell, M S; Schnabel, R; Williams, J L

    2006-01-01

    In the absence of a complete and annotated bovine genome sequence, detailed human-bovine comparative maps are one of the most effective tools for identification of positional candidate genes contributing to quantitative trait loci (QTL) in cattle. In the present study, eight genes from human chromosome 8 were selected for mapping in cattle to improve breakpoint resolution and confirm gene order on the comparative map near the 40 cM region of the BTA27 linkage map where a QTL affecting dairy form had previously been identified. The resulting map identified ADRB3 as a positional candidate gene for the QTL contributing to the dairy form trait based on its estimated position between 40 and 45 cM on the linkage map. It is also a functional candidate gene due to its role in fat metabolism, and polymorphisms in the ADRB3 gene associated with obesity and metabolic disease in humans, as well as, carcass fat in sheep. Further studies are underway to investigate the existence of polymorphisms in the bovine ADRB3 gene and their association with traits related to fat deposition in cattle. PMID:16276096

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

    PubMed Central

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

    2007-01-01

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

  16. QTL Mapping of Leafy Heads by Genome Resequencing in the RIL Population of Brassica rapa

    PubMed Central

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

    2013-01-01

    Leaf heads of cabbage (Brassica oleracea), Chinese cabbage (B. rapa), and lettuce (Lactuca sativa) are important vegetables that supply mineral nutrients, crude fiber and vitamins in the human diet. Head size, head shape, head weight, and heading time contribute to yield and quality. In an attempt to investigate genetic basis of leafy head in Chinese cabbage (B. rapa), we took advantage of recent technical advances of genome resequencing to perform quantitative trait locus (QTL) mapping using 150 recombinant inbred lines (RILs) derived from the cross between heading and non-heading Chinese cabbage. The resequenced genomes of the parents uncovered more than 1 million SNPs. Genotyping of RILs using the high-quality SNPs assisted by Hidden Markov Model (HMM) generated a recombination map. The raw genetic map revealed some physical assembly error and missing fragments in the reference genome that reduced the quality of SNP genotyping. By deletion of the genetic markers in which recombination rates higher than 20%, we have obtained a high-quality genetic map with 2209 markers and detected 18 QTLs for 6 head traits, from which 3 candidate genes were selected. These QTLs provide the foundation for study of genetic basis of leafy heads and the other complex traits. PMID:24204591

  17. A combined linkage and regional association mapping validation and fine mapping of two major pleiotropic QTLs for seed weight and silique length in rapeseed (Brassica napus L.)

    PubMed Central

    2014-01-01

    Background Seed weight (SW) and silique length (SL) are important determinants of the yield potential in rapeseed (Brassica napus L.). However, the genetic basis of both traits is poorly understood. The main objectives of this study were to dissect the genetic basis of SW and SL in rapeseed through the preliminary mapping of quantitative trait locus (QTL) by linkage analysis and fine mapping of the target major QTL by regional association analysis. Results Preliminary linkage mapping identified thirteen and nine consensus QTLs for SW and SL, respectively. These QTLs explained 0.7-67.1% and 2.1-54.4% of the phenotypic variance for SW and SL, respectively. Of these QTLs, three pairs of SW and SL QTLs were co-localized and integrated into three unique QTLs. In addition, the significance level and genetic effect of the three co-localized QTLs for both SW and SL showed great variation before and after the conditional analysis. Moreover, the allelic effects of the three QTLs for SW were highly consistent with those for SL. Two of the three co-localized QTLs, uq.A09-1 (mean R2?=?20.1% and 19.0% for SW and SL, respectively) and uq.A09-3 (mean R2?=?13.5% and 13.2% for SW and SL, respectively), were detected in all four environments and showed the opposite additive-effect direction. These QTLs were validated and fine mapped (their confidence intervals were narrowed down from 5.3 cM to 1 cM for uq.A09-1 and 13.2 cM to 2.5 cM for uq.A09-3) by regional association analysis with a panel of 576 inbred lines, which has a relatively rapid linkage disequilibrium decay (0.3 Mb) in the target QTL region. Conclusions A few QTLs with major effects and several QTLs with moderate effects might contribute to the natural variation of SW and SL in rapeseed. The meta-, conditional and allelic effect analyses suggested that pleiotropy, rather than tight linkage, was the genetic basis of the three pairs of co-localized of SW and SL QTLs. Regional association analysis was an effective and highly efficient strategy for the direct fine mapping of target major QTL identified by preliminary linkage mapping. PMID:24779415

  18. Fine mapping of loci involved with glucosinolate biosynthesis in oilseed mustard ( Brassica juncea ) using genomic information from allied species

    Microsoft Academic Search

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

    2009-01-01

    Fine mapping of six seed glucosinolate QTL (J2Gsl1, J3Gsl2, J9Gsl3, J16Gsl4, J17Gsl5 and J3Gsl6) (Ramchiary et al. in Theor Appl Genet 116:77–85, 2007a) was undertaken by the candidate gene approach. Based on the DNA sequences from Arabidopsis and Brassica oleracea for the different genes involved in the aliphatic glucosinolate biosynthesis, candidate genes were amplified and sequenced\\u000a from high to low

  19. The genetic architecture of zinc and iron content in maize grains as revealed by QTL mapping and meta-analysis.

    PubMed

    Jin, Tiantian; Zhou, Jinfeng; Chen, Jingtang; Zhu, Liying; Zhao, Yongfeng; Huang, Yaqun

    2013-09-01

    Micronutrient malnutrition, especially zinc (Zn) and iron (Fe) deficiency in diets, has aroused worldwide attention. Biofortification of food crops has been considered as a promising approach for alleviating this deficiency. Quantitative trait locus (QTL) analysis was performed to dissect the genetic mechanism of Zn and Fe content in maize grains using a total of 218 F2:3 families derived from a cross between inbred lines 178 and P53. Meta-analysis was used to integrate genetic maps and detect Meta-QTL (MQTL) across several independent QTL researches for traits related to Zn or Fe content. Five significant QTLs and 10 MQTLs were detected. Two informative genomic regions, bins 2.07 and 2.08, showed a great importance for Zn and Fe content QTLs. The correlation between Zn and Fe level in maize grains was proposed by MQTLs as 8 of the 10 involved both traits. The results of this study suggest that QTL mapping and meta-analysis is an effective approach to understand the genetic basis of Zn and Fe accumulation in maize grains. PMID:24273427

  20. Genetic mapping reveals a single major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.).

    PubMed

    Studer, Bruno; Boller, Beat; Herrmann, Doris; Bauer, Eva; Posselt, Ulrich K; Widmer, Franco; Kölliker, Roland

    2006-08-01

    Bacterial wilt caused by Xanthomonas translucens pv. graminis (Xtg) is a major disease of economically important forage crops such as ryegrasses and fescues. Targeted breeding based on seedling inoculation has resulted in cultivars with considerable levels of resistance. However, the mechanisms of inheritance of resistance are poorly understood and further breeding progress is difficult to obtain. This study aimed to assess the relevance of the seedling screening in the glasshouse for adult plant resistance in the field and to investigate genetic control of resistance to bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.). A mapping population consisting of 306 F1 individuals was established and resistance to bacterial wilt was assessed in glasshouse and field experiments. Highly correlated data (r = 0.67-0.77, P < 0.01) between trial locations demonstrated the suitability of glasshouse screens for phenotypic selection. Analysis of quantitative trait loci (QTL) based on a high density genetic linkage map consisting of 368 amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers revealed a single major QTL on linkage group (LG) 4 explaining 67% of the total phenotypic variance (Vp). In addition, a minor QTL was observed on LG 5. Field experiments confirmed the major QTL on LG 4 to explain 43% (in 2004) to 84% (in 2005) of Vp and also revealed additional minor QTLs on LG 1, LG 4 and LG 6. The identified QTLs and the closely linked markers represent important targets for marker-assisted selection of Italian ryegrass. PMID:16799808

  1. Construction of an integrative linkage map and QTL mapping of grain yield-related traits using three related wheat RIL populations.

    PubMed

    Cui, Fa; Zhao, Chunhua; Ding, Anming; Li, Jun; Wang, Lin; Li, Xingfeng; Bao, Yinguang; Li, Junming; Wang, Honggang

    2014-03-01

    A novel high-density consensus wheat genetic map was obtained based on three related RIL populations, and the important chromosomal regions affecting yield and related traits were specified. A prerequisite for mapping quantitative trait locus (QTL) is to build a genetic linkage map. In this study, three recombinant inbred line populations (represented by WL, WY, and WJ) sharing one common parental line were used for map construction and subsequently for QTL detection of yield-related traits. PCR-based and diversity arrays technology markers were screened in the three populations. The integrated genetic map contains 1,127 marker loci, which span 2,976.75 cM for the whole genome, 985.93 cM for the A genome, 922.16 cM for the B genome, and 1,068.65 cM for the D genome. Phenotypic values were evaluated in four environments for populations WY and WJ, but three environments for population WL. Individual and combined phenotypic values across environments were used for QTL detection. A total of 165 putative additive QTL were identified, 22 of which showed significant additive-by-environment interaction effects. A total of 65 QTL (51.5%) were stable across environments, and 23 of these (35.4%) were common stable QTL that were identified in at least two populations. Notably, QTkw-5B.1, QTkw-6A.2, and QTkw-7B.1 were common major stable QTL in at least two populations, exhibiting 11.28-16.06, 5.64-18.69, and 6.76-21.16% of the phenotypic variance, respectively. Genetic relationships between kernel dimensions and kernel weight and between yield components and yield were evaluated. Moreover, QTL or regions that commonly interact across genetic backgrounds were discussed by comparing the results of the present study with those of previous similar studies. The present study provides useful information for marker-assisted selection in breeding wheat varieties with high yield. PMID:24326459

  2. QTL mapping of yield-associated traits in Brassica juncea: meta-analysis and epistatic interactions using two different crosses between east European and Indian gene pool lines.

    PubMed

    Yadava, Satish Kumar; Arumugam, N; Mukhopadhyay, Arundhati; Sodhi, Yashpal Singh; Gupta, Vibha; Pental, Deepak; Pradhan, Akshay K

    2012-11-01

    Genetic analysis of 12 yield-associated traits was undertaken by dissection of quantitative trait loci (QTL) through meta-analysis and epistatic interaction studies in Brassica juncea. A consensus (integrated) map in B. juncea was constructed using two maps. These were VH map, developed earlier in the laboratory by using a DH population from the cross between Varuna and Heera (Pradhan et al. in Theor Appl Genet 106:607-614, 2003; Ramchiary et al. in Theor Appl Genet. 115:807-817, 2007; Panjabi et al. in BMC Genomics 9:113, 2008), and the TD map, developed in the present study using a DH population of 100 lines from the cross between TM-4 and Donskaja-IV. The TD map was constructed with 911 markers consisting of 585 AFLP, 8 SSR and 318 IP markers covering a total genome length of 1,629.9 cM. The consensus map constructed by using the common markers between the two maps contained a total of 2,662 markers and covered a total genome length of 1,927.1 cM. Firstly, QTL analysis of 12 yield-associated traits was undertaken for the TD population based on three-environment phenotypic data. Secondly, the three-environment phenotypic data for the same 12 quantitative traits generated by Ramchiary et al. (2007) were re-analyzed for the QTL detection in the VH map. Comparative analysis identified both common and population-specific QTL. The study revealed the presence of QTL clusters on LG A7, A8 and A10 in both TD and VH maps. Meta-analyses resolved 187 QTL distributed over nine linkage groups of TD and VH maps into 20 meta-QTL. Maximum resolution was recorded for the LG A10 wherein all the 54 QTL were mapped to a single meta-QTL within a confidence interval of 3.0 cM. Digenic epistatic interactions of QTL in both TD and VH maps revealed substantial additive × additive interactions showing a higher frequency of Type 1 and Type 2 interactions than Type 3 interactions. Some of the loci interacted with more than one locus indicating the presence of higher order epistatic interactions. These findings provided some detailed insight into the genetic architecture of the yield-associated traits in B. juncea. PMID:22821338

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2015-02-01

    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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    2010-01-01

    Background Azalea (Rhododendron simsii hybrids) is the most important flowering pot plant produced in Belgium, being exported world-wide. In the breeding program, flower color is the main feature for selection, only in later stages cultivation related plant quality traits are evaluated. As a result, plants with attractive flowering are kept too long in the breeding cycle. The inheritance of flower color has been well studied; information on the heritability of cultivation related quality traits is lacking. For this purpose, QTL mapping in diverse genetic backgrounds appeared to be a must and therefore 4 mapping populations were made and analyzed. Results An integrated framework map on four individual linkage maps in Rhododendron simsii hybrids was constructed. For genotyping, mainly dominant scored AFLP (on average 364 per population) and MYB-based markers (15) were combined with co-dominant SSR (23) and EST markers (12). Linkage groups were estimated in JoinMap. A consensus grouping for the 4 mapping populations was made and applied in each individual mapping population. Finally, 16 stable linkage groups were set for the 4 populations; the azalea chromosome number being 13. A combination of regression mapping (JoinMap) and multipoint-likelihood maximization (Carthagène) enabled the construction of 4 maps and their alignment. A large portion of loci (43%) was common to at least two populations and could therefore serve as bridging markers. The different steps taken for map optimization and integration into a reference framework map for QTL mapping are discussed. Conclusions This is the first map of azalea up to our knowledge. AFLP and SSR markers are used as a reference backbone and functional markers (EST and MYB) were added as candidate genes for QTL analysis. The alignment of the 4 maps on the basis of framework markers will facilitate in turn the alignment of QTL regions detected in each of the populations. The approach we took is thoroughly different than the recently published integrated maps and well-suited for mapping in a non-model crop. PMID:20070894

  7. Construction of a linkage map with TRAP markers and identification of QTL for four morphological traits in sunflower (Helianthus annuus L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic maps have been constructed using RFLP, AFLP, RAPD and SSR markers in sunflower, and quantitative trait loci (QTL) underlying agronomically important traits have been positioned on these maps. In this study, a linkage map containing 202 target region amplification polymorphism (TRAP) and 24 S...

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

    2014-01-01

    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

  10. ISOLATION AND RADIATION HYBRID MAPPING OF 213 PORCINE MICROSATELLITES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Considerable effort is now being put into mapping Quantitative Trait Loci in swine. When a QTL region has been identified the next step is to fine map the region and narrow the chromosomal location harboring the QTL. One of the limiting factors to this approach has been lack of informative genetic m...

  11. Genetic Diversity and QTL Mapping of Thermostability of Limit Dextrinase in Barley.

    PubMed

    Wang, Xiaolei; Zhang, Xuelei; Cai, Shengguan; Ye, Lingzhen; Zhou, Meixue; Chen, Zhonghua; Zhang, Guoping; Dai, Fei

    2015-04-15

    Limit dextrinase (LD) is an essential amylolytic enzyme for the complete degradation of starch, and it is closely associated with malt quality. A survey of 51 cultivated barley and 40 Tibetan wild barley genotypes showed a wide genetic diversity of LD activity and LD thermostability. Compared with cultivated barley, Tibetan wild barley showed lower LD activity and higher LD thermostability. A doubled haploid population composed of 496 DArT and 28 microsatellite markers was used for mapping Quantitative Trait Loci (QTLs). Parental line Yerong showed low LD activity and high LD thermostability, but Franklin exhibited high LD activity and low LD thermostability. Three QTLs associated with thermostable LD were identified. The major QTL is close to the LD gene on chromosome 7H. The two minor QTLs colocalized with previously reported QTLs determining malt-extract and diastatic power on chromosomes 1H and 2H, respectively. These QTLs may be useful for a better understanding of the genetic control of LD activity and LD thermostability in barley. PMID:25816850

  12. QTL mapping and development of candidate gene-derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.).

    PubMed

    Kim, Suk-Man; Suh, Jung-Pil; Lee, Chung-Koon; Lee, Jeong-Heui; Kim, Yeong-Gyu; Jena, Kshirod Kumar

    2014-06-01

    Cold stress at the seedling stage is a major threat to rice production. Cold tolerance is controlled by complex genetic factors. We used an F7 recombinant inbred line (RIL) population of 123 individuals derived from a cross of the cold-tolerant japonica cultivar Jinbu and the cold-susceptible indica cultivar BR29 for QTL mapping. Phenotypic evaluation of the parents and RILs in an 18/8 °C (day/night) cold stress regime revealed continuous variation for cold tolerance. Six QTLs including two on chromosome 1 and one each on chromosomes 2, 4, 10, and 11 for seedling cold tolerance were identified with phenotypic variation (R(2)) ranging from 6.1 to 16.5 %. The QTL combinations (qSCT1 and qSCT11) were detected in all stable cold-tolerant RIL groups, which explained the critical threshold of 27.1 % for the R(2) value determining cold tolerance at the seedling stage. Two QTLs (qSCT1 and qSCT11) on chromosomes 1 and 11, respectively, were fine mapped. The markers In1-c3, derived from the open reading frame (ORF) LOC_Os01g69910 encoding calmodulin-binding transcription activator (CAMTA), and In11-d1, derived from ORF LOC_Os11g37720 (Duf6 gene), co-segregated with seedling cold tolerance. The result may provide useful information on seedling cold tolerance mechanism and provide DNA markers for a marker-assisted breeding program to improve seedling cold tolerance in indica rice varieties. PMID:24464311

  13. 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

    2013-01-01

    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

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

    PubMed

    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

    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

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

    PubMed Central

    2011-01-01

    Background Integrating QTL results from independent experiments performed on related species helps to survey the genetic diversity of loci/alleles underlying complex traits, and to highlight potential targets for breeding or QTL cloning. Potato (Solanum tuberosum L.) late blight resistance has been thoroughly studied, generating mapping data for many Rpi-genes (R-genes to Phytophthora infestans) and QTLs (quantitative trait loci). Moreover, late blight resistance was often associated with plant maturity. To get insight into the genomic organization of late blight resistance loci as compared to maturity QTLs, a QTL meta-analysis was performed for both traits. Results Nineteen QTL publications for late blight resistance were considered, seven of them reported maturity QTLs. Twenty-one QTL maps and eight reference maps were compiled to construct a 2,141-marker consensus map on which QTLs were projected and clustered into meta-QTLs. The whole-genome QTL meta-analysis reduced by six-fold late blight resistance QTLs (by clustering 144 QTLs into 24 meta-QTLs), by ca. five-fold maturity QTLs (by clustering 42 QTLs into eight meta-QTLs), and by ca. two-fold QTL confidence interval mean. Late blight resistance meta-QTLs were observed on every chromosome and maturity meta-QTLs on only six chromosomes. Conclusions Meta-analysis helped to refine the genomic regions of interest frequently described, and provided the closest flanking markers. Meta-QTLs of late blight resistance and maturity juxtaposed along chromosomes IV, V and VIII, and overlapped on chromosomes VI and XI. The distribution of late blight resistance meta-QTLs is significantly independent from those of Rpi-genes, resistance gene analogs and defence-related loci. The anchorage of meta-QTLs to the potato genome sequence, recently publicly released, will especially improve the candidate gene selection to determine the genes underlying meta-QTLs. All mapping data are available from the Sol Genomics Network (SGN) database. PMID:21247437

  16. Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map

    Microsoft Academic Search

    WANG Xu-sheng; ZHU Jun; MANSUETO Locedie; BRUSKIEWICH Richard

    2005-01-01

    Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL)

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

    PubMed

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

    2011-08-01

    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

  18. Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping

    PubMed Central

    Yang, Can; Wang, Lin; Zhang, Shuqin; Zhao, Hongyu

    2013-01-01

    Motivation: Expression quantitative trait loci (eQTL) studies investigate how gene expression levels are affected by DNA variants. A major challenge in inferring eQTL is that a number of factors, such as unobserved covariates, experimental artifacts and unknown environmental perturbations, may confound the observed expression levels. This may both mask real associations and lead to spurious association findings. Results: In this article, we introduce a LOw-Rank representation to account for confounding factors and make use of Sparse regression for eQTL mapping (LORS). We integrate the low-rank representation and sparse regression into a unified framework, in which single-nucleotide polymorphisms and gene probes can be jointly analyzed. Given the two model parameters, our formulation is a convex optimization problem. We have developed an efficient algorithm to solve this problem and its convergence is guaranteed. We demonstrate its ability to account for non-genetic effects using simulation, and then apply it to two independent real datasets. Our results indicate that LORS is an effective tool to account for non-genetic effects. First, our detected associations show higher consistency between studies than recently proposed methods. Second, we have identified some new hotspots that can not be identified without accounting for non-genetic effects. Availability: The software is available at: http://bioinformatics.med.yale.edu/software.aspx. Contact: hongyu.zhao@yale.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23419377

  19. Mapping and Introgression of QTL Involved in Fruit Shape Transgressive Segregation into ‘Piel de Sapo’ Melon (Cucucumis melo L.)

    PubMed Central

    Díaz, Aurora; Zarouri, Belkacem; Fergany, Mohamed; Eduardo, Iban; Álvarez, José M.; Picó, Belén; Monforte, Antonio J.

    2014-01-01

    A mapping F2 population from the cross ‘Piel de Sapo’ × PI124112 was selectively genotyped to study the genetic control of morphological fruit traits by QTL (Quantitative Trait Loci) analysis. Ten QTL were identified, five for FL (Fruit Length), two for FD (Fruit Diameter) and three for FS (Fruit Shape). At least one robust QTL per character was found, flqs8.1 (LOD?=?16.85, R2?=?34%), fdqs12.1 (LOD?=?3.47, R2?=?11%) and fsqs8.1 (LOD?=?14.85, R2?=?41%). flqs2.1 and fsqs2.1 cosegregate with gene a (andromonoecious), responsible for flower sex determination and with pleiotropic effects on FS. They display a positive additive effect (a) value, so the PI124112 allele causes an increase in FL and FS, producing more elongated fruits. Conversely, the negative a value for flqs8.1 and fsqs8.1 indicates a decrease in FL and FS, what results in rounder fruits, even if PI124112 produces very elongated melons. This is explained by a significant epistatic interaction between fsqs2.1 and fsqs8.1, where the effects of the alleles at locus a are attenuated by the additive PI124112 allele at fsqs8.1. Roundest fruits are produced by homozygous for PI124112 at fsqs8.1 that do not carry any dominant A allele at locus a (PiPiaa). A significant interaction between fsqs8.1 and fsqs12.1 was also detected, with the alleles at fsqs12.1 producing more elongated fruits. fsqs8.1 seems to be allelic to QTL discovered in other populations where the exotic alleles produce elongated fruits. This model has been validated in assays with backcross lines along 3 years and ultimately obtaining a fsqs8.1-NIL (Near Isogenic Line) in ‘Piel de Sapo’ background which yields round melons. PMID:25126852

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

    PubMed

    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

    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

  1. Using a limited mapping strategy to identify major QTL’s for resistance to grapevine powdery mildew (Erysiphe necator) and their use in marker-assisted breeding.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A limited genetic mapping strategy was used to develop genetic markers in populations segregating for powdery mildew (Erysiphe necator) resistance. A genetic map was constructed and QTL analysis completed on a population derived from Muscadinia rotundifolia cv. Magnolia. In two additional populati...

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

    PubMed

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

    2015-04-01

    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

  3. Expression Quantitative Trait Loci (eQTL) Mapping in Puerto Rican Children

    PubMed Central

    Chen, Wei; Brehm, John M.; Lin, Jerome; Wang, Ting; Forno, Erick; Acosta-Pérez, Edna; Boutaoui, Nadia; Canino, Glorisa; Celedón, Juan C.

    2015-01-01

    Background Expression quantitative trait loci (eQTL) have been identified using tissue or cell samples from diverse human populations, thus enhancing our understanding of regulation of gene expression. However, few studies have attempted to identify eQTL in racially admixed populations such as Hispanics. Methods We performed a systematic eQTL study to identify regulatory variants of gene expression in whole blood from 121 Puerto Rican children with (n = 63) and without (n = 58) asthma. Genome-wide genotyping was conducted using the Illumina Omni2.5M Bead Chip, and gene expression was assessed using the Illumina HT-12 microarray. After completing quality control, we performed a pair-wise genome analysis of ~15 K transcripts and ~1.3 M SNPs for both local and distal effects. This analysis was conducted under a regression framework adjusting for age, gender and principal components derived from both genotypic and mRNA data. We used a false discovery rate (FDR) approach to identify significant eQTL signals, which were next compared to top eQTL signals from existing eQTL databases. We then performed a pathway analysis for our top genes. Results We identified 36,720 local pairs in 3,391 unique genes and 1,851 distal pairs in 446 unique genes at FDR <0.05, corresponding to unadjusted P values lower than 1.5x10-4 and 4.5x10-9, respectively. A significant proportion of genes identified in our study overlapped with those identified in previous studies. We also found an enrichment of disease-related genes in our eQTL list. Conclusions We present results from the first eQTL study in Puerto Rican children, who are members of a unique Hispanic cohort disproportionately affected with asthma, prematurity, obesity and other common diseases. Our study confirmed eQTL signals identified in other ethnic groups, while also detecting additional eQTLs unique to our study population. The identified eQTLs will help prioritize findings from future genome-wide association studies in Puerto Ricans. PMID:25816334

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

    PubMed

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

    2013-11-01

    Improvement of resistance to Fusarium head blight (FHB) is a continuous challenge for durum wheat breeders, particularly due to the limited genetic variation within this crop species. We accordingly generated a backcross-derived mapping population using the type 2 FHB resistant Triticum dicoccoides line Mt. Gerizim #36 as donor and the modern Austrian T. durum cultivar Helidur as recipient; 103 BC1F6:7 lines were phenotyped for type 2 FHB resistance using single-spikelet inoculations and genotyped with 421 DNA markers (SSR and AFLP). QTL mapping revealed two highly significant QTL, mapping to chromosomes 3A and 6B, respectively. For both QTL the T. dicoccoides allele improved type 2 FHB resistance. Recombinant lines with both favorable alleles fixed conferred high resistance to FHB similar to that observed in the T. dicoccoides parent. The results appear directly applicable for durum wheat resistance breeding. PMID:23921957

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

    PubMed Central

    2014-01-01

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

  6. Fine-mapping natural alleles: quantitative complementation to the rescue

    PubMed Central

    Turner, Thomas L.

    2014-01-01

    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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  9. A fast algorithm for estimating transmission probabilities in QTL detection designs with dense maps

    PubMed Central

    2009-01-01

    Background In the case of an autosomal locus, four transmission events from the parents to progeny are possible, specified by the grand parental origin of the alleles inherited by this individual. Computing the probabilities of these transmission events is essential to perform QTL detection methods. Results A fast algorithm for the estimation of these probabilities conditional to parental phases has been developed. It is adapted to classical QTL detection designs applied to outbred populations, in particular to designs composed of half and/or full sib families. It assumes the absence of interference. Conclusion The theory is fully developed and an example is given. PMID:19919698

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2014-02-15

    A preliminary linkage map was constructed by applying backcross and testcross strategy using microsatellite (SSR) markers developed for Xiphophorus and Poecilia reticulata in ornamental fish, molly Poecilia sp. The linkage map having 18 SSR loci consisted of four linkage groups that spanned a map size of 516.1cM. Association between genotypes and phenotypes was tested in a random fashion and QTL for dorsal fin length was found to be linked to locus Msb069 on linkage group 2. Coincidentally, locus Msb069 was also reported as putative homologue primer pairs containing SSRs repeat motif which encoded hSMP-1, a sex determining locus. Dorsal fin length particularly in males of Poecilia latipinna is an important feature during courtship display. Therefore, we speculate that both dorsal fin length and putative hSMP-1 gene formed a close proximity to male sexual characteristics. PMID:24333858

  12. QTL Mapping Based on Different Genetic Systems for Essential Amino Acid Contents in Cottonseeds in Different Environments

    PubMed Central

    Chen, Jinhong; Li, Jinrong; Huang, Zhuangrong; He, Qiuling; Zhu, Shuijin; Shi, Chunhai

    2013-01-01

    Cottonseeds are rich in various essential amino acids. However, the inheritance of them at molecular level are still not defined across various genetic systems. In the present study, using a newly developed mapping model that can analyze the embryo and maternal main effects as well as QTL × environment interaction effects on quantitative quality trait loci (QTLs) in cottonseeds, a study on QTL located in the tetraploid embryo and tetraploid maternal plant genomes for essential amino acid contents in cottonseeds under different environments was carried out, using the immortal F2 (IF2) populations from a set of 188 recombinant inbred lines derived from an intraspecific hybrid cross of two upland cotton germplasms HS46 and MARKCBUCAG8US-1-88 as experimental materials. The results showed a total of 35 QTLs associated with these quality traits in cottonseeds. Nineteen QTLs were subsequently mapped on chromosome 5, 6 and 8 in sub-A genome and chromosome 15, 18, 22 and 23 in sub-D genome. Eighteen QTLs were also found having QTL × environment (QE) interaction effects. The genetic main effects from QTLs located on chromosomes in the embryo and maternal plant genomes and their QE effects in different environments were all important for these essential amino acids in cottonseeds. The results suggested that the influence of environmental factors on the expression of some QTLs located in different genetic systems should be considered when improving for these amino acids. This study can serve as the foundation for the improvement of these essential amino acids in cottonseeds. PMID:23555562

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines

    E-print Network

    Weigel, Detlef

    two closely linked loci are detected as a single QTL. One strategy to increase the power of precisely-Term Fellowship ALTF-473 (SB), NIH grant GM62932 (JC & DW), ERA- PG (BMBF) Grant ARABRAS, and a Gottfried Wilhelm Leibniz Award from the DFG (DW), the Howard Hughes Medical Institute, and the Max Planck Society

  15. Tests of candidate genes in breed cross populations for QTL mapping in livestock

    Microsoft Academic Search

    Honghua Zhao; Max F. Rothschild; Rohan L. Fernando; Jack C. M. Dekkers

    2003-01-01

    In recent years, several F 2 crosses between outbred lines of livestock have been developed to identify quantitative trait loci (QTL). These populations are valuable for further genetic analysis, including positional candidate gene loci (CGL). Analysis of CGL in F 2 populations is, however, hindered by extensive between-breed linkage disequilibrium (LD). The objectives here were to develop and evaluate three

  16. COMPARATIVE MAPPING OF A REGION ON CHROMOSOME 10 CONTAINING QTL FOR REPRODUCTION IN SWINE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several quantitative trait loci (QTL) for important reproductive traits (age of puberty, ovulation rate, nipple number and plasma FSH) have been identified on the long arm of porcine chromosome 10. Bi-directional chromosome painting has shown that this region is homologous to human chromosome 10p. ...

  17. SEED PROTEIN AND OIL QTL MAPPING IN THREE BACKCROSS SOYBEAN POPULATIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean seed has the highest concentration of crude protein among all sources of vegetable protein. Currently, soybean meal accounts for two-thirds of the total value seed. The objectives of this study were to identify QTL associated with protein and oil in three backcross populations and to asses...

  18. MAPPING OF FUSARIUM HEAD BLIGHT QTL IN THE CHINESE WHEAT LINE FUJIAN 5114

    Microsoft Academic Search

    D. E. Bowen; S. Liu; R. Dill-Macky; C. K. Evans; J. A. Anderson

    Many Chinese wheat lines have been introduced into wheat breeding programs because of their resistance to Fusarium head blight (FHB). It is anticipated that these lines will provide diversity for resistance genes. Sumai 3, a popular resistance source from China, has been well characterized for scab resistance QTL. Fujian 5114, a Chinese wheat derived from the cross Longxi18\\/Ning8017, has resistance

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

    PubMed Central

    2012-01-01

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

  20. QTL analysis for rice grain length and fine mapping of an identified QTL with stable and major effects

    Microsoft Academic Search

    X. Y. Wan; J. M. Wan; L. Jiang; J. K. Wang; H. Q. Zhai; J. F. Weng; H. L. Wang; C. L. Lei; X. Zhang; Z. J. Cheng; X. P. Guo

    2006-01-01

    Grain length in rice plays an important role in determining rice appearance, milling, cooking and eating quality. In this\\u000a study, the genetic basis of grain length was dissected into six main-effect quantitative trait loci (QTLs) and twelve pairs\\u000a of epistatic QTLs. The stability of these QTLs was evaluated in four environments using an F7 recombinant inbred line (RIL) population derived

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    2013-01-01

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

  3. Development of genetic markers linked to straighthead resistance through fine mapping in rice (Oryza sativa L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Straighthead, characterized by sterile florets and distorted spikelets, results in significant yield losses in rice and occurs in many countries. The current prevention method of draining paddies early in the season stresses plants, is costly and wastes water. We mapped QTL for straighthead resistan...

