Chum Salmon Genetic Diversity in the Northeastern Pacific Ocean Assessed with Single Nucleotide Polymorphisms (SNPs): Applications to Fishery Management

We examined genetic diversity patterns among 55 collections of Chum Salmon from the northeastern Pacific Ocean using 89 single nucleotide polymorphisms (SNPs). The distribution of Chum Salmon samples extended from the Nass River along the coast of British Columbia and along the coast of Washington as far south as the Columbia River. Chum Salmon represented three previously defined run-groups: fall (primarily), summer, and winter. Genetic variation at SNP loci, as measured by FST, ranged from 0.002 to 0.279 over all collections and averaged 0.062 over all loci. Similar to the genetic patterns detected with microsatellites and allozymes, genetic variation followed a regional structure along geographic distance, with genetic diversity being highest in the north and decreasing southward, then increasing in and near the Columbia River. Within Puget Sound, Washington, genetic variation was structured further according to run timing (fall, summer, and winter) and shared ancestry. Simulations indicated that this suite of SNPs is powerful for identifying regional components in a Chum Salmon mixed fishery. Because of the transferability of SNP data, the growing SNP baseline for Chum Salmon will be useful for multiple agencies managing Chum Salmon around the Pacific Rim.Received December 19, 2014; accepted May 20, 2015

本研究利用89个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点，对东北太平洋海域55份狗鲑（Chum Salmon）采集样本的遗传多样性模式展开分析。样本的采集范围涵盖从纳斯河（Nass River）沿岸的不列颠哥伦比亚省海岸，向南延伸至华盛顿州沿岸直至哥伦比亚河（Columbia River）流域。所有采样的狗鲑可划分为3个此前已界定的洄游类群：秋季洄游（占比最高）、夏季洄游以及冬季洄游。以固定指数（fixation index, FST）衡量的SNP位点遗传变异水平，在所有采集样本中介于0.002至0.279之间，所有位点的平均变异水平为0.062。与微卫星标记及同工酶检测得到的遗传模式一致，遗传变异呈现出随地理距离变化的区域结构特征：北部的遗传多样性最高，向南逐渐降低，而在哥伦比亚河流域及其周边区域遗传多样性又出现回升。在华盛顿州普吉特海湾（Puget Sound）范围内，遗传变异进一步按照洄游时间（秋季、夏季、冬季）及共享祖先谱系进行划分。模拟实验结果表明，这套SNP位点组合可有效识别狗鲑混合渔业中的区域类群组分。由于SNP数据具有良好的可转移性，不断完善的狗鲑SNP基准数据集将对环太平洋地区多个狗鲑资源管理机构具有重要应用价值。收稿日期：2014年12月19日；录用日期：2015年5月20日