Integrating GBS-Derived SNP Markers with Phytochemical Profiling and Anti-Obesity Enzyme Inhibition in Phyllanthus emblica

Phyllanthus emblica L. is a nutraceutically important medicinal plant; however, the relationship between genetic variation and bioactive potential remains poorly understood. This study integrates genome-wide SNP analysis, phytochemical profiling, and functional bioassays to investigate cross-scale differentiation among fourteen cultivars. Genotyping-by-sequencing (GBS) identified 5644 high-quality SNPs from an initial dataset of 9018 SNPs, revealing moderate but structured genomic divergence (0.0275–0.0845). Phytochemical analysis of five commercial cultivars demonstrated significant variation (p < 0.05) in total phenolic content (6.58–15.53 mg GAE/gDW) and tannin content (284.52–333.81 mg TAE/gDW). Functional assays revealed strong anti-obesity potential, with crude extracts exhibiting superior α-glucosidase inhibition (up to 98.75%), while tannin-enriched extracts showed enhanced pancreatic lipase inhibition (up to 46.26%). Importantly, enzyme inhibition did not correlate directly with total phenolic or tannin content, indicating compound-specific bioactivity. LC-MS/QTOF analysis identified flavonoids (e.g., quercetin and kaempferol), phenolic acids, and other candidate metabolites potentially associated with enzyme inhibitory activity. These findings demonstrate a non-proportional association among genomic variation, metabolite composition, and functional bioactivity, suggesting that bioactivity may be influenced more strongly by compound-specific metabolite composition than by genome-wide similarity alone.