  4. Genet. Res., Camb. (1998), 71, pp. 133141. With 2 figures. Printed in the United Kingdom # 1998 Cambridge University Press 133 QTL mapping of genotypeenvironment interaction for

    E-print Network

    Mackay, Trudy F.C.

    1998-01-01

    recombinant inbred (RI) lines derived from a cross between two D. melanogaster laboratory strains. The threeGenet. Res., Camb. (1998), 71, pp. 133­141. With 2 figures. Printed in the United Kingdom # 1998 Cambridge University Press 133 QTL mapping of genotype­environment interaction for fitness in Drosophila

  5. Fine mapping of the major Soybean dwarf virus resistance gene Rsdv1 of the soybean cultivar ‘Wilis’

    PubMed Central

    Yamashita, Yoko; Takeuchi, Toru; Ohnishi, Shizen; Sasaki, Jun; Tazawa, Akiko

    2013-01-01

    Soybean dwarf virus (SbDV), a Luteoviridae family member, causes dwarfing, yellowing and sterility of soybean (Glycine max), leading to one of the most serious problems in soybean production in northern Japan. Previous studies revealed that the Indonesian soybean cultivar ‘Wilis’ is resistant to SbDV and that the resistance can be introduced into Japanese cultivars. A major QTL for SbDV resistance has been reported between SSR markers Sat_217 and Satt211 on chromosome 5. In this study, we named this QTL Rsdv1 (resistance to SbDV) and developed near-isogenic lines incorporating Rsdv1 (Rsdv1-NILs) using Sat_217 and Satt211 markers. The Rsdv1-NILs were resistant to SbDV in greenhouse inoculation and field tests, indicating that Rsdv1 alone is sufficient for the resistance phenotype. We fine-mapped Rsdv1 within the 44-kb region between Sat_11 and Sct_13. None of the six genes predicted in this region was closely related to known virus resistance genes in plants. Thus, Rsdv1 may confer resistance by a previously unknown mechanism. We suggest that Rsdv1 may be a useful source for the Japanese soybean breeding program to introduce SbDV resistance. PMID:24399914

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

    PubMed

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

    2013-11-01

    Advancements in genotyping are rapidly decreasing marker costs and increasing marker density. This opens new possibilities for mapping quantitative trait loci (QTL), in particular by combining linkage disequilibrium information and linkage analysis (LDLA). In this study, we compared different approaches to detect QTL for four traits of agronomical importance in two large multi-parental datasets of maize (Zea mays L.) of 895 and 928 testcross progenies composed of 7 and 21 biparental families, respectively, and genotyped with 491 markers. We compared to traditional linkage-based methods two LDLA models relying on the dense genotyping of parental lines with 17,728 SNP: one based on a clustering approach of parental line segments into ancestral alleles and one based on single marker information. The two LDLA models generally identified more QTL (60 and 52 QTL in total) than classical linkage models (49 and 44 QTL in total). However, they performed inconsistently over datasets and traits suggesting that a compromise must be found between the reduction of allele number for increasing statistical power and the adequacy of the model to potentially complex allelic variation. For some QTL, the model exclusively based on linkage analysis, which assumed that each parental line carried a different QTL allele, was able to capture remaining variation not explained by LDLA models. These complementarities between models clearly suggest that the different QTL mapping approaches must be considered to capture the different levels of allelic variation at QTL involved in complex traits. PMID:23975245

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

    PubMed Central

    2013-01-01

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

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

    PubMed

    Rogers, S M; Bernatchez, L

    2005-02-01

    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

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

    PubMed

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

    2013-07-01

    Fire blight, incited by the enterobacterium Erwinia amylovora, is a destructive disease of Rosaceae, particularly of apples and pears. There are reports on the molecular mechanisms underlying E. amylovora pathogenesis and how the host activates its resistance mechanism. The host's resistance mechanism is quantitatively controlled, although some major genes might also be involved. Thus far, quantitative trait loci (QTL) mapping and differential expression studies have been used to elucidate those genes and/or genomic regions underlying quantitative resistance present in the apple genome. In this study, an effort is undertaken to dissect the genetic basis of fire blight resistance in apple using both QTL and genome-wide association mapping. On the basis of an F1 pedigree of 'Coop 16'?×?'Coop 17' and a genome-wide association study (GWAS) mapping population of Malus accessions (species, old and new cultivars and selections), new QTLs and associations have been identified. A total of three QTLs for resistance to fire blight, with above 95% significant logarithm of odds threshold value of 2.5, have been identified on linkage groups (LGs) 02, 06, and 15 of the apple genome with phenotypic variation explained values of 14.7, 20.1 and 17.4, respectively. Although elevated P-values with signals for marker-trait associations are observed for some LGs, these are not found to be significant. However, a total of 34 significant associations, with P-values ?0.02, have been detected including 8 for lesion length at 7?days following inoculation (PL1), 14 for lesion length at 14?days following inoculation (PL2), and 12 for shoot length. PMID:23627651

  10. mQTL.NMR: An Integrated Suite for Genetic Mapping of Quantitative Variations of (1)H NMR-Based Metabolic Profiles.

    PubMed

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

    2015-04-21

    High-throughput (1)H nuclear magnetic resonance (NMR) is an increasingly popular robust approach for qualitative and quantitative metabolic profiling, which can be used in conjunction with genomic techniques to discover novel genetic associations through metabotype quantitative trait locus (mQTL) mapping. There is therefore a crucial necessity to develop specialized tools for an accurate detection and unbiased interpretability of the genetically determined metabolic signals. Here we introduce and implement a combined chemoinformatic approach for objective and systematic analysis of untargeted (1)H NMR-based metabolic profiles in quantitative genetic contexts. The R/Bioconductor mQTL.NMR package was designed to (i) perform a series of preprocessing steps restoring spectral dependency in collinear NMR data sets to reduce the multiple testing burden, (ii) carry out robust and accurate mQTL mapping in human cohorts as well as in rodent models, (iii) statistically enhance structural assignment of genetically determined metabolites, and (iv) illustrate results with a series of visualization tools. Built-in flexibility and implementation in the powerful R/Bioconductor framework allow key preprocessing steps such as peak alignment, normalization, or dimensionality reduction to be tailored to specific problems. The mQTL.NMR package is freely available with its source code through the Comprehensive R/Bioconductor repository and its own website ( http://www.ican-institute.org/tools/ ). It represents a significant advance to facilitate untargeted metabolomic data processing and quantitative analysis and their genetic mapping. PMID:25803548

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

    PubMed Central

    Andriantahina, Farafidy; Liu, Xiaolin; Huang, Hao

    2013-01-01

    Growth is a priority trait from the point of view of genetic improvement. Molecular markers linked to quantitative trait loci (QTL) have been regarded as useful for marker-assisted selection (MAS) in complex traits as growth. Using an intermediate F2 cross of slow and fast growth parents, a genetic linkage map of Pacific whiteleg shrimp, Litopenaeusvannamei, based on amplified fragment length polymorphisms (AFLP) and simple sequence repeats (SSR) markers was constructed. Meanwhile, QTL analysis was performed for growth-related traits. The linkage map consisted of 451 marker loci (429 AFLPs and 22 SSRs) which formed 49 linkage groups with an average marker space of 7.6 cM; they spanned a total length of 3627.6 cM, covering 79.50% of estimated genome size. 14 QTLs were identified for growth-related traits, including three QTLs for body weight (BW), total length (TL) and partial carapace length (PCL), two QTLs for body length (BL), one QTL for first abdominal segment depth (FASD), third abdominal segment depth (TASD) and first abdominal segment width (FASW), which explained 2.62 to 61.42% of phenotypic variation. Moreover, comparison of linkage maps between L. vannamei and Penaeusjaponicus was applied, providing a new insight into the genetic base of QTL affecting the growth-related traits. The new results will be useful for conducting MAS breeding schemes in L. vannamei. PMID:24086466

  12. A Molecular Genetic Linkage Map of Eucommia ulmoides and Quantitative Trait Loci (QTL) Analysis for Growth Traits

    PubMed Central

    Li, Yu; Wang, Dawei; Li, Zhouqi; Wei, Junkun; Jin, Cangfu; Liu, Minhao

    2014-01-01

    Eucommia ulmoides is an economically important tree species for both herbal medicine and organic chemical industry. Effort to breed varieties with improved yield and quality is limited by the lack of knowledge on the genetic basis of the traits. A genetic linkage map of E. ulmoides was constructed from a full-sib family using sequence-related amplified polymorphism, amplified fragment length polymorphism, inter-simple sequence repeat and simple sequence repeat markers. In total, 706 markers were mapped in 25 linkage groups covering 2133 cM. The genetic linkage map covered approximately 89% of the estimated E. ulmoides genome with an average of 3.1 cM between adjacent markers. The present genetic linkage map was used to identify quantitative trait loci (QTL) affecting growth-related traits. Eighteen QTLs were found to explain 12.4%–33.3% of the phenotypic variance. This genetic linkage map provides a tool for marker-assisted selection and for studies of genome in E. ulmoides. PMID:24477264

  13. Linkage Relationships Among Multiple QTL for Horticultural Traits and Late Blight (P. infestans) Resistance on Chromosome 5 Introgressed from Wild Tomato Solanum habrochaites

    PubMed Central

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

    2013-01-01

    When the allele of a wild species at a quantitative trait locus (QTL) conferring a desirable trait is introduced into cultivated species, undesirable effects on other traits may occur. These negative phenotypic effects may result from the presence of wild alleles at other closely linked loci that are transferred along with the desired QTL allele (i.e., linkage drag) and/or from pleiotropic effects of the desired allele. Previously, a QTL for resistance to Phytophthora infestans on chromosome 5 of Solanum habrochaites was mapped and introgressed into cultivated tomato (S. lycopersicum). Near-isogenic lines (NILs) were generated and used for fine-mapping of this resistance QTL, which revealed coincident or linked QTL with undesirable effects on yield, maturity, fruit size, and plant architecture traits. Subsequent higher-resolution mapping with chromosome 5 sub-NILs revealed the presence of multiple P. infestans resistance QTL within this 12.3 cM region. In our present study, these 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 the course of two years. Each previously detected single horticultural trait QTL fractionated into two or more QTL. A total of 41 QTL were detected across all traits, with ?30% exhibiting significant QTL × environment interactions. Colocation of QTL for multiple traits suggests either pleiotropy or tightly linked genes control these traits. The complex genetic architecture of horticultural and P. infestans resistance trait QTL within this S. habrochaites region of chromosome 5 presents challenges and opportunities for breeding efforts in cultivated tomato. PMID:24122052

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

    PubMed Central

    2013-01-01

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

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

    PubMed Central

    2012-01-01

    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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2013-03-01

    Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be 'adaptive' to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes. PMID:23124431

  19. 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

    2013-01-01

    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

  20. 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)

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

    2015-01-01

    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.

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

    PubMed

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

    2004-07-01

    The different response to growth on serpentine soil is a major autecological difference between the annual asteracean species Microseris douglasii and M. bigelovii, with nearly non-overlapping distribution ranges in California. Early flowering and seed set is regarded as a crucial character contributing to escape drought and thus is strongly correlated with survival and reproductive success on serpentine as naturally toxic soil. M. bigelovii (strain C94) from non-serpentine soil produces more leaves at the expense of bud production in the first growing phase than M. douglasii (B14) from serpentine soil. A QTL mapping study for this trade-off and for other growth-related traits was performed after six generations of inbreeding (F7) from a single interspecific hybrid between B14 and C94 on plants that were grown on serpentine and alternatively on normal potting soil. The trade-off is mainly correlated with markers on one map region on linkage group 03a (lg03a) with major phenotypic effects (phenotypic variance explained [PVE] = 18.8 - 31.7 %). Plants with the M. douglasii allele in QTL-B1 (QTL-NL1) produce more buds but fewer leaves in the first 119 days on both soil types. Three modifier QTL could be mapped for bud and leaf production. In one modifier (QTL-B2 = QTL-NL4) the M. douglasii allele is again associated with more buds but fewer leaves. QTL mapped for bud set in the F6 co-localize with QTL-B1 (major QTL) and QTL-B3. Two additional QTL for leaf length and red coloration of leaves could be mapped to one map region on lg03a. Co-localization of the two QTL loci with major phenotypic effects on bud and leaf production strongly suggests that a major genetic locus controls the trade-off between the two adaptive traits. The importance of mutational changes in major genes for the adaptation to stressful environments is discussed. PMID:15248127

  2. ORIGINAL PAPER Fine mapping QMi-C11 a major QTL controlling root-knot

    E-print Network

    Chee, Peng W.

    of five individuals, with each being homozygous for the two parental alleles. From a survey of 1,152 AFLP primer combinations, 9 AFLP markers closely linked to the target region were identified. By screening to a 3.6-cM interval flanked by the SSR marker CIR069 and the AFLP marker E14M27-375. These results

  3. Fine mapping of the grain chalkiness QTL qPGWC-7 in rice ( Oryza sativa L.)

    Microsoft Academic Search

    Lijun Zhou; Liangming Chen; Ling Jiang; Wenwei Zhang; Linglong Liu; Xi Liu; Zhigang Zhao; Shijia Liu; Lujun Zhang; Jiankang Wang; Jianmin Wan

    2009-01-01

    s  Chalkiness of rice grain is an important quality component of rice, as it has a profound influence on eating and milling qualities.\\u000a We has determined the inheritance of percentage of grain with chalkiness (PGWC) using a set of chromosome segment substitution\\u000a lines, made from a cross between cv. PA64s and cv. 9311. Two loci controlling PGWC, designated as qPGWC-6 and

  4. Meta-QTL analysis of the genetic control of ear emergence in elite European winter wheat germplasm.

    PubMed

    Griffiths, Simon; Simmonds, James; Leverington, Michelle; Wang, Yingkun; Fish, Lesley; Sayers, Liz; Alibert, Leodie; Orford, Simon; Wingen, Luzie; Herry, Laurence; Faure, Sebastien; Laurie, David; Bilham, Lorelei; Snape, John

    2009-08-01

    Variation in ear emergence time is critical for the adaptation of wheat (Triticum aestivum L.) to specific environments. The aim of this study was to identify genes controlling ear emergence time in elite European winter wheat germplasm. Four doubled haploid populations derived from the crosses: Avalon x Cadenza, Savannah x Rialto, Spark x Rialto, and Charger x Badger were selected which represent diversity in European winter wheat breeding programmes. Ear emergence time was recorded as the time from 1st May to heading in replicated field trials in the UK, France and Germany. Genetic maps based on simple sequence repeat (SSR) and Diversity Arrays Technology (DArT) markers were constructed for each population. One hundred and twenty-seven significant QTL were identified in the four populations. These effects were condensed into 19 meta-QTL projected onto a consensus SSR map of wheat. These effects are located on chromosomes 1B (2 meta-QTL), 1D, 2A (2 meta-QTL), 3A, 3B (2 meta-QTL), 4B, 4D, 5A (2 meta-QTL), 5B, 6A, 6B 7A (2 meta-QTL), 7B and 7D. The identification of environmentally robust earliness per se effects will facilitate the fine tuning of ear emergence in predictive wheat breeding programmes. PMID:19430758

  5. 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

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

    2014-01-01

    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

  6. Genetic and epigenetic fine mapping of causal autoimmune disease variants.

    PubMed

    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

    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

  7. A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea.

    PubMed

    Bajaj, Deepak; Upadhyaya, Hari D; Khan, Yusuf; Das, Shouvik; Badoni, Saurabh; Shree, Tanima; Kumar, Vinod; Tripathi, Shailesh; Gowda, C L L; Singh, Sube; Sharma, Shivali; Tyagi, Akhilesh K; Chattopdhyay, Debasis; Parida, Swarup K

    2015-01-01

    High experimental validation/genotyping success rate (94-96%) and intra-specific polymorphic potential (82-96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94?cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8-25.8% with LOD: 7.0-13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8?kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1-171.3?cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea. PMID:25786576

  8. A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea

    PubMed Central

    Bajaj, Deepak; Upadhyaya, Hari D.; Khan, Yusuf; Das, Shouvik; Badoni, Saurabh; Shree, Tanima; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Singh, Sube; Sharma, Shivali; Tyagi, Akhilesh K.; Chattopdhyay, Debasis; Parida, Swarup K.

    2015-01-01

    High experimental validation/genotyping success rate (94–96%) and intra-specific polymorphic potential (82–96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94?cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8–25.8% with LOD: 7.0–13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8?kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1–171.3?cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea. PMID:25786576

  9. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight

    Microsoft Academic Search

    Jianfeng Weng; Suhai Gu; Xiangyuan Wan; He Gao; Tao Guo; Ning Su; Cailin Lei; Xin Zhang; Zhijun Cheng; Xiuping Guo; Jiulin Wang; Ling Jiang; Huqu Zhai; Jianmin Wan

    2008-01-01

    Grain weight is a major determinant of crop grain yield and is controlled by naturally occurring quantitative trait loci (QTLs). We earlier identified a major QTL that controls rice grain width and weight, GW5, which was mapped to a recombination hotspot on rice chromosome 5. To gain a better understanding of how GW5 controls rice grain width, we conducted fine

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

    PubMed Central

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

    2013-01-01

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

  11. Microarray-assisted fine-mapping of quantitative trait loci for cold tolerance in rice.

    PubMed

    Liu, Fengxia; Xu, Wenying; Song, Qian; Tan, Lubin; Liu, Jiayong; Zhu, Zuofeng; Fu, Yongcai; Su, Zhen; Sun, Chuanqing

    2013-05-01

    Many important agronomic traits, including cold stress resistance, are complex and controlled by quantitative trait loci (QTLs). Isolation of these QTLs will greatly benefit the agricultural industry but it is a challenging task. This study explored an integrated strategy by combining microarray with QTL-mapping in order to identify cold-tolerant QTLs from a cold-tolerant variety IL112 at early-seedling stage. All the early seedlings of IL112 survived normally for 9 d at 4-5°C, while Guichao2 (GC2), an indica cultivar, died after 4 d under the same conditions. Using the F2:3 population derived from the progeny of GC2 and IL112, we identified seven QTLs for cold tolerance. Furthermore, we performed Affymetrix rice whole-genome array hybridization and obtained the expression profiles of IL112 and GC2 under both low-temperature and normal conditions. Four genes were selected as cold QTL-related candidates, based on microarray data mining and QTL-mapping. One candidate gene, LOC_Os07g22494, was shown to be highly associated with cold tolerance in a number of rice varieties and in the F2:3 population, and its overexpression transgenic rice plants displayed strong tolerance to low temperature at early-seedling stage. The results indicated that overexpression of this gene (LOC_Os07g22494) could increase cold tolerance in rice seedlings. Therefore, this study provides a promising strategy for identifying candidate genes in defined QTL regions. PMID:23267004

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

    PubMed Central

    2012-01-01

    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

  13. 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...

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

    PubMed

    Ma, Xuexia; Ding, Yezhang; Zhou, Baoliang; Guo, Wangzhen; Lv, Yanhui; Zhu, Xiefei; Zhang, Tianzhen

    2008-12-01

    Asiatic cotton (Gossypium arboreum L.) is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species was replaced by the New World allotetraploid cotton G. hirsutum L. Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs. In addition, G. arboreum serves as a model for genomic research in Gossypium. In the present study, we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 13 linkage groups. The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci. A population containing 176 F(2:3) families was used to perform quantitative trait loci (QTL) mapping for 17 phenotypes using Multiple QTL Model (MQM) of MapQTL ver 5.0. Overall, 108 QTLs were detected on 13 chromosomes. Thirty-one QTLs for yield and its components were detected in the F2 population. Forty-one QTLs for yield and its components were detected in the F(2:3) families with a total of 43 QTLs for fiber qualities. Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F2 and F(2:3). Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals. These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes. PMID:19103431

  15. Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities.

    PubMed

    Dixit, Shalabh; Swamy, B P Mallikarjuna; Vikram, Prashant; Ahmed, H U; Sta Cruz, M T; Amante, Modesto; Atri, Dinesh; Leung, Hei; Kumar, Arvind

    2012-06-01

    Fine-mapping studies on four QTLs, qDTY(2.1), qDTY(2.2), qDTY(9.1) and qDTY(12.1), for grain yield (GY) under drought were conducted using four different backcross-derived populations screened in 16 experiments from 2006 to 2010. Composite and bayesian interval mapping analyses resolved the originally identified qDTY(2.1) region of 42.3 cM into a segment of 1.6 cM, the qDTY(2.2) region of 31.0 cM into a segment of 6.7 cM, the qDTY(9.1) region of 32.1 cM into two segments of 9.4 and 2.4 cM and the qDTY(12.1) region of 10.6 cM into two segments of 3.1 and 0.4 cM. Two of the four QTLs (qDTY(9.1) and qDTY(12.1)) having effects under varying degrees of stress severity showed the presence of more than one region within the original QTL. The study found the presence of a donor allele at RM262 within qDTY(2.1) and RM24334 within qDTY(9.1) showing a negative effect on GY under drought, indicating the necessity of precise fine mapping of QTL regions before using them in marker-assisted selection (MAS). However, the presence of sub-QTLs together in close vicinity to each other provides a unique opportunity to breeders to introgress such regions together as a unit into high-yielding drought-susceptible varieties through MAS. PMID:22361948

  16. Resistance loci affecting distinct stages of fungal pathogenesis: use of introgression lines for QTL mapping and characterization in the maize - Setosphaeria turcica pathosystem

    PubMed Central

    2010-01-01

    Background Studies on host-pathogen interactions in a range of pathosystems have revealed an array of mechanisms by which plants reduce the efficiency of pathogenesis. While R-gene mediated resistance confers highly effective defense responses against pathogen invasion, quantitative resistance is associated with intermediate levels of resistance that reduces disease progress. To test the hypothesis that specific loci affect distinct stages of fungal pathogenesis, a set of maize introgression lines was used for mapping and characterization of quantitative trait loci (QTL) conditioning resistance to Setosphaeria turcica, the causal agent of northern leaf blight (NLB). To better understand the nature of quantitative resistance, the identified QTL were further tested for three secondary hypotheses: (1) that disease QTL differ by host developmental stage; (2) that their performance changes across environments; and (3) that they condition broad-spectrum resistance. Results Among a set of 82 introgression lines, seven lines were confirmed as more resistant or susceptible than B73. Two NLB QTL were validated in BC4F2 segregating populations and advanced introgression lines. These loci, designated qNLB1.02 and qNLB1.06, were investigated in detail by comparing the introgression lines with B73 for a series of macroscopic and microscopic disease components targeting different stages of NLB development. Repeated greenhouse and field trials revealed that qNLB1.06Tx303 (the Tx303 allele at bin 1.06) reduces the efficiency of fungal penetration, while qNLB1.02B73 (the B73 allele at bin 1.02) enhances the accumulation of callose and phenolics surrounding infection sites, reduces hyphal growth into the vascular bundle and impairs the subsequent necrotrophic colonization in the leaves. The QTL were equally effective in both juvenile and adult plants; qNLB1.06Tx303 showed greater effectiveness in the field than in the greenhouse. In addition to NLB resistance, qNLB1.02B73 was 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

  17. Genetic dissection of rice blast resistance by QTL mapping approach using an F3 population.

    PubMed

    Ashkani, S; Rafii, M Y; Rahim, H A; Latif, M A

    2013-03-01

    Rice blast is one of the major fungal diseases that badly reduce rice production in Asia including Malaysia. There is not much information on identification of QTLs as well as linked markers and their association with blast resistance within local rice cultivars. In order to understanding of the genetic control of blast in the F3 families from indica rice cross Pongsu seribu2/Mahsuri, an analysis of quantitative trait loci against one of the highly virulent Malaysian rice blast isolate Magnaporthe oryzae, P5.0 was carried out. Result indicated that partial resistance to this pathotype observed in the present study was controlled by multiple loci or different QTLs. In QTL analysis in F3 progeny fifteen QTLs on chromosomes 1, 2, 3, 5, 6, 11 and 12 for resistance to blast nursery tests was identified. Three of detected QTLs (qRBr-6.1, qRBr-11.4, and qRBr-12.1) had significant threshold (LOD >3) and approved by both IM and CIM methods. Twelve suggestive QTLs, qRBr-1.2, qRBr-2.1, qRBr-4.1, qRBr-5.1, qRBr-6.2, qRBr-6.3, qRBr-8.1, qRBr-10.1, qRBr-10.2, qRBr-11.1, qRBr-11.2 and qRBr-11.3) with Logarithmic of Odds (LOD) <3.0 or LRS <15) were distributed on chromosomes 1, 2, 4, 5, 6, 8, 10, and 11. Most of the QTLs detected using single isolate had the resistant alleles from Pongsu seribu 2 which involved in the resistance in the greenhouse. We found that QTLs detected for deferent traits for the using isolate were frequently located in similar genomic regions. Inheritance study showed among F3 lines resistance segregated in the expected ratio of 15: 1 for resistant to susceptible. The average score for blast resistance measured in the green house was 3.15, 1.98 and 29.95 % for three traits, BLD, BLT and % DLA, respectively. PMID:23203411

  18. THE SEARCH FOR QTL IN BARLEY (HORDEUM VULGARE L.) USING A NEW MAPPING POPULATION

    Microsoft Academic Search

    GERHARD H. BUCK-SORLIN

    2002-01-01

    Ninety-nine different lines of the Doubled-Haploid F2 winter barley population W766 ('Angora' x 'W704\\/137') were genetically fingerprinted using AFLP, microsatellite, morphological and resistance markers. A preliminary map consisting of seven linkage groups is presented. The map contains a highly distorted region on the long arm of chromosome 3H reflecting preselection of the genotypes for resistance against barley mild mosaic virus.

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

    PubMed Central

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common garden experiment. The F2 offspring of a hybrid poplar (Populus trichocarpa x P. deltoides) cross were assessed for seven categories of insect leaf damage at two time points, June and August. Positive and negative correlations were detected among damage categories and between sampling times. For example, sap suckers on leaves in June were positively correlated with sap suckers on leaves (P<0.001) but negatively correlated with skeletonizer damage (P<0.01) in August. The seven forms of leaf damage were used as a proxy for seven functional groups of insect species. Significant variation in insect association occurred among the hybrid offspring, including transgressive segregation of susceptibility to damage. NMDS analyses revealed significant variation and modest broad-sense heritability in insect community structure among genets. QTL analyses identified 14 genomic regions across 9 linkage groups that correlated with insect association. We used three genomics tools to test for putative mechanisms underlying the QTL. First, shikimate-phenylpropanoid pathway genes co-located to 9 of the 13 QTL tested, consistent with the role of phenolic glycosides as defensive compounds. Second, two insect association QTL corresponded to genomic hotspots for leaf trait QTL as identified in previous studies, indicating that, in addition to biochemical attributes, leaf morphology may influence insect preference. Third, network analyses identified categories of gene models over-represented in QTL for certain damage types, providing direction for future functional studies. These results provide insight into the genetic components involved in insect community structure in a fast-growing forest tree. PMID:24260320

  1. A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits

    Microsoft Academic Search

    Rosemarie Weikard; Tom Goldammer; Pascal Laurent; James E Womack; Christa Kuehn

    2006-01-01

    BACKGROUND: A number of different quantitative trait loci (QTL) for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits in meat cattle, have been mapped consistently in the middle region of bovine chromosome 6 (BTA6). Dense genetic and physical maps and, ultimately, a fully annotated genome sequence as

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

    PubMed Central

    2012-01-01

    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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  4. Genetic Mapping of Sulfur Assimilation Genes Reveals a QTL for Onion Bulb Pungency

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Onion exhibits wide genetic and environmental variation in bioactive organosulfur compounds that impart pungency and health benefits. A PCR-based molecular marker map that included candidate genes for sulfur assimilation was used to identify genomic regions affecting pungency in the cross 'W202A' x ...

  5. Mapping of a novel QTL for resistance to cereal cyst nematode in wheat.

    PubMed

    Williams, K J; Willsmore, K L; Olson, S; Matic, M; Kuchel, H

    2006-05-01

    Cereal cyst nematode (CCN; Heterodera avenae Woll.) is a root pathogen of cereals that can cause severe yield losses in intolerant wheat cultivars. Loci for resistance to CCN, measured by a seedling bioassay, were identified by creating a genetic map based on a Trident/Molineux doubled haploid population of 182 lines. A novel locus accounting for up to 14% of the resistance to CCN was mapped to chromosome 1B of Molineux by association with microsatellite marker loci Xwmc719 and Xgwm140. This locus acts additively with the previously identified CCN resistance loci identified on chromosomes 6B (Cre8) and 2A (Cre5 on the VPM1 segment) in this population to explain 44% of the genetic variance for this major wheat pathogen. PMID:16538511

  6. Mapping QTL for Biomass Yield and Its Components in Rice ( Oryza sativa L.)

    Microsoft Academic Search

    Gui-Fu LIU; Jian YANG; Jun ZHU

    2006-01-01

    Addicive effects, additive by additive epistatic effects, and their environmental interactions of QTLs are important genetic components of quantitative traits. Genetic architecture underlying rice biomass yield and its two component traits (straw yield and grain yield) were analyzed for a population of 125 DH lines from an inter-subspecific cross of IR64\\/Azucena. The mixed-model based composite interval mapping approach (MCIM) was

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

    Microsoft Academic Search

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

    2004-01-01

    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

  8. 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

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

    1999-01-01

    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

  9. Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources

    PubMed Central

    Cridland, Julie M.; Macdonald, Stuart J.; Long, Anthony D.; Thornton, Kevin R.

    2013-01-01

    Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster. The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that “burden tests” that test for the effect of TEs as a class may be more fruitful. PMID:23883524

  10. Mapping the quantitative trait loci (QTL) controlling seed morphology and disk diameter in sunflower (Helianthus annuus L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several seed morphological traits, along with disk diameter, differ greatly between oilseed and confection sunflower types, which are bred for different end-use purposes. This paper reports the results of analyzing the quantitative trait loci (QTL) underlying seed morphological traits and disk diam...

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

    E-print Network

    Abraham, Nader G.

    chromosome that was 220 kb long. This small segment still contained the primary candidate locus Cyp11b1 (11 in the Dahl rat model of hypertension. This QTL accounts for about 23 mm Hg under the condition of 2% NaCl diet for 24 days. © 2001 Academic Press INTRODUCTION Human essential hypertension is a complex, multi

  12. Mapping QTL tolerance to Phytophthora root rot in soybean using microsatellite and RAPD\\/SCAR derived markers

    Microsoft Academic Search

    Yingpeng Han; Weili Teng; Kangfu Yu; Vaino Poysa; Terry Anderson; Lijuan Qiu; David A. Lightfoot; Wenbin Li

    2008-01-01

    Broad tolerance to phytophthora root rot (PRR) caused by Phytophthora sojae has become an important goal for the improvement of soybean (Glycine max) because of the rapid spread of races that defeat the available resistance genes. The aim of this research was to identify the location of quantitative trait loci (QTL) in ‘Conrad’, a soybean cultivar with\\u000a broad tolerance to

  13. Mapping QTL controlling southern leaf blight resistance by combined analysis of three related recombinant inbred line populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative trait loci (QTL) for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O were identified in three maize recombinant inbred populations assed in two environments. Each population derived from a cross between a temperate and a tropical maize li...

