Phenotypic Diversity and Genome-Wide Association Analysis of Decaploid Camellia hainanica Germplasm from Hainan Island

Camellia hainanica is an endemic woody oil species from Hainan Island, but the phenotypic and genomic bases of its agronomic and ornamental variation remain poorly understood. Here, 31 phenotypic traits were evaluated in 100 accessions from Changjiang, Hainan, and flower-diameter variation guided the selection of 30 accessions for whole-genome resequencing and genome-wide association analysis. Coefficients of variation ranged from 8.81% to 56.85%, with flower density and first-branch height showing the greatest variation. Cluster analysis separated five groups with contrasting phenotypic characteristics, including groups characterized by large fruits and thick pericarps and ornamental groups characterized by dense flowering and large flowers. Flow cytometry classified the 30 selected accessions as decaploid, and resequencing showed that most variants occurred in non-coding regions. Genome-wide association analysis identified 9 significant SNPs (−log10(P) > 8.63) associated with petal number, flower diameter, locule number, and flower density (3, 1, 3, and 2 SNPs, respectively), including a flower-diameter signal on GWHERBT00000039 and signals on GWHERBT00000008 and GWHERBT00000036. These results integrate phenotypic and genomic evidence for C. hainanica and provide germplasm resources and preliminary candidate regions for further validation and ornamental improvement alongside fruit-trait evaluation.