Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as "integrated" with the founding wild stock, with ongoing gene flow, and as "segregated" with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F2 -F4 ; inbreeding F2 ). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.

中文翻译：

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奇努克鲑鱼在两种不同的孵化场管理制度中进行近亲繁殖的基因组和表型效应。

基因组学方法可以直接估计近交及其对适应性的影响。我们使用基于基因组的近交估计来调查它们与圈养的太平洋鲑鱼中的八个成年性状的关系，该鲑鱼被释放到野外。估计值还用于确定亲鱼替代管理方法是否降低了近亲繁殖的风险。具体而言，使用1100个未链接的限制性位点相关（RAD）位点比较从关系矩阵得出的成对关联性，并通过比较在两个奇努克鲑鱼孵化场中四代的个体近亲繁殖，通过比较观察到的纯合性和预期纯合性来估计来自同一来源。这些品系与已建立的野生种群“整合”，持续的基因流以及“分离的”种群进行管理 没有基因流动。虽然这两个系的第一代中的亲缘关系和近亲繁殖都增加了，这可能是由于孵化场启动引起的种群细分所致，但综合系在某些后代中的水平明显较低（关联性：F2-F4；近亲繁殖F2）。通常，尽管育种者的有效数量差异很大，但品系之间的近交相似。近亲繁殖不影响繁殖力，生殖力，返回时间，叉长，体重，条件因子和日生长系数。但是，F的每标准偏差增加（〜0.16）将产卵时间延迟1.75天。结果表明，综合管理可以减少近亲繁殖，但同时也表明，在一个隔离的孵化场中，繁殖者数量最大化，繁殖率相对较低。