  14. Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon

    PubMed Central

    2010-01-01

    Background For decades, linkage mapping has been one of the most powerful and widely used approaches for elucidating the genetic architecture of phenotypic traits of medical, agricultural and evolutionary importance. However, successful mapping of Mendelian and quantitative phenotypic traits depends critically on the availability of fast and preferably high-throughput genotyping platforms. Several array-based single nucleotide polymorphism (SNP) genotyping platforms have been developed for genetic model organisms during recent years but most of these methods become prohibitively expensive for screening large numbers of individuals. Therefore, inexpensive, simple and flexible genotyping solutions that enable rapid screening of intermediate numbers of loci (~75-300) in hundreds to thousands of individuals are still needed for QTL mapping applications in a broad range of organisms. Results Here we describe the discovery of and application of insertion-deletion (INDEL) polymorphisms for cost-efficient medium throughput genotyping that enables analysis of >75 loci in a single automated sequencer electrophoresis column with standard laboratory equipment. Genotyping of INDELs requires low start-up costs, includes few standard sample handling steps and is applicable to a broad range of species for which expressed sequence tag (EST) collections are available. As a proof of principle, we generated a partial INDEL linkage map in Atlantic salmon (Salmo salar) and rapidly identified a number of quantitative trait loci (QTLs) affecting early life-history traits that are expected to have important fitness consequences in the natural environment. Conclusions The INDEL genotyping enabled fast coarse-mapping of chromosomal regions containing QTL, thus providing an efficient means for characterization of genetic architecture in multiple crosses and large pedigrees. This enables not only the discovery of larger number of QTLs with relatively smaller phenotypic effect but also provides a cost-effective means for evaluation of the frequency of segregating QTLs in outbred populations which is important for further understanding how genetic variation underlying phenotypic traits is maintained in the wild. PMID:20210987

  15. A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire ...

  16. QTL for resistance in Lolium perenne to a mixed population of Puccinia graminis subsp. graminicola: use of RAD (restriction site associated DNA) markers to rapidly populate a new linkage map

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. Susceptible and resistant plants were crossed to produce a pseudo-testcross population. Markers were produced by the Restriction-sit...

  17. Power and Precision of Alternate Methods for Linkage Disequilibrium Mapping of Quantitative Trait Loci

    PubMed Central

    Zhao, H. H.; Fernando, R. L.; Dekkers, J. C. M.

    2007-01-01

    Linkage disequilibrium (LD) analysis in outbred populations uses historical recombinations to detect and fine map quantitative trait loci (QTL). Our objective was to evaluate the effect of various factors on power and precision of QTL detection and to compare LD mapping methods on the basis of regression and identity by descent (IBD) in populations of limited effective population size (Ne). An 11-cM region with 6–38 segregating single-nucleotide polymorphisms (SNPs) and a central QTL was simulated. After 100 generations of random mating with Ne of 50, 100, or 200, SNP genotypes and phenotypes were generated on 200, 500, or 1000 individuals with the QTL explaining 2 or 5% of phenotypic variance. To detect and map the QTL, phenotypes were regressed on genotypes or (assumed known) haplotypes, in comparison with the IBD method. Power and precision to detect QTL increased with sample size, marker density, and QTL effect. Power decreased with Ne, but precision was affected little by Ne. Single-marker regression had similar or greater power and precision than other regression models, and was comparable to the IBD method. Thus, for rapid initial screening of samples of adequate size in populations in which drift is the primary force that has created LD, QTL can be detected and mapped by regression on SNP genotypes without recovering haplotypes. PMID:17277369

  18. Zero-inflated Poisson regression models for QTL mapping applied to tick-resistance in a Gyr × Holstein F2 population

    PubMed Central

    Silva, Fabyano Fonseca; Tunin, Karen P.; Rosa, Guilherme J.M.; da Silva, Marcos V.B.; Azevedo, Ana Luisa Souza; da Silva Verneque, Rui; Machado, Marco Antonio; Packer, Irineu Umberto

    2011-01-01

    Now a days, an important and interesting alternative in the control of tick-infestation in cattle is to select resistant animals, and identify the respective quantitative trait loci (QTLs) and DNA markers, for posterior use in breeding programs. The number of ticks/animal is characterized as a discrete-counting trait, which could potentially follow Poisson distribution. However, in the case of an excess of zeros, due to the occurrence of several noninfected animals, zero-inflated Poisson and generalized zero-inflated distribution (GZIP) may provide a better description of the data. Thus, the objective here was to compare through simulation, Poisson and ZIP models (simple and generalized) with classical approaches, for QTL mapping with counting phenotypes under different scenarios, and to apply these approaches to a QTL study of tick resistance in an F2 cattle (Gyr × Holstein) population. It was concluded that, when working with zero-inflated data, it is recommendable to use the generalized and simple ZIP model for analysis. On the other hand, when working with data with zeros, but not zero-inflated, the Poisson model or a data-transformation-approach, such as square-root or Box-Cox transformation, are applicable. PMID:22215960

  19. Zero-inflated Poisson regression models for QTL mapping applied to tick-resistance in a Gyr × Holstein F2 population.

    PubMed

    Silva, Fabyano Fonseca; Tunin, Karen P; Rosa, Guilherme J M; da Silva, Marcos V B; Azevedo, Ana Luisa Souza; da Silva Verneque, Rui; Machado, Marco Antonio; Packer, Irineu Umberto

    2011-10-01

    Now a days, an important and interesting alternative in the control of tick-infestation in cattle is to select resistant animals, and identify the respective quantitative trait loci (QTLs) and DNA markers, for posterior use in breeding programs. The number of ticks/animal is characterized as a discrete-counting trait, which could potentially follow Poisson distribution. However, in the case of an excess of zeros, due to the occurrence of several noninfected animals, zero-inflated Poisson and generalized zero-inflated distribution (GZIP) may provide a better description of the data. Thus, the objective here was to compare through simulation, Poisson and ZIP models (simple and generalized) with classical approaches, for QTL mapping with counting phenotypes under different scenarios, and to apply these approaches to a QTL study of tick resistance in an F2 cattle (Gyr × Holstein) population. It was concluded that, when working with zero-inflated data, it is recommendable to use the generalized and simple ZIP model for analysis. On the other hand, when working with data with zeros, but not zero-inflated, the Poisson model or a data-transformation-approach, such as square-root or Box-Cox transformation, are applicable. PMID:22215960

  20. Four rice QTL controlling number of spikelets per panicle expressed the characteristics of single Mendelian gene in near isogenic backgrounds

    Microsoft Academic Search

    Yushan Zhang; Lijun Luo; Touming Liu; Caiguo Xu; Yongzhong Xing

    2009-01-01

    Development of quantitative trait loci (QTL) near isogenic lines is a crucial step to QTL isolation using the strategy of\\u000a map-based cloning. In this study, a recombinant inbred line (RIL) population derived from two indica rice varieties, Zhenshan 97 and HR5, was employed to map QTL for spikelets per panicle (SPP). One major QTL (qSPP7) and three minor QTL (qSPP1,

  1. 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...

  2. Fine-scale mapping using Hardy-Weinberg disequilibrium

    Microsoft Academic Search

    R. JIANG; J. DONG; D. WANG; F. Z. SUN

    2001-01-01

    (Received 12.9.00. Accepted 22.12.00) summary Hardy{Weinberg disequilibrium (HWD) among affected individuals has recently been proposed for ne-scale mapping of disease susceptibility genes. We investigate the statistical properties of several available HWD measures and develop a new HWD measure J for ne-scale mapping. It is shown both theoretically and through simulations that the available HWD measures depend not only on the

  3. Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping

    PubMed Central

    Rowan, Beth A.; Patel, Vipul; Weigel, Detlef; Schneeberger, Korbinian

    2015-01-01

    The reshuffling of existing genetic variation during meiosis is important both during evolution and in breeding. The reassortment of genetic variants relies on the formation of crossovers (COs) between homologous chromosomes. The pattern of genome-wide CO distributions can be rapidly and precisely established by the short-read sequencing of individuals from F2 populations, which in turn are useful for quantitative trait locus (QTL) mapping. Although sequencing costs have decreased precipitously in recent years, the costs of library preparation for hundreds of individuals have remained high. To enable rapid and inexpensive CO detection and QTL mapping using low-coverage whole-genome sequencing of large mapping populations, we have developed a new method for library preparation along with Trained Individual GenomE Reconstruction, a probabilistic method for genotype and CO predictions for recombinant individuals. In an example case with hundreds of F2 individuals from two Arabidopsis thaliana accessions, we resolved most CO breakpoints to within 2 kb and reduced a major flowering time QTL to a 9-kb interval. In addition, an extended region of unusually low recombination revealed a 1.8-Mb inversion polymorphism on the long arm of chromosome 4. We observed no significant differences in the frequency and distribution of COs between F2 individuals with and without a functional copy of the DNA helicase gene RECQ4A. In summary, we present a new, cost-efficient method for large-scale, high-precision genotyping-by-sequencing. PMID:25585881

  4. Rapid and inexpensive whole-genome genotyping-by-sequencing for crossover localization and fine-scale genetic mapping.

    PubMed

    Rowan, Beth A; Patel, Vipul; Weigel, Detlef; Schneeberger, Korbinian

    2015-03-01

    The reshuffling of existing genetic variation during meiosis is important both during evolution and in breeding. The reassortment of genetic variants relies on the formation of crossovers (COs) between homologous chromosomes. The pattern of genome-wide CO distributions can be rapidly and precisely established by the short-read sequencing of individuals from F2 populations, which in turn are useful for quantitative trait locus (QTL) mapping. Although sequencing costs have decreased precipitously in recent years, the costs of library preparation for hundreds of individuals have remained high. To enable rapid and inexpensive CO detection and QTL mapping using low-coverage whole-genome sequencing of large mapping populations, we have developed a new method for library preparation along with Trained Individual GenomE Reconstruction, a probabilistic method for genotype and CO predictions for recombinant individuals. In an example case with hundreds of F2 individuals from two Arabidopsis thaliana accessions, we resolved most CO breakpoints to within 2 kb and reduced a major flowering time QTL to a 9-kb interval. In addition, an extended region of unusually low recombination revealed a 1.8-Mb inversion polymorphism on the long arm of chromosome 4. We observed no significant differences in the frequency and distribution of COs between F2 individuals with and without a functional copy of the DNA helicase gene RECQ4A. In summary, we present a new, cost-efficient method for large-scale, high-precision genotyping-by-sequencing. PMID:25585881

  5. Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology

    PubMed Central

    2014-01-01

    Background The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causative mutations in a QTL region. For this, a concordance analysis was applied for a leg conformation trait in dairy cattle. Several QTL were detected for which the QTL status (homozygous or heterozygous for the QTL) was inferred for each individual. Subsequently, the inferred QTL status was used in a concordance analysis to reduce the number of candidate mutations. Methods Twenty QTL for rear leg set side view were mapped using Bayes C. Marker effects estimated during QTL mapping were used to infer the QTL status for each individual. Subsequently, polymorphisms present in the QTL regions were extracted from the whole-genome sequences of 71 Holstein bulls. Only polymorphisms for which the status was concordant with the QTL status were kept as candidate causative mutations. Results QTL status could be inferred for 15 of the 20 QTL. The number of concordant polymorphisms differed between QTL and depended on the number of QTL statuses that could be inferred and the linkage disequilibrium in the QTL region. For some QTL, the concordance analysis was efficient and narrowed down to a limited number of candidate mutations located in one or two genes, while for other QTL a large number of genes contained concordant polymorphisms. Conclusions For regions for which the concordance analysis could be performed, we were able to reduce the number of candidate mutations. For part of the QTL, the concordant analyses narrowed QTL regions down to a limited number of genes, of which some are known for their role in limb or skeletal development in humans and mice. Mutations in these genes are good candidates for QTN (quantitative trait nucleotides) influencing rear leg set side view. PMID:24884971

  6. FINE MAPPING OF GENES REGULATING HEAT LOSS IN MICE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three mapping populations have been produced from lines of mice that have undergone 16 generations of divergent selection for high and low heat loss using direct calorimetry. Two populations consisted of F2 intercrosses originating from either outbred (MH x ML, n=560) or inbred (IH x IL, n=640) high...

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

    PubMed Central

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

    2014-01-01

    Annual fish of the genus Nothobranchius show large variations in lifespan and expression of age-related phenotypes between closely related populations. We studied N. kadleci and its sister species N. furzeri GRZ strain, and found that N.kadleci is longer-lived than the N. furzeri. Lipofuscin and apoptosis measured in the liver increased with age in N. kadleci with different profiles: lipofuscin increased linearly, while apoptosis declined in the oldest animals. More lipofuscin (P < 0.001) and apoptosis (P < 0.001) was observed in N. furzeri than in N. kadleci at 16w age. Lipofuscin and apoptotic cells were then quantified in hybrids from the mating of N. furzeri to N. kadleci. F1 individuals showed heterosis for lipofuscin but additive effects for apoptosis. These two age-related phenotypes were not correlated in F2 hybrids. Quantitative trait loci analysis of 287 F2 fish using 237 markers identified two QTL accounting for 10% of lipofuscin variance (P < 0.001) with overdominance effect. Apoptotic cells revealed three significant- and two suggestive QTL explaining 19% of variance (P < 0.001), showing additive and dominance effects, and two interacting loci. Our results show that lipofuscin and apoptosis are markers of different age-dependent biological processes controlled by different genetic mechanisms. PMID:25093339

  8. QTL Model Selection 1. Bayesian strategyy gy

    E-print Network

    Yandell, Brian S.

    : key players · observed measurements ­ y = phenotypic trait ­ m = markers & linkage map ­ i q Model Selection Seattle SISG: Yandell © 2012 2 ­ grounded by linkage map, experimental cross here) ­ unknown parameters (could be non-parametric) after Sen Churchill (2001) #12;QTL mapping (from

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

    PubMed Central

    2014-01-01

    Background Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and strawberry. Early studies on lactone biosynthesis suggest that several enzymatic pathways could be responsible for the diversity of lactones, but detailed information on them remained elusive. In this study, we have integrated genetic mapping and genome-wide transcriptome analysis to investigate the molecular basis of natural variation in ?-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

  10. Isolation, mapping and identification of SNPs for four genes (ACP6, CGN, ANXA9, SLC27A3) from a bovine QTL region on BTA3

    Microsoft Academic Search

    J. H. Calvo; A. Martínez-Royo; L. Silveri; S. Floriot; A. Eggen; A. Marcos-Carcavilla; M. Serrano

    2006-01-01

    On the basis of fine mapping of a quantitative trait loci region of BTA3 for milk fat content, an examination of the comparative map between cattle and human indicates that the annexin 9 protein gene (ANXA9) and the fatty acid transport protein type 3 gene (SLC27A3) are two strong candidate genes. The objective of the present study is to isolate,

  11. Accuracy of mapping the Earth's gravity field fine structure with a spaceborne gravity gradiometer mission

    NASA Technical Reports Server (NTRS)

    Kahn, W. D.

    1984-01-01

    The spaceborne gravity gradiometer is a potential sensor for mapping the fine structure of the Earth's gravity field. Error analyses were performed to investigate the accuracy of the determination of the Earth's gravity field from a gravity field satellite mission. The orbital height of the spacecraft is the dominating parameter as far as gravity field resolution and accuracies are concerned.

  12. Fine Genetic Mapping Localizes Cucumber Scab Resistance Gene Ccu into an R Gene Cluster

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The scab caused by Cladosporium cucumerinum, is an important disease of cucumber, Cucumis sativus. In this study, we conducted fine genetic mapping of the single dominant scab resistance gene, Ccu, with 148 F9 recombination inbreeding lines (RILs) and 1,944 F2 plants derived from the resistant cucum...

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

    E-print Network

    van der Knaap, Esther

    ORIGINAL PAPER Fine mapping of fw3.2 controlling fruit weight in tomato Na Zhang · Marin Talbot: 10 March 2012 � Springer-Verlag 2012 Abstract Tomato (Solanum lycopersicum) is an impor- tant crop for fruit mass in tomato. Identification of the underlying gene will improve our understanding

  14. Brief Genetics Report Fine-Mapping Gene-by-Diet Interactions on Chromosome

    E-print Network

    Hrbek, Tomas - Department of Biology, Universidad de Puerto Rico

    Brief Genetics Report Fine-Mapping Gene-by-Diet Interactions on Chromosome 13 in a LG/J SM/J Murine of obesity in humans range as high as 70% based on twin studies (1). However, obesity in the developed world is increasing too rapidly to be caused by changes in genetic background (2). Moreover, some human geno- types

  15. 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

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

    2011-01-01

    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

  16. 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

    2013-01-01

    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

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

    E-print Network

    Gilad, Yoav

    genome-wide association analysis in the combined population of F2 and AI identified 2241 quantitative). Because of the world's growing geriatric population, age-related loss of strength and55 muscle mass of health and fitness as it inversely associated with the risk for coronary heart disease54 and stroke (33

  18. Separation of base allele and sampling term effects gives new insights in variance component QTL analysis

    Microsoft Academic Search

    Lars Rönnegård; Örjan Carlborg

    2007-01-01

    BACKGROUND: Variance component (VC) models are commonly used for Quantitative Trait Loci (QTL) mapping in outbred populations. Here, the QTL effect is given as a random effect and a critical part of the model is the relationship between the phenotypic values and the random effect. In the traditional VC model, each individual has a unique QTL effect and the relationship

  19. Fine mapping and marker development for the crossability gene SKr on chromosome 5BS of hexaploid wheat (Triticum aestivum L.).

    PubMed

    Alfares, Walid; Bouguennec, Annaig; Balfourier, François; Gay, Georges; Bergès, Hélène; Vautrin, Sonia; Sourdille, Pierre; Bernard, Michel; Feuillet, Catherine

    2009-10-01

    Most elite wheat varieties cannot be crossed with related species thereby restricting greatly the germplasm that can be used for alien introgression in breeding programs. Inhibition to crossability is controlled genetically and a number of QTL have been identified to date, including the major gene Kr1 on 5BL and SKr, a strong QTL affecting crossability between wheat and rye on chromosome 5BS. In this study, we used a recombinant SSD population originating from a cross between the poorly crossable cultivar Courtot (Ct) and the crossable line MP98 to characterize the major dominant effect of SKr and map the gene at the distal end of the chromosome near the 5B homeologous GSP locus. Colinearity with barley and rice was used to saturate the SKr region with new markers and establish orthologous relationships with a 54-kb region on rice chromosome 12. In total, five markers were mapped within a genetic interval of 0.3 cM and 400 kb of BAC contigs were established on both sides of the gene to lay the foundation for map-based cloning of SKr. Two SSR markers completely linked to SKr were used to evaluate a collection of crossable wheat progenies originating from primary triticale breeding programs. The results confirm the major effect of SKr on crossability and the usefulness of the two markers for the efficient introgression of crossability in elite wheat varieties. PMID:19652174

  20. Cross-genome map based dissection of a nitrogen use efficiency ortho-metaQTL in bread wheat unravels concerted cereal genome evolution.

    PubMed

    Quraishi, Umar Masood; Abrouk, Michael; Murat, Florent; Pont, Caroline; Foucrier, Séverine; Desmaizieres, Gregory; Confolent, Carole; Rivière, Nathalie; Charmet, Gilles; Paux, Etienne; Murigneux, Alain; Guerreiro, Laurent; Lafarge, Stéphane; Le Gouis, Jacques; Feuillet, Catherine; Salse, Jerome

    2011-03-01

    Monitoring nitrogen use efficiency (NUE) in plants is becoming essential to maintain yield while reducing fertilizer usage. Optimized NUE application in major crops is essential for long-term sustainability of agriculture production. Here, we report the precise identification of 11 major chromosomal regions controlling NUE in wheat that co-localise with key developmental genes such as Ppd (photoperiod sensitivity), Vrn (vernalization requirement), Rht (reduced height) and can be considered as robust markers from a molecular breeding perspective. Physical mapping, sequencing, annotation and candidate gene validation of an NUE metaQTL on wheat chromosome 3B allowed us to propose that a glutamate synthase (GoGAT) gene that is conserved structurally and functionally at orthologous positions in rice, sorghum and maize genomes may contribute to NUE in wheat and other cereals. We propose an evolutionary model for the NUE locus in cereals from a common ancestral region, involving species specific shuffling events such as gene deletion, inversion, transposition and the invasion of repetitive elements. PMID:21251102

  1. Fine mapping of the lesion mimic and early senescence 1 (lmes1) in rice (Oryza sativa).

    PubMed

    Li, Zhi; Zhang, Yingxin; Liu, Lin; Liu, Qunen; Bi, Zhenzhen; Yu, Ning; Cheng, Shihua; Cao, Liyong

    2014-07-01

    A novel rice mutant, lesion mimic and early senescence 1 (lmes1), was induced from the rice 93-11 cultivar in a ?-ray field. This mutant exhibited spontaneous disease-like lesions in the absence of pathogen attack at the beginning of the tillering stage. Moreover, at the booting stage, lmes1 mutants exhibited a significantly increased MDA but decreased chlorophyll content, soluble protein content and photosynthetic rate in the leaves, which are indicative of an early senescence phenotype. The lmes1 mutant was significantly more resistant than 93-11 against rice bacterial blight infection, which was consistent with a marked increase in the expression of three resistance-related genes. Here, we employed a map-based cloning approach to finely map the lmes1 gene. In an initial mapping with 94 F2 individuals derived from a cross between the lmes1 mutant and Nipponbare, the lmes1 gene was located in a 10.6-cM region on the telomere of the long arm of chromosome 7 using simple sequence repeat (SSR) markers. To finely map lmes1, we derived two F2 populations with 940 individuals from two crosses between the lmes1 mutant and two japonica rice varieties, Nipponbare and 02428. Finally, the lmes1 gene was mapped to an 88-kb region between two newly developed inDel markers, Zl-3 and Zl-22, which harbored 15 ORFs. PMID:24832615

  2. Fine mapping of a male sterility gene MS-cd1 in Brassica oleracea

    Microsoft Academic Search

    Xinmei Zhang; Jian Wu; Hui Zhang; Yuan Ma; Aiguang Guo; Xiaowu Wang

    2011-01-01

    A dominant male sterility (DGMS) line 79-399-3, developed from a spontaneous mutation in Brassica oleracea var. capitata, has been widely used in production of hybrid cultivars in China. In this line, male sterility is controlled by a dominant\\u000a gene Ms-cd1. In the present study, fine mapping of Ms-cd1 was conducted by screening a segregating population Ms79-07 with 2,028 individuals developed

  3. Fine mapping of an incomplete recessive gene for leaf rolling in rice ( Oryza sativa L.)

    Microsoft Academic Search

    Yuanjian Shao; Cunhong Pan; Zongxiang Chen; Shimin Zuo; Yafang Zhang; Xuebiao Pan

    2005-01-01

    Genetic analysis and fine mapping of genes controlling leaf rolling were conducted using two backcrossed generations (BC4F2, BC4F3) derived from a cross between QMX, a non-rolled leaf cultivar as a recurrent parent, and JZB, a rolled leaf NIL of ZB as\\u000a a donor parent. Results indicated that leaf rolling was mainly controlled by an incompletely recessive major gene, namelyrl\\u000a (t),

  4. Fine-mapping QTLs in advanced intercross lines and other outbred populations.

    PubMed

    Gonzales, Natalia M; Palmer, Abraham A

    2014-08-01

    Quantitative genetic studies in model organisms, particularly in mice, have been extremely successful in identifying chromosomal regions that are associated with a wide variety of behavioral and other traits. However, it is now widely understood that identification of the underlying genes will be far more challenging. In the last few years, a variety of populations have been utilized in an effort to more finely map these chromosomal regions with the goal of identifying specific genes. The common property of these newer populations is that linkage disequilibrium spans relatively short distances, which permits fine-scale mapping resolution. This review focuses on advanced intercross lines (AILs) which are the simplest such population. As originally proposed in 1995 by Darvasi and Soller, an AIL is the product of intercrossing two inbred strains beyond the F2 generation. Unlike recombinant inbred strains, AILs are maintained as outbred populations; brother-sister matings are specifically avoided. Each generation of intercrossing beyond the F2 further degrades linkage disequilibrium between adjacent makers, which allows for fine-scale mapping of quantitative trait loci (QTLs). Advances in genotyping technology and techniques for the statistical analysis of AILs have permitted rapid advances in the application of AILs. We review some of the analytical issues and available software, including QTLRel, EMMA, EMMAX, GEMMA, TASSEL, GRAMMAR, WOMBAT, Mendel, and others. PMID:24906874

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

    PubMed

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

    2014-05-01

    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

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

    PubMed Central

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

    2014-01-01

    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

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

    Microsoft Academic Search

    D. K. Santra; X. M. Chen; M. Santra; K. G. Campbell; K. K. Kidwell

    2008-01-01

    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 quantitative trait loci (QTL) for HTAP resistance in Stephens\\u000a through genetic linkage analysis and identify DNA markers linked to the QTL for use

  8. Extensive genomic characterization of a set of near-isogenic lines for heterotic QTL in maize (Zea mays L.)

    PubMed Central

    2013-01-01

    Background Despite the crucial role that heterosis has played in crop improvement, its genetic and molecular bases are still elusive. Several types of structured populations were used to discover the genetic architecture underlying complex phenotypes, and several QTL related to heterosis were detected. However, such analyses generally lacked the statistical power required for the detailed characterization of individual QTL. Currently, QTL introgression into near-isogenic materials is considered the most effective strategy to this end, despite such materials inevitably contain a variable, unknown and undesired proportion of non-isogenic genome. An introgression program based on residual heterozygous lines allowed us to develop five pairs of maize (Zea mays L.) near-isogenic lines (NILs) suitable for the fine characterization of three major heterotic QTL previously detected. Here we describe the results of the detailed genomic characterization of these NILs that we undertook to establish their genotypic structure, to verify the presence of the expected genotypes within target QTL regions, and to determine the extent and location of residual non-isogenic genomic regions. Results The SNP genotyping approach allowed us to determine the parent-of-origin allele for 14,937 polymorphic SNPs and to describe in detail the genotypic structure of all NILs. The correct introgression was confirmed for all target QTL in the respective NIL and several non-isogenic regions were detected genome-wide. Possible linkage drag effects associated to the specific introgressed regions were observed. The extent and position of other non-isogenic regions varied among NIL pairs, probably deriving from random segregating sections still present at the separation of lineages within pairs. Conclusions The results of this work strongly suggest that the actual isogenicity and the genotypic architecture of near-isogenic materials should be monitored both during the introgression procedure and on the final materials as a paramount requisite for a successful mendelization of target QTL. The information here gathered on the genotypic structure of NILs will be integrated in future experimental programs aimed at the fine mapping and isolation of major heterotic QTL, a crucial step towards the understanding of the molecular bases of heterosis in maize. PMID:23360375

  9. Genetic mapping and QTL analysis of fruit and flower related traits in cucumber ( Cucumis sativus L.) using recombinant inbred lines

    Microsoft Academic Search

    X. J. Yuan; J. S. Pan; R. Cai; Y. Guan; L. Z. Liu; W. W. Zhang; Z. Li; H. L. He; C. Zhang; L. T. Si; L. H. Zhu

    2008-01-01

    A set of 224 recombinant inbred lines (RILs) derived from a narrow cross between two fresh eaten types (S94 (Northern China\\u000a type) × S06 (Northern European type)) (Cucumis sativus L.) was used to construct a genetic linkage map. With the RILs a 257-point genetic map was constructed including 206 SRAPs,\\u000a 22 SSRs, 25 SCARs, 1 STS, and three economically important morphological markers

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

    PubMed

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

    2009-11-01

    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

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

    PubMed Central

    2013-01-01

    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

  12. Increasing the density of markers around a major QTL controlling resistance to angular leaf spot in common bean.

    PubMed

    Oblessuc, Paula Rodrigues; Cardoso Perseguini, Juliana Morini Kupper; Baroni, Renata Moro; Chiorato, Alisson Fernando; Carbonell, Sérgio Augusto Morais; Mondego, Jorge Mauricio Costa; Vidal, Ramon Oliveira; Camargo, Luis Eduardo Aranha; Benchimol-Reis, Luciana Lasry

    2013-10-01

    Angular leaf spot (ALS) causes major yield losses in the common bean (Phaseolus vulgaris L.), an important protein source in the human diet. This study describes the saturation around a major quantitative trait locus (QTL) region, ALS10.1, controlling resistance to ALS located on linkage group Pv10 and explores the genomic context of this region using available data from the P. vulgaris genome sequence. DArT-derived markers (STS-DArT) selected by bulk segregant analysis and SCAR and SSR markers were used to increase the resolution of the QTL, reducing the confidence interval of ALS10.1 from 13.4 to 3.0 cM. The position of the SSR ATA220 coincided with the maximum LOD score of the QTL. Moreover, a new QTL (ALS10.2(UC)) was identified at the end of the same linkage group. Sequence analysis using the P. vulgaris genome located ten SSRs and seven STS-DArT on chromosome 10 (Pv10). Coincident linkage and genome positions of five markers enabled the definition of a core region for ALS10.1 spanning 5.3 Mb. These markers are linked to putative genes related to disease resistance such as glycosyl transferase, ankyrin repeat-containing, phospholipase, and squamosa-promoter binding protein. Synteny analysis between ALS10.1 markers and the genome of soybean suggested a dynamic evolution of this locus in the common bean. The present study resulted in the identification of new candidate genes and markers closely linked to a major ALS disease resistance QTL, which can be used in marker-assisted selection, fine mapping and positional QTL cloning. PMID:23832048

  13. Quantitative trait loci identification, fine mapping and gene expression profiling for ovicidal response to whitebacked planthopper (Sogatella furcifera Horvath) in rice (Oryza sativa L.)

    PubMed Central

    2014-01-01

    Background The whitebacked planthopper (WBPH), Sogatella furcifera Horváth, is a serious rice pest in Asia. Ovicidal resistance is a natural rice defense mechanism against WBPH and is characterized by the formation of watery lesions (WLs) and increased egg mortality (EM) at the WBPH oviposition sites. Results This study aimed to understand the genetic and molecular basis of rice ovicidal resistance to WBPH by combining genetic and genomic analyses. First, the ovicidal trait in doubled haploid rice lines derived from a WBPH-resistant cultivar (CJ06) and a WBPH-susceptible cultivar (TN1) were phenotyped based on the necrotic symptoms of the leaf sheaths and EM. Using a constructed molecular linkage map, 19 quantitative trait loci (QTLs) associated with WLs and EM were identified on eight chromosomes. Of them, qWL6 was determined to be a major QTL for WL. Based on chromosome segment substitution lines and a residual heterozygous population, a high-resolution linkage analysis further defined the qWL6 locus to a 122-kb region on chromosome 6, which was annotated to encode 20 candidate genes. We then conducted an Affymetrix microarray analysis to determine the transcript abundance in the CJ06 and TN1 plants. Upon WBPH infestation, 432 genes in CJ06 and 257 genes in TN1 were significantly up-regulated, while 802 genes in CJ06 and 398 genes in TN1 were significantly down-regulated. This suggests that remarkable global changes in gene expression contribute to the ovicidal resistance of rice. Notably, four genes in the 122-kb region of the qWL6 locus were differentially regulated between CJ06 and TN1 in response to the WBPH infestation, suggesting they may be candidate resistance genes. Conclusions The information obtained from the fine mapping of qWL6 and the microarray analyses will facilitate the isolation of this important resistance gene and its use in breeding WBPH-resistant rice. PMID:24886295

  14. Fine Mapping and Candidate Gene Search of Quantitative Trait Loci for Growth and Obesity Using Mouse Intersubspecific Subcongenic Intercrosses and Exome Sequencing

    PubMed Central

    Ishikawa, Akira; Okuno, Sin-ichiro

    2014-01-01

    Although growth and body composition traits are quantitative traits of medical and agricultural importance, the genetic and molecular basis of those traits remains elusive. Our previous genome-wide quantitative trait locus (QTL) analyses in an intersubspecific backcross population between C57BL/6JJcl (B6) and wild Mus musculus castaneus mice revealed a major growth QTL (named Pbwg1) on a proximal region of mouse chromosome 2. Using the B6.Cg-Pbwg1 intersubspecific congenic strain created, we revealed 12 closely linked QTLs for body weight and body composition traits on an approximately 44.1-Mb wild-derived congenic region. In this study, we narrowed down genomic regions harboring three (Pbwg1.12, Pbwg1.3 and Pbwg1.5) of the 12 linked QTLs and searched for possible candidate genes for the QTLs. By phenotypic analyses of F2 intercross populations between B6 and each of four B6.Cg-Pbwg1 subcongenic strains with overlapping and non-overlapping introgressed regions, we physically defined Pbwg1.12 affecting body weight to a 3.8-Mb interval (61.5–65.3 Mb) on chromosome 2. We fine-mapped Pbwg1.3 for body length to an 8.0-Mb interval (57.3–65.3) and Pbwg1.5 for abdominal white fat weight to a 2.1-Mb interval (59.4–61.5). The wild-derived allele at Pbwg1.12 and Pbwg1.3 uniquely increased body weight and length despite the fact that the wild mouse has a smaller body size than that of B6, whereas it decreased fat weight at Pbwg1.5. Exome sequencing and candidate gene prioritization suggested that Gcg and Grb14 are putative candidate genes for Pbwg1.12 and that Ly75 and Itgb6 are putative candidate genes for Pbwg1.5. These genes had nonsynonymous SNPs, but the SNPs were predicted to be not harmful to protein functions. These results provide information helpful to identify wild-derived quantitative trait genes causing enhanced growth and resistance to obesity. PMID:25398139

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

    PubMed

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

    2007-05-01

    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

  16. 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...

