Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 9169
Title: Genome-wide association analyses of fitness traits in captive reared Chinook salmon: Applications in evaluating conservation strategies
Author: Charles D. Waters, Jeffrey J. Hard, M. S. O. Brieuc, D. E. Fast, Kenneth I. Warheit, Curtis M. Knudsen, W. J. Bosch, Kerry A. Naish
Publication Year: 2018
Journal: Evolutionary Applications
Abstract:

A novel application of genome-wide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha), and then determined how two alternative management approaches affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return time), fork length, weight, age at maturity, spawn time, and daily growth coefficient were identified using 9108 restriction site-associated markers and an analytical approach suitable for polygenic traits, Random Forest. Mapping of trait-associated loci, gene annotations, and the integration of results across multiple studies revealed candidate regions involved in several fitness-related traits. Genotypes at trait-associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad scale change was detected across four generations, there were numerous regions where trait-associated loci overlapped with signatures of adaptive divergence from previous studies. Many of these regions, primarily with loci linked to return and spawn time, were either unique to, or more divergent in, the segregated hatchery line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait-associated ¿ and potentially adaptive ¿ loci. The results will help promote the development of trait-specific tools to better monitor genetic change in captive and wild populations.

Description:

This paper uses a set of genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait-associated ¿ and potentially adaptive ¿ loci in a population of a threatened species, Columbia River spring Chinook salmon. The analyses are intended to promote the development of trait-specific tools to better monitor genetic change in captive and wild populations.

Theme: Recovery and rebuilding of marine and coastal species
Foci: Evaluate the effects of artificial propagation on recovery, rebuilding and sustainability of marine and anadromous species.