Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations

Abstract

A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype-phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom(®) myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information.

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

“…The density of the 6K chip used here was too low to effectively detect fine‐scale patterns of among population divergence and within population homozygosity in response to population‐specific directional selection. More precise detection of long haplotype blocks from selective sweeps is now possible using the 220K SNP chip (Yáñez et al., 2016) and the high‐density 132K SNP chip (Houston et al., 2014) that have been developed for European Atlantic salmon.…”

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…Some outlier loci at these regions were near QTL for growth, appetite, maturity, or disease resistance, which exhibited the effects of strong artificial selection in hatchery stocks. In order to develop a high-density SNP, taking genome duplication and across-continent genetic variation of complex traits in Atlantic salmon into account, de novo SNP discovery and validation was performed using specimens from Chilean, European and North American populations, including fish from wild and farmed origins (Yáñez et al, 2016). A 200K SNPs array can be used for assessment of gene flow from farmed stocks to wild salmon populations worldwide.…”

“…Forty four markers were identified as outliers, and were associated with molecular functions that could be related to selection for growth, response to pathogens and environmental stressors, and with an undesirable early sexual maturation À grilsing trait, that is economically important traits and domestication. A 200K SNP custom array can be applied for carrying genomic selection in breeding programmes and genetic studies in wild populations (Yáñez et al, 2016). An Atlantic salmon 15K SNP chip was evaluated as a potential genomic tool for application in a Tasmanian Atlantic salmon (S. salar) breeding population and was found useful for carrying within-family selection (Dominik et al, 2010).…”

Future directions in breeding for disease resistance in aquaculture species

“…In all studies of aquaculture species to date, the use of GS has resulted in higher prediction accuracy of breeding values than the use of pedigree information alone (Odegård et al, 2014;Tsai et al, 2015;Dou et al, 2016). A prerequisite for genomic selection is a platform to generate high-density SNP marker genotypes across populations of animals and SNP arrays have been developed for several aquaculture species, including Atlantic salmon Yáñez et al, 2016), rainbow trout (Palti et al, 2015), common carp (Xu et al, 2014), and catfish . A major downside to GS is the cost, due to the expense of high-density genotyping in large numbers of individuals.…”