ARS | Publication request: Analysis of genetic diversity using SNP markers in oat

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: October 29, 2010
Publication Date: January 14, 2011
Citation: Chao, S., Oliver, R.E., Lazo, G.R., Tinker, N., Jannink, J., Redman, R.R., Jackson, E.W. 2011. Analysis of genetic diversity using SNP markers in oat. Meeting Abstract. pg. 209.

Technical Abstract: A large-scale single nucleotide polymorphism (SNP) discovery was carried out in cultivated oat using Roche 454 sequencing methods. DNA sequences were generated from cDNAs originating from a panel of 20 diverse oat cultivars, and from Diversity Array Technology (DArT) genomic complexity reductions from the same 20 cultivars and an additional 5 cultivars. Two oligo pooled assays (OPAs) comprised of 3,072 in silico SNPs were developed and the candidate SNPs were validated using Illumina’s GoldenGate genotyping system. The performance of two OPAs in terms of data quality and assay conversion rates was evaluated based on a set of 109 oat germplasm originating from wide geographic regions in the world. The average assay conversion rate was at 65%. Approximately 1,100 SNPs that gave unambiguous genotype calls were found polymorphic with an average PIC value of 0.32 among all the germplasm investigated. The allele frequency distribution among germplasm showed that over 80% of the polymorphic SNPs had minor allele frequency >0.10, indicating that the SNPs discovered in our study represent common alleles present among germplasm of wide origin. The estimate of LD decay revealed that LD decayed rapidly to r2 = 0.2 between linked markers at a map distance of 2cM in this set of germplasm. Our results also suggested that the highly parallel SNP genotyping system generally worked well for oat, despite its complex genome structure, and can be used to apply population-based genetic studies and breeding applications in polyploid crops such as oat.