A new method for studying population genetics of cyst nematodes based on Pool-Seq and genome-wide allele frequency analysis

Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of SNPs and allowed us to study the relationships between populations of different origins or pathotypes. Validation of the method on well-characterized populations also demonstrated that it was a powerful and accurate tool for population genetics. The genomewide allele frequencies of 23 populations of golden nematode, from nine countries and representing the five known pathotypes, were compared. A clear separation of the pathotypes and fine genetic relatio...胞囊线虫（Cyst nematodes）是一类重要的农业害虫，每年造成的经济损失高达数十亿美元。植物抗性是当前最为有效的防治手段，但该策略需对种群遗传学开展密切监测。当前用于胞囊线虫致病型鉴定（pathotyping）与基因型分型（genotyping）的技术普遍存在耗时长、成本高昂且精度不足的缺陷。本研究利用胞囊线虫的繁殖特性，开发了一套基于测序分型（genotyping-by-sequencing）与混合测序（Pool-Seq）的简易种群遗传分析流程。该方法可获得数千个单核苷酸多态性（SNPs）位点，能够用于分析不同来源或不同致病型的种群间亲缘关系。通过对特征明确的种群开展方法验证，结果表明该工具在种群遗传学研究中兼具高效性与准确性。本研究对来自9个国家、涵盖5种已知致病型的23个金线虫（golden nematode）种群的全基因组等位基因频率进行了比较分析，实现了不同致病型的清晰区分，并可解析精细的遗传关联……