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

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.