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

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 re-sequencing were examined in 50 individuals from four populations of Rhl with a depth of similar to 34x 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.