Genetic diversity, population structure, and genome-wide association study show genetic differentiation and trait improvements in Alpinia oxyphylla Miquel

Alpinia oxyphylla Miquel, a medicinally and culinarily valuable Zingiberaceae plant, faces germplasm challenges due to limited genetic insights. To address this gap and provide a theoretical basis for its germplasm innovation and molecular breeding, we systematically analyzed 220 A. oxyphylla germplasms from five Chinese provinces via whole-genome resequencing to characterize genetic diversity, population structure, and trait-associated loci. Resequencing generated 3.96 Tb of clean data, identifying 112,638,653 SNPs, among which 4604,480 were high-quality SNPs and indels with uneven chromosomal distribution (chromosome 11 had the most SNP loci: 6222,032, average density 59.07 SNPs/kb; chromosome 18 had the fewest: 3485,184, average density 60.27 SNPs/kb). Phylogenetic, population structure, and principal component analysis (PCA) analyses revealed six geography-linked subpopulations, with Hainan Island as the main genetic diversity center (θπ = 5.81 ×10⁻⁴-5.94 ×10⁻⁴ vs. Guangdong’s 3.2 ×10⁻⁴) and domestication hub (faster LD decay, r2 = 0.2). Genome-wide association studies (GWAS) identified 21 significant SNPs linked to fruit number per panicle (ranging from 2 to 45 among germplasms, coefficient of variation 38.86 %), highlighting candidate genes (e.g., ethylene-responsive transcription factor). For medicinal traits, GWAS linked yakuchinone A and nootkatone to cinnamoyl-CoA reductase (phenylpropanoid pathway) and flavin-containing monooxygenase (FMO), respectively. Heterologous expression of AoFMO in tobacco confirmed its role in nootkatone biosynthesis. This study provides a genomic foundation for A. oxyphylla breeding, highlights Hainan as a germplasm resource center, and identifies yield and pharmacodynamic trait-related genes, offering a framework for underexplored medicinal plant molecular breeding.