A new single-nucleotide polymorphism database for rainbow trout generated through whole genome re-sequencing

Authors: Gao, Guangtu; NOME, TORFINN - Centre For Integrative Genetics (CIGENE); PEARSE, DEVON - National Oceanic & Atmospheric Administration (NOAA); MOEN, TOMAS - Aquagen; NAISH, KERRY - University Of Washington; THORGAARD, GARY - Washington State University; LIEN, SIGBJORN - Centre For Integrative Genetics (CIGENE); Palti, Yniv

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/9/2018
Publication Date: 4/24/2018
Citation: Gao, G., Nome, T., Pearse, D.E., Moen, T., Naish, K.A., Thorgaard, G.H., Lien, S., Palti, Y. 2018. A new single-nucleotide polymorphism database for rainbow trout generated through whole genome re-sequencing. Frontiers in Genetics. 9:147. https://doi.org/10.3389/fgene.2018.00147.
DOI: https://doi.org/10.3389/fgene.2018.00147

Interpretive Summary: Rainbow trout is one of the most important aquaculture species in the United States and around the world. Recent biotechnological advancements have enhanced our ability to improve selective breeding in rainbow trout and other aquaculture species through the utilization of molecular genetics and genomics. To this end, an assay called high-density single nucleotide polymorphism (SNP) chip is used to assess relationships between the DNA make-up of the animal and desired production traits, which enables accurate prediction of the genetic merit and breeding potential of the animal. Here we report on the development of a very large database of SNP markers towards the improvement of current resources for genetic analyses in rainbow trout and the development of new high-density SNP chip assays. This resource will facilitate the identification of genes affecting important aquaculture production traits, wild fisheries management and basic biological research, and will enhance strategies targeting the genetic improvement of this species for production efficiency.

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 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway) that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup. SNPs were filtered based on SNP quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs) and multi-sequence variants (MSVs). Overall, 30,302,087 SNPs were identified on 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25). The average SNP rate in the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. These SNPs form a new database which provides an important resource for a new high density SNP array design and for other SNP genotyping platforms used for genetic and genomics studies of this iconic salmonid fish species.