A genome-wide association study on resistance to iron deficiency chlorosis in soybean using whole genome resequencing data

Abstract

Iron deficiency chlorosis (IDC) is a nutritional stress prevalent in high pH and high calcium soils, significantly reducing soybean productivity. This study aimed to identify genetic variants associated with IDC resistance using high-resolution markers. In this research, we analyzed 426 G. max accession using 1.4 M markers, incorporating comprehensive IDC phenotyping across four environments and accounting for spatial field variation. Additionally, we examined the phylogenetic relationships within the panel and the distribution of IDC resistance. Our analysis identified six significant loci associated with IDC resistance, including three previously mapped regions and three novel associations. Furthermore, we found one association in chromosome 13 for IDC recovery, located near a previously mapped maturity locus. Notably, one of the significant hits for IDC resistance found in chromosome 5 was co-localized within a previously fine-mapped 75 kb region. Within this region, we conducted candidate locus association and analyzed the effects of different haplotype combinations involving transposable elements and TATA box insertions for potential epistatic interactions. We found that lines carrying the ‘Fiskeby III’ type alleles with the significant SNP, L1-13, and TATA insertions exhibited significantly lower IDC scores than those carrying the Wm82 type alleles. We also validated a putative candidate gene using CRISPR-Cas9 knock-out experiments but found no significant phenotypic differences between the knock-out line and the wild type. Finally, these findings reinforce the importance of chromosome 5 QTL in IDC resistance. However, our results suggest that the genetic mechanism is very complex for this trait, warranting further investigation to fully understand the underlying genetics behind this QTL.