ARS | Publication request: TaqMan assays exploring allelic diversity in USDA pea core collection.

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 15, 2008
Publication Date: January 12, 2009
Citation: Coyne, C.J., Brown, A.F., Timmerman-Vaughn, G. 2009. TaqMan assays exploring allelic diversity in USDA pea core collection. Plant and Animal Genome XVII Conference Abstract p. 150.

Interpretive Summary: Allelic diversity of the USDA pea collection was studied by first resequencing 32 diverse pea germplasm accessions using 62 loci from published pea genes and developing assays using the TaqMan® SNP Genotyping Assay platform. Previously, De La Vega et al. (2005) has published that ‘the TaqMan assay format is suitable for low- to mid-throughput applications in which a high assay conversion rate, simple assay workflow, and low cost of automation are desirable’ making it ideal for the USDA National Plant Germplasm Stations. The SNP/INDEL discovery rate averaged 12.2 SNPs and 0.76 INDEL per 13 loci presented. Next, 310 pea core accessions from one population based on the program STRUCTURE (Pritchard et al. 2000) will be analyzed for fluorescence emission directly in 96-well plates using the ABI PRISM 7500 Sequence Detection System, which provides allele assignment at a 99.7% confidence level. We will report on successful assays developed 10 loci (Aubert et al. 2006; Gilpin et al 1997; Hecht et al 2005): Agpl1, AspS2, Cwi1, DRR206c, Gpt, O2like, PPlike, PsFCA, PsAS2, SOD9, Thaumatin1, PsLD, and Viola2.

Technical Abstract: N/A