Genetic diversity of Rhododendron henanense subsp. lingbaoense revealed by whole-genome resequencing

Abstract Rhododendron henanense subsp. lingbaoense Fang (Rhl) is a subspecies endemic to China with important ornamental value. Recently, the Rhl population has been shrinking as a result of its limited distribution range, poor natural regeneration, and rising human exploitation. In this study, high-quality single nucleotide polymorphisms (SNPs) identified through whole-genome resequencing were examined in 50 individuals from four populations of Rhl with a depth of ~34× to evaluate genome-level diversity and population structure. Population structure profiling, principal component analysis, and phylogenetic analysis clustered the Rhl samples into two groups corresponding to their geographical distributions. Analysis of SNPs indicated that Rhl populations have high genetic diversity and little genetic differentiation. Additionally, demographic history indicated that all four populations of Rhl have experienced long-term population decline. The above findings showed that we should take action to protect this rare species.

摘要 河南杜鹃灵宝亚种（Rhododendron henanense subsp. lingbaoense Fang，简称Rhl）是中国特有的珍稀亚种，兼具重要的观赏价值。近年来，受限于其狭窄的分布范围、较弱的自然更新能力以及日益加剧的人类开发活动，Rhl种群规模正持续缩减。本研究通过全基因组重测序（whole-genome resequencing）技术鉴定得到高质量单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点，对采自4个种群的50株Rhl个体开展分析，测序深度约为34×，以此评估该物种的基因组水平遗传多样性与种群结构。种群结构分析、主成分分析（principal component analysis）与系统发育分析（phylogenetic analysis）结果显示，Rhl样本可依据地理分布划分为两个类群。单核苷酸多态性位点分析表明，Rhl种群具有较高的遗传多样性且遗传分化程度较低。此外，种群历史动态分析显示，所有4个Rhl种群均经历了长期的种群衰退过程。上述研究结果表明，亟需采取有效措施对这一珍稀物种开展保护工作。