Nutritional and Biochemical Diversity in Beans Accessions from Three <i>Phaseolus</i> Species Using Multiomics Characterization

Comprehensive profiling of <i>Phaseolus</i> species revealed key biochemical differences relevant to nutrition and crop improvement. Genotyping confirmed species-level separation and two gene pools in <i>P. vulgaris</i>, with evidence of introgression. Proteomic analysis identified over 11100 proteins, with <i>P. vulgaris</i> showing the highest diversity. Functional proteins, storage proteins, digestive enzymes, and protease inhibitors were linked to amino acid composition and digestibility. All 20 standard and nine essential amino acids were detected, with <i>P. lunatus</i> displaying a distinct essentials profile. Metabolomics identified 6717 compounds, 57% shared across species, dominated by flavonoids, polyphenols, and terpenoids. <i>P. lunatus</i> had 592 unique metabolites, while <i>P. acutifolius</i> had 98, suggesting a conserved, drought-adapted metabolome. Although the total fat was low, <i>P. vulgaris</i> accessions had higher omega-3 content and favorable omega-6/omega-3. Ionomic profiling revealed a variation in Ca, Fe, and Zn, with one <i>P. vulgaris</i> line accumulating unsafe Pb and Cd. Multiomics enables identification of nutrient-rich, climate-resilient, food-safe accessions.