Waters Charles D, Hard Jeffrey J, Brieuc Marine S O, Fast David E, Warheit Kenneth I, Knudsen Curtis M, Bosch William J, Naish Kerry A
School of Aquatic and Fishery Sciences University of Washington Seattle WA USA.
Conservation Biology Division Northwest Fisheries Science Center National Oceanic and Atmospheric Administration Seattle WA USA.
Evol Appl. 2018 Mar 5;11(6):853-868. doi: 10.1111/eva.12599. eCollection 2018 Jul.
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 () 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.
全基因组关联分析的一个新应用是利用与性状相关的基因座来监测保护策略对潜在适应性遗传变异的影响。例如，比较圈养来源和野生来源个体之间的适应性，并不能揭示圈养饲养如何影响适应性性状背后的遗传变异，或者哪些性状最容易受到驯化选择的影响。在这里，我们利用四代收集的数据，确定了与成年奇努克鲑（）的六个性状相关的基因座，然后确定了两种圈养饲养的替代管理方法如何影响这些基因座的变异。使用9108个限制性位点相关标记和随机森林（一种适用于多基因性状的方法），确定了与返回淡水产卵场的日期（返回时间）、返回时的长度和体重、成熟年龄、产卵时间和每日生长系数相关的基因座。性状相关基因座的定位、基因注释以及多项研究结果的整合揭示了涉及几个适应性相关性状的候选区域。然后，在两个孵化场种群之间比较了性状相关基因座的基因型，这两个种群来自同一来源，但现在作为独立品系进行管理，一个与野生种群整合，另一个与野生种群隔离。虽然在四代中未检测到大规模变化，但有许多区域的性状相关基因座与之前在这两个品系中确定的适应性分化特征重叠。许多区域，主要是与返回和产卵时间相关的基因座，在隔离品系中要么是独特的，要么差异更大，这表明这些性状可能正在对驯化选择做出反应。这项研究是首批利用基因组方法证明一种保护策略——管理基因流动——对性状相关且可能具有适应性的基因座有效性的研究之一。研究结果将促进开发特定性状的工具，以更好地监测圈养和野生种群的遗传变化。