  17. Validation of rice blast resistance genes in barley using a QTL mapping population and near-isolines.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are prior reports of Pyricularia grisea – the causal agent of blast of rice – causing disease in barley. In order to determine the specificity of this resistance in barley, we extended our previous mapping efforts to include blast isolates from barley and rice grown in Thailand and we assesse...

  18. Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic

    E-print Network

    Gepts, Paul

    associated with the domestication syndrome in bean. Since the bean and cowpea maps were developed importance in bean and cowpea J.D. Kellya,* , P. Geptsb , P.N. Miklasc , D.P. Coyned a Crop and Soil Sciences.V. All rights reserved. Keywords: Domestication; Disease resistance; Epistasis; Indirect selection

  19. 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...

  20. Fine-scale genetic mapping based on linkage disequilibrium: theory and applications.

    PubMed Central

    Xiong, M; Guo, S W

    1997-01-01

    Linkage-disequilibrium mapping (LDM) recently has been hailed as a powerful statistical method for fine-scale mapping of disease genes. After reviewing its historical background and methodological development, we present a general, mathematical, and conceptually coherent framework for LDM that incorporates multilocus and multiallelic markers and mutational processes at the marker and disease loci. With this framework, we address several issues relevant to fine-scale mapping and propose some efficient computational methods for LDM. We implement various LDM methods that incorporate population growth, recurrent mutation, and marker mutations, on the basis of a general framework. We demonstrate these methods by applying them to published data on cystic fibrosis, Huntington disease, Friedreich ataxia, and progressive myoclonus epilepsy. Since the genes responsible for these diseases all have been cloned, we can evaluate the performance of our methods and can compare ours with that of other methods. Using the proposed methods, we successfully and accurately predicted the locations of genes responsible for these diseases, on the basis of published data only. PMID:9199574

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

    PubMed Central

    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

    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

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

    SciTech Connect

    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

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    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.

  4. Favorable QTL alleles for yield and its components identified by association mapping in Chinese Upland cotton cultivars.

    PubMed

    Mei, Hongxian; Zhu, Xiefei; Zhang, Tianzhen

    2013-01-01

    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 (r(2) = 0.1182, P ? 0.01), r(2) = 0.1 and r(2) = 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, -log10 P ? 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

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

    PubMed Central

    Mei, Hongxian; Zhu, Xiefei; Zhang, Tianzhen

    2013-01-01

    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

  6. QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice

    Microsoft Academic Search

    S. Fukuoka; K. Okuno

    2001-01-01

    Field resistance is defined as the resistance that allows effective control of a parasite under natural field conditions and\\u000a is durable when exposed to new races of that parasite. To identify the genes for field resistance to rice blast, quantitative\\u000a trait loci (QTLs) conferring field resistance to rice blast in Japanese upland rice were detected and mapped using RFLP and

  7. Recalculation of 23 mouse HDL QTL datasets improves accuracy and allows for better candidate gene analysis.

    PubMed

    Ackert-Bicknell, Cheryl; Paigen, Beverly; Korstanje, Ron

    2013-04-01

    In the past 15 years, the quantitative trait locus (QTL) mapping approach has been applied to crosses between different inbred mouse strains to identify genetic loci associated with plasma HDL cholesterol levels. Although successful, a disadvantage of this method is low mapping resolution, as often several hundred candidate genes fall within the confidence interval for each locus. Methods have been developed to narrow these loci by combining the data from the different crosses, but they rely on the accurate mapping of the QTL and the treatment of the data in a consistent manner. We collected 23 raw datasets used for the mapping of previously published HDL QTL and reanalyzed the data from each cross using a consistent method and the latest mouse genetic map. By utilizing this approach, we identified novel QTL and QTL that were mapped to the wrong part of chromosomes. Our new HDL QTL map allows for reliable combining of QTL data and candidate gene analysis, which we demonstrate by identifying Grin3a and Etv6, as candidate genes for QTL on chromosomes 4 and 6, respectively. In addition, we were able to narrow a QTL on Chr 19 to five candidates. PMID:23393305

  8. Hitchhiking mapping: A population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster

    PubMed Central

    Harr, Bettina; Kauer, Max; Schlötterer, Christian

    2002-01-01

    The identification of genes contributing to the adaptation of local populations is of great biological interest. In an attempt to characterize functionally important differences among African and non-African Drosophila melanogaster populations, we surveyed neutral microsatellite variation in an 850-kb genomic sequence. Three genomic regions were identified that putatively bear an adaptive mutation associated with the habitat expansion of D. melanogaster. A further inspection of two regions by sequence analysis of multiple fragments confirmed the presence of a recent beneficial mutation in the non-African populations. Our study suggests that hitchhiking mapping is a universal approach for the identification of ecologically important mutations. PMID:12351680

  9. Fine-resolution mapping of micro-meteorological features in regions with heterogeneous landscapes

    NASA Astrophysics Data System (ADS)

    Esau, Igor; Varentsov, Mikhail

    2014-05-01

    Human socioeconomic activity and wild life conservation tasks frequently require meteorological information at fine (about 100 m) spatial resolution. For instance, this information is needed for assessment of wind load, wind gustiness, air quality and urban comfort in high latitudes where the atmospheric convection is limited. Neither sparse observational network nor operational meteorological models are able to directly provide this information to end-users. Methods of geo-statistical weighted interpolation (kriging) have been already successfully applied to reconstruct fine-resolution maps in geophysics. In this study, we applied a kriging with external drive to micro-meteorological reconstructions. As kriging is a statistical interpolation method, its application requires information from a more or less uniformly distributed network of observational stations. This condition is rarely satisfied. We propose use of a turbulence-resolving large-eddy simulation model (LES) to: (i) obtain variograms for each station; (ii) correct extrapolation of the data outside the domain covered with observations. The proposed fine-resolution method with external drive from the LES is demonstrated for the surface air temperature distribution (resolution 50 m) in the central valley of Bergen.

  10. Chromatin marks identify critical cell types for fine mapping complex trait variants.

    PubMed

    Trynka, Gosia; Sandor, Cynthia; Han, Buhm; Xu, Han; Stranger, Barbara E; Liu, X Shirley; Raychaudhuri, Soumya

    2013-02-01

    If trait-associated variants alter regulatory regions, then they should fall within chromatin marks in relevant cell types. However, it is unclear which of the many marks are most useful in defining cell types associated with disease and fine mapping variants. We hypothesized that informative marks are phenotypically cell type specific; that is, SNPs associated with the same trait likely overlap marks in the same cell type. We examined 15 chromatin marks and found that those highlighting active gene regulation were phenotypically cell type specific. Trimethylation of histone H3 at lysine 4 (H3K4me3) was the most phenotypically cell type specific (P < 1 × 10(-6)), driven by colocalization of variants and marks rather than gene proximity (P < 0.001). H3K4me3 peaks overlapped with 37 SNPs for plasma low-density lipoprotein concentration in the liver (P < 7 × 10(-5)), 31 SNPs for rheumatoid arthritis within CD4(+) regulatory T cells (P = 1 × 10(-4)), 67 SNPs for type 2 diabetes in pancreatic islet cells (P = 0.003) and the liver (P = 0.003), and 14 SNPs for neuropsychiatric disease in neuronal tissues (P = 0.007). We show how cell type-specific H3K4me3 peaks can inform the fine mapping of associated SNPs to identify causal variation. PMID:23263488

  11. Evaluation of multispectral, fine scale digital imagery as a tool for mapping stream morphology

    NASA Astrophysics Data System (ADS)

    Wright, Andrea; Marcus, W. Andrew; Aspinall, Richard

    2000-05-01

    Multispectral digital imagery acquired from Soda Butte and Cache Creeks, Montana and Wyoming was used in conjunction with field data to classify and map hydrogeomorphic stream units on four stream reaches. The morphologic units that were field mapped were eddy drop zones, glides, low gradient riffles, high gradient riffles, lateral scour pools, attached bars, detached bars, and large woody debris. Unsupervised and supervised classifications of the imagery were used to develop a Maximum Joint Probability classification and an Alternative Joint Probability classification of the stream reaches. The Maximum Joint Probability classification allowed only one of the image classes to represent each hydrogeomorphic unit on the field map and resulted in relatively low overall accuracies for identification of these units of 10% to 50%. The Alternative Joint Probability classification allowed each image class to represent any geomorphic unit where the probability of a correct classification was greater than random. In this technique, two or three image classes were assigned to represent each hydrogeomorphic unit, resulting in higher overall accuracies of 28% to 80%. Accurate classification of hydrogeomorphic units was hampered by poor rectification of imagery with the field maps because of inadequate ground control points. In general, the largest hydrogeomorphic units were most accurately classified, whereas units that were small in area or spatially linear were least likely to be accurately classified. The results of this study demonstrated that multispectral digital imagery has the potential to be a useful tool for mapping hydrogeomorphic stream units at fine scales. Imagery to be an effective tool, however, careful measures such as accurate documentation of ground control points must be taken to ensure accurate rectification of the imagery with field maps.

  12. Characterization of the effect of a QTL for drought resistance in rice, qtl12.1 , over a range of environments in the Philippines and eastern India

    Microsoft Academic Search

    Jérôme Bernier; Arvind Kumar; Ramaiah Venuprasad; Dean Spaner; Satish Verulkar; Nimai P. Mandal; Pramod K. Sinha; Puvvada Peeraju; Praba R. Dongre; R. N. Mahto; Gary Atlin

    2009-01-01

    A large-effect QTL for grain yield under drought conditions (qtl12.1) was reported in a rice mapping population derived from Vandana and Way Rarem. Here, we measured the effect of qtl12.1 on grain yield and associated traits in 21 field trials: ten at IRRI in the Philippines and 11 in the target environment\\u000a of eastern India. The relative effect of the

  13. 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...

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

    PubMed

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

    2014-04-01

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

  15. Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags

    Microsoft Academic Search

    K. Ishimaru; M. Yano; N. Aoki; K. Ono; T. Hirose; S. Y. Lin; L. Monna; T. Sasaki; R. Ohsugi

    2001-01-01

    We have constructed a rice function map by collating the results on quantitative trait loci (QTLs) for 23 important physiological\\u000a and agronomic characters (including 13 newly measured traits) obtained using backcross inbred lines of japonica Nipponbare×indica Kasalath. Using these materials, The Rice Genome project (RGP) has developed a high-density genetic map. QTLs controlling\\u000a yield did not overlap with those controlling

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

    PubMed

    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

    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

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

    PubMed

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

    2013-07-15

    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

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

    PubMed Central

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

    2013-01-01

    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

  19. Empirical threshold values for quantitative trait mapping

    Microsoft Academic Search

    G. A. Churchill; R. W. Doerge

    1994-01-01

    The detection of genes that control quantitative characters is a problem of great interest to the genetic mapping community. Methods for locating these quantitative trait loci (QTL) relative to maps of genetic markers are now widely used. This paper addresses an issue common to all QTL mapping methods, that of determining an appropriate threshold value for declaring significant QTL effects.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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.

  1. An anchored linkage map for sugar beet based on AFLP, SNP and RAPD markers and QTL mapping of a new source of resistance to Beet necrotic yellow vein virus

    Microsoft Academic Search

    M. K. Grimmer; S. Trybush; S. Hanley; S. A. Francis; A. Karp; M. J. C. Asher

    2007-01-01

    Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), is an important sugar-beet disease worldwide and can result in severe losses of root yield and sugar content. We\\u000a have identified a major QTL for BNYVV resistance from a new source in a segregating population of 158 individuals. The QTL\\u000a explained an estimated 78% of the observed phenotypic variation and the

  2. Multi-ethnic fine-mapping of 14 central adiposity loci.

    PubMed

    Liu, Ching-Ti; Buchkovich, Martin L; Winkler, Thomas W; Heid, Iris M; Borecki, Ingrid B; Fox, Caroline S; Mohlke, Karen L; North, Kari E; Adrienne Cupples, L

    2014-09-01

    The Genetic Investigation of Anthropometric Traits (GIANT) consortium identified 14 loci in European Ancestry (EA) individuals associated with waist-to-hip ratio (WHR) adjusted for body mass index. These loci are wide and narrowing the signals remains necessary. Twelve of 14 loci identified in GIANT EA samples retained strong associations with WHR in our joint EA/individuals of African Ancestry (AA) analysis (log-Bayes factor >6.1). Trans-ethnic analyses at five loci (TBX15-WARS2, LYPLAL1, ADAMTS9, LY86 and ITPR2-SSPN) substantially narrowed the signals to smaller sets of variants, some of which are in regions that have evidence of regulatory activity. By leveraging varying linkage disequilibrium structures across different populations, single-nucleotide polymorphisms (SNPs) with strong signals and narrower credible sets from trans-ethnic meta-analysis of central obesity provide more precise localizations of potential functional variants and suggest a possible regulatory role. Meta-analysis results for WHR were obtained from 77 167 EA participants from GIANT and 23 564 AA participants from the African Ancestry Anthropometry Genetics Consortium. For fine mapping we interrogated SNPs within ± 250 kb flanking regions of 14 previously reported index SNPs from loci discovered in EA populations by performing trans-ethnic meta-analysis of results from the EA and AA meta-analyses. We applied a Bayesian approach that leverages allelic heterogeneity across populations to combine meta-analysis results and aids in fine-mapping shared variants at these locations. We annotated variants using information from the ENCODE Consortium and Roadmap Epigenomics Project to prioritize variants for possible functionality. PMID:24760767

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

    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.

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

    PubMed Central

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

    2014-01-01

    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

  5. Fine Mapping Major Histocompatibility Complex Associations in Psoriasis and Its Clinical Subtypes

    PubMed Central

    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

    2014-01-01

    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

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

    PubMed

    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

    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

  7. Discovery and Fine Mapping of Serum Protein Loci through Transethnic Meta-analysis

    PubMed Central

    Franceschini, Nora; van Rooij, Frank J.A.; Prins, Bram P.; Feitosa, Mary F.; Karakas, Mahir; Eckfeldt, John H.; Folsom, Aaron R.; Kopp, Jeffrey; Vaez, Ahmad; Andrews, Jeanette S.; Baumert, Jens; Boraska, Vesna; Broer, Linda; Hayward, Caroline; Ngwa, Julius S.; Okada, Yukinori; Polasek, Ozren; Westra, Harm-Jan; Wang, Ying A.; Del Greco M., Fabiola; Glazer, Nicole L.; Kapur, Karen; Kema, Ido P.; Lopez, Lorna M.; Schillert, Arne; Smith, Albert V.; Winkler, Cheryl A.; Zgaga, Lina; Bandinelli, Stefania; Bergmann, Sven; Boban, Mladen; Bochud, Murielle; Chen, Y.D.; Davies, Gail; Dehghan, Abbas; Ding, Jingzhong; Doering, Angela; Durda, J. Peter; Ferrucci, Luigi; Franco, Oscar H.; Franke, Lude; Gunjaca, Grog; Hofman, Albert; Hsu, Fang-Chi; Kolcic, Ivana; Kraja, Aldi; Kubo, Michiaki; Lackner, Karl J.; Launer, Lenore; Loehr, Laura R.; Li, Guo; Meisinger, Christa; Nakamura, Yusuke; Schwienbacher, Christine; Starr, John M.; Takahashi, Atsushi; Torlak, Vesela; Uitterlinden, André G.; Vitart, Veronique; Waldenberger, Melanie; Wild, Philipp S.; Kirin, Mirna; Zeller, Tanja; Zemunik, Tatijana; Zhang, Qunyuan; Ziegler, Andreas; Blankenberg, Stefan; Boerwinkle, Eric; Borecki, Ingrid B.; Campbell, Harry; Deary, Ian J.; Frayling, Timothy M.; Gieger, Christian; Harris, Tamara B.; Hicks, Andrew A.; Koenig, Wolfgang; O’Donnell, Christopher J.; Fox, Caroline S.; Pramstaller, Peter P.; Psaty, Bruce M.; Reiner, Alex P.; Rotter, Jerome I.; Rudan, Igor; Snieder, Harold; Tanaka, Toshihiro; van Duijn, Cornelia M.; Vollenweider, Peter; Waeber, Gerard; Wilson, James F.; Witteman, Jacqueline C.M.; Wolffenbuttel, Bruce H.R.; Wright, Alan F.; Wu, Qingyu; Liu, Yongmei; Jenny, Nancy S.; North, Kari E.; Felix, Janine F.; Alizadeh, Behrooz Z.; Cupples, L. Adrienne; Perry, John R.B.; Morris, Andrew P.

    2012-01-01

    Many disorders are associated with altered serum protein concentrations, including malnutrition, cancer, and cardiovascular, kidney, and inflammatory diseases. Although these protein concentrations are highly heritable, relatively little is known about their underlying genetic determinants. Through transethnic meta-analysis of European-ancestry and Japanese genome-wide association studies, we identified six loci at genome-wide significance (p < 5 × 10?8) for serum albumin (HPN-SCN1B, GCKR-FNDC4, SERPINF2-WDR81, TNFRSF11A-ZCCHC2, FRMD5-WDR76, and RPS11-FCGRT, in up to 53,190 European-ancestry and 9,380 Japanese individuals) and three loci for total protein (TNFRS13B, 6q21.3, and ELL2, in up to 25,539 European-ancestry and 10,168 Japanese individuals). We observed little evidence of heterogeneity in allelic effects at these loci between groups of European and Japanese ancestry but obtained substantial improvements in the resolution of fine mapping of potential causal variants by leveraging transethnic differences in the distribution of linkage disequilibrium. We demonstrated a functional role for the most strongly associated serum albumin locus, HPN, for which Hpn knockout mice manifest low plasma albumin concentrations. Other loci associated with serum albumin harbor genes related to ribosome function, protein translation, and proteasomal degradation, whereas those associated with serum total protein include genes related to immune function. Our results highlight the advantages of transethnic meta-analysis for the discovery and fine mapping of complex trait loci and have provided initial insights into the underlying genetic architecture of serum protein concentrations and their association with human disease. PMID:23022100

  8. Discovery and fine mapping of serum protein loci through transethnic meta-analysis.

    PubMed

    Franceschini, Nora; van Rooij, Frank J A; Prins, Bram P; Feitosa, Mary F; Karakas, Mahir; Eckfeldt, John H; Folsom, Aaron R; Kopp, Jeffrey; Vaez, Ahmad; Andrews, Jeanette S; Baumert, Jens; Boraska, Vesna; Broer, Linda; Hayward, Caroline; Ngwa, Julius S; Okada, Yukinori; Polasek, Ozren; Westra, Harm-Jan; Wang, Ying A; Del Greco M, Fabiola; Glazer, Nicole L; Kapur, Karen; Kema, Ido P; Lopez, Lorna M; Schillert, Arne; Smith, Albert V; Winkler, Cheryl A; Zgaga, Lina; Bandinelli, Stefania; Bergmann, Sven; Boban, Mladen; Bochud, Murielle; Chen, Y D; Davies, Gail; Dehghan, Abbas; Ding, Jingzhong; Doering, Angela; Durda, J Peter; Ferrucci, Luigi; Franco, Oscar H; Franke, Lude; Gunjaca, Grog; Hofman, Albert; Hsu, Fang-Chi; Kolcic, Ivana; Kraja, Aldi; Kubo, Michiaki; Lackner, Karl J; Launer, Lenore; Loehr, Laura R; Li, Guo; Meisinger, Christa; Nakamura, Yusuke; Schwienbacher, Christine; Starr, John M; Takahashi, Atsushi; Torlak, Vesela; Uitterlinden, André G; Vitart, Veronique; Waldenberger, Melanie; Wild, Philipp S; Kirin, Mirna; Zeller, Tanja; Zemunik, Tatijana; Zhang, Qunyuan; Ziegler, Andreas; Blankenberg, Stefan; Boerwinkle, Eric; Borecki, Ingrid B; Campbell, Harry; Deary, Ian J; Frayling, Timothy M; Gieger, Christian; Harris, Tamara B; Hicks, Andrew A; Koenig, Wolfgang; O' Donnell, Christopher J; Fox, Caroline S; Pramstaller, Peter P; Psaty, Bruce M; Reiner, Alex P; Rotter, Jerome I; Rudan, Igor; Snieder, Harold; Tanaka, Toshihiro; van Duijn, Cornelia M; Vollenweider, Peter; Waeber, Gerard; Wilson, James F; Witteman, Jacqueline C M; Wolffenbuttel, Bruce H R; Wright, Alan F; Wu, Qingyu; Liu, Yongmei; Jenny, Nancy S; North, Kari E; Felix, Janine F; Alizadeh, Behrooz Z; Cupples, L Adrienne; Perry, John R B; Morris, Andrew P

    2012-10-01

    Many disorders are associated with altered serum protein concentrations, including malnutrition, cancer, and cardiovascular, kidney, and inflammatory diseases. Although these protein concentrations are highly heritable, relatively little is known about their underlying genetic determinants. Through transethnic meta-analysis of European-ancestry and Japanese genome-wide association studies, we identified six loci at genome-wide significance (p < 5 × 10(-8)) for serum albumin (HPN-SCN1B, GCKR-FNDC4, SERPINF2-WDR81, TNFRSF11A-ZCCHC2, FRMD5-WDR76, and RPS11-FCGRT, in up to 53,190 European-ancestry and 9,380 Japanese individuals) and three loci for total protein (TNFRS13B, 6q21.3, and ELL2, in up to 25,539 European-ancestry and 10,168 Japanese individuals). We observed little evidence of heterogeneity in allelic effects at these loci between groups of European and Japanese ancestry but obtained substantial improvements in the resolution of fine mapping of potential causal variants by leveraging transethnic differences in the distribution of linkage disequilibrium. We demonstrated a functional role for the most strongly associated serum albumin locus, HPN, for which Hpn knockout mice manifest low plasma albumin concentrations. Other loci associated with serum albumin harbor genes related to ribosome function, protein translation, and proteasomal degradation, whereas those associated with serum total protein include genes related to immune function. Our results highlight the advantages of transethnic meta-analysis for the discovery and fine mapping of complex trait loci and have provided initial insights into the underlying genetic architecture of serum protein concentrations and their association with human disease. PMID:23022100

  9. Three QTL in the honey bee Apis mellifera L. suppress reproduction of the parasitic mite Varroa destructor.

    PubMed

    Behrens, Dieter; Huang, Qiang; Geßner, Cornelia; Rosenkranz, Peter; Frey, Eva; Locke, Barbara; Moritz, Robin F A; Kraus, F B

    2011-12-01

    Varroa destructor is a highly virulent ectoparasitic mite of the honey bee Apis mellifera and a major cause of colony losses for global apiculture. Typically, chemical treatment is essential to control the parasite population in the honey bee colony. Nevertheless a few honey bee populations survive mite infestation without any treatment. We used one such Varroa mite tolerant honey bee lineage from the island of Gotland, Sweden, to identify quantitative trait loci (QTL) controlling reduced mite reproduction. We crossed a queen from this tolerant population with drones from susceptible colonies to rear hybrid queens. Two hybrid queens were used to produce a mapping population of haploid drones. We discriminated drone pupae with and without mite reproduction, and screened the genome for potential QTL using a total of 216 heterozygous microsatellite markers in a bulk segregant analysis. Subsequently, we fine mapped three candidate target regions on chromosomes 4, 7, and 9. Although the individual effect of these three QTL was found to be relatively small, the set of all three had significant impact on suppression of V. destructor reproduction by epistasis. Although it is in principle possible to use these loci for marker-assisted selection, the strong epistatic effects between the three loci complicate selective breeding programs with the Gotland Varroa tolerant honey bee stock. PMID:22393513

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

    Microsoft Academic Search

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

    2010-01-01

    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\\u000a lines and the tepary bean (P. acutifolius L.) line PI319443. This source of CBB resistance is widely used in bean breeding. Several other

  11. Assessing the importance of genotype × environment interaction for root traits in rice using a mapping population III: QTL analysis by mixed models

    Microsoft Academic Search

    Katharina Emrich; Adam Price; Hans Peter Piepho

    2008-01-01

    The phenotypic analysis of field experiments includes information about the experimental design, the randomization structure\\u000a and a number of putative dependencies of environment and design factors on the trait investigated. In QTL studies, the genetic\\u000a correlation across environments, which arises when the same set of lines is tested in multiple environments, plays an important\\u000a role. This paper investigates the effect

  12. Fine Mapping of 14q24.1 Breast Cancer Susceptibility Locus

    PubMed Central

    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

    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

  13. Analysis of QTL×environment interaction for yield components and plant height in rice

    Microsoft Academic Search

    J.-Y. Zhuang; H.-X. Lin; J. Lu; H.-R. Qian; S. Hittalmani; N. Huang; K.-L. Zheng

    1997-01-01

    An F2 and two equivalent F3 populations of an indica-indica cross of rice, Tesanai 2\\/CB, were constructed and grown in different environments. The identification of quantitative trait\\u000a loci (QTL) for yield components and plant height and an analysis of QTL?environment interaction were conducted for three trials.\\u000a Interval mapping of QTL for eight traits was employed with a threshold of LOD=2

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

    PubMed Central

    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

    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

  15. Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens.

    PubMed

    Wragg, D; Mwacharo, J M; Alcalde, J A; Hocking, P M; Hanotte, O

    2012-07-01

    Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r(2) ? 0.3) in both traditional and village chickens at pairwise marker distances of ~10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling ~75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions. PMID:22395157

  16. QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum  ×  Gossypium barbadense

    Microsoft Academic Search

    Dao-Hua He; Zhong-Xu Lin; Xian-Long Zhang; Yi-Chun Nie; Xiao-Ping Guo; Yan-Xin Zhang; Wu Li

    2007-01-01

    A high-density molecular marker linkage map of cotton based entirely on polymerase chain reaction-based markers is useful\\u000a for a marker-assisted breeding program. Four kinds of markers—simple sequence repeats (SSRs), sequence-related amplified polymorphism\\u000a (SRAP), random amplified polymorphic DNA (RAPD), and retrotransposon-microsatellite amplified polymorphism (REMAP)—were used\\u000a to assay an F2 population from a cross between “Handan208” (Gossypium hirsutum) and “Pima90” (Gossypium barbadense).

  17. A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L

    PubMed Central

    2010-01-01

    Background Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea. Results We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 ×) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL. Conclusion The physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes. PMID:20849583

  18. Am. J. Hum. Genet. 76:349357, 2005 Fine Mapping and Positional Candidate Studies Identify HLA-G

    E-print Network

    Das, Soma

    Am. J. Hum. Genet. 76:349­357, 2005 349 Report Fine Mapping and Positional Candidate Studies Identify HLA-G as an Asthma Susceptibility Gene on Chromosome 6p21 Dan Nicolae,1 Nancy J. Cox,2,3 Lucille A Kogut,3 Nina M. Patel,3 Jeffrey Goodenbour,2 Timothy Howard,7,8 Raoul Wolf,4 Gerard H. Koppelman,11

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

    PubMed

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

    2014-11-28

    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

  20. High-resolution quantitative trait locus analysis reveals multiple diabetes susceptibility loci mapped to intervals<800 kb in the species-conserved Niddm1i of the GK rat.

    PubMed

    Granhall, Charlotte; Park, Hee-Bok; Fakhrai-Rad, Hossein; Luthman, Holger

    2006-11-01

    Niddm1i, a 16-Mb locus within the major diabetes QTL in the diabetic GK rat, causes impaired glucose tolerance in the congenic NIDDM1I strain. Niddm1i is homologous to both human and mouse regions linked with type 2 diabetes susceptibility. We employed multiple QTL analyses of congenic F2 progeny selected for one recombination event within Niddm1i combined with characterization of subcongenic strains. Fine mapping located one hyperglycemia locus within 700 kb (Niddm1i4, P=5x10(-6)). Two adjacent loci were also detected, and the GK allele at Niddm1i2 (500 kb) showed a glucose-raising effect, whereas it had a glucose-lowering effect at Niddm1i3 (400 kb). Most proximally, Niddm1i1 (800 kb) affecting body weight was identified. Experimental data from subcongenics supported the four loci. Sorcs1, one of the two known diabetes susceptibility genes in the region, resides within Niddm1i3, while Tcf7l2 maps outside all four loci. Multiple-marker QTL analysis incorporating the effect of cosegregating QTL as cofactors together with genetically selected progeny can remarkably enhance resolution of QTL. The data demonstrate that the species-conserved Niddm1i is a composite of at least four QTL affecting type 2 diabetes susceptibility and that two adjacent QTL (Niddm1i2GK and Niddm1i3GK) act in opposite directions. PMID:16951059

  1. Trans-Ancestral Studies Fine Map the SLE-Susceptibility Locus TNFSF4

    PubMed Central

    Manku, Harinder; Langefeld, Carl D.; Guerra, Sandra G.; Malik, Talat H.; Alarcon-Riquelme, Marta; Anaya, Juan-Manuel; Bae, Sang-Cheol; Boackle, Susan A.; Brown, Elizabeth E.; Criswell, Lindsey A.; Freedman, Barry I.; Gaffney, Patrick M.; Gregersen, Peter A.; Guthridge, Joel M.; Han, Sang-Hoon; Harley, John B.; Jacob, Chaim O.; James, Judith A.; Kamen, Diane L.; Kaufman, Kenneth M.; Kelly, Jennifer A.; Martin, Javier; Merrill, Joan T.; Moser, Kathy L.; Niewold, Timothy B.; Park, So-Yeon; Pons-Estel, Bernardo A.; Sawalha, Amr H.; Scofield, R. Hal; Shen, Nan; Stevens, Anne M.; Sun, Celi; Gilkeson, Gary S.; Edberg, Jeff C.; Kimberly, Robert P.; Nath, Swapan K.; Tsao, Betty P.; Vyse, Tim J.

    2013-01-01

    We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls), African-Americans (AA) (1529, 2048) and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122). The best evidence of association comes from two adjacent markers: rs2205960-T (P?=?1.71×10?34, OR?=?1.43[1.26–1.60]) and rs1234317-T (P?=?1.16×10?28, OR?=?1.38[1.24–1.54]). Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5? region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3) imputation. Conditional regression analyses delineate the 5? risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-?Bp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-?B interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and lymphopenia. Our data confirm a global signal at TNFSF4 and a role for the expressed product at multiple stages of lymphocyte dysregulation during SLE pathogenesis. We confirm the validity of trans-ancestral mapping in a complex trait. PMID:23874208

  2. Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4.

