Data from: Multiplex preamplification PCR and microsatellite validation allows accurate single nucleotide polymorphism (SNP) genotyping of historical fish scales

Incorporating historical tissues into the study of ecological, conservation, and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for preexisting DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for preexisting DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect preexisting DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Preexisting contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The potential for automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA.

将历史组织样本纳入生态学、保护生物学与资源管理相关研究议题，可通过深化对自然种群演化过程及人为活动影响的认知，拓宽种群遗传学研究的范畴。针对历史样本与低质量样本开展基因分型（genotyping）的工作长期面临诸多挑战，包括模板DNA含量极低，以及样本间存在预先存在的DNA污染的风险。本文介绍了一套两步法流程，可实现两大目标：（1）以高通量方式对大量历史来源的低质量鱼鳞样本实现精准基因分型；（2）筛查样本中是否存在预先存在的DNA污染。首先，我们阐明了针对45个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点开展高效多重预扩增聚合酶链式反应（PCR），可在后续对红大马哈鱼（Oncorhynchus nerka）个体历史鱼鳞样本的SNP基因分型反应中，获得高准确率的基因型数据，且失败率与错误率均控制在较低水平。其次，我们验证了该方法可经改造用于扩增微卫星位点（microsatellite loci），以检测样本中预先存在的DNA污染。本研究共对760份历史鱼鳞样本与182份当代鳍剪样本开展了基因分型及污染筛查。结果显示，历史样本与当代样本的基因分型失败率及错误率均极低，且二者水平相近。通过对扩增后的微卫星位点进行筛查，研究团队成功在21%的历史样本中鉴定出预先存在的DNA污染。该实验流程具备自动化潜力，失败率与错误率低，且可同时对预扩增及后续基因分型反应进行多重化处理，这些优势使其非常适合高效对大量可能受污染的低质量DNA来源样本开展基因分型工作。