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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #311710

Title: The development and characterization of a 57K SNP array for Rainbow Trout

item Palti, Yniv
item Gao, Guangtu
item MOEN, THOMAS - Aquagen
item Liu, Sixin
item KENT, MATTHEW - Centre For Integrative Genetics (CIGENE)
item SIGBJORN, LIEN - Centre For Integrative Genetics (CIGENE)
item MILLER, MICHAEL - University Of California
item Rexroad, Caird

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/29/2014
Publication Date: 1/14/2015
Citation: Palti, Y., Gao, G., Moen, T., Liu, S., Kent, M., Sigbjorn, L., Miller, M., Rexroad Iii, C.E. 2015. The development and characterization of a 57K SNP array for Rainbow Trout. Plant and Animal Genome Conference. P354.

Interpretive Summary:

Technical Abstract: In this paper we describe the development and characterization of the first high density single nucleotide polymorphism (SNP) genotyping array for rainbow trout. The SNP array is publically available from a commercial vendor (Affymetrix). The SNP genotyping quality was high and validation rate was close to 90%. This is comparable to other farm animals and is much higher than previous smaller scale SNP validation studies in rainbow trout. High quality and integrity of the genotypes is evident from sample reproducibility and from nearly 100% agreement in genotyping results from other methods. The array is very useful for rainbow trout aquaculture populations with more than 40,900 polymorphic markers per population. For wild populations that were confounded by a smaller sample size the number of polymorphic markers was between 10,577 and 24,330. Comparison between genotypes from individual populations suggest good potential for identifying candidate markers for populations' traceability. Linkage analysis and mapping of the SNPs to the reference genome assembly provide strong evidence for a wide distribution throughout the genome with good representation in all 29 chromosomes. A total of 68% of the genome scaffolds and contigs were anchored through linkage analysis using the SNP array genotypes, including ~20% of the genome assembly that has not been previously anchored to chromosomes.