Armstrong Ellie E, Li Chenyang, Campana Michael G, Ferrari Tessa, Kelley Joanna L, Petrov Dmitri A, Solari Katherine A, Mooney Jazlyn A
School of Biological Sciences, Washington State University, Pullman, Washington, USA.
Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, Riverside, California, USA.
Mol Ecol Resour. 2025 Apr;25(3):e14048. doi: 10.1111/1755-0998.14048. Epub 2024 Nov 29.
Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.
尽管在过去十年中测序成本大幅降低，但基因检测板因其成本效益和在各种样本类型中的灵活性而仍然具有相关性。特别是，单核苷酸多态性（SNP）检测板在保护应用中越来越受到青睐。SNP检测板经常被使用，是因为它们具有适应性、对低质量样本有效，以及在种群监测和法医学方面具有成本效益。然而，选择用于种群归属和个体识别的诊断性SNP可能具有挑战性。SNP选择不当的后果是检测板效能不足、结果不准确和金钱损失。在这里，我们开发了一种新颖且用户友好的SNP选择流程（mPCRselect），可用于选择用于种群归属和/或个体识别的SNP。mPCRselect允许任何拥有足够SNP水平数据的研究人员为一个受保护的二倍体物种设计一个成功且具有成本效益的SNP检测板。