    PubMed

    Manku, Harinder; Langefeld, Carl D; Guerra, Sandra G; Malik, Talat H; Alarcon-Riquelme, Marta; Anaya, Juan-Manuel; Bae, Sang-Cheol; Boackle, Susan A; Brown, Elizabeth E; Criswell, Lindsey A; Freedman, Barry I; Gaffney, Patrick M; Gregersen, Peter A; Guthridge, Joel M; Han, Sang-Hoon; Harley, John B; Jacob, Chaim O; James, Judith A; Kamen, Diane L; Kaufman, Kenneth M; Kelly, Jennifer A; Martin, Javier; Merrill, Joan T; Moser, Kathy L; Niewold, Timothy B; Park, So-Yeon; Pons-Estel, Bernardo A; Sawalha, Amr H; Scofield, R Hal; Shen, Nan; Stevens, Anne M; Sun, Celi; Gilkeson, Gary S; Edberg, Jeff C; Kimberly, Robert P; Nath, Swapan K; Tsao, Betty P; Vyse, Tim J

    2013-01-01

    We previously established an 80 kb haplotype upstream of TNFSF4 as a susceptibility locus in the autoimmune disease SLE. SLE-associated alleles at this locus are associated with inflammatory disorders, including atherosclerosis and ischaemic stroke. In Europeans, the TNFSF4 causal variants have remained elusive due to strong linkage disequilibrium exhibited by alleles spanning the region. Using a trans-ancestral approach to fine-map the locus, utilising 17,900 SLE and control subjects including Amerindian/Hispanics (1348 cases, 717 controls), African-Americans (AA) (1529, 2048) and better powered cohorts of Europeans and East Asians, we find strong association of risk alleles in all ethnicities; the AA association replicates in African-American Gullah (152,122). The best evidence of association comes from two adjacent markers: rs2205960-T (P=1.71 × 10(-34) , OR=1.43[1.26-1.60]) and rs1234317-T (P=1.16 × 10(-28) , OR=1.38[1.24-1.54]). Inference of fine-scale recombination rates for all populations tested finds the 80 kb risk and non-risk haplotypes in all except African-Americans. In this population the decay of recombination equates to an 11 kb risk haplotype, anchored in the 5' region proximal to TNFSF4 and tagged by rs2205960-T after 1000 Genomes phase 1 (v3) imputation. Conditional regression analyses delineate the 5' risk signal to rs2205960-T and the independent non-risk signal to rs1234314-C. Our case-only and SLE-control cohorts demonstrate robust association of rs2205960-T with autoantibody production. The rs2205960-T is predicted to form part of a decameric motif which binds NF-?Bp65 with increased affinity compared to rs2205960-G. ChIP-seq data also indicate NF-?B interaction with the DNA sequence at this position in LCL cells. Our research suggests association of rs2205960-T with SLE across multiple groups and an independent non-risk signal at rs1234314-C. rs2205960-T is associated with autoantibody production and lymphopenia. Our data confirm a global signal at TNFSF4 and a role for the expressed product at multiple stages of lymphocyte dysregulation during SLE pathogenesis. We confirm the validity of trans-ancestral mapping in a complex trait. PMID:23874208

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

    PubMed Central

    2010-01-01

    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

  4. Revealing the genetic architecture of FHB resistance in hexaploid wheat ( Triticum aestivum L.) by QTL meta-analysis

    Microsoft Academic Search

    Martin Löffler; Chris-Carolin Schön; Thomas Miedaner

    2009-01-01

    Fusarium head blight (FHB) in wheat results in reduced yield and quality and in accumulation of mycotoxins. The objective of this\\u000a study was to identify genomic regions in wheat involved in the control of FHB resistance applying a QTL meta-analysis approach\\u000a by combining QTL of 30 mapping populations to propose independent meta-QTL (MQTL). A consensus map was created on which

  5. Meta-analysis of QTL involved in silage quality of maize and comparison with the position of candidate genes.

    PubMed

    Truntzler, M; Barrière, Y; Sawkins, M C; Lespinasse, D; Betran, J; Charcosset, A; Moreau, L

    2010-11-01

    A meta-analysis of quantitative trait loci (QTL) associated with plant digestibility and cell wall composition in maize was carried out using results from 11 different mapping experiments. Statistical methods implemented in "MetaQTL" software were used to build a consensus map, project QTL positions and perform meta-analysis. Fifty-nine QTL for traits associated with digestibility and 150 QTL for traits associated with cell wall composition were included in the analysis. We identified 26 and 42 metaQTL for digestibility and cell wall composition traits, respectively. Fifteen metaQTL with confidence interval (CI) smaller than 10 cM were identified. As expected from trait correlations, 42% of metaQTL for digestibility displayed overlapping CIs with metaQTL for cell wall composition traits. Coincidences were particularly strong on chromosomes 1 and 3. In a second step, 356 genes selected from the MAIZEWALL database as candidates for the cell wall biosynthesis pathway were positioned on our consensus map. Colocalizations between candidate genes and metaQTL positions appeared globally significant based on ?(2) tests. This study contributed in identifying key chromosomal regions involved in silage quality and potentially associated genes for most of these regions. These genes deserve further investigation, in particular through association mapping. PMID:20658277

  6. Identification and independent validation of a stable yield and thousand grain weight QTL on chromosome 6A of hexaploid wheat (Triticum aestivum L.)

    PubMed Central

    2014-01-01

    Background Grain yield in wheat is a polygenic trait that is influenced by environmental and genetic interactions at all stages of the plant’s growth. Yield is usually broken down into three components; number of spikes per area, grain number per spike, and grain weight (TGW). In polyploid wheat, studies have identified quantitative trait loci (QTL) which affect TGW, yet few have been validated and fine-mapped using independent germplasm, thereby having limited impact in breeding. Results In this study we identified a major QTL for TGW, yield and green canopy duration on wheat chromosome 6A of the Spark x Rialto population, across 12 North European environments. Using independent germplasm in the form of BC2 and BC4 near isogenic lines (NILs), we validated the three QTL effects across environments. In four of the five experiments the Rialto 6A introgression gave significant improvements in yield (5.5%) and TGW (5.1%), with morphometric measurements showing that the increased grain weight was a result of wider grains. The extended green canopy duration associated with the high yielding/TGW Rialto allele was comprised of two independent effects; earlier flowering and delayed final maturity, and was expressed stably across the five environments. The wheat homologue (TaGW2) of a rice gene associated with increased TGW and grain width was mapped within the QTL interval. However, no polymorphisms were identified in the coding sequence between the parents. Conclusion The discovery and validation through near-isogenic lines of robust QTL which affect yield, green canopy duration, thousand grain weight, and grain width on chromosome 6A of hexaploid wheat provide an important first step to advance our understanding of the genetic mechanisms regulating the complex processes governing grain size and yield in polyploid wheat. PMID:25034643

  7. Fine mapping of genes within the IDDM8 region in rheumatoid arthritis

    PubMed Central

    Hinks, Anne; Barton, Anne; John, Sally; Shephard, Neil; Worthington, Jane

    2006-01-01

    The IDDM8 region on chromosome 6q27, first identified as a susceptibility locus for type 1 diabetes, has previously been linked and associated with rheumatoid arthritis (RA). The region contains a number of potential candidate genes, including programmed cell death 2 (PDCD2), the proteosome subunit beta type 1 (PSMB1), delta-like ligand 1 (DLL-1) and TATA box-binding protein (TBP) amongst others. The aim of this study was to fine map the IDDM8 region on chromosome 6q27, focusing on the genes in the region, to identify polymorphisms that may contribute to susceptibility to RA and potentially to other autoimmune diseases. Validated single nucleotide polymorphisms (SNPs; n = 65) were selected from public databases from the 330 kb region of IDDM8. These were genotyped using Sequenom MassArray genotyping technology in two datasets; the test dataset comprised 180 RA cases and 180 controls. We tested 50 SNPs for association with RA and any significant associations were genotyped in a second dataset of 174 RA cases and 192 controls, and the datasets were combined before analysis. Association analysis was performed by chi-square test implemented in Stata software and linkage disequilibrium and haplotype analysis was performed using Helix tree version 4.1. There was initial weak evidence of association, with RA, of a number of SNPs around the loc154449 putative gene and within the KIAA1838 gene; however, these associations were not significant in the combined dataset. Our study has failed to detect evidence of association with any of the known genes mapping to the IDDM8 locus with RA. PMID:16945141

  8. Fine mapping and isolation of Bc7(t), allelic to OsCesA4.

    PubMed

    Yan, Changjie; Yan, Song; Zeng, Xiuhong; Zhang, Zhengqiu; Gu, Minghong

    2007-11-01

    Several brittle culm mutants of rice were identified and characterized. In this study, we characterized a brittle mutant (bc7(t)) identified from japonica variety Zhonghua 11 by means of 60Co-gamma radiation. This mutant displays normal phenotype similar to its wild type plants except for the fragility of all plant body, with approximately 10% decrease in the cellulose content. The genetic analysis and gene fine mapping showed that the bc7(t) mutant was controlled by a recessive gene, residing on an 8.4 kb region of the long arm of chromosome 1. The gene annotation indicated that there was only one putative gene encoding cellulose synthase catalytic subunit (CesA) in this region, which was allelic to OsCesA4. Furthermore, the sequence analysis was carried out and 7 bases deletion in the junction of exon 10 and intron 10 was done in bc7(t) mutant, resulting in the change of reading frame and the consequent failure to generate functional protein. In addition, the result of RNA interference experiment showed that when the Bc7(t) was knocked down, the transplants exhibited fragility, similar to bc7(t) mutant. The finding of novel allele of OsCesA4 locus will facilitate the understanding of the mechanism of cell wall biosynthesis. The potential utilization of the bc7(t) mutant in animal food was discussed as well. PMID:18037139

  9. Fine resolution mapping of population age-structures for health and development applications.

    PubMed

    Alegana, V A; Atkinson, P M; Pezzulo, C; Sorichetta, A; Weiss, D; Bird, T; Erbach-Schoenberg, E; Tatem, A J

    2015-04-01

    The age-group composition of populations varies considerably across the world, and obtaining accurate, spatially detailed estimates of numbers of children under 5 years is important in designing vaccination strategies, educational planning or maternal healthcare delivery. Traditionally, such estimates are derived from population censuses, but these can often be unreliable, outdated and of coarse resolution for resource-poor settings. Focusing on Nigeria, we use nationally representative household surveys and their cluster locations to predict the proportion of the under-five population in 1 × 1 km using a Bayesian hierarchical spatio-temporal model. Results showed that land cover, travel time to major settlements, night-time lights and vegetation index were good predictors and that accounting for fine-scale variation, rather than assuming a uniform proportion of under 5 year olds can result in significant differences in health metrics. The largest gaps in estimated bednet and vaccination coverage were in Kano, Katsina and Jigawa. Geolocated household surveys are a valuable resource for providing detailed, contemporary and regularly updated population age-structure data in the absence of recent census data. By combining these with covariate layers, age-structure maps of unprecedented detail can be produced to guide the targeting of interventions in resource-poor settings. PMID:25788540

  10. Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis.

    PubMed

    Liu, Jimmy Z; Almarri, Mohamed A; Gaffney, Daniel J; Mells, George F; Jostins, Luke; Cordell, Heather J; Ducker, Samantha J; Day, Darren B; Heneghan, Michael A; Neuberger, James M; Donaldson, Peter T; Bathgate, Andrew J; Burroughs, Andrew; Davies, Mervyn H; Jones, David E; Alexander, Graeme J; Barrett, Jeffrey C; Sandford, Richard N; Anderson, Carl A

    2012-10-01

    We genotyped 2,861 cases of primary biliary cirrhosis (PBC) from the UK PBC Consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified 3 loci newly associated with PBC (at P<5×10(-8)), increasing the number of known susceptibility loci to 25. The most associated variant at 19p12 is a low-frequency nonsynonymous SNP in TYK2, further implicating JAK-STAT and cytokine signaling in disease pathogenesis. An additional five loci contained nonsynonymous variants in high linkage disequilibrium (LD; r2>0.8) with the most associated variant at the locus. We found multiple independent common, low-frequency and rare variant association signals at five loci. Of the 26 independent non-human leukocyte antigen (HLA) signals tagged on the Immunochip, 15 have SNPs in B-lymphoblastoid open chromatin regions in high LD (r2>0.8) with the most associated variant. This study shows how data from dense fine-mapping arrays coupled with functional genomic data can be used to identify candidate causal variants for functional follow-up. PMID:22961000

  11. Fine mapping analysis confirms and strengthens linkage of four chromosomal regions in familial hypospadias.

    PubMed

    Söderhäll, Cilla; Körberg, Izabella Baranowska; Thai, Hanh T T; Cao, Jia; Chen, Yougen; Zhang, Xufeng; Shulu, Zu; van der Zanden, Loes F M; van Rooij, Iris A L M; Frisén, Louise; Roeleveld, Nel; Markljung, Ellen; Kockum, Ingrid; Nordenskjöld, Agneta

    2015-04-01

    Hypospadias is a common male genital malformation and is regarded as a complex disease affected by multiple genetic as well as environmental factors. In a previous genome-wide scan for familial hypospadias, we reported suggestive linkage in nine chromosomal regions. We have extended this analysis by including new families and additional markers using non-parametric linkage. The fine mapping analysis displayed an increased LOD score on chromosome 8q24.1 and 10p15 in altogether 82 families. On chromosome 10p15, with the highest LOD score, we further studied AKR1C2, AKR1C3 and AKR1C4 involved in steroid metabolism, as well as KLF6 expressed in preputial tissue from hypospadias patients. Mutation analysis of the AKR1C3 gene showed a new mutation, c.643G>A (p.(Ala215Thr)), in a boy with penile hypospadias. This mutation is predicted to have an impact on protein function and structure and was not found in controls. Altogether, we homed in on four chromosomal regions likely to harbor genes for hypospadias. Future studies will aim for studying regulatory sequence variants in these regions. PMID:24986825

  12. A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster.

    PubMed

    Bastide, Héloïse; Betancourt, Andrea; Nolte, Viola; Tobler, Raymond; Stöbe, Petra; Futschik, Andreas; Schlötterer, Christian

    2013-06-01

    Various approaches can be applied to uncover the genetic basis of natural phenotypic variation, each with their specific strengths and limitations. Here, we use a replicated genome-wide association approach (Pool-GWAS) to fine-scale map genomic regions contributing to natural variation in female abdominal pigmentation in Drosophila melanogaster, a trait that is highly variable in natural populations and highly heritable in the laboratory. We examined abdominal pigmentation phenotypes in approximately 8000 female European D. melanogaster, isolating 1000 individuals with extreme phenotypes. We then used whole-genome Illumina sequencing to identify single nucleotide polymorphisms (SNPs) segregating in our sample, and tested these for associations with pigmentation by contrasting allele frequencies between replicate pools of light and dark individuals. We identify two small regions near the pigmentation genes tan and bric-à-brac 1, both corresponding to known cis-regulatory regions, which contain SNPs showing significant associations with pigmentation variation. While the Pool-GWAS approach suffers some limitations, its cost advantage facilitates replication and it can be applied to any non-model system with an available reference genome. PMID:23754958

  13. Fine resolution mapping of population age-structures for health and development applications

    PubMed Central

    Alegana, V. A.; Atkinson, P. M.; Pezzulo, C.; Sorichetta, A.; Weiss, D.; Bird, T.; Erbach-Schoenberg, E.; Tatem, A. J.

    2015-01-01

    The age-group composition of populations varies considerably across the world, and obtaining accurate, spatially detailed estimates of numbers of children under 5 years is important in designing vaccination strategies, educational planning or maternal healthcare delivery. Traditionally, such estimates are derived from population censuses, but these can often be unreliable, outdated and of coarse resolution for resource-poor settings. Focusing on Nigeria, we use nationally representative household surveys and their cluster locations to predict the proportion of the under-five population in 1 × 1 km using a Bayesian hierarchical spatio-temporal model. Results showed that land cover, travel time to major settlements, night-time lights and vegetation index were good predictors and that accounting for fine-scale variation, rather than assuming a uniform proportion of under 5 year olds can result in significant differences in health metrics. The largest gaps in estimated bednet and vaccination coverage were in Kano, Katsina and Jigawa. Geolocated household surveys are a valuable resource for providing detailed, contemporary and regularly updated population age-structure data in the absence of recent census data. By combining these with covariate layers, age-structure maps of unprecedented detail can be produced to guide the targeting of interventions in resource-poor settings. PMID:25788540

  14. Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis

    PubMed Central

    Liu, Jimmy Z; Almarri, Mohamed A; Gaffney, Daniel J; Mells, George F; Jostins, Luke; Cordell, Heather J; Ducker, Samantha J; Day, Darren B; Heneghan, Michael A; Neuberger, James M.; Donaldson, Peter T; Bathgate, Andrew J; Burroughs, Andrew; Davies, Mervyn H; Jones, David E; Alexander, Graeme J; Barrett, Jeffrey C; Sandford, Richard N; Anderson, Carl A

    2012-01-01

    We genotyped 2,861 cases from the UK PBC consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified three loci newly associated with primary biliary cirrhosis (PBC) (with P<5×10?8), increasing the number of known susceptibility loci to 25. The most associated variant at 19p12 is a low-frequency non-synonymous SNP in TYK2, further implicating JAK/STAT and cytokine signalling in disease pathogenesis. A further five loci contained non-synonymous variants in high linkage disequilibrium (LD) (r2>0.8) with the most associated variant at the locus. We found multiple independent common, low-frequency and rare variant association signals at five loci. Of the 26 independent non-HLA signals tagged on Immunochip, 15 have SNPs in B-lymphoblastoid open-chromatin regions in high LD (r2>0.8) with the most associated variant. This study demonstrates how dense fine-mapping arrays coupled with functional genomic data can be utilized to identify candidate causal variants for functional follow-up. PMID:22961000

  15. Fine map of the Gct1 spontaneous ovarian granulosa cell tumor locus.

    PubMed

    Smith, Kerri N; Halfyard, Sarah J; Yaskowiak, Edward S; Shultz, Kathryn L; Beamer, Wesley G; Dorward, Ann M

    2013-02-01

    The spontaneous development of juvenile-onset, ovarian granulosa cell (GC) tumors in the SWR/Bm (SWR) inbred mouse strain is a model for juvenile-type GC tumors that appear in infants and young girls. GC tumor susceptibility is supported by multiple Granulosa cell tumor (Gct) loci, but the Gct1 locus on Chr 4 derived from SWR strain background is fundamental for GC tumor development and uniquely responsive to the androgenic precursor dehydroepiandrosterone (DHEA). To resolve the location of Gct1 independently from other susceptibility loci, Gct1 was isolated in a congenic strain that replaces the distal segment of Chr 4 in SWR mice with a 47 × 10(6)-bp genomic segment from the Castaneus/Ei (CAST) strain. SWR females homozygous for the CAST donor segment were confirmed to be resistant to DHEA- and testosterone-induced GC tumorigenesis, indicating successful exchange of CAST alleles (Gct1 ( CA )) for SWR alleles (Gct1 ( SW )) at this tumor susceptibility locus. A series of nested, overlapping, congenic sublines was created to fine-map Gct1 based on GC tumor susceptibility under the influence of pubertal DHEA treatment. Twelve informative lines have resolved the Gct1 locus to a 1.31 × 10(6)-bp interval on mouse Chr 4, a region orthologous to human Chr 1p36.22. PMID:23179634

  16. Replication and fine mapping of asthma-associated loci in individuals of African ancestry.

    PubMed

    Kantor, David B; Palmer, Cameron D; Young, Taylor R; Meng, Yan; Gajdos, Zofia K; Lyon, Helen; Price, Alkes L; Pollack, Samuela; London, Stephanie J; Loehr, Laura R; Smith, Lewis J; Kumar, Rajesh; Jacobs, David R; Petrini, Marcy F; O'Connor, George T; White, Wendy B; Papanicolaou, George; Burkart, Kristin M; Heckbert, Susan R; Barr, R Graham; Hirschhorn, Joel N

    2013-09-01

    Asthma originates from genetic and environmental factors with about half the risk of disease attributable to heritable causes. Genome-wide association studies, mostly in populations of European ancestry, have identified numerous asthma-associated single nucleotide polymorphisms (SNPs). Studies in populations with diverse ancestries allow both for identification of robust associations that replicate across ethnic groups and for improved resolution of associated loci due to different patterns of linkage disequilibrium between ethnic groups. Here we report on an analysis of 745 African-American subjects with asthma and 3,238 African-American control subjects from the Candidate Gene Association Resource (CARe) Consortium, including analysis of SNPs imputed using 1,000 Genomes reference panels and adjustment for local ancestry. We show strong evidence that variation near RAD50/IL13, implicated in studies of European ancestry individuals, replicates in individuals largely of African ancestry. Fine mapping in African ancestry populations also refined the variants of interest for this association. We also provide strong or nominal evidence of replication at loci near ORMDL3/GSDMB, IL1RL1/IL18R1, and 10p14, all previously associated with asthma in European or Japanese populations, but not at the PYHIN1 locus previously reported in studies of African-American samples. These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry. PMID:23666277

  17. Replication and fine mapping of asthma-associated loci in individuals of African ancestry

    PubMed Central

    Kantor, David B.; Palmer, Cameron D.; Young, Taylor R.; Meng, Yan; Gajdos, Zofia K.; Lyon, Helen; Price, Alkes L.; Pollack, Samuela; London, Stephanie J.; Loehr, Laura R.; Smith, Lewis J.; Kumar, Rajesh; Jacobs, David R.; Petrini, Marcy F.; O’Connor, George T.; White, Wendy B.; Papanicolaou, George; Burkart, Kristin M.; Heckbert, Susan R.; Barr, R. Graham

    2013-01-01

    Asthma originates from genetic and environmental factors with about half the risk of disease attributable to heritable causes. Genome-wide association studies, mostly in populations of European ancestry, have identified numerous asthma-associated single nucleotide polymorphisms (SNPs). Studies in populations with diverse ancestries allow both for identification of robust associations that replicate across ethnic groups and for improved resolution of associated loci due to different patterns of linkage disequilibrium between ethnic groups. Here we report on an analysis of 745 African-American subjects with asthma and 3,238 African-American control subjects from the Candidate Gene Association Resource (CARe) Consortium, including analysis of SNPs imputed using 1,000 Genomes reference panels and adjustment for local ancestry. We show strong evidence that variation near RAD50/IL13, implicated in studies of European ancestry individuals, replicates in individuals largely of African ancestry. Fine mapping in African ancestry populations also refined the variants of interest for this association. We also provide strong or nominal evidence of replication at loci near ORMDL3/GSDMB, IL1RLML18R1, and 10pl4, all previously associated with asthma in European or Japanese populations, but not at the PYHIN1 locus previously reported in studies of African-American samples. These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry. PMID:23666277

  18. 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...

  19. Epistasis in allelic expression at upper temperature tolerance QTL in rainbow trout

    Microsoft Academic Search

    Roy G. Danzmann; Timothy R. Jackson; Moira M. Ferguson

    1999-01-01

    We have mapped the location of QTL affecting upper temperature tolerance in three backcross families of rainbow trout (Oncorhynchus mykiss) derived from matings between an F1 male (high (H)×low (L) temperature tolerance selected lines) and two H and one L line females using variation at 61 microsatellite loci. Physiological epistasis was observed among paternally inherited QTL alleles and this depended

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

    PubMed Central

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

    2014-01-01

    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

  1. Re-Sequencing Data for Refining Candidate Genes and Polymorphisms in QTL Regions Affecting Adiposity in Chicken

    PubMed Central

    Roux, Pierre-François; Boutin, Morgane; Désert, Colette; Djari, Anis; Esquerré, Diane; Klopp, Christophe

    2014-01-01

    In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments. PMID:25333370

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

    PubMed Central

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

    2012-01-01

    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

  3. Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice.

    PubMed

    Xie, Lixia; Tan, Zhengwei; Zhou, Yuan; Xu, Rongbao; Feng, Laibao; Xing, Yongzhong; Qi, Xiaoquan

    2014-08-01

    Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establishment of strong seedlings in any environmental conditions. Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci (QTLs) for seed vigor by using a recombinant inbred population from a cross between rice (Oryza sativa L. ssp. indica) cultivars ZS97 and MH63. Conditional QTL analysis identified qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-11 influenced seedling establishment and that qSV-5a, qSV-5c, and qSV-8 influenced only germination. Of these, qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-8 were low-temperature-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5c were narrowed down to 1.13-Mbp and 400-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive alleles for increased seed vigor in both normal and low-temperature germination environments. PMID:24571491

  4. Lineage-specific mapping of quantitative trait loci

    PubMed Central

    Chen, C; Ritland, K

    2013-01-01

    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

  5. Fine-mapping IGF1 and prostate cancer risk in African Americans: the multiethnic cohort study.

    PubMed

    Giorgi, Elena E; Stram, Daniel O; Taverna, Darin; Turner, Stephen D; Schumacher, Fredrick; Haiman, Christopher A; Lum-Jones, Annette; Tirikainen, Maarit; Caberto, Christian; Duggan, David; Henderson, Brian E; Le Marchand, Loic; Cheng, Iona

    2014-09-01

    Genetic variation at insulin-like growth factor 1 (IGF1) has been linked to prostate cancer risk. However, the specific predisposing variants have not been identified. In this study, we fine-mapped the IGF1 locus for prostate cancer risk in African Americans. We conducted targeted Roche GS-Junior 454 resequencing of a 156-kb region of IGF1 in 80 African American aggressive prostate cancer cases. Three hundred and thirty-four IGF1 SNPs were examined for their association with prostate cancer risk in 1,000 African American prostate cancer cases and 991 controls. The top associated SNP in African Americans, rs148371593, was examined in an additional 3,465 prostate cancer cases and 3,425 controls of non-African American ancestry-European Americans, Japanese Americans, Latinos, and Native Hawaiians. The overall association of 334 IGF1 SNPs and prostate cancer risk was assessed using logistic kernel-machine methods. The association between each SNP and prostate cancer risk was evaluated through unconditional logistic regression. A false discovery rate threshold of q < 0.1 was used to determine statistical significance of associations. We identified 8 novel IGF1 SNPs. The cumulative effect of the 334 IGF1 SNPs was not associated with prostate cancer risk (P = 0.13) in African Americans. Twenty SNPs were nominally associated with prostate cancer at P < 0.05. The top associated SNP among African Americans, rs148371593 [minor allele frequency (MAF) = 0.03; P = 0.0014; q > 0.1], did not reach our criterion of statistical significance. This polymorphism was rare in non-African Americans (MAF < 0.003) and was not associated with prostate cancer risk (P = 0.98). Our findings do not support the role of IGF1 variants and prostate cancer risk among African Americans. PMID:24904019

  6. Fine-Mapping an Association of FSHR with Preterm Birth in a Finnish Population

    PubMed Central

    Chun, Sung; Plunkett, Jevon; Teramo, Kari; Muglia, Louis J.; Fay, Justin C.

    2013-01-01

    Preterm birth is a complex disorder defined by gestations of less than 37 weeks. While preterm birth is estimated to have a significant genetic component, relative few genes have been associated with preterm birth. Polymorphism in one such gene, follicle-stimulating hormone receptor (FSHR), has been associated with preterm birth in Finnish and African American mothers but not other populations. To refine the genetic association of FSHR with preterm birth we conducted a fine-mapping study at the FSHR locus in a Finnish cohort. We sequenced a total of 44 kb, including protein-coding and conserved non-coding regions, in 127 preterm and 135 term mothers. Overall, we identified 288 single nucleotide variants and 65 insertion/deletions of 1–2 bp across all subjects. While no common SNPs in protein-coding regions were associated with preterm birth, including one previously associated with timing of fertilization, multiple SNPs spanning the first and second intron showed the strongest associations. Analysis of the associated SNPs revealed that they form both a protective (OR?=?0.50, 95% CI?=?0.25–0.93) as well as a risk (OR?=?1.89, 95% CI?=?1.08–3.39) haplotype with independent effects. In these haplotypes, two SNPs, rs12052281 and rs72822025, were predicted to disrupt ZEB1 and ELF3 transcription factor binding sites, respectively. Our results show that multiple haplotypes at FSHR are associated with preterm birth and we discuss the frequency and structure of these haplotypes outside of the Finnish population as a potential explanation for the absence of FSHR associations in some populations. PMID:24205076

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2014-08-01

    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

  9. Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2.

