ARS | Publication request: Large-Scale SNP Marker Development and Genotyping in Oat

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: May 28, 2010
Publication Date: August 31, 2010
Citation: Chao, S., Oliver, R.E., Lazo, G.R., Tinker, N., Jackson, E.W. 2010. Large-Scale SNP Marker Development and Genotyping in Oat. Proceedings of The 5th European Oat Conference, September 1-3, 2010, Ystad, Sweden. P.43.

Technical Abstract: In this study, our goals are to develop genome-wide SNP markers using next generation sequencing technologies and to apply a highly parallel SNP genotyping system developed by Illumina for genetics and breeding applications in oat. The large amount of DNA sequence sources generated from cDNAs and Diversity Array Technology (DArT) from a diverse set of oat varieties were assembled and evaluated, and the candidate SNPs were subsequently discovered. The sequence information from 9280 assembled contigs with each containing one candidate SNP was submitted to Illumina for custom genotyping assay design. Among them, 8009 (86%) passed Illumina’s assay design criteria. After filtering the redundant sequences and sequences matched to organelle genomes, a set of 1536 SNPs was selected and comprised of the first pilot oat oligo pooled assay (OPA). The pilot oat OPA1 was validated by genotyping a set of 576 oat samples, including 109 oat germplasm lines and six mapping populations, using Illumina’s GoldenGate assay techniques. The performance of 1536-plex SNP assay in terms of data quality and assay conversion rates was evaluated based on a set of 109 oat germplasm originated from North America and Europe. The assay success rate was at 74%. Approximately 650 SNPs that gave unambiguous genotype calls were found polymorphic among all the germplasm investigated. Our results also suggested that the highly parallel SNP genotyping system generally worked well for oat, and can be used to apply population-based genetic studies and breeding applications in polyploid crops such as oat.