Genetic architecture of iron and zinc concentration and identification of candidate markers for biofortification in common bean (Phaseolus vulgaris L.) populations

Abstract Background Iron (Fe) and zinc (Zn) deficiencies remain important nutritional challenges, particularly where common bean ( Phaseolus vulgaris L.) is an important dietary staple. Understanding the genetic basis of seed micronutrient accumulation can facilitate development of nutritionally improved cultivars. This study aimed to identify genomic regions and marker–trait associations associated with seed Fe and Zn concentrations in a genetically diverse collection of common bean germplasm from Burundi using genome-wide association analysis. Results Significant phenotypic variation was observed for both micronutrients, with Fe showing greater dispersion than Zn. Broad-sense heritability ranged from 0.73 to 0.81 for Fe and 0.70–0.81 for Zn, while genotypic effects accounted for 85.24% and 84.61% of total variation, respectively. Fe and Zn exhibited moderate positive phenotypic (rp = 0.58) and genetic (rg = 0.55) correlations, indicating potential for simultaneous improvement. Principal component analysis revealed pronounced differentiation between Andean ( n = 62) and Mesoamerican ( n = 101) gene pools, with PC1 explaining 44.12% of molecular variation. Linkage disequilibrium remained extended, with predicted r² = 0.2717 at 250 kb. Genome-wide association analysis identified no SNPs reaching the Bonferroni threshold for either trait. For Fe, 20 SNPs were significant under the Benjamini–Hochberg false discovery rate, and 16 Fe-associated SNPs were retained for detailed interpretation and candidate-gene analysis. These loci were distributed across Pv01, Pv04, Pv06, and Pv07 and individually explained 12.61–16.28% of phenotypic variance. In contrast, no significant or suggestive marker–trait associations were detected for Zn. LD-informed candidate-gene analysis identified 145 unique putative candidate genes within ± 100-kb regions surrounding the 16 Fe-associated SNPs. These genes represented diverse functional categories, including metal/mineral homeostasis, signalling, transcriptional regulation, redox processes, protein processing, RNA-related processes, and photosynthesis/chloroplast functions. Conclusion The findings demonstrate substantial genetic variation and complex genetic control of seed Fe and Zn accumulation in Burundi common bean germplasm. The identified Fe-associated SNPs and candidate genes provide useful genomic resources for Fe biofortification, whereas the absence of detectable Zn associations highlights the potential value of genomic selection and multi-locus approaches for Zn improvement. Independent validation and functional characterization will be necessary to confirm the stability and biological relevance of the identified Fe-associated regions.