    PubMed

    Orr, Nick; Dudbridge, Frank; Dryden, Nicola; Maguire, Sarah; Novo, Daniela; Perrakis, Eleni; Johnson, Nichola; Ghoussaini, Maya; Hopper, John L; Southey, Melissa C; Apicella, Carmel; Stone, Jennifer; Schmidt, Marjanka K; Broeks, Annegien; Van't Veer, Laura J; Hogervorst, Frans B; Fasching, Peter A; Haeberle, Lothar; Ekici, Arif B; Beckmann, Matthias W; Gibson, Lorna; Aitken, Zoe; Warren, Helen; Sawyer, Elinor; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Burwinkel, Barbara; Marme, Frederik; Schneeweiss, Andreas; Sohn, Chistof; Guénel, Pascal; Truong, Thérèse; Cordina-Duverger, Emilie; Sanchez, Marie; Bojesen, Stig E; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Benitez, Javier; Zamora, Maria Pilar; Arias Perez, Jose Ignacio; Menéndez, Primitiva; Anton-Culver, Hoda; Neuhausen, Susan L; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Hamann, Ute; Brauch, Hiltrud; Justenhoven, Christina; Brüning, Thomas; Ko, Yon-Dschun; Nevanlinna, Heli; Aittomäki, Kristiina; Blomqvist, Carl; Khan, Sofia; Bogdanova, Natalia; Dörk, Thilo; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Chenevix-Trench, Georgia; Beesley, Jonathan; Lambrechts, Diether; Moisse, Matthieu; Floris, Guiseppe; Beuselinck, Benoit; Chang-Claude, Jenny; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Radice, Paolo; Peterlongo, Paolo; Peissel, Bernard; Pensotti, Valeria; Couch, Fergus J; Olson, Janet E; Slettedahl, Seth; 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; Kristensen, Vessela; Alnæs, Grethe Grenaker; Nord, Silje; Borresen-Dale, Anne-Lise; Zheng, Wei; Deming-Halverson, Sandra; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Andrulis, Irene L; Knight, Julia A; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robertus A E M; Seynaeve, Caroline M; Van Asperen, Christi J; Garcia-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J; Lissowska, Jolanta; Czene, Kamila; Darabi, Hatef; Eriksson, Mikael; Klevebring, Daniel; Hooning, Maartje J; Hollestelle, Antoinette; van Deurzen, Carolien H M; Kriege, Mieke; Hall, Per; Li, Jingmei; Liu, Jianjun; Humphreys, Keith; Cox, Angela; Cross, Simon S; Reed, Malcolm W R; Pharoah, Paul D P; Dunning, Alison M; Shah, Mitul; Perkins, Barbara J; Jakubowska, Anna; Lubinski, Jan; Jaworska-Bieniek, Katarzyna; Durda, Katarzyna; Ashworth, Alan; Swerdlow, Anthony; Jones, Michael; Schoemaker, Minouk J; Meindl, Alfons; Schmutzler, Rita K; Olswold, Curtis; Slager, Susan; Toland, Amanda E; Yannoukakos, Drakoulis; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Matsuo, Keitaro; Ito, Hidema; Iwata, Hiroji; Ishiguro, Junko; Wu, Anna H; Tseng, Chiu-Chen; Van Den Berg, David; Stram, Daniel O; Teo, Soo Hwang; Yip, Cheng Har; Kang, Peter; Ikram, Mohammad Kamran; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K; Noh, Dong-Young; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Lee, Soo Chin; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; Mckay, James; Wu, Pei-Ei; Hou, Ming-Feng; Yu, Jyh-Cherng; Shen, Chen-Yang; Blot, William; Cai, Qiuyin; Signorello, Lisa B; Luccarini, Craig; Bayes, Caroline; Ahmed, Shahana; Maranian, Mel; Healey, Catherine S; González-Neira, Anna; Pita, Guillermo; Alonso, M Rosario; Álvarez, Nuria; Herrero, Daniel; Tessier, Daniel C; Vincent, Daniel; Bacot, Francois; Hunter, David J; Lindstrom, Sara; Dennis, Joe; Michailidou, Kyriaki; Bolla, Manjeet K; Easton, Douglas F; Dos Santos Silva, Isabel; Fletcher, Olivia; Peto, Julian

    2015-05-15

    We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88-0.92]; P-value = 1.58 × 10(-25)). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ?14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08-1.17]; P-value = 7.89 × 10(-09)) and rs13294895 (OR = 1.09 [1.06-1.12]; P-value = 2.97 × 10(-11)). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06-1.18]; P-value = 2.77 × 10(-05)). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-?, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis. PMID:25652398

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

    PubMed

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

    2014-11-01

    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

  11. Dynamic QTL analysis of linolenic acid content in different developmental stages of soybean seed.

    PubMed

    Han, Yingpeng; Xie, Dongwei; Teng, Weili; Zhang, Shuzheng; Chang, Wei; Li, Wenbin

    2011-05-01

    Linolenic acid (LN) in soybean (Glycine max L. Merr.) seed mainly contributes to the undesirable odors and flavors commonly associated with poor oil quality. LN deposition at various stages of soybean seed development had not been reported by 2010. The objects of this study were (1) to identify and measure quantitative trait loci (QTL) underlying LN content and (2) to estimate the QTL effects expressed from earlier seed developmental stages to drying seed of soybean. One hundred and twenty-five F(5:8) and F(5:9) recombinant inbred lines derived from the cross of soybean cultivars 'Hefeng 25' and 'Dongnong L5' were used for the identification of QTL underlying LN content from the 37 day (D) to 86D stages after flowering, at Harbin in 2008 and 2009. QTL × Environment interactions (QE) effects were evaluated using a mixed genetic model (Zhu in J Zhejiang Univ (Natural Science) 33:327-335, 1999). Twelve unconditional QTL and 12 conditional QTL associated with LN content were identified at different developmental stages. Most of the QTL explained <10% of phenotypic variation of LN content. Unconditional QTL QLNF-1, QLNC2-1, QLND1b-1, QLNA2-1 and QLNH-1 influenced LN content across different development stages and environments. Conditional QTL QLNF-1, QLNC2-1 and QLNH-1 were identified in multiple developmental stages and environments. Conditional and unconditional QTL clustered in neighboring intervals on linkage groups A2, C2 and D1b. Ten QTL with conditional additive main effects (a) and/or conditional additive × environment interaction effects (ae) at specific developmental stage were identified on nine linkage groups. Of them, six QTL only possessed additive main effects and seven QTL had significant ae effects in different developmental stages. A total of 13 epistatic pairwise QTL were identified by conditional mapping in different developmental stages. Two pairs of QTL only showed aa effects and five pairs of QTL only showed aae effects at different developmental stages. QTL with aa effects, as well as their environmental interaction effects, appeared to vary at different developmental stages. PMID:21344183

  12. Genomic correlates of relationship QTL involved in fore- versus hind limb divergence in mice.

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  14. Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement

    Microsoft Academic Search

    E. S. Mace; D. R. Jordan

    2011-01-01

    A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical\\u000a sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In\\u000a total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals

  15. Fine mapping and identification of candidate Bo-or gene controlling orange head of Chinese cabbage (Brassica rapa L. ssp. Pekinensis)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Orange head Chinese cabbage accumulates significant amounts of carotenoids with enhanced nutritional quality. To develop molecular markers for breeding of Chinese cabbage lines with high carotenoid content and to isolate the candidate gene underlying carotenoid synthesis, we performed fine mapping ...

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

    PubMed Central

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

    2014-01-01

    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

  17. Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea

    Microsoft Academic Search

    J. D. Kelly; P. Gepts; P. N. Miklas; D. P. Coyne

    2003-01-01

    Bean\\/Cowpea Collaborative Research Support Program (B\\/C CRSP) scientists have successfully developed integrated consensus maps of the 11 linkage groups (LGs) in both bean (Phaseolus vulgaris L.) and cowpea (Vigna unguiculata L. Walp). The bean map is approximately 1200cM with some 500 markers and an additional 500 markers shared with other bean maps. The cowpea map spans 2670cM with over 400

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

    PubMed Central

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

    2013-01-01

    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

  19. CONSENSUS QUANTITATIVE TRAIT MAPS IN MAIZE: A DATABASE STRATEGY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report a strategy for consensus QTL maps that leverages the highly curated data in MaizeGDB, in particular, the numerous QTL studies and maps that are integrated with other genome data on a common coordinate system. In addition, we exploit a systematic QTL nomenclature and a hierarchical categori...

  20. QTL x Genetic Background Interaction: Application to Predicting Progeny Value

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Failures of the additive infinitesimal model continue to provide incentive to study other modes of gene action, in particular, epistasis. Epistasis can be modeled as a QTL by genetic background interaction. Association mapping models lend themselves to fitting such an interaction because they often ...

  1. Fine-scale mapping of vector habitats using very high resolution satellite imagery: a liver fluke case-study.

    PubMed

    De Roeck, Els; Van Coillie, Frieke; De Wulf, Robert; Soenen, Karen; Charlier, Johannes; Vercruysse, Jozef; Hantson, Wouter; Ducheyne, Els; Hendrickx, Guy

    2014-01-01

    The visualization of vector occurrence in space and time is an important aspect of studying vector-borne diseases. Detailed maps of possible vector habitats provide valuable information for the prediction of infection risk zones but are currently lacking for most parts of the world. Nonetheless, monitoring vector habitats from the finest scales up to farm level is of key importance to refine currently existing broad-scale infection risk models. Using Fasciola hepatica, a parasite liver fluke, as a case in point, this study illustrates the potential of very high resolution (VHR) optical satellite imagery to efficiently and semi-automatically detect detailed vector habitats. A WorldView2 satellite image capable of <5m resolution was acquired in the spring of 2013 for the area around Bruges, Belgium, a region where dairy farms suffer from liver fluke infections transmitted by freshwater snails. The vector thrives in small water bodies (SWBs), such as ponds, ditches and other humid areas consisting of open water, aquatic vegetation and/or inundated grass. These water bodies can be as small as a few m2 and are most often not present on existing land cover maps because of their small size. We present a classification procedure based on object-based image analysis (OBIA) that proved valuable to detect SWBs at a fine scale in an operational and semi-automated way. The classification results were compared to field and other reference data such as existing broad-scale maps and expert knowledge. Overall, the SWB detection accuracy reached up to 87%. The resulting fine-scale SWB map can be used as input for spatial distribution modelling of the liver fluke snail vector to enable development of improved infection risk mapping and management advice adapted to specific, local farm situations. PMID:25599638

  2. Detection and modelling of time-dependent QTL in animal populations

    PubMed Central

    Lund, Mogens S; Sorensen, Peter; Madsen, Per; Jaffrézic, Florence

    2008-01-01

    A longitudinal approach is proposed to map QTL affecting function-valued traits and to estimate their effect over time. The method is based on fitting mixed random regression models. The QTL allelic effects are modelled with random coefficient parametric curves and using a gametic relationship matrix. A simulation study was conducted in order to assess the ability of the approach to fit different patterns of QTL over time. It was found that this longitudinal approach was able to adequately fit the simulated variance functions and considerably improved the power of detection of time-varying QTL effects compared to the traditional univariate model. This was confirmed by an analysis of protein yield data in dairy cattle, where the model was able to detect QTL with high effect either at the beginning or the end of the lactation, that were not detected with a simple 305 day model. PMID:18298934

  3. Fine Mapping of the Bsr1 Barley Stripe Mosaic Virus Resistance Gene in the Model Grass Brachypodium distachyon

    PubMed Central

    Cui, Yu; Lee, Mi Yeon; Huo, Naxin; Bragg, Jennifer; Yan, Lijie; Yuan, Cheng; Li, Cui; Holditch, Sara J.; Xie, Jingzhong; Luo, Ming-Cheng; Li, Dawei; Yu, Jialin; Martin, Joel; Schackwitz, Wendy; Gu, Yong Qiang; Vogel, John P.; Jackson, Andrew O.; Liu, Zhiyong; Garvin, David F.

    2012-01-01

    The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25°C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F6?7 recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F2 population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits. PMID:22675544

  4. Precision mapping of quantitative trait loci

    Microsoft Academic Search

    Zhao-Bang Zeng

    1994-01-01

    Adequate separation of effects of possible multiple linked quantitative trait loci (QTLs) on mapping QTLs is the key to increasing the precision of QTL mapping. A new method of QTL mapping is proposed and analyzed in this paper by combining interval mapping with multiple regression. The basis of the proposed method is an interval test in which the test statistic

  5. Fourteen Years of R/qtl: Just Barely Sustainable

    PubMed Central

    Broman, Karl W.

    2014-01-01

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

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

    PubMed Central

    2013-01-01

    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

  7. Fine mapping in tomato using microsynteny with the Arabidopsis genome: the Diageotropica (Dgt) locus

    Microsoft Academic Search

    KwangChul Oh; Kristine Hardeman; Maria G Ivanchenko; Mary Ellard-Ivey; Andreas Nebenführ; TJ White; Terri L Lomax

    2002-01-01

    BACKGROUND: The Arabidopsis thaliana genome sequence provides a catalog of reference genes applicable to comparative microsynteny analysis of other species, facilitating map-based cloning in economically important crops. We have applied such an analysis to the tomato expressed sequence tag (EST) database to expedite high-resolution mapping of the Diageotropica (Dgt) gene within the distal end of chromosome 1 in tomato (Lycopersicon

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

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

    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.

  9. Fine resolution topographic mapping of the Jovian moons: a Ka-band high resolution topographic mapping interferometric synthetic aperture radar

    NASA Technical Reports Server (NTRS)

    Madsen, Soren N.; Carsey, Frank D.; Turtle, Elizabeth P.

    2003-01-01

    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 us 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 100 km 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.

  10. 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...

  11. A mixed model QTL analysis for sugarcane multiple-harvest-location trial data.

    PubMed

    Pastina, M M; Malosetti, M; Gazaffi, R; Mollinari, M; Margarido, G R A; Oliveira, K M; Pinto, L R; Souza, A P; van Eeuwijk, F A; Garcia, A A F

    2012-03-01

    Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane. PMID:22159754

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. The lack of informative and saturated linkage maps associated with well characterized populations s...

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

    E-print Network

    Broman, Karl W.

    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

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

    SciTech Connect

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

    1992-02-01

    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.

  15. Fine-mapping of a locus on linkage group 23 for sex determination in Nile tilapia (Oreochromis niloticus).

    PubMed

    Eshel, O; Shirak, A; Weller, J I; Slossman, T; Hulata, G; Cnaani, A; Ron, M

    2011-04-01

    Genetic markers in tilapia species associated with loci affecting sex determination (SD), sex-specific mortality or both were mapped to linkage groups (LG) 1, 2, 3, 6 and 23. The objective of this study was to use these markers to fine-map the locus with the greatest effect on SD in Oreochromis niloticus. Our parental stock, full-sibs of Nile tilapia (Swansea origin), were divided into three groups: (i) untreated, (ii) feminized by diethylstilbestrol and (iii) masculinized by 17?-methyltestosterone. We analysed the first group for association of microsatellite markers representing these five LGs. The strongest association with gender was found on LG23 for marker UNH898 (?(2) ; P=8.6×10(-5) ). Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Sex-reversed individuals were used for mating experiments with and without the segregating MAA. Mating of individuals lacking the MAA resulted in all-female progeny. Mating of two heterozygotes for MAA gave rise to 81 males and 30 females. Analysis of association between gender and genotypes identified the MAA in 98.6% of males as opposed to 8.0% of females (?(2) ; P=2.5×10(-18) ). Eight markers that flank UNH898 were genotyped to map the locus on LG23 within a confidence interval of 16-21 cM. Mating of homozygous individuals for MAA is underway for production of all-male populations. PMID:24725231

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

    PubMed

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

    2007-08-01

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

  17. Fine mapping of the congenital chloride diarrhea gene by linkage disequilibrium.

    PubMed Central

    Höglund, P; Sistonen, P; Norio, R; Holmberg, C; Dimberg, A; Gustavson, K H; de la Chapelle, A; Kere, J

    1995-01-01

    Congenital chloride diarrhea is a recessively inherited intestinal disorder affecting electrolyte transportation. The clinical presentation is a life-threatening watery diarrhea with a high chloride content. Recently, the congenital chloride diarrhea gene (CLD) was assigned to chromosome 7 by linkage in eight Finnish families. In the present study, refined mapping of CLD was performed by studying linkage and linkage disequilibrium in 24 Finnish and 4 Swedish families. Recombination mapping assigned CLD to an approximately 10-cM region flanked by D7S515 and D7S799. Linkage disequilibrium was detected over this large genetic region, with the strongest allelic association at D7S496. Application of the Luria and Delbrück-derived analysis allowed for a further narrowing of the CLD region to approximately 0.37 cM from the marker D7S496. Haplotype analysis placed CLD unequivocally between D7S501 and D7S692, very close to D7S496 and most likely on the distal side of D7S496. This combined analytical approach allowed highly accurate mapping of CLD, each component adding complementary and consistent mapping information. Images Figure 1 PMID:7611301

  18. Fine Mapping the Soybean Aphid Resistance Gene Rag1 in Soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The soybean aphid [Aphis glycines Matsumura] is an important soybean [Glycine max (L.) Merr.] pest in North America. The dominant aphid resistance gene Rag1 was previously mapped from the cultivar ‘Dowling’ to a 12 centiMorgan (cM) marker interval on soybean chromosome 7 [formerly linkage group (LG)...

  19. Fine mapping of the friend retrovirus resistance gene, Rfv3, on mouse chromosome 15.

    PubMed

    Super, H J; Hasenkrug, K J; Simmons, S; Brooks, D M; Konzek, R; Sarge, K D; Morimoto, R I; Jenkins, N A; Gilbert, D J; Copeland, N G; Frankel, W; Chesebro, B

    1999-09-01

    Rfv3 is a host resistance gene that operates through an unknown mechanism to control the development of the virus-neutralizing antibody response required for recovery from infection with Friend retrovirus. The Rfv3 gene was previously mapped to an approximately 20-centimorgan (cM) region of chromosome 15. More refined mapping was not possible, due to a lack of microsatellite markers and leakiness in the Rfv3 phenotype, which prevented definitive phenotyping of individual recombinant mice. In the present study, we overcame these difficulties by taking advantage of seven new microsatellite markers in the Rfv3 region and by using progeny tests to accurately determine the Rfv3 phenotype of recombinant mice. Detailed linkage analysis of relevant crossovers narrowed the location of Rfv3 to a 0.83-cM region. Mapping of closely linked genes in an interspecific backcross panel allowed us to exclude two previous candidate genes, Ly6 and Wnt7b. These studies also showed for the first time that the Hsf1 gene maps to the Rfv3-linked cluster of genes including Il2rb, Il3rb, and Pdgfb. This localization of Rfv3 to a region of less than 1 cM now makes it feasible to attempt the cloning of Rfv3 by physical methods. PMID:10438878

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

    Microsoft Academic Search

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

    2009-01-01

    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

  1. 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....

  2. Fine mapping and conservation analysis of linear B-cell epitopes of peste des petits ruminants virus nucleoprotein.

    PubMed

    Yu, Ruisong; Fan, Xiaoming; Xu, Wanxiang; Li, Wentao; Dong, Shijuan; Zhu, Yumin; He, Yaping; Tang, Haiping; Du, Rong; Li, Zhen

    2015-01-30

    Nucleoprotein (NP) is the most abundant and highly immunogenic protein of morbillivirus, and is presently the basis of most diagnostic assays for peste des petits ruminants virus (PPRV). In this study, fine epitope mapping and conservation analysis of linear B-cell epitopes on the PPRV NP has been undertaken using biosynthetic peptides. Nineteen linear B-cell epitopes were identified and their corresponding minimal motifs were located on the NP of PPRV China/Tibet/Geg/07-30. Conservation analysis indicated that ten of the 19 minimal motifs were conserved among 46 PPRV strains. Peptides containing the minimal motifs were recognized using anti-PPRV serum from a goat immunized with PPRV vaccine strain Nigeria 75/1. Identified epitopes and their motifs improve our understanding of the antigenic characteristics of PPRV NP and provide a basis for the development of epitope-based diagnostic assays. PMID:25465659

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

    PubMed

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

    2013-01-01

    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

  4. Fine Time Course Expression Analysis Identifies Cascades of Activation and Repression and Maps a Putative Regulator of Mammalian Sex Determination

    PubMed Central

    Looger, Loren L.; Ohler, Uwe; Capel, Blanche

    2013-01-01

    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

  5. Fine mapping of breast cancer genome-wide association studies loci in women of African ancestry identifies novel susceptibility markers.

    PubMed

    Zheng, Yonglan; Ogundiran, Temidayo O; Falusi, Adeyinka G; Nathanson, Katherine L; John, Esther M; Hennis, Anselm J M; Ambs, Stefan; Domchek, Susan M; Rebbeck, Timothy R; Simon, Michael S; Nemesure, Barbara; Wu, Suh-Yuh; Leske, Maria Cristina; Odetunde, Abayomi; Niu, Qun; Zhang, Jing; Afolabi, Chibuzor; Gamazon, Eric R; Cox, Nancy J; Olopade, Christopher O; Olopade, Olufunmilayo I; Huo, Dezheng

    2013-07-01

    Numerous single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility have been identified by genome-wide association studies (GWAS). However, these SNPs were primarily discovered and validated in women of European and Asian ancestry. Because linkage disequilibrium is ancestry-dependent and heterogeneous among racial/ethnic populations, we evaluated common genetic variants at 22 GWAS-identified breast cancer susceptibility loci in a pooled sample of 1502 breast cancer cases and 1378 controls of African ancestry. None of the 22 GWAS index SNPs could be validated, challenging the direct generalizability of breast cancer risk variants identified in Caucasians or Asians to other populations. Novel breast cancer risk variants for women of African ancestry were identified in regions including 5p12 (odds ratio [OR] = 1.40, 95% confidence interval [CI] = 1.11-1.76; P = 0.004), 5q11.2 (OR = 1.22, 95% CI = 1.09-1.36; P = 0.00053) and 10p15.1 (OR = 1.22, 95% CI = 1.08-1.38; P = 0.0015). We also found positive association signals in three regions (6q25.1, 10q26.13 and 16q12.1-q12.2) previously confirmed by fine mapping in women of African ancestry. In addition, polygenic model indicated that eight best markers in this study, compared with 22 GWAS-identified SNPs, could better predict breast cancer risk in women of African ancestry (per-allele OR = 1.21, 95% CI = 1.16-1.27; P = 9.7 × 10(-16)). Our results demonstrate that fine mapping is a powerful approach to better characterize the breast cancer risk alleles in diverse populations. Future studies and new GWAS in women of African ancestry hold promise to discover additional variants for breast cancer susceptibility with clinical implications throughout the African diaspora. PMID:23475944

  6. Fine Physical and Genetic Mapping of Powdery Mildew Resistance Gene MlIW172 Originating from Wild Emmer (Triticum dicoccoides)

    PubMed Central

    Han, Jun; Zhao, Xiaojie; Cui, Yu; Song, Wei; Huo, Naxin; Liang, Yong; Xie, Jingzhong; Wang, Zhenzhong; Wu, Qiuhong; Chen, Yong-Xing; Lu, Ping; Zhang, De-Yun; Wang, Lili; Sun, Hua; Yang, Tsomin; Keeble-Gagnere, Gabriel; Appels, Rudi; Doležel, Jaroslav; Ling, Hong-Qing; Luo, Mingcheng; Gu, Yongqiang; Sun, Qixin; Liu, Zhiyong

    2014-01-01

    Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90) via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172. PMID:24955773

  7. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides).

    PubMed

    Ouyang, Shuhong; Zhang, Dong; Han, Jun; Zhao, Xiaojie; Cui, Yu; Song, Wei; Huo, Naxin; Liang, Yong; Xie, Jingzhong; Wang, Zhenzhong; Wu, Qiuhong; Chen, Yong-Xing; Lu, Ping; Zhang, De-Yun; Wang, Lili; Sun, Hua; Yang, Tsomin; Keeble-Gagnere, Gabriel; Appels, Rudi; Doležel, Jaroslav; Ling, Hong-Qing; Luo, Mingcheng; Gu, Yongqiang; Sun, Qixin; Liu, Zhiyong

    2014-01-01

    Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90) via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172. PMID:24955773

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

    Microsoft Academic Search

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

    2006-01-01

    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

  9. The mapping of fine and ultrafine particle concentrations in an engine machining and assembly facility.

    PubMed

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

    2006-04-01

    Aerosol mapping was used to assess particle number and mass concentration in an engine machining and assembly facility in the winter and spring. Number and mass concentration maps were constructed from data collected with two mobile sampling carts, each equipped with a condensation particle counter (10 nm < diameter < 1 microm) and an optical particle counter (300 nm < diameter < 20 microm). Number concentrations inside the facility ranged from 15 to 150 times greater than that outside the facility and were highly dependent on season. The greatest number concentration (>1,000,000 particles cm(-3)) occurred in winter in an area where mass concentration was low (<0.10 mg m(-3)). The increased number of particles was attributed to the exhaust of direct-fire, natural-gas burners used to heat the supply air. The greatest mass concentrations were found around metalworking operations that were poorly enclosed. The larger particles that dominated particle mass in this area were accompanied by ultrafine particles, probably generated through evaporation and subsequent condensation of metalworking fluid components. Repeat mapping events demonstrated that these ultrafine particles persist in workplace air over long time periods. PMID:16361396

  10. Construction of a chromosome-assigned, sequence-tagged linkage map for the radish, Raphanus sativus L. and QTL analysis of morphological traits

    PubMed Central

    Hashida, Tomoko; Nakatsuji, Ryoichi; Budahn, Holger; Schrader, Otto; Peterka, Herbert; Fujimura, Tatsuhito; Kubo, Nakao; Hirai, Masashi

    2013-01-01

    The radish displays great morphological variation but the genetic factors underlying this variability are mostly unknown. To identify quantitative trait loci (QTLs) controlling radish morphological traits, we cultivated 94 F4 and F5 recombinant inbred lines derived from a cross between the rat-tail radish and the Japanese radish cultivar ‘Harufuku’ inbred lines. Eight morphological traits (ovule and seed numbers per silique, plant shape, pubescence and root formation) were measured for investigation. We constructed a map composed of 322 markers with a total length of 673.6 cM. The linkage groups were assigned to the radish chromosomes using disomic rape-radish chromosome-addition lines. On the map, eight and 10 QTLs were identified in 2008 and 2009, respectively. The chromosome-linkage group correspondence, the sequence-specific markers and the QTLs detected here will provide useful information for further genetic studies and for selection during radish breeding programs. PMID:23853517

  11. An SSR-based linkage map of yardlong bean (Vigna unguiculata (L.) Walp. subsp. unguiculata Sesquipedalis Group) and QTL analysis of pod length.

    PubMed

    Kongjaimun, Alisa; Kaga, Akito; Tomooka, Norihiko; Somta, Prakit; Shimizu, Takehiko; Shu, Yujian; Isemura, Takehisa; Vaughan, Duncan A; Srinives, Peerasak

    2012-02-01

    Yardlong bean (Vigna unguiculata (L.) Walp. subsp. unguiculata Sesquipedalis Group) (2n = 2x = 22) is one of the most important vegetable legumes of Asia. The objectives of this study were to develop a genetic linkage map of yardlong bean using SSR makers from related Vigna species and to identify QTLs for pod length. The map was constructed from 226 simple sequence repeat (SSR) markers from cowpea (Vigna unguiculata (L.) Walp. subsp. unguiculata Unguiculata Group), azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi), and mungbean (Vigna radiata (L.) Wilczek) in a BC(1)F(1) ((JP81610 × TVnu457) × JP81610) population derived from the cross between yardlong bean accession JP81610 and wild cowpea (Vigna unguiculata subsp. unguiculata var. spontanea) accession TVnu457. The markers were clustered into 11 linkage groups (LGs) spanning 852.4 cM in total length with a mean distance between adjacent markers of 3.96 cM. All markers on LG11 showed segregation distortion towards the homozygous yardlong bean JP81610 genotype. The markers on LG11 were also distorted in the rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) map, suggesting the presence of common segregation distortion factors in Vigna species on this LG. One major and six minor QTLs were identified for pod length variation between yardlong bean and wild cowpea. Using flanking markers, six of the seven QTLs were confirmed in an F(2) population of JP81610 × TVnu457. The molecular linkage map developed and markers linked to pod length QTLs would be potentially useful for yardlong bean and cowpea breeding. PMID:22242703

  12. 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

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

    2013-01-01

    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

  13. High congruency of QTL positions for heterosis of grain yield in three crosses of maize.

    PubMed

    Schön, Chris C; Dhillon, Baldev S; Utz, H Friedrich; Melchinger, Albrecht E

    2010-01-01

    The genetic basis of heterosis in maize has been investigated in a number of studies but results have not been conclusive. Here, we compare quantitative trait loci (QTL) mapping results for grain yield, grain moisture, and plant height from three populations derived from crosses of the heterotic pattern Iowa Stiff Stalk Synthetic x Lancaster Sure Crop, investigated with the Design III, and analyzed with advanced statistical methods specifically developed to examine the genetic basis of mid-parent heterosis (MPH). In two populations, QTL analyses were conducted with a joint fit of linear transformations Z (1) (trait mean across pairs of backcross progenies) and Z (2) (half the trait difference between pairs of backcross progenies) to estimate augmented additive and augmented dominance effects of each QTL, as well as their ratio. QTL results for the third population were obtained from the literature. For Z (2) of grain yield, congruency of QTL positions was high across populations, and a large proportion of the genetic variance (~70%) was accounted for by QTL. This was not the case for Z (1) or the other two traits. Further, almost all congruent grain yield QTL were located in the same or an adjacent bin encompassing the centromere. We conclude that different alleles have been fixed in each heterotic pool, which in combination with allele(s) from the opposite heterotic pool lead to high MPH for grain yield. Their positive interactions very likely form the base line for the superior performance of the heterotic pattern under study. PMID:19911156

  14. Disentangling two QTL on porcine chromosome 12 for backfat fatty acid composition.

    PubMed

    Muñoz, María; Fernández, Ana Isabel; Benítez, Rita; Pena, Ramona N; Folch, Josep María; Rodríguez, María del Carmen; Silió, Luis; Alves, Estefânia

    2013-01-01

    A previous study allowed the identification of two QTL regions at positions 11-34 cM (QTL1) and 68-76 cM (QTL2) on porcine chromosome SSC12 affecting several backfat fatty acids in an Iberian x Landrace F2 intercross. In the current study, different approaches were performed in order to better delimit the quoted QTL regions and analyze candidate genes. A new chromosome scan, using 81 SNPs selected from the Porcine 60KBeadChip and six previously genotyped microsatellites have refined the QTL positions. Three new functional candidate genes (ACOX1, ACLY, and SREBF1) have been characterized. Moreover, two putative promoters of porcine ACACA gene have also been investigated. New isoforms and 24 SNPs were detected in the four candidate genes, 19 of which were genotyped in the population. ACOX1 and ACLY SNPs failed to explain the effects of QTL1 on palmitic and gadoleic fatty acids. QTL2, affecting palmitoleic, stearic, and vaccenic fatty acids, maps close to the ACACA gene location. The most significant associations have been detected between one intronic (g.53840T > C) and one synonymous (c.5634T > C) ACACA SNPs and these fatty acids. Complementary analyses including ACACA gene expression quantification and association studies in other porcine genetic types do not support the expected causal effect of ACACA SNPs. PMID:23777347

  15. Fine-resolution multiscale mapping of clay minerals in Australian soils measured with near infrared spectra

    NASA Astrophysics Data System (ADS)

    Viscarra Rossel, R. A.

    2011-12-01

    Clay minerals are the most reactive inorganic components of soils. They help to determine soil properties and largely govern their behaviors and functions. Clay minerals also play important roles in biogeochemical cycling and interact with the environment to affect geomorphic processes such as weathering, erosion and deposition. This paper provides new spatially explicit clay mineralogy information for Australia that will help to improve our understanding of soils and their role in the functioning of landscapes and ecosystems. I measured the abundances of kaolinite, illite and smectite in Australian soils using near infrared (NIR) spectroscopy. Using a model-tree algorithm, I built rule-based models for each mineral at two depths (0-20 cm, 60-80 cm) as a function of predictors that represent the soil-forming factors (climate, parent material, relief, vegetation and time), their processes and the scales at which they vary. The results show that climate, parent material and soil type exert the largest influence on the abundance and spatial distribution of the clay minerals; relief and vegetation have more local effects. I digitally mapped each mineral on a 3 arc-second grid. The maps show the relative abundances and distributions of kaolinite, illite and smectite in Australian soils. Kaolinite occurs in a range of climates but dominates in deeply weathered soils, in soils of higher landscapes and in regions with more rain. Illite is present in varied landscapes and may be representative of colder, more arid climates, but may also be present in warmer and wetter soil environments. Smectite is often an authigenic mineral, formed from the weathering of basalt, but it also occurs on sediments and calcareous substrates. It occurs predominantly in drier climates and in landscapes with low relief. These new clay mineral maps fill a significant gap in the availability of soil mineralogical information. They provide data to for example, assist with research into soil fertility and food production, carbon sequestration, land degradation, dust and climate modeling and paleoclimatic change.

