Heritability and genomic basis of age-at-maturity in Chinook Salmon

Intrapopulation variation in the age at return and reproduction of Chinook Salmon (Oncorhynchus tshawytscha), or age-at-maturity, acts as a buffer against stochastic environmental variation. We investigated the genetic component of this trait by estimating the heritability of age-at-maturity and the genomic basis of both sex and age-at-maturity in stocks representing the 3 major lineages of the Columbia River Basin. We found that heritability of age-at-maturity was generally stronger for fathers with male offspring (mean h2 = 0.37, SD = 0.164) than mothers with female offspring (mean h2 = 0.29, SD = 0.077), fathers with female offspring (mean h2 = 0.29, SD = 0.155), or mothers with male offspring (mean h2 = 0.25, SD = 0.100). We identified several regions of the genome that were consistently associated with sex across all 3 lineages that included expected sex-chromosomes (Chr17 and 18), but also putative copies of sex-linked regions in several autosomal chromosomes. Furthermore, large regions of the same 2 chromosomes (17 and 18) were associated with age-at-maturity in a lineage-specific manner. Patterns of genotype by phenotype with multi-marker haplotypes confirmed the association of SNPs on chromosome 17 with both sizes (fork length) in natural-origin males from the 2 interior lineages, and age-at-maturity (ocean age) in interior ocean-type males, but not in females. Further studies will be necessary to verify other candidate regions and polygenic effects on size and age-at-maturity in this species. Although the rearing environment and growth play a major role in age-at-maturity, these results provided evidence for genetic heritability and candidate genes associated with this trait that will assist in monitoring genetic variation to maintain life history variation in Chinook Salmon.