Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

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dc.contributor.author Wang, Shichen
dc.contributor.author Wong, Debbie
dc.contributor.author Forrest, Kerrie
dc.contributor.author Allen, Alexandra
dc.contributor.author Chao, Shiaoman
dc.contributor.author Huang, Bevan E.
dc.contributor.author Maccaferri, Marco
dc.contributor.author Salvi, Silvio
dc.contributor.author Milner, Sara G.
dc.contributor.author Cattivelli, Luigi
dc.contributor.author Mastrangelo, Anna M.
dc.contributor.author Whan, Alex
dc.contributor.author Stephen, Stuart
dc.contributor.author Barker, Gary
dc.contributor.author Wieseke, Ralf
dc.contributor.author Plieske, Joerg
dc.contributor.author International Wheat Genome Sequencing Consortium
dc.contributor.author Lillemo, Morten
dc.contributor.author Mather, Diane
dc.contributor.author Appels, Rudi
dc.contributor.author Dolferus, Rudy
dc.contributor.author Brown-Guedira, Gina
dc.contributor.author Korol, Abraham
dc.contributor.author Akhunova, Alina
dc.contributor.author Feuillet, Catherine
dc.contributor.author Salse, Jerome
dc.contributor.author Morgante, Michele
dc.contributor.author Pozniak, Curtis
dc.contributor.author Luo, Ming-Cheng
dc.contributor.author Dvorak, Jan
dc.contributor.author Morell, Matthew
dc.contributor.author Dubcovsky, Jorge
dc.contributor.author Ganal, Martin
dc.contributor.author Tuberosa, Roberto
dc.contributor.author Lawley, Cindy
dc.contributor.author Mikoulitch, Ivan
dc.contributor.author Cavanagh, Colin
dc.contributor.author Edwards, Keith J.
dc.contributor.author Hayden, Matthew
dc.contributor.author Akhunov, Eduard D.
dc.date.accessioned 2014-10-01T18:34:34Z
dc.date.available 2014-10-01T18:34:34Z
dc.date.issued 2014-10-01
dc.identifier.uri http://hdl.handle.net/2097/18356
dc.description.abstract 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. en_US
dc.language.iso en_US en_US
dc.relation.uri http://onlinelibrary.wiley.com/doi/10.1111/pbi.12183/full en_US
dc.rights This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. en_US
dc.subject Single nucleotide polymorphism en_US
dc.subject Polyploid wheat en_US
dc.subject Wheat iSelect array en_US
dc.subject Genotyping en_US
dc.subject High-density map en_US
dc.subject Genetic diversity en_US
dc.title Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array en_US
dc.type Article (publisher version) en_US
dc.date.published 2014 en_US
dc.citation.doi doi:10.1111/pbi.12183 en_US
dc.citation.epage 796 en_US
dc.citation.issue 6 en_US
dc.citation.jtitle Plant Biotechnology Journal en_US
dc.citation.spage 787 en_US
dc.citation.volume 12 en_US
dc.contributor.authoreid wangsc en_US
dc.contributor.authoreid akhunova en_US
dc.contributor.authoreid eakhunov en_US


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