Unveiling genetic loci and natural alleles for seed iron accumulation in adzuki bean via genome-wide association study​

BACKGROUND: Iron is an essential micronutrient for both plant growth and human health and iron deficiency affects over 30% of the global population. Adzuki bean (Vigna angularis), an iron-rich legume, serves as a strategic dietary iron source to combat global iron deficiency anemia. Despite its nutritional significance, the genetic basis of iron accumulation in legumes remains unexplored. RESULTS: This study addresses this gap by performing the first genome-wide association study (GWAS) targeting seed iron content in a diverse panel of 320 adzuki accessions (220 cultivated, 100 wild/semi-wild), representing seven genetic subpopulations across East Asia. Multi-environment phenotyping (2014–2019) revealed extensive iron content variation, with wild adzuki bean exhibiting significantly higher concentrations than cultivated types. No significant difference was found between landraces and improved cultivars. GWAS identified 39 quantitative trait loci (QTLs) associated with iron content, distributed across chromosomes 1 to 11, with chromosomes 3 and 10 harboring the most loci. Twelve candidate genes were prioritized within QTL intervals, including genes involved in iron transport (e.g., Vigan01g178400, homologous to iron-regulated transporter IRT1), metabolism (e.g., Vigan07g168200, a nicotinamidase aminotransferase), and regulation (e.g., Vigan03g004100, a bZIP transcription factor). Haplotype analysis of key genes uncovered functional variations: for example, VaIRT1 haplotypes with a promoter SNP showed significant differences in iron content, likely due to altered cis-acting elements affecting gene expression. CONCLUSIONS: This study provides the first genetic blueprint for iron biofortification in adzuki bean, identifying key haplotypes and regulatory variants that modulate iron homeostasis. These findings clarify the genetic architecture of iron accumulation in adzuki bean and provide valuable resources for breeding high-iron varieties to address global iron deficiency.