Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP‐chip

Abstract

Genetic interactions between farmed and wild conspecifics are of special concern in fisheries where large numbers of domesticated individuals are released into the wild. In the Atlantic salmon (Salmo salar), selective breeding since the 1970's has resulted in rapid genetic changes in commercially important traits, such as a doubling of the growth rate. Each year, farmed salmon escape from net pens, enter rivers, and interbreed with wild salmon. Field experiments demonstrate that genetic introgression may weaken the viability of recipient populations. However, due to the lack of diagnostic genetic markers, little is known about actual rates of gene flow from farmed to wild populations. Here we present a panel of 60 single nucleotide polymorphisms (SNPs) that collectively are diagnostic in identifying individual salmon as being farmed or wild, regardless of their populations of origin. These were sourced from a pool of 7000 SNPs comparing historical wild and farmed salmon populations, and were distributed on all but two of the 29 chromosomes. We suggest that the generic differences between farmed and wild salmon at these SNPs have arisen due to domestication. The identified panel of SNPs will permit quantification of gene flow from farmed to wild salmon populations, elucidating one of the most controversial potential impacts of aquaculture. With increasing global interest in aquaculture and increasing pressure on wild populations, results from our study have implications for a wide range of species.

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

“…Therefore, the mining of highly informative SNPs from such high genomic resolution data sets is a common approach for developing reduced SNP assays capable of reliable ancestry estimation (Amirisetty, Khurana Hershey, & Baye, 2012; Judge, Kelleher, Kearney, Sleator, & Berry, 2017). While different metrics and approaches (e.g., Delta, I n , PCA, outlier tests) can be used for ranking SNPs by information content, the fixation index ( F ST ) has been the metric of choice perhaps due to its power (Ding et al., 2011; Karlsson, Moen, Lien, Glover, & Hindar, 2011; Wilkinson et al., 2011), especially when comparing only two highly divergent populations (Hulsegge et al., 2013). Furthermore, some metrics are correlated regarding information content, in particular those based on allele frequencies (Ding et al., 2011; Wilkinson et al., 2011).…”

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

“…Recent outlier locus studies of salmonid fishes have primarily compared wild populations at different spatial scales (Freamo, O'Reilly, Berg, Lien, & Boulding, 2011; Vasemägi & Primmer, 2005) or have correlated outlier loci of wild populations with specific environmental variables (Bourret, Kent, et al., 2013; Bourret, Dionne, Kent, Lien, & Bernatchez, 2013; Narum, Campbell, Kozfkay, & Meyer, 2010; Perrier, Bourret, Kent, & Bernatchez et al., 2013). Of more relevance to Atlantic salmon domestication are four outlier studies comparing aquaculture strains with wild populations from the same region as their putative founder population(s) (Gutierrez, Yáñez, & Davidson, 2016; Karlsson, Moen, Lien, Glover, & Hindar, 2011; Mäkinen, Vasemägi, McGinnity, Cross, & Primmer, 2015; Vasemägi, Nilsson, & Primmer, 2005). …”

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

“…Offering less variability per locus than STRs, SNPs provide a substantial number of advantages, namely: (i) reduced propensity for homoplasy due to lower mutation rates; (ii) higher density and more uniform distribution in genomes; (iii) suitability for successful high-throughput genotyping and straightforward comparability and transportability across laboratories and detection protocols; and (iv) highly successful application in fragmented DNA samples, for example, noninvasive and historical DNA (see Brumfield et al, 2003;Morin et al, 2004;Garvin et al, 2010 for reviews). Nonetheless, the successful application of genome-wide batteries of nuclear SNPs in studies of wild populations is still limited to a few cases such as wolf-like species for studying their evolutionary history (vonHoldt et al, 2011), wild sheep for detecting population structure and linkage disequilibrium (Miller et al, 2011) and wild Atlantic salmon for the differentiation of farmed and wild individuals (Karlsson et al, 2011). Recently, Monzón et al (2013) used species-diagnostic SNPs to quantify the relative contributions of parental populations and better understand the complex hybrid Toward a genome-wide approach for detecting hybrids R Oliveira et al ancestry of the northeastern coyote.…”