Location: Cereal Crops ResearchTitle: A SNP genotyping array for hexaploid oat Author
Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/13/2014
Publication Date: 6/19/2014
Publication URL: http://handle.nal.usda.gov/10113/60961
Citation: Tinker, N.A., Chao, S., Lazo, G.R., Oliver, R.E., Huang, Y.-F., Poland, J.A., Jellen, E.N., Maughan, P.J., Kilian, A., Jackson, E.W. 2014. A SNP genotyping array for hexaploid oat. The Plant Genome. 7(3). doi: 10.3835/plantgenome2014.03.0010 Interpretive Summary: DNA marker development generally has lagged behind in cultivated hexaploid oat because of its complex genome structure and polyploidy. Recognizing a need in oat for a reliable set of reference DNA markers, we have developed a marker design in an array format based on the genetic differences found at a single nucleotide level known as single nucleotide polymorphism (SNP). A total of 4,975 SNP markers on this array were validated using 1,100 samples, and approximately 3,500 of those detected discernable polymorphisms among the samples investigated. Our study has also determined the genetic positions for 4100 markers on oat chromosomes. This oat SNP array is expected to provide the entire oat community with a much needed marker resource.
Technical Abstract: Recognizing a need in cultivated hexaploid oat (Avena sativa L.) for a reliable set of reference SNPs, we have developed a 6K BeadChip design containing 257 Infinium I and 5,486 Infinium II designs corresponding to 5,743 SNPs. Of those, 4,975 SNPs yielded successful assays after array manufacturing. These SNPs were discovered based on a variety of bioinformatics pipelines in cDNA and genomic DNA originating from 20 or more diverse oat cultivars. The array was validated in 1100 samples from six RIL mapping populations and sets of diverse oat cultivars and breeding lines, and provided approximately 3500 discernable Mendelian polymorphisms. Here, we present a detailed annotation of these SNPs, including gene identification and orthology, population-genetic characteristics, and tentative positions on an oat consensus map. We also evaluate a new cluster-based method of calling SNPs. The SNP design sequences are made publically available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.