Barney Bryan T, Munkholm Christiane, Walt David R, Palumbi Stephen R
Department of Biology, Hopkins Marine Station, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA, 92950, USA.
Gloucester Marine Genomics Institute, 55 Blackburn Center, Gloucester, MA, 01930, USA.
BMC Genomics. 2017 Mar 31;18(1):271. doi: 10.1186/s12864-017-3660-3.
Atlantic cod (Gadus morhua), is known to vary genetically across the North Atlantic, Greenland, and Newfoundland. This genetic variation occurs both spatially and temporally through decades of heavy fishing, and is concentrated in three linkage disequilibrium blocks, previously defined by pedigreed linkage mapping analysis. Variation within these genomic regions is correlated with both seawater temperature and behavioral ecotype. The full extent and nature of these linkage groups is important information for interpreting cod genetic structure as a tool for future fisheries management.
We conducted whole genome sequencing for 31 individual cod from three sub-populations in the Gulf of Maine. Across the genome, we found 3,390,654 intermediate to high frequency Single Nucleotide Polymorphisms (SNPs). We show that pairwise linkage analysis among these SNPs is a powerful tool to detect linkage disequilibrium clusters by recovering the three previously detected linkage groups and identifying the 1031 genes contained therein. Across these genes, we found significant population differentiation among spawning groups in the Gulf of Maine and between Georges Bank and Gulf of Maine. Coordinated divergence among these genes and their differentiation at both short and long spatial scales suggests that they are acting as linked supergenes in local adaptation of cod populations.
Differentiation between SNPs in linkage disequilibrium blocks is the major signal of genetic differentiation between all groups tested within the Gulf of Maine. Our data provide a map of genes contained in these blocks, allowing an enhanced search for neutral genetic structure for demographic inference and fisheries modeling. Patterns of selection and the history of populations may be possible to identify in cod using this description of linkage disequilibrium blocks and future data sets to robustly separate neutral and selected genetic markers.
已知大西洋鳕鱼（Gadus morhua）在北大西洋、格陵兰岛和纽芬兰岛的基因存在差异。这种基因变异在几十年的过度捕捞过程中在空间和时间上都有发生，并且集中在三个连锁不平衡区域，这些区域先前是通过系谱连锁图谱分析确定的。这些基因组区域内的变异与海水温度和行为生态型都相关。这些连锁群的完整范围和性质是解释鳕鱼遗传结构作为未来渔业管理工具的重要信息。
我们对缅因湾三个亚种群的31条个体鳕鱼进行了全基因组测序。在整个基因组中，我们发现了3390654个中高频单核苷酸多态性（SNP）。我们表明，这些SNP之间的成对连锁分析是检测连锁不平衡簇的有力工具，通过恢复先前检测到的三个连锁群并识别其中包含的1031个基因。在这些基因中，我们发现缅因湾产卵群体之间以及乔治斯浅滩和缅因湾之间存在显著的种群分化。这些基因之间的协同分化以及它们在短距离和长距离空间尺度上的差异表明，它们在鳕鱼种群的局部适应中作为连锁的超级基因发挥作用。
连锁不平衡区域内SNP之间的差异是缅因湾内所有测试群体之间遗传分化的主要信号。我们的数据提供了这些区域中包含的基因图谱，有助于更有效地搜索用于人口统计学推断和渔业建模的中性遗传结构。利用这种连锁不平衡区域的描述以及未来的数据集，有可能在鳕鱼中识别选择模式和种群历史，以可靠地区分中性和选择的遗传标记。
