Loci and natural alleles for leaf length and width revealed by a genome wide association study in adzuki bean

Leaf size and shape are crucial for photosynthesis and consequently, yield in adzuki beans (Vigna angularis L.). This study utilized 321 adzuki bean germplasm accessions (100 wild/semi-wild and 221 cultivated varieties) to analyze leaf length (LL) and leaf width (LW) phenotypes across two locations (Beijing and Anhui, China) from 2014 to 2017. Genome-wide association studies (GWAS) were then employed to elucidate the underlying genetic mechanisms.

The results demonstrated that cultivated adzuki beans exhibited significantly larger leaves (LL: 6.64-10.84 cm; LW: 5.22-9.23 cm) compared to wild populations (LL: 5.65-6.21 cm; LW: 4.52-4.83 cm). Improved cultivars consistently displayed greater leaf width across multiple growing seasons than landraces, highlighting the effects of domestication and breeding improvement on leaf morphology. A significant geographic effect was also observed, with adzuki beans grown in Beijing generally exhibiting larger leaves than those grown in Anhui, indicating the influence of environmental factors. GWAS identified 100 quantitative trait loci (QTLs) associated with leaf morphology across the entire population (72 for LL and 28 for LW), distributed across chromosomes 1-11, with chromosome 4 showing the highest number of QTLs (16). Eight candidate genes were selected based on gene annotation, cross-species homology comparisons, and haplotype analysis. For example, Vigan01g073100, a candidate gene for LL, encodes a receptor protein kinase involved in regulating cell division and elongation, thus impacting organ development. Vigan07g22880, a candidate gene for LW, encodes an auxin efflux carrier, and its haplotype variation (Val-Ala substitution) led to significantly wider leaves in cultivated populations compared to wild populations. Haplotype analysis revealed genetic differentiation of these genes between cultivated and wild subpopulations, with some advantageous haplotypes (e.g., Hap.1 of Vigan02g058600) showing significant associations with leaf morphology phenotypes.

This study presents the first comprehensive analysis of the genetic basis of leaf morphology in adzuki beans, identifying key candidate genes involved in cell proliferation, auxin transport, and transcription regulation. These findings provide valuable genetic resources and theoretical support for understanding the molecular mechanisms of leaf development and improving leaf morphology in adzuki bean breeding programs.