Genome-wide association study, population structure, and core germplasm construction of Rongjiang tea (Camellia yungkiangensis H. T. Chang)

Camellia yungkiangensis H. T. Chang (Rongjiang tea, RJ) is a distinctive wild tea germplasm characterized by its naturally low caffeine and high theobromine content, holding significant potential for breeding novel tea cultivars. However, the lack of genomic insights into its population structure and the genetic basis of key traits has hindered its effective utilization. In this study, a comprehensive genome-wide analysis of 121 RJ accessions was conducted using double-digest restriction-site-associated DNA sequencing (ddRAD-seq). A total of 1304,248 high-quality single-nucleotide polymorphisms (SNPs) were identified. Population structure analysis revealed that the RJ germplasm could be clearly divided into two genetic groups (GP1 and GP2) with moderate differentiation ( Fst = 0.327), exhibiting high genetic diversity (nucleotide diversity, pi = 0.190). A core germplasm collection comprising 36 accessions was established, capturing over 92% of the genetic diversity of the original population, thus providing a manageable resource for future breeding and research. Genome-wide association studies (GWAS) of 40 agronomic and biochemical traits identified 72 significant SNP markers associated with 15 traits, including leaf morphology (e.g., texture, margin) and key secondary metabolites (e.g., gallocatechin gallate, epigallocatechin gallate). Functional annotation of nearby candidate genes revealed their potential roles in stress response, plant development, and metabolic pathways. This study provides the first comprehensive genomic insights into the population genetics and trait associations of the low-caffeine RJ tea, establishing a valuable resource and genetic foundation for its conservation, marker-assisted breeding, and future genetic improvement.