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A SNP Genotyping Array for Hexaploid Oat

Permanent URL:
http://handle.nal.usda.gov/10113/60961
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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 discernible 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 publicly available, and the full SNP genotyping platform is available for commercial purchase from an independent third party.
Author(s):
Nicholas A. Tinker , Shiaoman Chao , Gerard R. Lazo , Rebekah E. Oliver , Yung-Fen Huang , Jesse A. Poland , Eric N. Jellen , Peter J. Maughan , Andrzej Kilian , Eric W. Jackson
Note:
USDA Scientist Submission
Source:
Plant genome 2014 Aug. 15 v.7 no.3
Language:
English
Year:
2014
Collection:
Journal Articles, USDA Authors, Peer-Reviewed
Rights:
Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.