Genome-wide association for precocial maturation in juvenile male Spring Chinook salmon (Oncorhynchus tshawytscha)

Abstract Fish conservation through hatchery supplementation involves maintaining population structure similar to natural populations. High proportions of precociously mature two-year-old male Chinook salmon (i.e. minijacks) observed in hatchery populations reduces the number of anadromous males in the population. Understanding the genetic architecture of this trait could be used to adjust hatchery practices to reduce precocious maturation. The genetic control of this trait was examined in a hatchery population of Columbia River Spring Chinook salmon over two replicate year classes (brood years BY2018 and BY2019). Genome wide allele frequencies from millions of single nucleotide polymorphisms (SNPs) were compared between immature males and minijacks identified by plasma 11-ketotestosterone levels. Genome scans identified 1,917 SNPs within and between brood years. Within brood years, there were two and four notable peaks of significance in BY2018 and BY2019, respectively. Combining the same phenotypes between brood years resulted in candidate regions on multiple chromosomes associated with precocial maturation as a minijack. The strongest signals from the combined year analysis were on chromosomes 15 (617 SNPs, five genes) and 18 (922 SNPs, nine genes). Individuals representing the extreme ends of the phenotypic distributions had notable signals on chromosomes 17 and 18, which have been previously identified as age-of-maturity candidates in this species. These analyses indicated that genetic control of minijack maturation is influenced by many regions of small effect including markers that may be sex-linked on chromosomes 17 and 18. The regions identified in this study will aid in conservation and broodstock monitoring relating to abundances of minijacks in hatchery origin populations.