Genomic SSR markers elucidate genetic architecture and phenotypic trait associations in Rhododendron Linnaeus

The genus Rhododendron Linnaeus, comprising over 1,000 species distributed across temperate and alpine regions of Asia, Europe, and North America, holds significant value for its ornamental characteristics, ecological adaptability, and medicinal potential. Despite its importance, the genus presents persistent challenges in taxonomic classification and phylogenetic resolution, compounded by the current insufficiency of genomic SSR markers (g-SSRs) for comprehensive genetic studies. In this study, we conducted the first comprehensive genome-wide identification of SSR markers using whole-genome sequencing data of Rhododendron × pulchrum Sweet. Our analysis identified 324,674 SSR loci across the 509.49 Mb genome. From 190 synthesized primer pairs, 124 (65.3 %) demonstrated successful amplification, with 30 (24.2 %) showing high polymorphism. These polymorphic g-SSR markers generated 597 polymorphic bands, exhibiting polymorphic information content (PIC) values ranging from 0.240 to 0.949 (mean = 0.748), reflecting substantial genetic diversity among the studied accessions. Genetic structure, cluster analysis, and principal coordinates analysis of 96 Rhododendron accessions revealed three distinct clades that correlated with geographic origins, hybrid relationships, and utilization values. Association mapping identified 17 SSR markers significantly linked (P < 0.05) to 10 key morphological traits, explaining 5.68-13.35 % of phenotypic variance. The number of significantly associated markers for each trait was as follows: leaf length (1), remontant (3), corolla lobe shape (2), initial flowering period (3), flower diameter (3), leaf shape (1), petal type (3), petiole length (2), stamen number (4), and flower shape (1). This study provides valuable genomic resources for marker-assisted breeding and establishes a foundation for systematic characterization, conservation, and utilization of Rhododendron genetic resources.