Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods

Abstract

Characterizing the role of different mutational effect sizes in the evolution of fitness-related traits has been a major goal in evolutionary biology for a century. Such characterization in a diversity of systems, both model and non-model, will help to understand the genetic processes underlying fitness variation. However, well-characterized genetic architectures of such traits in wild populations remain uncommon. In this study, we used haplotype-based and multi-SNP Bayesian association methods with sequencing data for 313 individuals from wild populations to test the mutational composition of known candidate regions for sea age at maturation in Atlantic salmon (Salmo salar). We detected an association at five loci out of 116 candidates previously identified in an aquaculture strain with maturation timing in wild Atlantic salmon. We found that at four of these five loci, variation explained by the locus was predominantly driven by a single SNP suggesting the genetic architecture of this trait includes multiple loci with simple, non-clustered alleles and a locus with potentially more complex alleles. This highlights the diversity of genetic architectures that can exist for fitness-related traits. Furthermore, this study provides a useful multi-SNP framework for future work using sequencing data to characterize genetic variation underlying phenotypes in wild populations.

Fig. 1. Plots displaying single SNP associations (black points) and haplotype associations (red line) scores from hapQTL for the five candidate regions with Bayes factors greater than 3.

Y-axis shows the Bayes factor indicating the association strength. X-axis shows the position on the respective chromosomes.

Fig. 2. PiMASS results for each of the tested candidate regions.

A ssa06:27541960-28218141, B ssa09:10915066-11415066, C ssa09:24636574-25136574, D ssa21:49390687-49890687, and E ssa25:28389273-28889273. Plots display the following results for each candidate region: (i) posterior inclusion probability (PIP) indicating the probability of a SNP being included in a model explaining sea age at maturity variation, (ii) truncated distribution of the number of SNPs included in a model explaining sea age at maturity variation, and (iii) distribution of proportion of variance explained per recorded iteration (2500). Red line indicates the median proportion of variance explained.