Nutritional and Biochemical Diversity in Beans Accessions from Three Phaseolus Species Using Multiomics Characterization

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