Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n=1485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation-based evaluations...

个体归属分析与遗传混合分析是当代野生动物与渔业管理领域的常用技术手段。尽管微卫星位点（microsatellite loci）单个位点可检测的等位基因数量优势突出，但其在个体归属分析应用中的局限性正日益凸显。不过，下一代测序（next-generation sequencing）技术结合新型生物信息学工具，可实现大规模微卫星位点的同步基因分型，为个体归属与遗传混合分析带来了全新的应用契机。
本研究通过检索已发表的大西洋鲑基因组序列，共鉴定出706个微卫星位点，最终筛选得到101个分布于全基因组的微卫星标记组合（平均每条染色体3.4个位点）。
研究使用加拿大拉布拉多沿海地区35个大西洋鲑种群的1485个个体样本（该区域内该物种的遗传分化水平较低），这套标记组合共检测到844个等位基因，平均每个位点8.4个等位基因。基于模拟的评估……