A novel intergenic dSH3-irr insertion mutation in Bradyrhizobium diazoefficiens causes its symbiotic incompatibility with soybean

Legumes and rhizobia collaborate to fix nitrogen in the host plant nodules, but some inadvertent mutation may generate unexpected symbiosis. We reported an altered host range symbiosis of Bradyrhizobium diazoefficiens USDA110 mutant dSH3_IP when associating with Sophora flavescens. Recently, we found SH3_IP cannot symbiose with original host soybean (Glycine max), and mutant influenced iron response regulator, which forms convergent gene pair with dSH3 in strain USDA110. The reason of symbiotic mismatching between soybean and dSH3_IP was explored through dual RNA-seq transcriptome and symbiotic characterization. We discovered dSH3_IP bacteroid assimilated more nutrition, triggered stronger immune responses and perturbed the symbiotic components in soybean nodules. Anyway, the incompatible symbiosis between dSH3_IP and soybean originated from intergenic insertion of dSH3-irr, which importance was not uncovered previously and may be used as a potential regulatory element in the future to regulate the SNF efficiency by artificial genetic design.