Data from: Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies

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 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.全基因组关联分析（Genome-wide Association Analyses）的一项创新性应用，是借助性状关联位点（trait-associated loci）来监测保护策略对潜在适应性遗传变异的影响。例如，仅比较圈养个体与野生个体的适合度，无法揭示圈养繁育如何影响适合度性状背后的遗传变异，也无法明确哪些性状最易受到驯化选择的作用。本研究借助四代繁育收集的数据，鉴定了成年奇努克鲑（Oncorhynchus tshawytscha）6个性状的关联位点，进而明确两种不同的圈养繁育管理方案如何影响这些位点的遗传变异。本研究利用9108个限制性酶切位点关联标记（Restriction Site-associated Markers）与随机森林（Random Forest）模型，鉴定出与淡水产卵洄游日期（洄游时间）、洄游时体长与体质量、成熟年龄、产卵时间以及日生长系数相关的位点，该方法适用于多基因性状（polygenic traits）的分析。通过性状关联位点的定位、基因注释以及多研究结果的整合，本研究鉴定出多个与适合度相关性状相关的候选基因组区域。随后，本研究对两个源自同一亲本群体但现已作为独立品系管理的孵化场种群的性状关联位点基因型进行了比较：其中一个品系与野生种群混合繁育，另一个则与野生种群隔离繁育。尽管在四代繁育过程中未检测到全基因组范围的显著变化，但多个基因组区域的性状关联位点与此前在两个品系中鉴定到的适应性分化信号存在重叠。多数（主要包含与洄游时间及产卵时间相关位点的）基因组区域仅在隔离品系中存在，或在隔离品系中分化程度更高，这表明这些性状可能正受到驯化选择的作用。本研究是首批利用基因组学方法，验证管理性基因流（managed gene flow）这一保护策略对性状关联且潜在具有适应性的位点的作用效果的研究之一。本研究结果将推动性状特异性监测工具的开发，以更好地监控圈养与野生种群的遗传变化。