Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits

Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, 3 of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease-resistance. Parallel comparisons using a wild, non-founder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.

比较基因组扫描（Comparative genome scans）可用于识别推测处于选择压力下的染色体区域，但无法直接鉴定性状。在以提升产量为目标的强人工选择的近期驯化种群中，目标性状的鉴定成功率往往更高。本研究利用北美大西洋鲑鱼6K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据集，对养殖群体（圣约翰河种群）与其推测野生创始群体（托比克河种群）之间分化程度极高的基因组区域进行定位。首先，借助STRUCTURE软件检测出携带部分欧洲血统的混合个体并将其从数据集中移除；随后，筛选出在养殖群体与创始群体间呈现极端分化的异常位点。所有Arlequin分析方法均鉴定出包含17个异常位点的重叠子集，其中3个位点同时被BayeScan软件鉴定到。多数异常位点紧邻候选基因，部分则位于已发表的生长、食欲、成熟度或抗病性相关数量性状位点（Quantitative Trait Loci, QTL）区域内。以野生非创始群体（斯蒂韦阿克河种群）开展平行比对分析，仅得到1个重叠的异常位点以及1个已知的成熟度相关QTL。本研究结论表明，将近期驯化的养殖群体与其野生创始群体进行比较基因组扫描，可助力鉴定受强人工选择的目标性状的候选基因。