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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #311786

Title: Development of a Fluidigm SNP panel for genetic analysis in rainbow trout

item Liu, Sixin
item Rexroad, Caird
item Gao, Guangtu
item Palti, Yniv

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/31/2014
Publication Date: 1/14/2015
Citation: Liu, S., Rexroad Iii, C.E., Gao, G., Palti, Y. 2015. Development of a Fluidigm SNP panel for genetic analysis in rainbow trout. Plant and Animal Genome Conference. P287.

Interpretive Summary:

Technical Abstract: Although microsatellite markers have been widely used in aquaculture species for genetic analysis such as parentage assignment and genetic mapping, SNPs (single nucleotide polymorphism) are the marker of choice as they are highly abundant and are amenable for high throughput genotyping. Recently we developed a 57K SNP Affymetrix array for rainbow trout. However, the high genotyping cost associated with this array prohibits its widespread use. Furthermore, not all genetic studies such as parentage analysis require such a large number of SNPs. Fluidigm SNPtype assays are based on allele specific PCR SNP detection chemistry, and provide low-cost and high-throughput genotyping and flexible assay choice. Our objective was to develop a Fluidigm SNP panel consisting of 96 SNPs that can be used for parentage analysis, estimating population genetic parameters, and evaluating the impact of SNP markers previously reported to be associated with growth and stress response. We analyzed marker polymorphism data from our recent characterization of the 57k SNP array to select markers. Initially, we selected 96 SNPs for the Fluidigm assay design. Sixty of the 96 SNPs are distributed across all 29 chromosomes (2-3 SNPs per chromosome) of rainbow trout, and the other 36 SNPs are associated with stress response or growth. Eighty of the 96 SNPs worked well in initial genotyping tests and parentage analysis. Replacement markers have been identified and are being incorporated. Once the panel is finalized, we will use it for applications in both research and commercial rainbow trout populations.