Abstract
A novel application of genomewide 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 for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site‐associated markers and random forest, an approach suitable for polygenic traits. Mapping of trait‐associated loci, gene annotations, and 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 previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to or more divergent in the segregated 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 promote the development of trait‐specific tools to better monitor genetic change in captive and wild populations.
Highlights
There is considerable interest in applying the results of genomewide association analyses to conservation and management (Bernatchez, 2016; Bernatchez et al, 2017; Funk, McKay, Hohenlohe, & Allendorf, 2012; Garner et al, 2016; Harrisson, Pavlova, Telonis-Scott, & Sunnucks, 2014; Hoffmann et al, 2015; Pearse, 2016; Shafer et al, 2015)
Markers associated with key phenotypic traits can provide further insights into the mechanisms by which adaptive variation is maintained in populations (Bernatchez, 2016) and may assist the delineation of conservation (Brieuc et al, 2015; Funk et al, 2012; Garner et al, 2016) and fisheries management units (Bernatchez et al, 2017)
Our findings demonstrate the future utility of genomic-based approaches in conservation monitoring
Summary
There is considerable interest in applying the results of genomewide association analyses to conservation and management (Bernatchez, 2016; Bernatchez et al, 2017; Funk, McKay, Hohenlohe, & Allendorf, 2012; Garner et al, 2016; Harrisson, Pavlova, Telonis-Scott, & Sunnucks, 2014; Hoffmann et al, 2015; Pearse, 2016; Shafer et al, 2015). Captive breeding remains one of the primary options for the conservation of threatened populations and species (e.g., Conde, Flesness, Colchero, Jones, & Scheuerlein, 2011; Griffiths & Pavajeau, 2008; Horne, Hervert, Woodruff, & Mills, 2016; Landa et al, 2017). This approach is controversial, because associated genetic and phenotypic changes may decrease the fitness of captive individuals when they are released into the wild and, reduce restoration success (Christie, Ford, & Blouin, 2014; Frankham, 2008; Jule, Leaver, & Lea, 2008). Trait-based monitoring could inform policy decisions that aim to minimize negative effects of captive breeding, including practices to reduce domestication selection
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
