The Experts below are selected from a list of 62271 Experts worldwide ranked by ideXlab platform
Edward S Buckler - One of the best experts on this subject based on the ideXlab platform.
-
lessons from dwarf8 on the strengths and weaknesses of structured Association Mapping
PLOS Genetics, 2013Co-Authors: Sara Larsson, Edward S Buckler, Alexander E LipkaAbstract:The strengths of Association Mapping lie in its resolution and allelic richness, but spurious Associations arising from historical relationships and selection patterns need to be accounted for in statistical analyses. Here we reanalyze one of the first generation structured Association Mapping studies of the Dwarf8 (d8) locus with flowering time in maize using the full range of new Mapping populations, statistical approaches, and haplotype maps. Because this trait was highly correlated with population structure, we found that basic structured Association methods overestimate phenotypic effects in the region, while mixed model approaches perform substantially better. Combined with analysis of the maize nested Association Mapping population (a multi-family crossing design), it is concluded that most, if not all, of the QTL effects at the general location of the d8 locus are from rare extended haplotypes that include other linked QTLs and that d8 is unlikely to be involved in controlling flowering time in maize. Previous independent studies have shown evidence for selection at the d8 locus. Based on the evidence of population bottleneck, selection patterns, and haplotype structure observed in the region, we suggest that multiple traits may be strongly correlated with population structure and that selection on these traits has influenced segregation patterns in the region. Overall, this study provides insight into how modern Association and linkage Mapping, combined with haplotype analysis, can produce results that are more robust.
-
genetic architecture of maize kernel composition in the nested Association Mapping and inbred Association panels
Plant Physiology, 2012Co-Authors: Jason P Cook, James B Holland, Michael D Mcmullen, Peter J Bradbury, Feng Tian, Jeffrey Rossibarra, Edward S BucklerAbstract:The maize (Zea mays) kernel plays a critical role in feeding humans and livestock around the world and in a wide array of industrial applications. An understanding of the regulation of kernel starch, protein, and oil is needed in order to manipulate composition to meet future needs. We conducted joint-linkage quantitative trait locus Mapping and genome-wide Association studies (GWAS) for kernel starch, protein, and oil in the maize nested Association Mapping population, composed of 25 recombinant inbred line families derived from diverse inbred lines. Joint-linkage Mapping revealed that the genetic architecture of kernel composition traits is controlled by 21–26 quantitative trait loci. Numerous GWAS Associations were detected, including several oil and starch Associations in acyl-CoA:diacylglycerol acyltransferase1-2, a gene that regulates oil composition and quantity. Results from nested Association Mapping were verified in a 282 inbred Association panel using both GWAS and candidate gene Association approaches. We identified many beneficial alleles that will be useful for improving kernel starch, protein, and oil content.
-
genome wide nested Association Mapping of quantitative resistance to northern leaf blight in maize
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Jesse Poland, Edward S Buckler, Peter J Bradbury, Rebecca J NelsonAbstract:Quantitative resistance to plant pathogens, controlled by multiple loci of small effect, is important for food production, food security, and food safety but is poorly understood. To gain insights into the genetic architecture of quantitative resistance in maize, we evaluated a 5,000-inbred-line nested Association Mapping population for resistance to northern leaf blight, a maize disease of global economic importance. Twenty-nine quantitative trait loci were identified, and most had multiple alleles. The large variation in resistance phenotypes could be attributed to the accumulation of numerous loci of small additive effects. Genome-wide nested Association Mapping, using 1.6 million SNPs, identified multiple candidate genes related to plant defense, including receptor-like kinase genes similar to those involved in basal defense. These results are consistent with the hypothesis that quantitative disease resistance in plants is conditioned by a range of mechanisms and could have considerable mechanistic overlap with basal resistance.
-
Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design
THE PLANT CELL ONLINE, 2009Co-Authors: S. Myles, J. Peiffer, Elhan S Ersoz, Denise E. Costich, P. J. Brown, Z. Zhang, Edward S BucklerAbstract:The goal of many plant scientists' research is to explain natural phenotypic variation in terms of simple changes in DNA sequence. Traditionally, linkage Mapping has been the most commonly employed method to reach this goal: experimental crosses are made to generate a family with known relatedness, and attempts are made to identify cosegregation of genetic markers and phenotypes within this family. In vertebrate systems, Association Mapping (also known as linkage disequilibrium Mapping) is increasingly being adopted as the Mapping method of choice. Association Mapping involves searching for genotype-phenotype correlations in unrelated individuals and often is more rapid and cost-effective than traditional linkage Mapping. We emphasize here that linkage and Association Mapping are complementary approaches and are more similar than is often assumed. Unlike in vertebrates, where controlled crosses can be expensive or impossible (e.g., in humans), the plant scientific community can exploit the advantages of both controlled crosses and Association Mapping to increase statistical power and Mapping resolution. While the time and money required for the collection of genotype data were critical considerations in the past, the increasing availability of inexpensive DNA sequencing and genotyping methods should prompt researchers to shift their attention to experimental design. This review provides thoughts on finding the optimal experimental mix of Association Mapping using unrelated individuals and controlled crosses to identify the genes underlying phenotypic variation.
