Buso Pauline, Diblasi Célian, Manousi Domniki, Kwak Jun Soung, Vera-Ponce de Leon Arturo, Stenløkk Kristina, Barson Nicola, Saitou Marie
IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France.
Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
Genome Biol Evol. 2025 Apr 3;17(4). doi: 10.1093/gbe/evaf063.
Domestication and artificial selection for desirable traits have driven significant phenotypic changes and left detectable genomic footprints in farmed animals. Since the 1960s, intensive breeding has led to the rapid domestication of Atlantic salmon (Salmo salar), with multiple independent events that make it a valuable model for studying early domestication stages and the parallel evolution of populations of different origins subjected to similar selection pressures. Some aquatic species, including Atlantic salmon, have undergone whole-genome duplication (WGD), raising the possibility that genetic redundancy resulting from WGD has contributed to adaptation in captive environments, as seen in plants. Here, we examined the genomic responses to domestication in Atlantic salmon, focusing on potential signatures of parallel selection, including those associated with WGD. Candidate genomic regions under selection were identified by comparing whole-genome sequences from aquaculture and wild populations across 2 independently domesticated lineages (Western Norway and North America) using a genome-wide scan that combined 3 statistical methods: allele frequencies (FST), site frequency (Tajima's D), and haplotype differentiation (XP-EHH). These analyses revealed shared selective sweeps on identical SNPs in major histocompatibility complex (MHC) genes across aquaculture populations. This suggests that a combination of long-term balancing selection and recent human-induced selection has shaped MHC gene evolution in domesticated salmon. Additionally, we observed selective sweeps on a small number of gene pairs in homeologous regions originating from WGD, offering insights into how historical genome duplication events may intersect with recent selection pressures in aquaculture species.
对理想性状的驯化和人工选择推动了养殖动物显著的表型变化，并在其基因组中留下了可检测的印记。自20世纪60年代以来，密集育种导致了大西洋鲑（Salmo salar）的快速驯化，多个独立事件使其成为研究早期驯化阶段以及不同起源种群在相似选择压力下平行进化的宝贵模型。包括大西洋鲑在内的一些水生物种经历了全基因组复制（WGD），这增加了一种可能性，即如在植物中所见，WGD导致的基因冗余有助于在圈养环境中的适应。在这里，我们研究了大西洋鲑对驯化的基因组反应，重点关注平行选择的潜在特征，包括与WGD相关的特征。通过使用结合了三种统计方法（等位基因频率（FST）、位点频率（Tajima's D）和单倍型分化（XP-EHH））的全基因组扫描，比较来自2个独立驯化谱系（挪威西部和北美）的养殖和野生种群的全基因组序列，确定了受选择的候选基因组区域。这些分析揭示了养殖种群中主要组织相容性复合体（MHC）基因相同单核苷酸多态性（SNP）上的共享选择性清除。这表明长期平衡选择和近期人为诱导选择的结合塑造了驯化鲑鱼中MHC基因的进化。此外，我们在源自WGD的同源区域的少数基因对上观察到了选择性清除，这为历史基因组复制事件如何与水产养殖物种近期的选择压力相互作用提供了见解。
