Mitigating the effects of escaped farmed Atlantic salmon: Combining single nucleotide polymorphisms, lipid acid profiling, and statistical methods to trace escaped salmon back to origin

Abstract

Comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10 samples/populations. Global FST ranged from 0.033-0.115 and -0.002-0.316 for the 14 STR and 300 SNP loci respectively. The best 15 SNPs (30 alleles) gave a similar level of selfassignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment. In 2003, a common garden experiment was initiated in the Guddal river to evaluate and compare the performance of Farm, Wild and Hybrid Salmon in the river habitat. Significant differences in growth, body shape (condition factor) and mortality were reported between these three types (Skaala et al. 2012). The aims of this two years post-doctoral project was to provide better understanding on the genetic bases for the observed differences in growth, body shape and mortality between wild, farm, and hybrid salmon. Genome scan for QTL affecting length (L), weight (W), and condition factor (CF) revealed several genomic regions significantly affecting these three phenotypes. The genomic positions of these QTL as well as proportion of the trait variance explained are identified. Weight is significantly affected by two QTL: one on chromosome 2 that explains 8.4% of the observed weight variance in our population, and one on chromosome 11 responsible for 7.7% of observed weight variance. Collectively, these two QTL are responsible for 14.8% of the weight variance. QTL position on chromosome 2 appears to be a particularly interesting region that both affects growth and survival in the river habitat. Moreover, this genomic region displays a strong reduction in genetic variability in the farm population whereas genetic variability is still very high in the wild population. QTL on chromosome 2 appears thus to be a genomic region potentially bearing the footprint of ongoing domestication in salmon. This study represents the first investigation into the genetic architecture underlying the relative performance of farmed and wild Atlantic salmon in the natural habitat.