-
status and prospects of Association Mapping in plants
The Plant Genome, 2008Co-Authors: Chengsong Zhu, Michael A Gore, Edward S BucklerAbstract:There is tremendous interest in using Association Mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and development of robust statistical analysis methods make Association Mapping appealing and affordable to plant research programs. Association Mapping identifi es quantitative trait loci (QTLs) by examining the marker-trait Associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. General understanding of Association Mapping has increased signifi cantly since its debut in plants. We have seen a more concerted effort in assembling various Association-Mapping populations and initiating experiments through either candidategene or genome-wide approaches in different plant species. In this review, we describe the current status of Association Mapping in plants and outline opportunities and challenges in complex trait dissection and genomics-assisted crop improvement. L arge-scale genome-wide Association analyses of major human diseases have yielded very promising results, corroborating fi ndings of previous candidategene Association studies and identifying novel disease loci that were previously unknown (Th e Wellcome Trust Case Control Consortium, 2007). Th e same strategy is being exploited in many plant species thanks to the dramatic reduction in costs of genomic technologies. In contrast to the widely used linkage analysis traditional Mapping research in plants, Association Mapping searches for functional variation in a much broader germplasm context. Association Mapping enables researchers to use modern genomic technologies to exploit natural diversity, the wealth of which is known to plant geneticists and breeders but has been utilized only on a small scale before the genomics era. Owing to the ease of producing large numbers of progenies from controlled crosses and conducting replicated trials with immortal individuals (inbreds and recombinant inbred lines, RILs), Association Mapping in plants may prove to be more promising than in human or animal genetics. In the current review,
Chase M Mason - One of the best experts on this subject based on the ideXlab platform.
-
genome wide Association Mapping of floral traits in cultivated sunflower helianthus annuus
Journal of Heredity, 2019Co-Authors: Jordan A Dowell, Erin C Reynolds, Tessa Pliakas, Jennifer R Mandel, John M Burke, Lisa A Donovan, Chase M MasonAbstract:Floral morphology and pigmentation are both charismatic and economically relevant traits associated with cultivated sunflower (Helianthus annuus L.). Recent work has linked floral morphology and pigmentation to pollinator efficiency and seed yield. Understanding the genetic architecture of such traits is essential for crop improvement, and gives insight into the role of genetic constraints in shaping floral diversity. A diversity panel of 288 sunflower genotypes was phenotyped for a variety of morphological, phenological, and color traits in both a greenhouse and a field setting. Association Mapping was performed using 5788 SNP markers using a mixed linear model approach. Several dozen markers across 10 linkage groups were significantly associated with variation in morphological and color trait variation. Substantial trait plasticity was observed between greenhouse and field phenotyping, and Associations differed between environments. Color traits mapped more strongly than morphology in both settings, with markers together explaining 16% of petal carotenoid content in the greenhouse, and 17% and 24% of variation in disc anthocyanin presence in the field and greenhouse, respectively. Morphological traits like disc size mapped more strongly in the field, with markers together explaining up to 19% of disc size variation. Loci identified here through Association Mapping within cultivated germplasm differ from those identified through biparental crosses between modern cultivated sunflower and either its wild progenitor or domesticated landraces. Several loci lie within genomic regions involved in domestication. Differences between phenotype expression under greenhouse and field conditions highlight the importance of plasticity in determining floral morphology and pigmentation.
Matthew P. Reynolds - One of the best experts on this subject based on the ideXlab platform.
-
Genome-wide Association Mapping of yield and yield components of spring wheat under contrasting moisture regimes
Theoretical and Applied Genetics, 2014Co-Authors: Erena A. Edae, Patrick F. Byrne, Scott D. Haley, Marta S. Lopes, Matthew P. ReynoldsAbstract:Key message A stable QTL that may be used in marker-assisted selection in wheat breeding programs was detected for yield, yield components and drought tolerance-related traits in spring wheat Association Mapping panel. Abstract Genome-wide Association Mapping has become a widespread method of quantitative trait locus (QTL) identification for many crop plants including wheat ( Triticum aestivum L.). Its benefit over traditional bi-parental Mapping approaches depends on the extent of linkage disequilibrium in the Mapping population. The objectives of this study were to determine linkage disequilibrium decay rate and population structure in a spring wheat Association Mapping panel ( n = 285–294) and to identify markers associated with yield and yield components, morphological, phenological, and drought tolerance-related traits. The study was conducted under fully irrigated and rain-fed conditions at Greeley, CO, USA and Melkassa, Ethiopia in 2010 and 2011 (five total environments). Genotypic data were generated using diversity array technology markers. Linkage disequilibrium decay rate extended over a longer genetic distance for the D genome (6.8 cM) than for the A and B genomes (1.7 and 2.0 cM, respectively). Seven subpopulations were identified with population structure analysis. A stable QTL was detected for grain yield on chromosome 2DS both under irrigated and rain-fed conditions. A multi-trait region significant for yield and yield components was found on chromosome 5B. Grain yield QTL on chromosome 1BS co-localized with harvest index QTL. Vegetation indices shared QTL with harvest index on chromosome 1AL and 5A. After validation in relevant genetic backgrounds and environments, QTL detected in this study for yield, yield components and drought tolerance-related traits may be used in marker-assisted selection in wheat breeding programs.
