Early survival in Atlantic salmon is associated with parental genotype at loci linked to timing of maturation late in life

Abstract

AbstractGenomic regions with large phenotypic effects often contain genes that may have critical roles as early as development, with potentially broad physiological and morphological effects across later life stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon (Salmo salar), variation in two large effect genomic regions,six6andvgll3, is linked to both age at maturity (a life-history trait with strong fitness effects) and several physiological and behavioural traits in early life. Here, by analysing offspring DNA samples from an experiment where fertilized eggs from known families of wild Atlantic salmon were planted into natural streams with manipulated nutrient levels, we tested if genetic variation in these loci is associated with survival in early life. We found that higher early life survival was linked to the genotype associated with late maturation in thevgll3locus, but with early maturation in thesix6locus. These effects were significant only in high-nutrient streams, while we observed no effect in low-nutrient streams. We also showed that the differences in early survival were not explained by additive effects of genes in the offspring generation, but by maternal genotypes in thesix6locus, and by both parents’ genotypes in thevgll3locus. These results suggest that indirect genetic effects are significant determinants of early life survival associated with these loci. Our study demonstrates an intriguing case of how large effect loci in the wild might exhibit complex fitness associations across life stages, and indicates that predicting evolutionary dynamics in the wild is likely difficult.