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

    PubMed Central

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

    2014-01-01

    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

  17. Fine-mapping the POLL locus in Brahman cattle yields the diagnostic marker CSAFG29.

    PubMed

    Mariasegaram, Maxy; Harrison, Blair E; Bolton, Jennifer A; Tier, Bruce; Henshall, John M; Barendse, William; Prayaga, Kishore C

    2012-12-01

    The POLL locus has been mapped to the centromeric region of bovine chromosome 1 (BTA1) in both taurine breeds and taurine-indicine crosses in an interval of approximately 1 Mb. It has not yet been mapped in pure-bred zebu cattle. Despite several efforts, neither causative mutations in candidate genes nor a singular diagnostic DNA marker has been identified. In this study, we genotyped a total of 68 Brahman cattle and 20 Hereford cattle informative for the POLL locus for 33 DNA microsatellites, 16 of which we identified de novo from the bovine genome sequence, mapping the POLL locus to the region of the genes IFNAR2 and SYNJ1. The 303-bp allele of the new microsatellite, CSAFG29, showed strong association with the POLL allele. We then genotyped 855 Brahman cattle for CSAFG29 and confirmed the association between the 303-bp allele and POLL. To determine whether the same association was found in taurine breeds, we genotyped 334 animals of the Angus, Hereford and Limousin breeds and 376 animals of the Brangus, Droughtmaster and Santa Gertrudis composite taurine-zebu breeds. The association between the 303-bp allele and POLL was confirmed in these breeds; however, an additional allele (305 bp) was also associated but not fully predictive of POLL. Across the data, CSAFG29 was in sufficient linkage disequilibrium to the POLL allele in Australian Brahman cattle that it could potentially be used as a diagnostic marker in that breed, but this may not be the case in other breeds. Further, we provide confirmatory evidence that the scur phenotype generally occurs in animals that are heterozygous for the POLL allele. PMID:22497221

  18. Fine Mapping of “Mini-Muscle,” a Recessive Mutation Causing Reduced Hindlimb Muscle Mass in Mice

    PubMed Central

    Hartmann, John; Garland, Theodore; Hannon, Robert M.; Kelly, Scott A.; Muñoz, Gloria

    2008-01-01

    Prolonged selective breeding of Hsd:ICR mice for high levels of voluntary wheel running has favored an unusual phenotype (mini-muscle [MM]), apparently caused by a single Mendelian recessive allele, in which hindlimb muscle mass is reduced by almost 50%. We recently described the creation and phenotypic characterization of a population suitable for mapping the genomic location of the MM gene. Specifically, we crossed females from a high-runner line fixed for the MM allele with male C57BL/6J. F1 males were then backcrossed to the MM parent females. Backcross (BC) mice exhibited a 50:50 ratio of normal to MM phenotypes. Here, we report on linkage mapping of MM in this BC population to a 2.6335-Mb interval on MMU11. This region harbors ?100 expressed or predicted genes, many of which have known roles in muscle development and/or function. Identification of the genetic variation that underlies MM could potentially be very important in understanding both normal muscle function and disregulation of muscle physiology leading to disease. PMID:18544554

  19. Fine-Scale Maps of Recombination Rates and Hotspots in the Mouse Genome

    PubMed Central

    Brunschwig, Hadassa; Levi, Liat; Ben-David, Eyal; Williams, Robert W.; Yakir, Benjamin; Shifman, Sagiv

    2012-01-01

    Recombination events are not uniformly distributed and often cluster in narrow regions known as recombination hotspots. Several studies using different approaches have dramatically advanced our understanding of recombination hotspot regulation. Population genetic data have been used to map and quantify hotspots in the human genome. Genetic variation in recombination rates and hotspots usage have been explored in human pedigrees, mouse intercrosses, and by sperm typing. These studies pointed to the central role of the PRDM9 gene in hotspot modulation. In this study, we used single nucleotide polymorphisms (SNPs) from whole-genome resequencing and genotyping studies of mouse inbred strains to estimate recombination rates across the mouse genome and identified 47,068 historical hotspots—an average of over 2477 per chromosome. We show by simulation that inbred mouse strains can be used to identify positions of historical hotspots. Recombination hotspots were found to be enriched for the predicted binding sequences for different alleles of the PRDM9 protein. Recombination rates were on average lower near transcription start sites (TSS). Comparing the inferred historical recombination hotspots with the recent genome-wide mapping of double-strand breaks (DSBs) in mouse sperm revealed a significant overlap, especially toward the telomeres. Our results suggest that inbred strains can be used to characterize and study the dynamics of historical recombination hotspots. They also strengthen previous findings on mouse recombination hotspots, and specifically the impact of sequence variants in Prdm9. PMID:22562932

  20. Fine-mapping of immunodominant linear B-cell epitopes of the Staphylococcus aureus SEB antigen using short overlapping peptides.

    PubMed

    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

    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

  1. Major histocompatibility complex haplotypes in Spanish immunoglobulin A deficiency patients: a comparative fine mapping microsatellite study.

    PubMed

    Gual, L; Martínez, A; Fernández-Arquero, M; García-Rodríguez, M C; Ferreira, A; Fontán, G; de la Concha, E G; Urcelay, E

    2004-12-01

    The most consistent finding in Immunoglobulin A deficiency (IgAD) genetics is the presence of susceptibility factors located in the major histocompatibility complex (MHC). We have described the existence of at least two distinct susceptibility genes in the MHC present in different haplotypes. The aim of the present study was to locate with precision the susceptibility genes present in DR1- and DR7-positive haplotypes, taking advantage of their structural diversity, as opposed to the conserved nature of the DR3-extended susceptibility haplotype (DR3/B8), that hampers a more exhaustive scrutiny. A detailed analysis with 20 markers along the MHC in the 400 haplotypes present in 100 IgAD families, with special density at Class II locations, was performed to define the minimal shared susceptibility region present in all haplotypes carrying DR1 and, on the other hand, in all DR7-positive haplotypes. A comparison of the fine microsatellite allele structure of DR-extended haplotypes in the Spanish population with those described for Swedish and British families revealed no difference in DRB1*0101 and DRB1*0102 haplotypes between both populations. Our data suggest that the etiologic mutation present in DRB1*0101 and DRB1*0102 in North Europe (Sweden and UK) is missing in the Spanish DRB1*0101 haplotypes but is present in the DQB1/DRB1 region in DRB1*0102 haplotypes. The results obtained also indicated that the most likely susceptibility gene in the DR7 haplotypes is either DQA1 or DRB1. PMID:15546340

  2. INTENSITY MAPPING OF THE [C II] FINE STRUCTURE LINE DURING THE EPOCH OF REIONIZATION

    SciTech Connect

    Gong Yan; Cooray, Asantha [Department of Physics and Astronomy, University of California, Irvine, CA 92697 (United States); Silva, Marta; Santos, Mario G. [CENTRA, Instituto Superior Tecnico, Technical University of Lisbon, Lisboa 1049-001 (Portugal); Bock, James; Bradford, C. Matt; Zemcov, Michael [California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 (United States)

    2012-01-20

    The atomic C II fine-structure line is one of the brightest lines in a typical star-forming galaxy spectrum with a luminosity {approx}0.1%-1% of the bolometric luminosity. It is potentially a reliable tracer of the dense gas distribution at high redshifts and could provide an additional probe to the era of reionization. By taking into account the spontaneous, stimulated, and collisional emission of the C II line, we calculate the spin temperature and the mean intensity as a function of the redshift. When averaged over a cosmologically large volume, we find that the C II emission from ionized carbon in individual galaxies is larger than the signal generated by carbon in the intergalactic medium. Assuming that the C II luminosity is proportional to the carbon mass in dark matter halos, we also compute the power spectrum of the C II line intensity at various redshifts. In order to avoid the contamination from CO rotational lines at low redshift when targeting a C II survey at high redshifts, we propose the cross-correlation of C II and 21 cm line emission from high redshifts. To explore the detectability of the C II signal from reionization, we also evaluate the expected errors on the C II power spectrum and C II-21 cm cross power spectrum based on the design of the future millimeter surveys. We note that the C II-21 cm cross power spectrum contains interesting features that capture physics during reionization, including the ionized bubble sizes and the mean ionization fraction, which are challenging to measure from 21 cm data alone. We propose an instrumental concept for the reionization C II experiment targeting the frequency range of {approx}200-300 GHz with 1, 3, and 10 m apertures and a bolometric spectrometer array with 64 independent spectral pixels with about 20,000 bolometers.

  3. Comparison of experimental fine-mapping to in silico prediction results of HIV-1 epitopes reveals ongoing need for mapping experiments.

    PubMed

    Roider, Julia; Meissner, Tim; Kraut, Franziska; Vollbrecht, Thomas; Stirner, Renate; Bogner, Johannes R; Draenert, Rika

    2014-10-01

    Methods for identifying physiologically relevant CD8 T-cell epitopes are critically important not only for the development of T-cell-based vaccines but also for understanding host-pathogen interactions. As experimentally mapping an optimal CD8 T-cell epitope is a tedious procedure, many bioinformatic tools have been developed that predict which peptides bind to a given MHC molecule. We assessed the ability of the CD8 T-cell epitope prediction tools syfpeithi, ctlpred and iedb to foretell nine experimentally mapped optimal HIV-specific epitopes. Randomly - for any of the subjects' HLA type and with any matching score - the optimal epitope was predicted in seven of nine epitopes using syfpeithi, in three of nine epitopes using ctlpred and in all nine of nine epitopes using iedb. The optimal epitope within the three highest ranks was given in four of nine epitopes applying syfpeithi, in two of nine epitopes applying ctlpred and in seven of nine epitopes applying iedb when screening for all of the subjects' HLA types. Knowing the HLA restriction of the peptide of interest improved the ranking of the optimal epitope within the predicted results. Epitopes restricted by common HLA alleles were more likely to be predicted than those restricted by uncommon HLA alleles. Epitopes with aberrant lengths compared with the usual HLA-class I nonamers were most likely not predicted. Application of epitope prediction tools together with literature searches for already described optimal epitopes narrows down the possibilities of optimal epitopes within a screening peptide of interest. However, in our opinion, the actual fine-mapping of a CD8 T-cell epitope cannot yet be replaced. PMID:24724694

  4. The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize (Zea mays L.).

    PubMed

    Zhang, J; Ku, L X; Han, Z P; Guo, S L; Liu, H J; Zhang, Z Z; Cao, L R; Cui, X J; Chen, Y H

    2014-09-01

    Maize architecture is a major contributing factor to their high level of productivity. Maize varieties with an erect-leaf-angle (LA) phenotype, which increases light harvesting for photosynthesis and grain-filling, have elevated grain yields. Although a large body of information is available on the map positions of quantitative trait loci (QTL) for LA, little is known about the molecular mechanism of these QTL. In this study, the ZmCLA4 gene, which is responsible for the qLA4-1 QTL associated with LA, was identified and isolated by fine mapping and positional cloning. The ZmCLA4 gene is an orthologue of LAZY1 in rice and Arabidopsis. Sequence analysis revealed two SNPs and two indel sites in ZmCLA4 between the D132 and D132-NIL inbred maize lines. Association analysis showed that C/T/mutation667 and CA/indel965 were strongly associated with LA. Subcellular localization verified the functions of a predicted transmembrane domain and a nuclear localization signal in ZmCLA4. Transgenic maize plants with a down-regulated ZmCLA4 RNAi construct and transgenic rice plants over-expressing ZmCLA4 confirmed that the ZmCLA4 gene located in the qLA4 QTL regulated LA. The allelic variants of ZmCLA4 in the D132 and D132-NIL lines exhibited significant differences in leaf angle. ZmCLA4 transcript accumulation was higher in D132-NIL than in D132 during all the developmental stages and was negatively correlated with LA. The gravitropic response was increased and cell shape and number at the leaf and stem junctions were altered in D132-NIL relative to D132. These findings suggest that ZmCLA4 plays a negative role in the control of maize LA through the alteration of mRNA accumulation, leading to altered shoot gravitropism and cell development. The cloning of the gene responsible for the qLA4-1 QTL provides information on the molecular mechanisms of LA in maize and an opportunity for the improvement of plant architecture with regard to LA through maize breeding. PMID:24987012

  5. New CRISM Along-Track Oversampled Observations and Implications for Spectral Mapping at Fine Spatial Scales

    NASA Astrophysics Data System (ADS)

    Coman, E. I.; Arvidson, R. E.; Stein, N.; Murchie, S. L.; McGovern, A.; Seelos, K. D.; Seelos, F. P.; Humm, D. C.

    2013-12-01

    The Mars Reconnaissance Orbiter (MRO) Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) is a hyperspectral line scanner imaging system (0.362-3.920 micrometers at 6.55 nm/channel) that was designed to acquire targeted images at ~18 m/pixel spatial sampling. Past experiments have shown that by appropriately commanding the gimbal system, CRISM can also collect Along-Track Oversampled (ATO) observations with overlapping pixels that can be sharpened to along-track spatial resolutions as fine as 5 m/pixel. These observations were impossible to sharpen to a constant along-track spatial resolution within scenes because pixel overlap varied significantly due to irregularities in gimbal motion during imaging of targets. A new observational scheme has been implemented in which gimbaling has been adjusted to keep overlap constant, allowing consistent regularization and sharpening across the entire scene. We demonstrate two processing approaches for spatial sharpening of several scenes acquired with the new gimbaling approach. The scenes are: 1. A recent crater with dark ejecta located at 23.7N, 220.1E (areocentric) ATO00029FC9; 2. Layered rocks uplifted in crater near Solis Dorsa located at 23.14N, 281.37E ATO00029F00, and 3. Dikes in Valles Marineris Coprates Chasma located at 15.02N, 306.96 ATO00029EFD. The two methods are Tikhonov damped least squares spatial sharpening implemented in one dimensional and two dimensional schemes. The Tikhonov method for spatial sharpening replaces the overlapping pixels with smaller, regularly spaced pixels by minimizing the sums of squares of deviations between the observed data matrix and a matrix of regularized, smaller-sized pixels premultiplied by the imaging system transfer function, including ground motion smear. A side constraint is introduced to minimize the sums of squares of deviations of first derivatives for the regularized pixel matrix. This side constraint minimizes noise, and the extent of this minimization is adjustable. The one dimensional approach focused on individual columns (i.e., vector approach), where the overlap was planned. Because of jitter, cross track overlap is also present and thus a 2-dimensional regularization (i.e., full 2D matrix) was also implemented. Examination of I/F spectra and noise patterns for the processed scenes demonstrates that the spatial overlap is sufficient to support 5 to 7 m/pixel along-track spatial sharpening.

  6. Beckwith-Wiedemann syndrome and uniparental disomy 11p: fine mapping of the recombination breakpoints and evaluation of several techniques.

    PubMed

    Romanelli, Valeria; Meneses, Heloisa N M; Fernández, Luis; Martínez-Glez, Victor; Gracia-Bouthelier, Ricardo; F Fraga, Mario; Guillén, Encarna; Nevado, Julián; Gean, Esther; Martorell, Loreto; Marfil, Victoria Esteban; García-Miñaur, Sixto; Lapunzina, Pablo

    2011-04-01

    Beckwith-Wiedemann syndrome (BWS) is a phenotypically and genotypically heterogeneous overgrowth syndrome characterized by somatic overgrowth, macroglossia and abdominal wall defects. Other usual findings are hemihyperplasia, embryonal tumours, adrenocortical cytomegaly, ear anomalies, visceromegaly, renal abnormalities, neonatal hypoglycaemia, cleft palate, polydactyly and a positive family history. BWS is a complex, multigenic disorder associated, in up to 90% of patients, with alteration in the expression or function of one or more genes in the 11p15.5 imprinted gene cluster. There are several molecular anomalies associated with BWS and the large proportion of cases, about 85%, is sporadic and karyotypically normal. One of the major categories of BWS molecular alteration (10-20% of cases) is represented by mosaic paternal uniparental disomy (pUPD), namely patients with two paternally derived copies of chromosome 11p15 and no maternal contribution for that. In these patients, in addition to the effects of IGF2 overexpression, a decreased level of the maternally expressed gene CDKN1C may contribute to the BWS phenotype. In this paper, we reviewed a series of nine patients with BWS because of pUPD using several methods with the aim to evaluate the percentage of mosaicism, the methylation status at both loci, the extension of the pUPD at the short arm and the breakpoints of recombination. Fine mapping of mitotic recombination breakpoints by single-nucleotide polymorphism-array in individuals with UPD and fine estimation of epigenetic defects will provide a basis for understanding the aetiology of BWS, allowing more accurate prognostic predictions and facilitating management and surveillance of individuals with this disorder. PMID:21248736

  7. Beckwith–Wiedemann syndrome and uniparental disomy 11p: fine mapping of the recombination breakpoints and evaluation of several techniques

    PubMed Central

    Romanelli, Valeria; Meneses, Heloisa N M; Fernández, Luis; Martínez-Glez, Victor; Gracia-Bouthelier, Ricardo; F Fraga, Mario; Guillén, Encarna; Nevado, Julián; Gean, Esther; Martorell, Loreto; Marfil, Victoria Esteban; García-Miñaur, Sixto; Lapunzina, Pablo

    2011-01-01

    Beckwith–Wiedemann syndrome (BWS) is a phenotypically and genotypically heterogeneous overgrowth syndrome characterized by somatic overgrowth, macroglossia and abdominal wall defects. Other usual findings are hemihyperplasia, embryonal tumours, adrenocortical cytomegaly, ear anomalies, visceromegaly, renal abnormalities, neonatal hypoglycaemia, cleft palate, polydactyly and a positive family history. BWS is a complex, multigenic disorder associated, in up to 90% of patients, with alteration in the expression or function of one or more genes in the 11p15.5 imprinted gene cluster. There are several molecular anomalies associated with BWS and the large proportion of cases, about 85%, is sporadic and karyotypically normal. One of the major categories of BWS molecular alteration (10–20% of cases) is represented by mosaic paternal uniparental disomy (pUPD), namely patients with two paternally derived copies of chromosome 11p15 and no maternal contribution for that. In these patients, in addition to the effects of IGF2 overexpression, a decreased level of the maternally expressed gene CDKN1C may contribute to the BWS phenotype. In this paper, we reviewed a series of nine patients with BWS because of pUPD using several methods with the aim to evaluate the percentage of mosaicism, the methylation status at both loci, the extension of the pUPD at the short arm and the breakpoints of recombination. Fine mapping of mitotic recombination breakpoints by single-nucleotide polymorphism-array in individuals with UPD and fine estimation of epigenetic defects will provide a basis for understanding the aetiology of BWS, allowing more accurate prognostic predictions and facilitating management and surveillance of individuals with this disorder. PMID:21248736

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

    PubMed Central

    2013-01-01

    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

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

    PubMed Central

    Villar-Garea, Ana; Imhof, Axel

    2008-01-01

    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

  10. Characterization and fine mapping of the rice premature senescence mutant ospse1.

    PubMed

    Wu, Hai-Bin; Wang, Bin; Chen, Yuanling; Liu, Yao-Guang; Chen, Letian

    2013-07-01

    Premature senescence can limit crop productivity by limiting the growth phase. In the present study, a spontaneous premature senescence mutant was identified in rice (Oryza sativa L.). Genetic analysis revealed that the premature senescence phenotype was controlled by a recessive mutation, which we named Oryza sativa premature senescence1 (ospse1). The ospse1 mutants showed premature leaf senescence from the booting stage and exhibited more severe symptoms during reproductive and ripening stages. Key yield-related agronomic traits such as 1,000-grain weight and seed-setting rate, but not panicle grain number, were significantly reduced in ospse1 plants. Chlorophyll content, net photosynthetic rate, and transpiration rate of ospse1 flag leaves were similar to the wild-type plants in vegetative stages, but these parameters decreased steeply in the mutant after the heading stage. Consistent with this, the senescence-associated genes OsNYC1 and OsSgr were up-regulated in ospse1 mutant during premature leaf senescence. The ospse1 locus was mapped to a 38-kb region on chromosome 1 and sequence analysis of this region identified a single-nucleotide deletion in the 3' region of an open reading frame (ORF) encoding a putative pectate lyase, leading to a frame shift and a longer ORF. Our results suggested that the premature senescence of the ospse1 may be regulated by a novel mechanism mediated by pectate lyase. PMID:23624440

  11. Fine mapping of qPAA8, a gene controlling panicle apical development in rice.

    PubMed

    Cheng, Zhi-Jun; Mao, Bi-Gang; Gao, Su-Wei; Zhang, Ling; Wang, Jiu-Lin; Lei, Cai-Lin; Zhang, Xin; Wu, Fu-Qing; Guo, Xiu-Ping; Wan, Jianmin

    2011-09-01

    In rice, one detrimental factor influencing single panicle yield is the frequent occurrence of panicle apical abortion (PAA) under unfavorable climatic conditions. Until now, no detailed genetic information has been available to avoid PAA in rice breeding. Here, we show that the occurrence of PAA is associated with the accumulation of excess hydrogen peroxide. Quantitative trait loci (QTLs) mapping for PAA in an F(2) population derived from the cross of L-05261 (PAA line) × IRAT129 (non-PAA variety) identified seven QTLs over a logarithm of the odd (LOD) threshold of 2.5, explaining approximately 50.1% of phenotypic variance for PAA in total. Five of the QTLs with an increased effect from L-05261, were designated as qPAA3-1, qPAA3-2, qPAA4, qPAA5 and qPAA8, and accounted for 6.8%, 5.9%, 4.2%, 13.0% and 12.2% of phenotypic variance, respectively. We found that the PAA in the early heading plants was mainly controlled by qPAA8. Subsequently, using the sub-populations specific for qPAA8 based on marker-assisted selection, we further narrowed qPAA8 to a 37.6-kb interval delimited by markers RM22475 and 8-In112. These results are beneficial for PAA gene clone. PMID:21605340

  12. Fine genetic mapping of the Hyp mutation on mouse chromosome X

    SciTech Connect

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

    1996-03-01

    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.

  13. Fine Specificity Mapping of Autoantigens Targeted by Anti-Centromere Autoantibodies

    PubMed Central

    Akbarali, Yasmin; Matousek-Ronck, Jennifer; Hunt, Laura; Staudt, Leslie; Reichlin, Morris; Guthridge, Joel M.; James, Judith A

    2007-01-01

    Summary Autoantibodies to centromeric proteins are commonly found in sera of limited scleroderma and other rheumatic disease patients. To better understand the inciting events and possible pathogenic mechanisms of these autoimmune responses, this study identified the common antigenic targets of CENP-A in scleroderma patient sera. Utilizing samples from 263 anti-centromere immunofluorescence positive patients, 93.5% were found to have anti-CENP-A reactivity and 95.4% had anti-CENP-B reactivity by ELISA. Very few patient samples exclusively targeted CENP-A (2.7%) or CENP-B (4.2%). Select patient sera were tested for reactivity with solid phase overlapping decapeptides of CENP-A. Four distinct epitopes of CENP-A were identified. Epitopes 2 and 3 were confirmed by additional testing of 263 patient sera by ELISA for reactivity with these sequences constructed as multiple antigenic peptides. Inhibition CENP-A Western blots also confirmed the specificity of these humoral peptide immune responses in a subset of patient sera. The first three arginine residues (aa 4-6) of CENP-A appear essential for antibody recognition, as replacing these arginines with glycine residues reduced antibody binding to the expressed CENP-A protein by an average of 93.2% (range 80-100%). In selected patients with serial samples spanning nearly a decade, humoral epitope binding patterns were quite stable and showed no epitope spreading over time. This epitope mapping study identifies key antigenic targets of the anti-centromere response and establishes that the majority of the responses depend on key amino-terminal residues. PMID:17210244

  14. SCAN database: facilitating integrative analyses of cytosine modification and expression QTL

    PubMed Central

    Zhang, Wei; Gamazon, Eric R.; Zhang, Xu; Konkashbaev, Anuar; Liu, Cong; Szilágyi, Keely L.; Dolan, M. Eileen; Cox, Nancy J.

    2015-01-01

    Functional annotation of genetic variants including single nucleotide polymorphisms (SNPs) and copy number variations (CNV) promises to greatly improve our understanding of human complex traits. Previous transcriptomic studies involving individuals from different global populations have investigated the genetic architecture of gene expression variation by mapping expression quantitative trait loci (eQTL). Functional interpretation of genome-wide association studies (GWAS) has identified enrichment of eQTL in top signals from GWAS of human complex traits. The SCAN (SNP and CNV Annotation) database was developed as a web-based resource of genetical genomic studies including eQTL detected in the HapMap lymphoblastoid cell line samples derived from apparently healthy individuals of European and African ancestry. Considering the critical roles of epigenetic gene regulation, cytosine modification quantitative trait loci (mQTL) are expected to add a crucial layer of annotation to existing functional genomic information. Here, we describe the new features of the SCAN database that integrate comprehensive mQTL mapping results generated in the HapMap CEU (Caucasian residents from Utah, USA) and YRI (Yoruba people from Ibadan, Nigeria) LCL samples and demonstrate the utility of the enhanced functional annotation system. Database URL: http://www.scandb.org/ PMID:25818895

  15. 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

    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

    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

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

    PubMed Central

    2011-01-01

    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

  17. Genetic Etiology of Renal Agenesis: Fine Mapping of Renag1 and Identification of Kit as the Candidate Functional Gene

    PubMed Central

    Samanas, Nyssa Becker; Commers, Tessa W.; Dennison, Kirsten L.; Harenda, Quincy Eckert; Kurz, Scott G.; Lachel, Cynthia M.; Wavrin, Kristen Leland; Bowler, Michael; Nijman, Isaac J.; Guryev, Victor; Cuppen, Edwin; Hubner, Norbert; Sullivan, Ruth; Vezina, Chad M.; Shull, James D.

    2015-01-01

    Congenital anomalies of the kidney and urogenital tract (CAKUT) occur in approximately 0.5% of live births and represent the most frequent cause of end-stage renal disease in neonates and children. The genetic basis of CAKUT is not well defined. To understand more fully the genetic basis of one type of CAKUT, unilateral renal agenesis (URA), we are studying inbred ACI rats, which spontaneously exhibit URA and associated urogenital anomalies at an incidence of approximately 10%. URA is inherited as an incompletely dominant trait with incomplete penetrance in crosses between ACI and Brown Norway (BN) rats and a single responsible genetic locus, designated Renag1, was previously mapped to rat chromosome 14 (RNO14). The goals of this study were to fine map Renag1, identify the causal genetic variant responsible for URA, confirm that the Renag1 variant is the sole determinant of URA in the ACI rat, and define the embryologic basis of URA in this rat model. Data presented herein localize Renag1 to a 379 kilobase (kb) interval that contains a single protein coding gene, Kit (v-kit Hardy-Zukerman 4 feline sarcoma viral oncogene homolog); identify an endogenous retrovirus-derived long terminal repeat located within Kit intron 1 as the probable causal variant; demonstrate aberrant development of the nephric duct in the anticipated number of ACI rat embryos; and demonstrate expression of Kit and Kit ligand (Kitlg) in the nephric duct. Congenic rats that harbor ACI alleles at Renag1 on the BN genetic background exhibit the same spectrum of urogenital anomalies as ACI rats, indicating that Renag1 is necessary and sufficient to elicit URA and associated urogenital anomalies. These data reveal the first genetic link between Kit and URA and illustrate the value of the ACI rat as a model for defining the mechanisms and cell types in which Kit functions during urogenital development. PMID:25693193

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

    PubMed Central

    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.

    2015-01-01

    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

  19. Genetic etiology of renal agenesis: fine mapping of renag1 and identification of kit as the candidate functional gene.

    PubMed

    Samanas, Nyssa Becker; Commers, Tessa W; Dennison, Kirsten L; Harenda, Quincy Eckert; Kurz, Scott G; Lachel, Cynthia M; Wavrin, Kristen Leland; Bowler, Michael; Nijman, Isaac J; Guryev, Victor; Cuppen, Edwin; Hubner, Norbert; Sullivan, Ruth; Vezina, Chad M; Shull, James D

    2015-01-01

    Congenital anomalies of the kidney and urogenital tract (CAKUT) occur in approximately 0.5% of live births and represent the most frequent cause of end-stage renal disease in neonates and children. The genetic basis of CAKUT is not well defined. To understand more fully the genetic basis of one type of CAKUT, unilateral renal agenesis (URA), we are studying inbred ACI rats, which spontaneously exhibit URA and associated urogenital anomalies at an incidence of approximately 10%. URA is inherited as an incompletely dominant trait with incomplete penetrance in crosses between ACI and Brown Norway (BN) rats and a single responsible genetic locus, designated Renag1, was previously mapped to rat chromosome 14 (RNO14). The goals of this study were to fine map Renag1, identify the causal genetic variant responsible for URA, confirm that the Renag1 variant is the sole determinant of URA in the ACI rat, and define the embryologic basis of URA in this rat model. Data presented herein localize Renag1 to a 379 kilobase (kb) interval that contains a single protein coding gene, Kit (v-kit Hardy-Zukerman 4 feline sarcoma viral oncogene homolog); identify an endogenous retrovirus-derived long terminal repeat located within Kit intron 1 as the probable causal variant; demonstrate aberrant development of the nephric duct in the anticipated number of ACI rat embryos; and demonstrate expression of Kit and Kit ligand (Kitlg) in the nephric duct. Congenic rats that harbor ACI alleles at Renag1 on the BN genetic background exhibit the same spectrum of urogenital anomalies as ACI rats, indicating that Renag1 is necessary and sufficient to elicit URA and associated urogenital anomalies. These data reveal the first genetic link between Kit and URA and illustrate the value of the ACI rat as a model for defining the mechanisms and cell types in which Kit functions during urogenital development. PMID:25693193

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

    PubMed

    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

    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

  1. The Flowering Repressor SVP Underlies a Novel Arabidopsis thaliana QTL Interacting with the Genetic Background

    PubMed Central

    Méndez-Vigo, Belén; Martínez-Zapater, José M.; Alonso-Blanco, Carlos

    2013-01-01

    The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments. Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species, but the molecular and evolutionary mechanisms underlying this genetic variation are mainly being determined in the model plant Arabidopsis thaliana. To find novel A. thaliana flowering QTL, we developed introgression lines from the Japanese accession Fuk, which was selected based on the substantial transgression observed in an F2 population with the reference strain Ler. Analysis of an early flowering line carrying a single Fuk introgression identified Flowering Arabidopsis QTL1 (FAQ1). We fine-mapped FAQ1 in an 11 kb genomic region containing the MADS transcription factor gene SHORT VEGETATIVE PHASE (SVP). Complementation of the early flowering phenotype of FAQ1-Fuk with a SVP-Ler transgen demonstrated that FAQ1 is SVP. We further proved by directed mutagenesis and transgenesis that a single amino acid substitution in SVP causes the loss-of-function and early flowering of Fuk allele. Analysis of a worldwide collection of accessions detected FAQ1/SVP-Fuk allele only in Asia, with the highest frequency appearing in Japan, where we could also detect a potential ancestral genotype of FAQ1/SVP-Fuk. In addition, we evaluated allelic and epistatic interactions of SVP natural alleles by analysing more than one hundred transgenic lines carrying Ler or Fuk SVP alleles in five genetic backgrounds. Quantitative analyses of these lines showed that FAQ1/SVP effects vary from large to small depending on the genetic background. These results support that the flowering repressor SVP has been recently selected in A. thaliana as a target for early flowering, and evidence the relevance of genetic interactions for the intraspecific evolution of FAQ1/SVP and flowering time. PMID:23382706

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

    PubMed Central

    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

    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

  3. Development of consistently crossable wheat genotypes for alien wheat gene transfer through fine-mapping of the Kr1 locus.

