The Genetic Basis of Age at Maturity in Hatchery and Natural Origin Chinook Salmon (Oncorhynchus tshawytscha)

Chinook salmon exhibit tremendous variation in age and size at sexual maturity. Hatchery and natural origin fish often have very different maturation schedules, with early maturation and “jacking” occurring in hatchery males relative to natural origin males.  Although environmental factors contribute to variation in age at maturity, substantial heritable genetic variation for age at sexual maturity also exists, though the number and distribution of associated genetic loci underlying this trait are unknown. We perform a genome-wide association analysis of thousands of RAD-tag SNP markers in two populations of Chinook salmon to examine the genome regions associated with age at sexual maturity and jacking in natural and hatchery origin males.  Analyses include 15,329 SNP loci in 428 individuals from the Wenatchee River and 12,882 loci in 391 individuals from Johnson Creek, both tributaries of the Columbia River (11,251 shared). Relative genomic position and distribution of loci were determined by aligning loci against a published Chinook salmon linkage map, and loci were further annotated for linkage to functional genes by alignment to related salmonid genome and transcriptome databases. Our results contribute to an understanding of the genetic basis to age at maturity and will assist conservation and management goals for Pacific salmon.