Genomic data: Nutritional and Biochemical Diversity in Bean Accessions from Three Phaseolus Species Using Multi-Omics Characterization

Beans (Phaseolus spp.) are vital food crops, providing essential nutrients and playing a crucial role in global food security. This study presents a multi-omics characterization of 46 accessions from Phaseolus vulgaris (n=35), P. lunatus (n=7), and P. acutifolius (n=4), selected for their morphological diversity from the Future Seeds Genebank. We analyzed their biochemical composition to assess nutritional quality and adaptive traits using proteomics, metabolomics, fatty acid profiling (FAMEs), and ionomics. Proteomic analysis identified over 11,000 unique proteins, with P. vulgaris exhibiting notable diversity. Essential amino acid content varied among species, with P. lunatus showing distinct profiles. Network analysis revealed conserved metabolic pathways and stress-response proteins across species. Metabolomic profiling detected 6,717 metabolites, with flavonoids, polyphenols, and terpenoids predominating. P. lunatus displayed showed a substantial number of unique metabolites, while P. acutifolius exhibited a more conserved metabolic profile, likely linked to its drought tolerance. Fatty acid profiling confirmed a predominance of unsaturated fatty acids, with notable omega-3 content and a favorable omega-6/omega-3 ratio observed in P. vulgaris, suggesting potential health benefits. Ionomic analysis revealed statistically significant variations in mineral composition, with some accessions exhibiting elevated calcium, iron, or zinc levels. One P. vulgaris accession showed concerning levels of lead and cadmium, highlighting the need for further monitoring. This study provides critical insights into Phaseolus species'' nutritional and biochemical diversity, informing health, nutrition sciences and also breeding programs aimed at enhancing food quality, stress resilience, and sustainable crop production. The genotypic data was used to explore the genetic diversity of the nutritionally characterized materials. Methodology:Genomic DNA was extracted from pooled young leaf tissue of 25 individuals per accession following Correa et al., (2024). DNA from 43 of 46 accessions was processed, excluding accession G7309 and cultivars KATB1 and PALOMINO. Samples were genotyped with DArTseq at medium sequencing density (~1.25 million reads/sample). DNA was digested with PstI and MseI enzymes, and libraries were sequenced on an Illumina NovaSeq 6000. SNP calling was performed de novo using DArT’s DS14 software, aligning reads with a 2–3 nucleotide mismatch threshold. SNPs were assessed for read depth, call rate, reproducibility, and minor allele frequency (maf).