Differences in genetic architecture between continents at a major locus previously associated with sea age at sexual maturity in European Atlantic salmon

Wild Atlantic salmon populations show heritable variation in the proportion of fish that mature early, as grilse, after one winter at sea. Grilse are undesirable in aquaculture, and in hatchery-supported recreational fisheries, but their frequency could be reduced using marker-assisted selection. SNP markers near vgll3 on Ssa25 are associated with 30-40% of the variation in early maturity in European (EU) Atlantic salmon. Our goal was to determine whether this association occurred in a major North America (NA) aquaculture strain from the Saint John River (SJR). Grilse reared entirely in freshwater tanks were heavier and longer two years post-hatching than normally-maturing post-smolts of the same sex. We first genotyped a large sample from a single year-class (YC-80) on a custom 80 SNP assay that included the four SNPs near vgll3. When no associations were found, our study was extended to include a genome-wide analysis (GWA) of another year-class using a custom 50 K SNP chip (YC-50 K). The GWA found no associations on Ssa25 but did detect a SNP with experiment-wide significance on its homeolog, Ssa21. The new SNP explained 6% of the variance in grilsing. Its association was not a by-product of the greater weights and lengths of grilse. GWA showed that the top SNP for weight was on Ssa01/23. The early-maturing allele at vgll3 had a higher frequency of homozygotes in European populations than in the North American populations. We conclude that differences in the genetic architecture of traits between highly diverged populations, such as these from different continents, can require re-estimation of marker-trait relationships.