Study on the characteristics of genetic diversity and population structure of a rare and endangered species of Rhododendron nymphaeoides (Ericaceae) based on microsatellite markers.

Background: Rhododendron nymphaeoides is explicitly listed as an endangered species in the "the International Union for Conservation of Nature's Red List (IUCN)", "The Red List of Rhododendrons", "Red List of China's Higher Plants" and "Threatened Species List of China's Higher Plants". It is also listed as a provincial-level key protected wild plant in Sichuan, with few individuals in the wild and significant conservation value. The genetic diversity and population structure have never been described, making it difficult to plan conservation strategies for this plant.

Results: This study utilized 15 pairs of microsatellite markers to examine the genetic diversity of 79 samples of R. nymphaeoides sourced from five different geographic populations. A total of 214 alleles were detected, with the average effective number of alleles (N) of 7.0324. The averages for the polymorphism information index (PIC) and expected heterozygosity (H) were 0.7832 and 0.8102, respectively, indicating that the R. nymphaeoides populations harbor a rich genetic information content, the genetic differentiation coefficients (F) average was 1.2607. There was high genetic diversity among populations, with average observed heterozygosity (H) and expected heterozygosity (H) values of 0.6375 and 0.6663, respectively, suggesting a degree of inbreeding within populations. Mantel test results showed a significant positive correlation between geographic distance and genetic distance amongst populations (r = 0.8456, P = 0.0021), which conforms to the isolation-by-distance (IBD) model. Due to geographical barriers, there is also a high level of genetic differentiation among populations, with an average genetic differentiation coefficient (F) of 0.2685. Analysis of molecular variance (AMOVA) indicated that the main source of molecular variance exists within populations (73%), rather than between populations (27%). There was higher historical gene flow (average = 1.0850) and lower contemporary gene flow (average = 1.2849), with seed and pollen dispersal being impeded. Under the Two-Phase Model (TPM) assumption, findings are consistent with the mutation-migration model, suggesting that there has been no genetic bottleneck. STRUCTURE analysis, principal coordinate analysis (PCoA), and UPGMA analysis all support the division of the five natural populations into three genetic clusters.

Conclusions: This is the first comprehensive analysis of the genetic diversity and population structure of the endangered plant R. nymphaeoides using microsatellite markers. The study results indicate that this endangered plant's natural populations maintain a high level of genetic diversity. Due to geographical barriers, there is also a high level of genetic differentiation, with the primary source of genetic variation originating within populations. There is higher historical gene flow and lower contemporary gene flow, with seed and pollen dispersal being obstructed. The five populations can be divided into three evolutionary units, for which corresponding conservation management units should be established. These findings will benefit the conservation and development of the species and provide a theoretical basis for further studies on its evolution and biogeography.