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

Life history variation acts as a buffer against stochastic environmental variation. When these variations represent distinct phenotypic optima for males and females there may be sexually antagonistic selection, and with high heritability, the opportunity for intralocus sexual conflict. The age at return migration for Chinook Salmon (Oncorhynchus tshawytscha), or age-at-maturity, is one such trait, since male age-at-maturity appears to experience a divergent selective landscape from females. We investigated the heritability of age-at-maturity, genomic basis of both sex and age-at-maturity, and potential for intralocus sexual conflict regarding age-at-maturity in stocks of Chinook Salmon from the Columbia River Basin representing the three major lineages present there. We found that heritability of age-at-maturity was positive for both sexes as well as in opposite sex comparisons but was generally stronger for males. We identified regions of the genome associated with sex across all three lineages, as well as large regions of a single chromosome, but which chromosome (17 or 18) varied across lineages as well as within the interior stream-type lineage. Regions of these same chromosomes were associated with age-at-maturity in natural-origin stocks of the interior lineages, but was associated with different chromosomes in natural-origin male and female interior stream-type fish. Analyses of genotyped markers, as well as multi-marker haplotypes, confirmed the association of chromosome 17 with age-at-maturity. Association of age-at-maturity with the sex-chromosome could mediate intralocus sexual conflict in these fish, but stocks which show polymorphism for the sex-chromosome could exhibit disjunction between complementary compensating modifiers on the X and Y chromosomes.

Methods
GT-seq on Illumina NextSeq 4000