Genomic selection in wheat breeding using genotyping-by-sequencing

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dc.contributor.author Poland, Jesse A.
dc.contributor.author Endelman, Jeffrey
dc.contributor.author Dawson, Julie
dc.contributor.author Rutkoski, Jessica
dc.contributor.author Wu, Shuangye
dc.contributor.author Manes, Yann
dc.contributor.author Dreisigacker, Susanne
dc.contributor.author Crossa, José
dc.contributor.author Sánchez-Villeda, Héctor
dc.contributor.author Sorrells, Mark
dc.contributor.author Jannink, Jean-Luc
dc.date.accessioned 2013-03-11T16:31:56Z
dc.date.available 2013-03-11T16:31:56Z
dc.date.issued 2013-03-11
dc.identifier.uri http://hdl.handle.net/2097/15344
dc.description.abstract Genomic selection (GS) uses genomewide molecular markers to predict breeding values and make selections of individuals or breeding lines prior to phenotyping. Here we show that genotyping-by-sequencing (GBS) can be used for de novo genotyping of breeding panels and to develop accurate GS models, even for the large, complex, and polyploid wheat (Triticum aestivum L.) genome. With GBS we discovered 41,371 single nucleotide polymorphisms (SNPs) in a set of 254 advanced breeding lines from CIMMYT’s semiarid wheat breeding program. Four different methods were evaluated for imputing missing marker scores in this set of unmapped markers, including random forest regression and a newly developed multivariate-normal expectation-maximization algorithm, which gave more accurate imputation than heterozygous or mean imputation at the marker level, although no signifi cant differences were observed in the accuracy of genomic-estimated breeding values (GEBVs) among imputation methods. Genomic-estimated breeding value prediction accuracies with GBS were 0.28 to 0.45 for grain yield, an improvement of 0.1 to 0.2 over an established marker platform for wheat. Genotyping-bysequencing combines marker discovery and genotyping of large populations, making it an excellent marker platform for breeding applications even in the absence of a reference genome sequence or previous polymorphism discovery. In addition, the flexibility and low cost of GBS make this an ideal approach for genomics-assisted breeding. en_US
dc.language.iso en_US en_US
dc.relation.uri https://www.crops.org/publications/tpg/abstracts/5/3/103 en_US
dc.subject Genomic selection en_US
dc.subject Genotyping-by-sequencing en_US
dc.subject Wheat genome en_US
dc.subject Wheat en_US
dc.subject Genomic-estimated breeding values en_US
dc.title Genomic selection in wheat breeding using genotyping-by-sequencing en_US
dc.type Article (publisher version) en_US
dc.date.published 2012 en_US
dc.citation.doi doi:10.3835/plantgenome2012.06.0006 en_US
dc.citation.epage 113 en_US
dc.citation.issue 3 en_US
dc.citation.jtitle Plant Genome en_US
dc.citation.spage 103 en_US
dc.citation.volume 5 en_US
dc.contributor.authoreid jpoland en_US
dc.contributor.authoreid swu4455 en_US


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