Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar

A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%). These markers included the sdy partial gene product to determine genetic sex, as well as three additional modules comprising SNPs for assessing neutral genetic variation (NSNP = 150), examining functional genetic variation associated with sea age at maturity (NSNP = 5), and for performing genetic subpopulation assignment (NSNP = 61). The assay was primarily developed to monitor long-term genetic changes in S. salar from the Teno River, but modules are likely suitable for application in a wide range of S. salar populations. Furthermore, the fast and versatile assay development pipeline offers a strategy for developing targeted sequencing assays in any species.

本研究针对离子激流（Ion Torrent）Ion PGM测序平台开发了一款基因分型检测方法，可快速且经济高效地对大西洋鲑（Salmo salar）中通过全基因组SNP芯片先期筛选得到的关键单核苷酸多态性（single nucleotide polymorphisms, SNPs）开展靶向基因分型。该方法包含简单的多重聚合酶链式反应（multiplex-polymerase chain reaction, PCR）引物设计步骤，随后进行两轮离子激流Ion PGM测序，以实证评估大规模多重扩增体系中标记物的扩增效能，并在必要时对标记物进行优化或剔除。在初始测试的282对引物中，217对成功实现扩增，扩增成功率超过75%，表现优异。该套标记物包含用于鉴定遗传性别的sdy部分基因产物，同时涵盖三个功能模块：分别为NSNP=150的中性遗传变异评估用SNP位点、NSNP=5的成熟海龄相关功能遗传变异分析用SNP位点，以及NSNP=61的遗传亚群分型用SNP位点。本检测方法最初主要用于监测泰诺河（Teno River）流域大西洋鲑的长期遗传变化，但其模块大概率可适用于绝大多数大西洋鲑种群。此外，该快速且通用的检测开发流程可为其他物种的靶向测序检测方法开发提供可行策略。