| Summary: | Large effects loci often contain genes with critical developmental functions with potentially broad effects across life-stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci, six6 and vgll3 , is linked to age at maturity, and several physiological and behavioural traits in early life. By genotyping the progeny of wild Atlantic salmon that were planted into natural streams with nutrient manipulations, 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 the vgll3 , but with early maturation in the six6 locus. These effects were significant in high-nutrient, but not in in low-nutrient streams. The differences in early survival were not explained by additive genetic effects in the offspring generation, but by maternal genotypes in the six6 locus, and by both parents' genotypes in the vgll3 locus. Our results suggest that indirect genetic effects by large-effect loci can be significant determinants of offspring fitness. This study demonstrates an intriguing case of how large-effect loci can exhibit complex fitness associations across life stages in the wild and indicates that predicting evolutionary dynamics is difficult. Funding provided by: Academy of Finland Crossref Funder Registry ID: https://ror.org/05k73zm37 Award Number: 353388 Funding provided by: Academy of Finland Crossref Funder Registry ID: https://ror.org/05k73zm37 Award Number: 325964 Funding provided by: Academy of Finland Crossref Funder Registry ID: https://ror.org/05k73zm37 Award Number: 348965 Funding provided by: European Research Council Crossref Funder Registry ID: https://ror.org/0472cxd90 Award Number: 322784 Funding provided by: European Research Council Crossref Funder Registry ID: https://ror.org/0472cxd90 Award Number: 834653
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