Integrated analysis of phenotypic and SSR data reveals the genetic structure differentiation of wild Rhododendron mariae Hance populations in Guangdong and the driving factors for conservation planning

Introduction Rhododendron mariae Hance is a traditional medicinal plant in the Lingnan region widely used for treating respiratory diseases. However, its wild germplasm resources are threatened by overharvesting and habitat destruction. To provide a scientific basis for conservation strategies, this study systematically investigated the genetic diversity and population structure of wild R. mariae populations. Methods We analyzed eight wild populations in Guangdong Province by integrating phenotypic traits and SSR molecular markers. Phenotypic diversity was assessed using the coefficient of variation (CV), nested analysis of variance, and Neighbor-Joining (NJ) clustering. Concurrently, SSR markers were employed to evaluate genetic diversity parameters (including number of alleles and Shannon’s information index), and population structure was further elucidated through genetic distance clustering, Principal Component Analysis (PCA), and Structure analysis. Results Phenotypic variation was primarily attributed to differences among populations (intraclass correlation coefficient ICC > 0.7 for all traits except leaf area). The GLS (CV = 0.26) and FLS (CV = 0.20) populations exhibited the most prominent phenotypic diversity. Molecular analysis confirmed high population differentiation (Fst = 0.1963). The DJS, FLS, XXC, and GLS populations displayed significantly higher genetic diversity parameters, identifying them as core germplasm resources. Both Structure and PCA analyses supported the division into three genetic subgroups, with GLS and XXC being highly differentiated populations, while others showed genetic admixture, highlighting the role of geographical isolation Conclusion Integrating both lines of evidence, the FLS, GLS, XXC, and DJS populations were identified as priority conservation units due to their rich genetic diversity and uniqueness at both phenotypic and molecular levels. This study provides a critical scientific foundation for the conservation and sustainable utilization of wild R. mariae germplasm resources.