Population genomic analysis and genome-wide association mapping of leaf morphology in Phyllanthus emblica L

Phyllanthus emblica L. is an important medicinal and edible fruit tree in tropical and subtropical regions, yet its population genetic structure and the genetic basis of key agronomic traits remain poorly understood. Here, we analyzed 112 accessions representing diverse germplasm collected from China and India. Using ddRAD-seq, we generated 73,405 high-quality SNPs to characterize population structure, genetic diversity, and the genetic architecture of leaf morphology. Population structure and phylogenetic reconstruction separated the accessions into two major genetic groups, which were further resolved into four subpopulations according to source. Genetic diversity varied markedly among groups, with one major source group retaining substantially higher diversity than the others, suggesting that the currently utilized germplasm of P. emblica has experienced uneven genetic utilization and limited systematic improvement. Genome-wide scans based on π ratios and F_ST identified multiple differentiated genomic regions, containing genes involved in protein turnover, stress response, hormone transport, and cell growth. We further conducted the first genome-wide association study of leaf traits in P. emblica and identified 85 loci significantly associated with leaf morphological variation. Several loci showed strong non-additive effects and clear allele-frequency differences among genetic groups. Candidate genes within these loci were functionally enriched in processes related to leaf development, leaf morphogenesis, auxin transport and hormone signaling, and cell wall biogenesis. Together, these results provide comprehensive insights into the population differentiation and leaf trait variation in P. emblica, and establish a valuable foundation for molecular marker-assisted breeding in this species.