Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon

Abstract

SummaryFarmed Atlantic salmon (Salmo salar) is a globally important production species, including in Australia where breeding and selection has been in progress since the 1960s. The recent development of SNP genotyping platforms means genome-wide association and genomic prediction can now be implemented to speed genetic gain. As a precursor, this study collected genotypes at 218 132 SNPs in 777 fish from a Tasmanian breeding population to assess levels of genetic diversity, the strength of linkage disequilibrium (LD) and imputation accuracy. Genetic diversity in Tasmanian Atlantic salmon was lower than observed within European populations when compared using four diversity metrics. The distribution of allele frequencies also showed a clear difference, with the Tasmanian animals carrying an excess of low minor allele frequency variants. The strength of observed LD was high at short distances (<25 kb) and remained above background for marker pairs separated by large chromosomal distances (hundreds of kb), in sharp contrast to the European Atlantic salmon tested. Genotypes were used to evaluate the accuracy of imputation from low density (0.5 to 5 K) up to increased density SNP sets (78 K). This revealed high imputation accuracies (0.89-0.97), suggesting that the use of low density SNP sets will be a successful approach for genomic prediction in this population. The long-range LD, comparatively low genetic diversity and high imputation accuracy in Tasmanian salmon is consistent with known aspects of their population history, which involved a small founding population and an absence of subsequent introgression. The findings of this study represent an important first step towards the design of methods to apply genomics in this economically important population.

Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon

“…, Hickey et al 2012b; Segelke et al 2012; Pausch et al 2013; Moghaddar et al 2015; Uemoto et al 2015; Kijas et al 2016). It is possible that the modest sample size of the current study ( n  = 624) may have been a limiting factor in determining the imputation accuracy.…”

“…When genotype imputation is employed in livestock populations, multiple generations of ancestral genotyped individuals, and pedigree information are typically available. Likewise, in the study of Kijas et al (2016), multiple generations of genotyped individuals were available for the Tasmanian salmon breeding population. These genotyped multi-generation pedigrees are more amenable to resolving the phase of whole chromosome haplotypes, and therefore result in more accurate genotype imputation.…”

“…While research into imputation methods and their application to breeding programs has been extensive for livestock and crop species, they have not yet been widely tested in aquaculture species (Kijas et al 2016; Tsai et al 2016a). In part, this is due to the previous lack of genomic resources ( e.g.…”

“…This combination of tools now facilitates the study and use of genotype imputation approaches to improve genomic selection. The potential of genotype imputation in salmon was highlighted in a recent study by Kijas et al (2016), who imputed from low density (0.5–5 K) up to high density (78 K) with high accuracy (0.89–0.97) based on a multi-generation reference population.…”

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

“…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). Genetic diversity and frequencies of alleles in Tasmanian Atlantic salmon was lower than observed within European populations as revealed by analysis with 218 132 SNPs array (Kijas et al, 2016). In contrast to the European Atlantic salmon, the strength of observed LD was high at short distances and remained above background for marker pairs separated by chromosomal distances of hundreds of kb.…”