    PubMed

    Bertin, Isabelle; Fish, Lesley; Foote, Tracie N; Knight, Emilie; Snape, John; Moore, Graham

    2009-11-01

    Breeders can force sexual hybridisation between wheat and related grass species to produce interspecific hybrids containing a dihaploid set of wheat and related chromosomes. This facilitates the introgression of desirable genes into wheat from the secondary gene pool. However, most elite European wheat varieties carry genes that suppress crossability, making the transfer of novel traits from exotic germplasm into elite wheat varieties difficult or impossible. Previous studies have identified at least five crossability loci in wheat. Here, the crossability locus with the largest effect, Kr1 on chromosome arm 5BL, was fine-mapped by developing a series of recombinant substitution lines in which the genome of the normally non-crossable wheat variety 'Hobbit sib' carries a recombinant 5BL chromosome arm containing segments from the crossable variety 'Chinese Spring'. These recombinant lines were scored for their ability to cross with rye over four seasons. Analysis revealed at least two regions on 5BL affecting crossability, including the Kr1 locus. However, the ability to set seed is highly dependent on prevailing environmental conditions. Typically, even crossable wheat lines exhibit little or no seed set when crossed with rye in winter, but show up to 90% seed set from similar crosses made in summer. By recombining different combinations of the two regions affecting crossability, wheat lines that consistently exhibit up to 50% seed set, whether crossed in the UK winter or summer conditions, were generated, thus creating a very important tool for increasing the efficiency of alien wheat transfer programmes. PMID:19727654

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

    PubMed

    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

    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

  5. Multi-environment mapping and meta-analysis of 100-seed weight in soybean.

    PubMed

    Sun, Ya-Nan; Pan, Jun-Bo; Shi, Xiang-Lin; Du, Xiang-Yu; Wu, Qiong; Qi, Zhao-Ming; Jiang, Hong-Wei; Xin, Da-Wei; Liu, Chun-Yan; Hu, Guo-Hua; Chen, Qing-Shan

    2012-10-01

    100-Seed weight (100-SW) of soybean is an important but complicated quantitative trait to yield. This study was focus on the quantitative trait loci (QTLs) of soybean 100-SW from 2006 to 2010, using recombination inbred lines population that was derived from a cross between Charleston and Dongnong 594. A total of 23 QTLs for 100-SW were detected in the linkage group C2, D1a, F, G and O. Nine QTLs were identified by composite interval mapping including one QTL with the minimum confidence interval (CI) of 1.3 cM, while 14 QTLs by multiple interval mapping. Furthermore, 94 reported QTLs of 100-SW were integrated with our QTL mapping results using BioMercator. As a result, 15 consensus QTLs and their corresponding markers were identified. The minimum CI was reduced to 1.52 cM by the combination of meta-analysis. These findings may merit fine-mapping of these QTL in soybean. PMID:22740134

  6. Polymorphism in the ELOVL6 Gene Is Associated with a Major QTL Effect on Fatty Acid Composition in Pigs

    PubMed Central

    Corominas, Jordi; Ramayo-Caldas, Yuliaxis; Puig-Oliveras, Anna; Pérez-Montarelo, Dafne; Noguera, Jose L.; Folch, Josep M.; Ballester, Maria

    2013-01-01

    Background The ELOVL fatty acid elongase 6 (ELOVL6), the only elongase related to de novo lipogenesis, catalyzes the rate-limiting step in the elongation cycle by controlling the fatty acid balance in mammals. It is located on pig chromosome 8 (SSC8) in a region where a QTL affecting palmitic, and palmitoleic acid composition was previously detected, using an Iberian x Landrace intercross. The main goal of this work was to fine-map the QTL and to evaluate the ELOVL6 gene as a positional candidate gene affecting the percentages of palmitic and palmitoleic fatty acids in pigs. Methodology and Principal Findings The combination of a haplotype-based approach and single-marker analysis allowed us to identify the main, associated interval for the QTL, in which the ELOVL6 gene was identified and selected as a positional candidate gene. A polymorphism in the promoter region of ELOVL6, ELOVL6:c.-533C>T, was highly associated with the percentage of palmitic and palmitoleic acids in muscle and backfat. Significant differences in ELOVL6 gene expression were observed in backfat when animals were classified by the ELOVL6:c.-533C>T genotype. Accordingly, animals carrying the allele associated with a decrease in ELOVL6 gene expression presented an increase in C16:0 and C16:1(n-7) fatty acid content and a decrease of elongation activity ratios in muscle and backfat. Furthermore, a SNP genome-wide association study with ELOVL6 relative expression levels in backfat showed the strongest effect on the SSC8 region in which the ELOVL6 gene is located. Finally, different potential genomic regions associated with ELOVL6 gene expression were also identified by GWAS in liver and muscle, suggesting a differential tissue regulation of the ELOVL6 gene. Conclusions and Significance Our results suggest ELOVL6 as a potential causal gene for the QTL analyzed and, subsequently, for controlling the overall balance of fatty acid composition in pigs. PMID:23341976

  7. Multiple interval mapping for quantitative trait loci.

    PubMed Central

    Kao, C H; Zeng, Z B; Teasdale, R D

    1999-01-01

    A new statistical method for mapping quantitative trait loci (QTL), called multiple interval mapping (MIM), is presented. It uses multiple marker intervals simultaneously to fit multiple putative QTL directly in the model for mapping QTL. The MIM model is based on Cockerham's model for interpreting genetic parameters and the method of maximum likelihood for estimating genetic parameters. With the MIM approach, the precision and power of QTL mapping could be improved. Also, epistasis between QTL, genotypic values of individuals, and heritabilities of quantitative traits can be readily estimated and analyzed. Using the MIM model, a stepwise selection procedure with likelihood ratio test statistic as a criterion is proposed to identify QTL. This MIM method was applied to a mapping data set of radiata pine on three traits: brown cone number, tree diameter, and branch quality scores. Based on the MIM result, seven, six, and five QTL were detected for the three traits, respectively. The detected QTL individually contributed from approximately 1 to 27% of the total genetic variation. Significant epistasis between four pairs of QTL in two traits was detected, and the four pairs of QTL contributed approximately 10.38 and 14.14% of the total genetic variation. The asymptotic variances of QTL positions and effects were also provided to construct the confidence intervals. The estimated heritabilities were 0.5606, 0.5226, and 0. 3630 for the three traits, respectively. With the estimated QTL effects and positions, the best strategy of marker-assisted selection for trait improvement for a specific purpose and requirement can be explored. The MIM FORTRAN program is available on the worldwide web (http://www.stat.sinica.edu.tw/chkao/). PMID:10388834

  8. Five QTL hotspots for yield in short rotation coppice bioenergy poplar: The Poplar Biomass Loci

    PubMed Central

    Rae, Anne M; Street, Nathaniel Robert; Robinson, Kathryn Megan; Harris, Nicole; Taylor, Gail

    2009-01-01

    Background Concern over land use for non-food bioenergy crops requires breeding programmes that focus on producing biomass on the minimum amount of land that is economically-viable. To achieve this, the maximum potential yield per hectare is a key target for improvement. For long lived tree species, such as poplar, this requires an understanding of the traits that contribute to biomass production and their genetic control. An important aspect of this for long lived plants is an understanding of genetic interactions at different developmental stages, i.e. how genes or genetic regions impact on yield over time. Results QTL mapping identified regions of genetic control for biomass yield. We mapped consistent QTL across multiple coppice cycles and identified five robust QTL hotspots on linkage groups III, IV, X, XIV and XIX, calling these 'Poplar Biomass Loci' (PBL 1–5). In total 20% of the variation in final harvest biomass yield was explained by mapped QTL. We also investigated the genetic correlations between yield related traits to identify 'early diagnostic' indicators of yield showing that early biomass was a reasonable predictor of coppice yield and that leaf size, cell number and stem and sylleptic branch number were also valuable traits. Conclusion These findings provide insight into the genetic control of biomass production and correlation to 'early diagnostic' traits determining yield in poplar SRC for bioenergy. QTL hotspots serve as useful targets for directed breeding for improved biomass productivity that may also be relevant across additional poplar hybrids. PMID:19245718

  9. Systematic Genetic Analysis Identifies Cis-eQTL Target Genes Associated with Glioblastoma Patient Survival

    PubMed Central

    Chen, Qing-Rong; Hu, Ying; Yan, Chunhua; Buetow, Kenneth; Meerzaman, Daoud

    2014-01-01

    Prior expression quantitative trait locus (eQTL) studies have demonstrated heritable variation determining differences in gene expression. The majority of eQTL studies were based on cell lines and normal tissues. We performed cis-eQTL analysis using glioblastoma multiforme (GBM) data sets obtained from The Cancer Genome Atlas (TCGA) to systematically investigate germline variation’s contribution to tumor gene expression levels. We identified 985 significant cis-eQTL associations (FDR<0.05) mapped to 978 SNP loci and 159 unique genes. Approximately 57% of these eQTLs have been previously linked to the gene expression in cell lines and normal tissues; 43% of these share cis associations known to be associated with functional annotations. About 25% of these cis-eQTL associations are also common to those identified in Breast Cancer from a recent study. Further investigation of the relationship between gene expression and patient clinical information identified 13 eQTL genes whose expression level significantly correlates with GBM patient survival (p<0.05). Most of these genes are also differentially expressed in tumor samples and organ-specific controls (p<0.05). Our results demonstrated a significant relationship of germline variation with gene expression levels in GBM. The identification of eQTLs-based expression associated survival might be important to the understanding of genetic contribution to GBM cancer prognosis. PMID:25133526

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

    PubMed Central

    2010-01-01

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

  11. Comparing the adaptive landscape across trait types: larger QTL effect size in traits under biotic selection

    PubMed Central

    2011-01-01

    Background In a spatially and temporally variable adaptive landscape, mutations operating in opposite directions and mutations of large effect should be commonly fixed due to the shifting locations of phenotypic optima. Similarly, an adaptive landscape with multiple phenotypic optima and deep valleys of low fitness between peaks will favor mutations of large effect. Traits under biotic selection should experience a more spatially and temporally variable adaptive landscape with more phenotypic optima than that experienced by traits under abiotic selection. To test this hypothesis, we assemble information from QTL mapping studies conducted in plants, comparing effect directions and effect sizes of detected QTL controlling traits putatively under abiotic selection to those controlling traits putatively under biotic selection. Results We find no differences in the fraction of antagonistic QTL in traits under abiotic and biotic selection, suggesting similar consistency in selection pressure on these two types of traits. However, we find that QTL controlling traits under biotic selection have a larger effect size than those under abiotic selection, supporting our hypothesis that QTL of large effect are more commonly detected in traits under biotic selection than in traits under abiotic selection. For traits under both abiotic and biotic selection, we find a large number of QTL of large effect, with 10.7% of all QTLs detected controlling more than 20% of the variance in phenotype. Conclusion These results suggest that mutations of large effect are more common in adaptive landscapes strongly determined by biotic forces, but that these types of adaptive landscapes do not result in a higher fraction of mutations acting in opposite directions. The high number of QTL of large effect detected shows that QTL of large effect are more common than predicted by the infinitesimal model of genetic adaptation. PMID:21385379

  12. Effect of family relatedness on characteristics of estimated IBD probabilities in relation to precision of QTL estimates

    PubMed Central

    2010-01-01

    Background A random QTL effects model uses a function of probabilities that two alleles in the same or in different animals at a particular genomic position are identical by descent (IBD). Estimates of such IBD probabilities and therefore, modeling and estimating QTL variances, depend on marker polymorphism, strength of linkage and linkage disequilibrium of markers and QTL, and the relatedness of animals in the pedigree. The effect of relatedness of animals in a pedigree on IBD probabilities and their characteristics was examined in a simulation study. Results The study based on nine multi-generational family structures, similar to a pedigree structure of a real dairy population, distinguished by an increased level of inbreeding from zero to 28% across the studied population. Highest inbreeding level in the pedigree, connected with highest relatedness, was accompanied by highest IBD probabilities of two alleles at the same locus, and by lower relative variation coefficients. Profiles of correlation coefficients of IBD probabilities along the marked chromosomal segment with those at the true QTL position were steepest when the inbreeding coefficient in the pedigree was highest. Precision of estimated QTL location increased with increasing inbreeding and pedigree relatedness. A method to assess the optimum level of inbreeding for QTL detection is proposed, depending on population parameters. Conclusions An increased overall relationship in a QTL mapping design has positive effects on precision of QTL position estimates. But the relationship of inbreeding level and the capacity for QTL detection depending on the recombination rate of QTL and adjacent informative marker is not linear. PMID:20868519

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

    PubMed Central

    2013-01-01

    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

  14. Fine mapping of a linkage peak with integration of lipid traits identifies novel coronary artery disease genes on chromosome 5

    PubMed Central

    2012-01-01

    Background Coronary artery disease (CAD), and one of its intermediate risk factors, dyslipidemia, possess a demonstrable genetic component, although the genetic architecture is incompletely defined. We previously reported a linkage peak on chromosome 5q31-33 for early-onset CAD where the strength of evidence for linkage was increased in families with higher mean low density lipoprotein-cholesterol (LDL-C). Therefore, we sought to fine-map the peak using association mapping of LDL-C as an intermediate disease-related trait to further define the etiology of this linkage peak. The study populations consisted of 1908 individuals from the CATHGEN biorepository of patients undergoing cardiac catheterization; 254 families (N = 827 individuals) from the GENECARD familial study of early-onset CAD; and 162 aorta samples harvested from deceased donors. Linkage disequilibrium-tagged SNPs were selected with an average of one SNP per 20 kb for 126.6-160.2 MB (region of highest linkage) and less dense spacing (one SNP per 50 kb) for the flanking regions (117.7-126.6 and 160.2-167.5 MB) and genotyped on all samples using a custom Illumina array. Association analysis of each SNP with LDL-C was performed using multivariable linear regression (CATHGEN) and the quantitative trait transmission disequilibrium test (QTDT; GENECARD). SNPs associated with the intermediate quantitative trait, LDL-C, were then assessed for association with CAD (i.e., a qualitative phenotype) using linkage and association in the presence of linkage (APL; GENECARD) and logistic regression (CATHGEN and aortas). Results We identified four genes with SNPs that showed the strongest and most consistent associations with LDL-C and CAD: EBF1, PPP2R2B, SPOCK1, and PRELID2. The most significant results for association of SNPs with LDL-C were: EBF1, rs6865969, p = 0.01; PPP2R2B, rs2125443, p = 0.005; SPOCK1, rs17600115, p = 0.003; and PRELID2, rs10074645, p = 0.0002). The most significant results for CAD were EBF1, rs6865969, p = 0.007; PPP2R2B, rs7736604, p = 0.0003; SPOCK1, rs17170899, p = 0.004; and PRELID2, rs7713855, p = 0.003. Conclusion Using an intermediate disease-related quantitative trait of LDL-C we have identified four novel CAD genes, EBF1, PRELID2, SPOCK1, and PPP2R2B. These four genes should be further examined in future functional studies as candidate susceptibility loci for cardiovascular disease mediated through LDL-cholesterol pathways. PMID:22369142

  15. Fine mapping of type 1 diabetes regions Idd9.1 and Idd9.2 reveals genetic complexity.

    PubMed

    Hamilton-Williams, Emma E; Rainbow, Daniel B; Cheung, Jocelyn; Christensen, Mikkel; Lyons, Paul A; Peterson, Laurence B; Steward, Charles A; Sherman, Linda A; Wicker, Linda S

    2013-10-01

    Nonobese diabetic (NOD) mice congenic for C57BL/10 (B10)-derived genes in the Idd9 region of chromosome 4 are highly protected from type 1 diabetes (T1D). Idd9 has been divided into three protective subregions (Idd9.1, 9.2, and 9.3), each of which partially prevents disease. In this study we have fine-mapped the Idd9.1 and Idd9.2 regions, revealing further genetic complexity with at least two additional subregions contributing to protection from T1D. Using the NOD sequence from bacterial artificial chromosome clones of the Idd9.1 and Idd9.2 regions as well as whole-genome sequence data recently made available, sequence polymorphisms within the regions highlight a high degree of polymorphism between the NOD and B10 strains in the Idd9 regions. Among numerous candidate genes are several with immunological importance. The Idd9.1 region has been separated into Idd9.1 and Idd9.4, with Lck remaining a candidate gene within Idd9.1. One of the Idd9.2 regions contains the candidate genes Masp2 (encoding mannan-binding lectin serine peptidase 2) and Mtor (encoding mammalian target of rapamycin). From mRNA expression analyses, we have also identified several other differentially expressed candidate genes within the Idd9.1 and Idd9.2 regions. These findings highlight that multiple, relatively small genetic effects combine and interact to produce significant changes in immune tolerance and diabetes onset. PMID:23934554

  16. Haplotyping a quantitative trait with a high-density map in experimental crosses

    Microsoft Academic Search

    Wei Hou; John Stephen F. Yap; Song Wu; Tian Liu; James M. Cheverud; Rongling Wu

    2007-01-01

    Background. The ultimate goal of genetic mapping of quantitative trait loci (QTL) is the positional cloning of genes involved in any agriculturally or medically important phenotype. However, only a small portion (# 1%) of the QTL detected have been characterized at the molecular level, despite the report of hundreds of thousands of QTL for different traits and populations. Methods\\/Results. We

  17. QTL mapping PLB152: Plant Genetics

    E-print Network

    Gepts, Paul

    Couch SR, Zhang QF (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant ­ Markers are qualitative traits · Quantitative: ­ Quantity: · Tallness · Yield ­ Generally more than one.g., affected siblings method Methods to detect QTLs · Single-marker analysis: ­ Divide population

  18. Linkage Disequilibrium Mapping of Meat Quality QTL

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previous studies based on linkage analysis have identified broad areas in the bovine genome associated with meat quality. Linkage disequilibrium (LD) analyses have the potential to identify narrower regions and point towards candidate genes. Tenderness and marbling were chosen to be evaluated in a ...

  19. Genetic, Physiological, and Gene Expression Analyses Reveal That Multiple QTL Enhance Yield of Rice Mega-Variety IR64 under Drought

    PubMed Central

    Swamy B. P., Mallikarjuna; Ahmed, Helal Uddin; Henry, Amelia; Mauleon, Ramil; Dixit, Shalabh; Vikram, Prashant; Tilatto, Ram; Verulkar, Satish B.; Perraju, Puvvada; Mandal, Nimai P.; Variar, Mukund; S., Robin; Chandrababu, Ranganath; Singh, Onkar N.; Dwivedi, Jawaharlal L.; Das, Sankar Prasad; Mishra, Krishna K.; Yadaw, Ram B.; Aditya, Tamal Lata; Karmakar, Biswajit; Satoh, Kouji; Moumeni, Ali; Kikuchi, Shoshi; Leung, Hei; Kumar, Arvind

    2013-01-01

    Background Rice (Oryza sativa L.) is a highly drought sensitive crop, and most semi dwarf rice varieties suffer severe yield losses from reproductive stage drought stress. The genetic complexity of drought tolerance has deterred the identification of agronomically relevant quantitative trait loci (QTL) that can be deployed to improve rice yield under drought in rice. Convergent evidence from physiological characterization, genetic mapping, and multi-location field evaluation was used to address this challenge. Methodology/Principal Findings Two pairs of backcross inbred lines (BILs) from a cross between drought-tolerant donor Aday Sel and high-yielding but drought-susceptible rice variety IR64 were produced. From six BC4F3 mapping populations produced by crossing the +QTL BILs with the ?QTL BILs and IR64, four major-effect QTL - one each on chromosomes 2, 4, 9, and 10 - were identified. Meta-analysis of transcriptome data from the +QTL/?QTL BILs identified differentially expressed genes (DEGs) significantly associated with QTL on chromosomes 2, 4, 9, and 10. Physiological characterization of BILs showed increased water uptake ability under drought. The enrichment of DEGs associated with root traits points to differential regulation of root development and function as contributing to drought tolerance in these BILs. BC4F3-derived lines with the QTL conferred yield advantages of 528 to 1875 kg ha?1 over IR64 under reproductive-stage drought stress in the targeted ecosystems of South Asia. Conclusions/Significance Given the importance of rice in daily food consumption and the popularity of IR64, the BC4F3 lines with multiple QTL could provide higher livelihood security to farmers in drought-prone environments. Candidate genes were shortlisted for further characterization to confirm their role in drought tolerance. Differential yield advantages of different combinations of the four QTL reported here indicate that future research should include optimizing QTL combinations in different genetic backgrounds to maximize yield advantage under drought. PMID:23667521

  20. QTL meta-analysis in Arabidopsis reveals an interaction between leaf senescence and resource allocation to seeds

    PubMed Central

    Chardon, Fabien; Jasinski, Sophie; Durandet, Monique; Lécureuil, Alain; Soulay, Fabienne; Bedu, Magali; Guerche, Philippe; Masclaux-Daubresse, Céline

    2014-01-01

    Sequential and monocarpic senescence are observed at vegetative and reproductive stages, respectively. Both facilitate nitrogen (N) remobilization and control the duration of carbon (C) fixation. Genetic and environmental factors control N and C resource allocation to seeds. Studies of natural variation in Arabidopsis thaliana revealed differences between accessions for leaf senescence phenotypes, seed N and C contents, and N remobilization efficiency-related traits. Here, a quantitative genetics approach was used to gain a better understanding of seed filling regulation in relation to leaf senescence and resource allocation. For that purpose, three Arabidopsis recombinant inbred line populations (Ct-1×Col-0, Cvi-0×Col-0, Bur-0×Col-0) were used to map QTL (quantitative trait loci) for ten traits related to senescence, resource allocation, and seed filling. The use of common markers across the three different maps allowed direct comparisons of the positions of the detected QTL in a single consensus map. QTL meta-analysis was then used to identify interesting regions (metaQTL) where QTL for several traits co-localized. MetaQTL were compared with positions of candidate genes known to be involved in senescence processes and flowering time. Finally, investigation of the correlation between yield and seed N concentration in the three populations suggests that leaf senescence disrupts the negative correlation generally observed between these two traits. PMID:24692652

  1. QTL meta-analysis in Arabidopsis reveals an interaction between leaf senescence and resource allocation to seeds.

    PubMed

    Chardon, Fabien; Jasinski, Sophie; Durandet, Monique; Lécureuil, Alain; Soulay, Fabienne; Bedu, Magali; Guerche, Philippe; Masclaux-Daubresse, Céline

    2014-07-01

    Sequential and monocarpic senescence are observed at vegetative and reproductive stages, respectively. Both facilitate nitrogen (N) remobilization and control the duration of carbon (C) fixation. Genetic and environmental factors control N and C resource allocation to seeds. Studies of natural variation in Arabidopsis thaliana revealed differences between accessions for leaf senescence phenotypes, seed N and C contents, and N remobilization efficiency-related traits. Here, a quantitative genetics approach was used to gain a better understanding of seed filling regulation in relation to leaf senescence and resource allocation. For that purpose, three Arabidopsis recombinant inbred line populations (Ct-1×Col-0, Cvi-0×Col-0, Bur-0×Col-0) were used to map QTL (quantitative trait loci) for ten traits related to senescence, resource allocation, and seed filling. The use of common markers across the three different maps allowed direct comparisons of the positions of the detected QTL in a single consensus map. QTL meta-analysis was then used to identify interesting regions (metaQTL) where QTL for several traits co-localized. MetaQTL were compared with positions of candidate genes known to be involved in senescence processes and flowering time. Finally, investigation of the correlation between yield and seed N concentration in the three populations suggests that leaf senescence disrupts the negative correlation generally observed between these two traits. PMID:24692652

  2. Mapping quantitative trait loci for downy mildew resistance in pearl millet

    Microsoft Academic Search

    E. S. Jones; C. J. Liu; M. D. Gale; C. T. Hash; J. R. Witcombe

    1995-01-01

    Quantitative trait loci (QTLs) for resistance to pathogen populations of Scelerospora graminicola from India, Nigeria, Niger and Senegal were mapped using a resistant x susceptible pearl millet cross. An RFLP map constructed using F2 plants was used to map QTLs for traits scored on F4 families. QTL analysis was carried out using the interval mapping programme Mapmaker\\/QTL. Independent inheritance of

  3. Connecting thermal performance curve variation to the genotype: a multivariate QTL approach.

    PubMed

    Latimer, C A L; Foley, B R; Chenoweth, S F

    2015-01-01

    Thermal performance curves (TPCs) are continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding trade-offs involved in thermal adaptation. Although thermal trade-offs such as those between generalists and specialists or between hot- and cold-adapted phenotypes are known to be genetically variable and evolve during thermal adaptation, little is known of the genetic basis to TPCs - specifically, the loci involved and the directionality of their effects across different temperatures. To address this, we took a multivariate approach, mapping quantitative trait loci (QTL) for locomotor activity TPCs in the fly, Drosophila serrata, using a panel of 76 recombinant inbred lines. The distribution of additive genetic (co)variance in the mapping population was remarkably similar to the distribution of mutational (co)variance for these traits. We detected 11 TPC QTL in females and 4 in males. Multivariate QTL effects were closely aligned with the major axes genetic (co)variation between temperatures; most QTL effects corresponded to variation for either overall increases or decreases in activity with a smaller number indicating possible trade-offs between activity at high and low temperatures. QTL representing changes in curve shape such as the 'generalist-specialist' trade-off, thought key to thermal adaptation, were poorly represented in the data. We discuss these results in the light of genetic constraints on thermal adaptation. PMID:25403928

  4. A Missense Mutation in PPARD Causes a Major QTL Effect on Ear Size in Pigs

    Microsoft Academic Search

    Jun Ren; Yanyu Duan; Ruimin Qiao; Fei Yao; Zhiyan Zhang; Bin Yang; Yuanmei Guo; Shijun Xiao; Rongxin Wei; Zixuan Ouyang; Nengshui Ding; Huashui Ai; Lusheng Huang

    2011-01-01

    Chinese Erhualian is the most prolific pig breed in the world. The breed exhibits exceptionally large and floppy ears. To identify genes underlying this typical feature, we previously performed a genome scan in a large scale White Duroc × Erhualian cross and mapped a major QTL for ear size to a 2-cM region on chromosome 7. We herein performed an

  5. 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 ...

  6. QTL ANALYSIS FOR YIELD COMPONENTS IN RICE (ORYZA SATIVA L.) UNDER DIFFERENT ENVIRONMENTS

    Microsoft Academic Search

    Mebrouk Benmoussa; Abderrahmane Achouch; Jun Zhu

    Quantitative trait loci (QTL) for yield components were identified based on an RFLP map from a double haploid population. The 123 DH lines with their parents IR64 and Azucena were evaluated in the field in two different environments (Hangzhou and Hainan). The study revealed that individual QTLs showed a range of sensibility to environments as some QTLs were detected only

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

    PubMed Central

    Vaughn, Laura M.; Masson, Patrick H.

    2011-01-01

    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

  8. QTL analysis of cleistogamy in soybean.

    PubMed

    Khan, Nisar A; Githiri, Stephen M; Benitez, Eduardo R; Abe, Jun; Kawasaki, Shinji; Hayashi, Takeshi; Takahashi, Ryoji

    2008-08-01

    Early-maturing cultivars of soybean [Glycine max (L.) Merr.] native to the shores of the Sea of Okhotsk (Sakhalin and Kuril Islands) and eastern Hokkaido (northern Japan) have a strong tendency to produce cleistogamous flowers throughout their blooming period. A previous study revealed that cleistogamy is controlled by a minimum of two genes with epistatic interaction, one of which is associated with a maturity gene responsible for insensitivity to incandescent long daylength (ILD). This study was conducted to determine the genetic basis of cleistogamy in more detail by QTL mapping. F2 to F4 progenies derived from a cross between a cleistogamous cv. Karafuto-1 and a chasmogamous cv. Toyosuzu were used. A molecular linkage map spanning 2,180 cM comprising 500 markers was constructed using 89 F2 plants. The markers were distributed in 25 linkage groups. An interval mapping method to analyze categorical traits identified four QTLs for cleistogamy, cl1, cl2, cl3 and cl4, in molecular linkage groups (MLGs) C2, D1a, I and L, respectively. Alleles derived from Karafuto-1 had additive effects to increase probability of cleistogamy at cl3 and cl4, whereas the alleles had additive effects to decrease the probablity at cl1 and cl2. Progeny test confirmed the effects of cl3, which had the highest LOD score (5.20). Composite interval mapping revealed four QTLs for flowering date, fd5-fd8. Judging from relative location with markers and association with ILD responses, fd7 and fd8 may correspond to maturity genes E4 and E3, respectively. cl3 and cl4 were located at similar positions as fd7 and fd8, suggesting that the two maturity genes may control cleistogamy by either pleiotropy or close linkage. PMID:18506418

  9. 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...

  10. A native QTL for Fusarium head blight resistance in North American barley (Hordeum vulgare L.) independent of height, maturity, and spike type loci.

    PubMed

    Yu, G T; Franckowiak, J D; Neate, S M; Zhang, B; Horsley, R D

    2010-02-01

    Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe (teleomorph Gibberella zeae (Schwein.) Petch), is one of the major diseases of barley (Hordeum vulgare L.) in eastern China, the Upper Midwest of the USA, and the eastern Prairie Provinces of Canada. To identify quantitative trait loci (QTL) controlling FHB resistance, a recombinant inbred line population (F6:7) was developed from the cross Zhenongda 7/PI 643302. The population was phenotyped for resistance to FHB in two experiments in China and four experiments in North Dakota. Accumulation of the mycotoxin deoxynivalenol was determined in one experiment in China and two in North Dakota. Simplified composite interval mapping was performed on the whole genome level using the software MQTL. The QTL FHB-2 from PI 643302 for FHB resistance was found on the distal portion of chromosome 2HL in all six FHB screening environments. This QTL accounted for 14% of phenotypic variation over six environments and was not associated with heading date or plant height. The FHB resistance QTL FHB-2 detected near the end of chromosome 2HL is in a different location from those found previously and is therefore probably unique. Because the QTL was not contributed by the Chinese cultivar Zhenongda 7, it is likely a native QTL present in North American barley. The QTL FHB-2 represents the first reported QTL for native FHB resistance in North American germ plasm and has been given the provisional name Qrgz-2H-14. This QTL should be considered for pyramiding with other FHB QTL previously mapped. PMID:20140029

  11. WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

    PubMed

    Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A

    2013-01-01

    Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers. PMID:23180786

  12. Mapping QTLs for plant phenology and production traits using indica rice (Oryza sativa L.) lines adapted to rainfed environment.

    PubMed

    Suji, K K; Biji, K R; Poornima, R; Prince, K Silvas Jebakumar; Amudha, K; Kavitha, S; Mankar, Sumeet; Babu, R Chandra

    2012-10-01

    Drought is a major abiotic stress limiting rice production and yield stability in rainfed ecosystems. Identifying quantitative trait loci (QTL) for rice yield and yield components under water limited environments will help to develop drought resilient cultivars using marker assisted breeding (MAB) strategy. A total of 232 recombinant inbred lines of IR62266/Norungan were used to map QTLs for plant phenology and production traits under rainfed condition in target population of environments. A total of 79 QTLs for plant phenology and production traits with phenotypic variation ranging from 4.4 to 72.8% were detected under non-stress and drought stress conditions across two locations. Consistent QTLs for phenology and production traits were detected across experiments and water regimes. The QTL region, RM204-RM197-RM217 on chromosome 6 was linked to days to 50% flowering and grain yield per plant under both rainfed and irrigated conditions. The same genomic region, RM585-RM204-RM197 was also linked to harvest index under rainfed condition with positive alleles from Norungan, a local landrace. QTLs for plant production and drought resistance traits co-located near RM585-RM204-RM197-RM217 region on chromosome 6 in several rice genotypes. Thus with further fine mapping, this region may be useful as a candidate QTL for MAB, map-based cloning of genes and functional genomics studies for rainfed rice improvement. PMID:22198727

  13. A high density linkage map of the bovine genome

    PubMed Central

    Arias, Juan A; Keehan, Mike; Fisher, Paul; Coppieters, Wouter; Spelman, Richard

    2009-01-01

    Background Recent technological advances have made it possible to efficiently genotype large numbers of single nucleotide polymorphisms (SNPs) in livestock species, allowing the production of high-density linkage maps. Such maps can be used for quality control of other SNPs and for fine mapping of quantitative trait loci (QTL) via linkage disequilibrium (LD). Results A high-density bovine linkage map was constructed using three types of markers. The genotypic information was obtained from 294 microsatellites, three milk protein haplotypes and 6769 SNPs. The map was constructed by combining genetic (linkage) and physical information in an iterative mapping process. Markers were mapped to 3,155 unique positions; the 6,924 autosomal markers were mapped to 3,078 unique positions and the 123 non-pseudoautosomal and 19 pseudoautosomal sex chromosome markers were mapped to 62 and 15 unique positions, respectively. The linkage map had a total length of 3,249 cM. For the autosomes the average genetic distance between adjacent markers was 0.449 cM, the genetic distance between unique map positions was 1.01 cM and the average genetic distance (cM) per Mb was 1.25. Conclusion There is a high concordance between the order of the SNPs in our linkage map and their physical positions on the most recent bovine genome sequence assembly (Btau 4.0). The linkage maps provide support for fine mapping projects and LD studies in bovine populations. Additionally, the linkage map may help to resolve positions of unassigned portions of the bovine genome. PMID:19393043

  14. QTL associated with Fusarium head blight resistance in the soft red winter wheat Ernie.

    PubMed

    Liu, S; Abate, Z A; Lu, H; Musket, T; Davis, G L; McKendry, A L

    2007-08-01

    Fusarium head blight (FHB), mainly caused by Fusarium graminearum Schwabe [telomorph: Gibberella zeae Schw. (Petch)], is an increasingly important disease of wheat (Triticum aestivum L.). Host-plant resistance provides the best hope for reducing economic losses associated with FHB, but new sources of resistance are limited. The moderately resistant winter wheat cultivar, Ernie, may provide a source of resistance that differs from Sumai 3 but these genes have not been mapped. Also hindering resistance breeding may be associations of resistance with agronomic traits such as late maturity that may be u