Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array
2014
Wang, Shichen | Wong, Debbie | Forrest, Kerrie | Allen, Alexandra | Chao, Shiaoman | Huang, Bevan | Maccaferri, Marco | Salvi, Silvio | Milner, Sara | Cattivelli, Luigi | Mastrangelo, Anna | Whan, Alex | Stephen, Stuart | Barker, Gary | Wieseke, Ralf | Plieske, Joerg | Lillemo, Morten | Mather, Diane, D. | Appels, Rudi | Dolferus, Rudy | Brown-Guedira, Gina | Korol, Abraham | Akhunova, Alina | Feuillet, Catherine | Salse, Jérôme | Morgante, Michèle | Pozniak, Curtis | Luo, Ming-Cheng | Dvorak, Jan | Morell, Matthew | Dubcovsky, Jorge | Ganal, Martin | Tuberosa, Roberto | Lawley, Cindy, T. | Mikoulitch, Ivan | Cavanagh, Colin | Edwards, Keith | Hayden, Matthew | Akhunov, Eduard | Department of Plant Pathology ; Shizuoka University | Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources ; AgriBio | USDA-ARS : Agricultural Research Service | Alma Mater Studiorum Università di Bologna = University of Bologna (UNIBO) | Department of Agricultural Sciences ; Alma Mater Studiorum Università di Bologna = University of Bologna (UNIBO) | Genomics Research Centre ; Consiglio per la Ricerca e Sperimentazione in Agricoltura | Commonwealth Scientific and Industrial Research Organisation [Australia] (CSIRO) | Waite Res Inst, Australian Ctr Plant Funct Genom ; University of Adelaide | Institute of Evolution and Department of Evolutionary and Environmental Biology ; Ǧāmiʿat͏̈ Hayfā = University of Haifa | Integrated Genomics Facility ; Kansas State University | Génétique Diversité et Ecophysiologie des Céréales (GDEC) ; Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP) | Dipartimento di Produzione Vegetale e Tecnologie Agrarie ; Università degli Studi di Udine - University of Udine [Italie] | Plant Genetics and Bioinformatics ; Department of Plant Sciences [Univ California Davis] (Plant - UC Davis) ; University of California [Davis] (UC Davis) ; University of California (UC)-University of California (UC)-University of California [Davis] (UC Davis) ; University of California (UC)-University of California (UC) | University of Hradec Kralove | CSIRO Plant Industry ; Commonwealth Scientific and Industrial Research Organisation [Australia] (CSIRO) | Department of Plant Sciences (DPS) ; University of Cambridge [UK] (CAM) | Illumina, Inc. ; Illumina, Inc. | CSIRO Plant Industrie ; Commonwealth Scientific and Industrial Research Organisation [Australia] (CSIRO) | Dept Plant Pathol ; Kansas State University
International audience
Show more [+] Less [-]English. High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
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