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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #327834

Title: Population structure and genotype-phenotype associations in a collection of oat landraces and historic cultivars.

item WINKLER, LOUISA - Washington State University
item Bonman, John
item Chao, Shiaoman
item YIMER, BELAYNEH - Orise Fellow
item Bockelman, Harold
item Esvelt Klos, Kathy

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/8/2016
Publication Date: 7/8/2016
Citation: Winkler, L., Bonman, J.M., Chao, S., Yimer, B.A., Bockelman, H.E., Esvelt Klos, K.L. 2016. Population structure and genotype-phenotype associations in a collection of oat landraces and historic cultivars. Frontiers in Plant Science. doi: 10.3389/fpls.2016.01077.

Interpretive Summary: In order to apply advanced genomic technologies to oat improvement, we must understand how past breeding efforts have impacted genetic diversity. We used molecular marker data on oat accessions in the USDA-ARS National Small Grains Collection to characterize the genetic diversity and population structure of un-improved oat and historical oat cultivars. We also used this data to find regions of the genome that influence kernel and flowering characteristics, and disease resistance. Understanding how and where genetic diversity may have been reduced can inform the selection of parents for breeding improved cultivars.

Technical Abstract: Population structure and genetic architecture of phenotypic traits in oat (Avena sativa L.) remain relatively under-researched compared to other small grain species. This study explores the historic context of current elite germplasm, including phenotypic and genetic characterization, with a particular focus on identifying under-utilized areas. A diverse panel of cultivated oat accessions was assembled from the US Department of Agriculture's National Small Grains Collection to represent a gene pool relatively unaffected by twentieth century breeding activity and unlikely to have been included in recent molecular studies. The panel was genotyped using an oat iSelect 6K beadchip SNP array. The final dataset included 759 unique individuals genotyped for 2,716 markers. Population structure appeared to be fairly strong, with the first three principal components accounting for 38.8% of variation and 73% of individuals belonging to one of three clusters. One cluster with high genetic distinctness appears to have been largely overlooked in twentieth century breeding. Phenotype data collected by the Germplasm Resources Information Network were evaluated for their relationship to population structure. Of the structuring variables evaluated, lemma color and region of origin showed the strongest explanatory power. Genome-wide association study of the panel generated novel indications of genomic regions associated with awn frequency, kernels per spikelet, lemma color and panicle type. Further results supported previous findings of loci associated with barley yellow dwarf virus tolerance, crown rust (Puccinia coronata f. sp. avenae) resistance, days to anthesis and growth habit (winter/spring). In addition, two novel loci were identified for crown rust resistance.