Skip to main content
ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #335753
Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: A new single-nucleotide polymorphisms database for rainbow trout generated through whole genome resequencing of selected samples

Author
item Gao, Guangtu
item LIEN, SIGBJORN - Centre For Integrative Genetics (CIGENE)
item NOME, TORFINN - Centre For Integrative Genetics (CIGENE)
item MOEN, THOMAS - Aquagen
item PEARSE, DEVON - National Marine Fisheries
item THORGAARD, GARY - Washington State University
item Palti, Yniv

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/28/2016
Publication Date: 1/14/2017
Citation: Gao, G., Lien, S., Nome, T., Moen, T., Pearse, D., Thorgaard, G., Palti, Y. 2017. A new single-nucleotide polymorphisms database for rainbow trout generated through whole genome resequencing of selected samples [abstract]. Plant and Animal Genome Conference. P1007.

Interpretive Summary:

Technical Abstract: Single-nucleotide polymorphisms (SNPs) are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout, SNP discovery has been done through sequencing of restriction-site associated DNA (RAD) libraries, reduced representation libraries (RRL), RNA sequencing, and whole-genome re-sequencing. Recently we have performed high coverage whole genome resequencing with 41 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 29 new samples from the US added to 12 samples that we previously used for SNP discovery from AquaGen (Norway). Of the 29 US samples, 11 were the Washington State University double-haploid lines and 18 represented wild populations with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout genome assembly which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMTools. SNPs were filtered based on their genome location, read depth on the locus, and read balance between the two alleles. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used in detection and filtering of paralogous sequence variants (PSV). This new SNP database provides an important resource for new SNP array designs and whole genome association analyses.