Genome-wide association study of common bean (Phaseolus vulgaris L.) unveils novel loci governing root-to-seed zinc allocation

Abstract

Micronutrient malnutrition is a global health concern, highlighting the importance of essential micronutrients like zinc in human diet, and enhancing zinc concentration in staple crops like common beans is a promising strategy. In this study, we performed genome-wide association studies to identify genetic loci associated with Zn accumulation in a diverse panel of 177 Turkish common bean landraces and six commercial varieties. Field trials were conducted across two locations over two years to assess Zn concentration variation. The results revealed significant genetic variability, with Zn concentrations ranging from 11.6 to 105.3 mg/kg. Two significant marker-trait associations (MTAs) were identified on chromosomes Pv06 and Pv08, with loci linked to Zn translocation and brassinosteroid-mediated cell-wall remodeling. Candidate genes, Vacuolar Iron Transporter 1 (VIT1) and Wall-Associated Kinase-Like 4 (WAKL4), were implicated in Zn homeostasis and distribution. In silico transcriptomics analysis further validated the role of these genes under Zn-deficient conditions in Arabidopsis. Protein-protein interaction (PPI) network analysis identified key regulatory pathways, including ZIP transporters, heavy metal ATPases, and cell-wall modification enzymes. These findings provide valuable genetic insights for biofortification strategies, facilitating the development of Zn-enriched common bean cultivars to enhance nutritional security. The study underscores the potential of GWAS in identifying stable genetic markers for Zn biofortification, paving the way for future breeding efforts aimed at improving dietary Zn intake through staple crops.

Keywords: Common bean; GWAS; Malnutrition; Zn biofortification.

Fig. 1

Frequency distribution of the Zn concentration of the studied Turkish common bean germplasm.

Fig. 2

Pearson correlation analysis for the studied environment.

Fig. 3

Constellation plot for Zn concentrations in Turkish common bean germplasm.

Fig. 4

Manhattan plot for Zn concentration in Turkish common bean germplasm.

Fig. 5

Physical map of chromosomes and physical base pair distance (bp) displaying the significantly associated markers to Zn concentration.

Fig. 6

PPI network of the core group of DEGs, VIT1 and WAKL4. VIT1 and WAKL4 are presented in red while the core group of DEGs were presented in gray.

Fig. 7

GO enrichment of WAKL4 and VIT1 PPI networks. (a) Biological process and molecular function ontologies of WAKL4 PPI network. (b) Biological process and molecular function ontologies of VIT1 PPI network.

Fig. 8

In silico expression levels of WAKL4 and VIT PPI networks in Zn deficiency and Zn homeostasis-related mutants. Expression levels of WAKL4 and VIT protein networks under zinc deficiency were analyzed in the roots and shoots of wild-type Col-0 after 7 days (GSE77286) and 21 days (GSE111443) in hydroponic conditions. Expression patterns in bzip19bzip23 and hma2hma4 double mutant roots and shoots were also evaluated. A heat map illustrating these expression patterns was generated using the “plotty” function in the ggplot2 package in R, utilizing Euclidean distance hierarchical clustering.