W469 Development of a High-Density SNP Genotyping Panel as a Community Resource for Genetic Analysis in Oat

Date: Saturday, January 14, 2012
Time: 3:50 PM
Room: Pacific Salon 6-7 (2nd Floor)
Shiaoman Chao , USDA-ARS, Fargo, ND
Rebekah Oliver , USDA ARS, Aberdeen,, ID
Gerard R. Lazo , USDA-ARS Western Regional Research Center, Albany, CA
Nick Tinker , AAFC, Ottawa, ON, Canada
Eric N. Jellen , Brigham Young University, Provo, UT
Jeff Maughan , Brigham Young University, Provo, UT
Eric Jackson , USDA ARS, Aberdeen, ID
The development and application of DNA markers in cultivated oat (Avena sativa L., 2n=6X=42), an important food and feed crop, has lagged behind many other major food crops. The recent breakthroughs in next generation sequencing technologies and the availability of highly parallel genotyping systems have greatly impacted the feasibility of large-scale SNP marker development and high density SNP marker genotyping in crops with complex genomes such as oat. In this study, SNP discovery was carried out based on sequencing cDNAs and genomic representations from 20 diverse oat accessions. Using Illumina's GoldenGate assay, we assessed genotyping performance of over 6,000 SNPs comprised of four pilot OPAs using 109 oat germplasm accessions of world-wide origin and six bi-parental mapping populations segregating for important agronomic traits. Polymorphic SNPs were identified and high density SNP-based genetic maps were constructed. Twenty one linkage groups were physically anchored to individual oat chromosomes using monosomic lines. Based on genotyping performance, allele frequency, and chromosome-wide distribution, 1536 SNPs were selected and included in a high density genotyping panel. This panel is expected to serve as a useful genomic tool for the oat community worldwide.