Abstract
Age at maturity is a key life‐history trait of most organisms. In anadromous salmonid fishes such as Atlantic Salmon (Salmo salar), age at sexual maturity is associated with sea age, the number of years spent at sea before the spawning migration. For the first time, we investigated the presence of two nonsynonymous vgll3 polymorphisms in North American Atlantic Salmon populations that relate to sea age in European salmon and quantified the natural variation at these and two additional candidate SNPs from two other genes. A targeted resequencing assay was developed and 1,505 returning adult individuals of size‐inferred sea age and sex from four populations were genotyped. Across three of four populations sampled in Québec, Canada, the late‐maturing component (MSW) of the population of a given sex exhibited higher proportions of SNP genotypes 54Thrvgll3 and 323Lysvgll3 compared to early‐maturing fish (1SW), for example, 85% versus 53% of females from Trinité River carried 323Lysvgll3 (n MSW = 205 vs. n 1SW = 30; p < .001). However, the association between vgll3 polymorphism and sea age was more pronounced in females than in males in the rivers we studied. Logistic regression analysis of vgll3 SNP genotypes revealed increased probabilities of exhibiting higher sea age for 54Thrvgll3 and 323Lysvgll3 genotypes compared to alternative genotypes, depending on population and sex. Moreover, individuals carrying the heterozygous vgll3 SNP genotypes were more likely (>66%) to be female. In summary, two nonsynonymous vgll3 polymorphisms were confirmed in North American populations of Atlantic Salmon and our results suggest that variation at those loci correlates with sea age and sex. Our results also suggest that this correlation varies among populations. Future work would benefit from a more balanced sampling and from adding data on juvenile riverine life stages to contrast our data.
Highlights
One of the largest contemporary challenges is to balance the availability of biological resources with an increasing demand for exploitation through a consistently growing world population (Ludwig, Hilborn, & Walters, 1993)
We assessed for the first time in North American Atlantic Salmon populations the natural variation at the previously identified loci associated with sea age
We developed targeted resequencing assays for the nonsynonymous mutations Met54Thrvgll3, Asn323Lysvgll3, and Val214Metakap11, as well as for SIX6TOP, and related genetic and phenotypic variation at the individual level in four Canadian rivers that varied in their 1SW to MSW ratios
Summary
One of the largest contemporary challenges is to balance the availability of biological resources with an increasing demand for exploitation through a consistently growing world population (Ludwig, Hilborn, & Walters, 1993). Variation in sea age in Atlantic Salmon has been attributed to a major selective sweep containing the candidate locus (vgll, vestigial-like family member 3, a 4-kb gene located on chromosome 25 consisting of 4 exons of 460, 440, 570, and 600 bp and no splicing variants) in European populations (Ayllon et al, 2015; Barson et al, 2015). We assessed for the first time in North American Atlantic Salmon populations the natural variation at the previously identified loci associated with sea age. The nonsynonymous single nucleotide variants in candidate genes vgll and akap were of particular interest because of their potential to alter protein function and structure and of their putative biological significance for sea age. The rationale was to find out whether these candidate SNPs existed in North American populations and how they associate with sea age
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