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

Abstract

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 ¼ 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.

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

“…(b) F CT . (c) QTL (with number showing chromosome and the letter the study “a” Baranski et al., 2010; “b” Boulding et al., 2008; “c” Gutierrez et al., 2012 males time 3, “d” QTL s from Gutierrez et al., 2012 females time 3. “e” Gutierrez et al., 2012 females time 4, “f” Gutierrez et al., 2012 Males time 4, “g” Houston et al., 2009; “h” Petersen et al.…”

“…eF1 hybrids (2001) and F1 backcrosses (2005) between NA and EU (Mowi) subspecies of Salmo salar (Boulding et al., 2008). …”

“…We attempted to identify outlier loci underlying traits known to have been under artificial selection by comparing their map position with that of published quantitative trait loci (QTL) for one classic quantitative trait—growth rate (Baranski, Moen, & Våge, 2010; Boulding et al., 2008; Gutierrez et al., 2012; Houston et al., 2009; Pedersen et al., 2013; Reid, Szanto, Glebe, Danzmann, & Ferguson, 2005; Tsai et al., 2015). The challenge was that, with the exception of Gutierrez et al.…”

Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss)

“…In the first case, a QTL for both BW and K detected on Atlantic salmon linkage group AS-8qa (markers Ssa401UoS, BHMS313A) appears to share homology to the short arm of rainbow trout linkage group RT-23 (i.e., RT-23p)[41]. Similarly, BW and K QTL have been localized to the duplicated homeologous linkage groups AS-22/24 [43]. These homeologs in Atlantic salmon share homology to the duplicated homeologs RT-7/15 [38].…”

Genotypic and phenotypic correlates with proliferative kidney disease-induced mortality in Atlantic salmon

“…Interestingly, Gilbey (2003) reported the markers Ssa14, Ssa48, and μ20.19 to be significantly associated with QTL affecting fish size during development from parr to smolt in backcrosses between Scottish and Canadian Atlantic salmon. Additionally, Boulding et al (2008) found SNP markers on linkage groups AS9, AS18, and AS22 (derived from ASalBASE; http://www. asalbase.org) to be associated with weight and condition factor and markers on AS10 and AS12 to be linked to morphometric variables in trans-Atlantic crosses of Atlantic salmon.…”