-
genome wide Association Mapping of yield and yield components of spring wheat under contrasting moisture regimes
Theoretical and Applied Genetics, 2014Co-Authors: Erena A. Edae, Patrick F. Byrne, Scott D. Haley, Marta S. Lopes, Matthew P. ReynoldsAbstract:Key message A stable QTL that may be used in marker-assisted selection in wheat breeding programs was detected for yield, yield components and drought tolerance-related traits in spring wheat Association Mapping panel.
Eric P Xing - One of the best experts on this subject based on the ideXlab platform.
-
Enhancing the usability and performance of structured Association Mapping algorithms using automation, parallelization, and visualization in the GenAMap software system
BMC Genetics, 2012Co-Authors: Ross E Curtis, Anuj Goyal, Eric P XingAbstract:Background Structured Association Mapping is proving to be a powerful strategy to find genetic polymorphisms associated with disease. However, these algorithms are often distributed as command line implementations that require expertise and effort to customize and put into practice. Because of the difficulty required to use these cutting-edge techniques, geneticists often revert to simpler, less powerful methods. Results To make structured Association Mapping more accessible to geneticists, we have developed an automatic processing system called Auto-SAM. Auto-SAM enables geneticists to run structured Association Mapping algorithms automatically, using parallelization. Auto-SAM includes algorithms to discover gene-networks and find population structure. Auto-SAM can also run popular Association Mapping algorithms, in addition to five structured Association Mapping algorithms. Conclusions Auto-SAM is available through GenAMap, a front-end desktop visualization tool. GenAMap and Auto-SAM are implemented in JAVA; binaries for GenAMap can be downloaded from http://sailing.cs.cmu.edu/genamap .
-
enhancing the usability and performance of structured Association Mapping algorithms using automation parallelization and visualization in the genamap software system
BMC Genetics, 2012Co-Authors: Ross E Curtis, Anuj Goyal, Eric P XingAbstract:Background: Structured Association Mapping is proving to be a powerful strategy to find genetic polymorphisms associated with disease. However, these algorithms are often distributed as command line implementations that require expertise and effort to customize and put into practice. Because of the difficulty required to use these cutting-edge techniques, geneticists often revert to simpler, less powerful methods. Results: To make structured Association Mapping more accessible to geneticists, we have developed an automatic
Sylvester Ndeda - One of the best experts on this subject based on the ideXlab platform.
-
Association Mapping of stem rust race TTKSK resistance in US barley breeding germplasm
Theoretical and Applied Genetics, 2014Co-Authors: Hao Zhou, Brian J Steffenson, R Wanyera, P Njau, Gary Muehlbauer, Sylvester NdedaAbstract:Key message Loci conferring resistance to the highly virulent African stem rust race TTKSK were identified in advanced barley breeding germplasm and positioned to chromosomes 5H and 7H using an Association Mapping approach. Abstract African races of the stem rust pathogen ( Puccinia graminis f. sp. tritici ) are a serious threat to barley production worldwide because of their wide virulence. To discover and characterize resistance to African stem rust race TTKSK in US barley breeding germplasm, over 3,000 lines/cultivars were assessed for resistance at the seedling stage in the greenhouse and also the adult plant stage in the field in Kenya. Only 12 (0.3 %) and 64 (2.1 %) lines exhibited a resistance level comparable to the resistant control at the seedling and adult plant stage, respectively. To map quantitative trait loci (QTL) for resistance to race TTKSK, an Association Mapping approach was conducted, utilizing 3,072 single nucleotide polymorphism (SNP) markers. At the seedling stage, two neighboring SNP markers (0.8 cM apart) on chromosome 7H (11_21491 and 12_30528) were found significantly associated with resistance. The most significant one found was 12_30528; thus, the resistance QTL was named Rpg - qtl - 7H - 12_30528. At the adult plant stage, two SNP markers on chromosome 5H (11_11355 and 12_31427) were found significantly associated with resistance. This resistance QTL was named Rpg - qtl - 5H - 11_11355 for the most significant marker identified. Adult plant resistance is of paramount importance for stem rust. The marker associated with Rpg - qtl - 5H - 11_11355 for adult plant resistance explained only a small portion of the phenotypic variation (0.02); however, this QTL reduced disease severity up to 55.0 % under low disease pressure and up to 21.1 % under heavy disease pressure. SNP marker 11_11355 will be valuable for marker-assisted selection of adult plant stem rust resistance in barley breeding.
-
Association Mapping of stem rust race ttksk resistance in us barley breeding germplasm
Theoretical and Applied Genetics, 2014Co-Authors: Hao Zhou, Brian J Steffenson, Gary J Muehlbauer, R Wanyera, P Njau, Sylvester NdedaAbstract:Key message Loci conferring resistance to the highly virulent African stem rust race TTKSK were identified in advanced barley breeding germplasm and positioned to chromosomes 5H and 7H using an Association Mapping approach.
