Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height

dc.contributor.author N'Diaye, Amidou
dc.contributor.author Haile, Jemanesh
dc.contributor.author Nilsen, Kirby
dc.contributor.author Walkowiak, Sean
dc.contributor.author Ruan, Yuefeng
dc.contributor.author Singh, Asheesh
dc.contributor.author Clarke, Fran
dc.contributor.author Clarke, John
dc.contributor.author Pozniak, Curtis
dc.contributor.department Department of Agronomy
dc.date 2018-12-09T15:53:44.000
dc.date.accessioned 2020-06-29T23:06:05Z
dc.date.available 2020-06-29T23:06:05Z
dc.date.copyright Mon Jan 01 00:00:00 UTC 2018
dc.date.issued 2018-11-01
dc.description.abstract <p>Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, <em>hap_4B_1</em> explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus <em>hap_2B_9</em>explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.</p>
dc.description.comments <p>This article is published as N'Diaye, Amidou, Jemanesh Kifetew Haile, Kirby Nilsen, Sean Walkowiak, Yuefeng Ruan, Asheesh K. Singh, Fran R. Clarke, John M. Clarke, and Curtis J. Pozniak. "Haplotype Loci under Selection in Canadian Durum Wheat Germplasm over 60 Years of Breeding: Association with Grain Yield, Quality Traits, Protein Loss and Plant Height." <em>Frontiers in Plant Science</em> 9 (2018): 1589. doi: <a href="https://doi.org/10.3389/fpls.2018.01589">10.3389/fpls.2018.01589</a>.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/agron_pubs/548/
dc.identifier.articleid 1592
dc.identifier.contextkey 13409865
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath agron_pubs/548
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/4914
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/agron_pubs/548/2018_Singh_HaplotypeLoci.pdf|||Sat Jan 15 00:54:29 UTC 2022
dc.source.uri 10.3389/fpls.2018.01589
dc.subject.disciplines Agriculture
dc.subject.disciplines Agronomy and Crop Sciences
dc.subject.disciplines Plant Breeding and Genetics
dc.subject.keywords haplotype
dc.subject.keywords loci under selection
dc.subject.keywords durum wheat
dc.subject.keywords quality traits
dc.subject.keywords grain yield
dc.subject.keywords protein loss
dc.subject.keywords plant height
dc.title Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height
dc.type article
dc.type.genre article
dspace.entity.type Publication
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relation.isOrgUnitOfPublication fdd5c06c-bdbe-469c-a38e-51e664fece7a
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