Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations. Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3). Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.

中文翻译：

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对四个驯化虹鳟鱼种群 (Oncorhynchus mykiss) 共有的正向和平衡选择特征进行全基因组检测


随着时间的推移，进化过程会在基因组上留下足迹。高度纯合的区域可能对应于有利等位基因的正选择，而杂合区域的维持可能是由于平衡选择现象。我们分析了来自四个不相连的国内虹鳟鱼种群的 176 条鱼的数据，这些鱼是使用高密度 Axiom Trout 基因分型 665K 单核苷酸多态性阵列进行基因分型的，其中 20 条来自美国，156 条来自三个法国品系。使用基于纯合性和扩展单倍型纯合性运行的方法，我们检测到了这四个群体中的选择特征。包括 253 个基因的 9 个基因组区域在所有四个群体中被鉴定为处于正选择状态。大多数位于 2 号染色体上，但也位于 12、15、16 和 20 号染色体上。此外，包含 29 个基因的 4 个杂合区域被推定为四个群体也共享平衡选择。它们位于 10、13 和 19 号染色体上。无论这些区域是纯合还是杂合，在每个区域中，我们都检测到了几个在脊椎动物中高度保守的基因，因为它们在细胞和核组织、胚胎发育中发挥着关键作用。 ，或免疫力。我们确定了与虹鳟鱼适应性相关的新候选基因，以及之前确定为正选择的 17 个基因，其中 10 个在其他鱼类中（auts2、atp1b3、zp4、znf135、igf-1α、brd2、col9a2、mrap2） 、pbx1 和 emilin-3）。 利用来自不同来源的不相关种群的材料，我们能够绘制这些虹鳟鱼种群之间共享的正选择特征的全基因组图谱，并确定几个可能处于平衡选择的区域。这些结果为未来研究驯化过程中遗传多样性和基因组进化的动态提供了宝贵的资源。