Abstract
BackgroundUnderstanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. In Atlantic salmon, age at maturity is an important life history trait that affects factors such as survival, reproductive success, and growth. Furthermore, age at maturity can seriously impact aquaculture production. Therefore, characterizing the genetic architecture that underlies variation in age at maturity is of key interest.ResultsHere, we refine our understanding of the genetic architecture for age at maturity of male Atlantic salmon using a genome-wide association study of 11,166 males from a single aquaculture strain, using imputed genotypes at 512,397 single nucleotide polymorphisms (SNPs). All individuals were genotyped with a 50K SNP array and imputed to higher density using parents genotyped with a 930K SNP array and pedigree information. We found significant association signals on 28 of 29 chromosomes (P-values: 8.7 × 10−133–9.8 × 10−8), including two very strong signals spanning the six6 and vgll3 gene regions on chromosomes 9 and 25, respectively. Furthermore, we identified 116 independent signals that tagged 120 candidate genes with varying effect sizes. Five of the candidate genes found here were previously associated with age at maturity in other vertebrates, including humans.DiscussionThese results reveal a mixed architecture of large-effect loci and a polygenic component that consists of multiple smaller-effect loci, suggesting a more complex genetic architecture of Atlantic salmon age at maturity than previously thought. This more complex architecture will have implications for selection on this key trait in aquaculture and for management of wild salmon populations.
Highlights
Understanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow
For single nucleotide polymorphisms (SNPs) with a minor allele effect that increased the odds of early maturation, the odds ratios (OR) ranged from 1.01 to 3.07 (0- to 3-fold)
The potential role of six6 in local adaptation may explain why its association signal was lost after population stratification correction in Barson et al [1]. This highlights the importance of examining genotype–phenotype associations within single populations, in addition to multi-population studies. These findings suggest that the role of the six6 gene in determining age at maturity may vary among populations, but it should not be ruled out as a candidate gene for maturation in Atlantic salmon
Summary
Understanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. The minimum effect size that can be detected increases [9] This limitation likely led to a bias in the reported distribution of the genetic architecture for quantitative traits in wild species, for which either very large effect loci are reported [1], or a highly polygenic architecture is concluded due to a lack of any significant association being detected [10]. Variability in age and size at maturity is thought to have evolved in order to maximize fitness in highly variable river and ocean environments [23] This variability aids in population stability in the face of environmental change and stochasticity via the portfolio effect—a phenomenon where biological diversity within a species reduces population size fluctuations [24]
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