Conservation genomics of Atlantic salmon: SNPs associated with QTLs for adaptive traits in parr from four trans-Atlantic backcrosses

European Atlantic salmon (Salmo salar) differ in skin pigmentation and shape from the North American lineage of Atlantic salmon but the genetic basis of these differences are poorly understood. We created four large (N=300) backcross families by crossing F1 hybrid male siblings to two females from the European and two from the North American aquacultural strains. We recorded 15 morphological landmarks and two skin pigmentation, three growth and three condition traits on parr. The backcross families were genotyped for at least 129 SNPs (single nucleotide polymorphisms) within expressed sequence tags (ESTs) spaced throughout the Atlantic salmon linkage map. The high polymorphism and low rates of crossover in our hybrid sires provided enough statistical power to detect 79 significant associations between SNP markers and quantitative traits after experiment-wide permutation analysis for all families within traits. Linkage group AS22 contained a quantitative trait loci (QTL) for parr mark number; its homolog AS24 contained a large QTL, which explained 26% of the phenotypic variance in parr mark contrast. We found 25 highly significant QTLs for body shape and fin position on seven different linkage groups, and 16 for growth and condition on six different linkage groups. QTL(s) for pectoral fin position, caudal peduncle position, late parr growth and condition index were associated with an SNP on linkage group AS1, which was linked to the sex-determining locus. Our work adds to the evidence that much of the variation in growth rate, shape and skin pigmentation observed among Atlantic salmon parr from different natal streams is genetic.