This study supports the idea that the evolution of type III secretion system (T3SS) is one of the factors that controls
Vigna radiata
–bradyrhizobia symbiosis. Based on phylogenetic tree data and gene arrangements, it seems that the T3SSs of the Thai bradyrhizobial strains SUTN9‐2, DOA1, and DOA9 and the Senegalese strain ORS3257 may share the same origin. Therefore, strains SUTN9‐2, DOA1, DOA9, and ORS3257 may have evolved their T3SSs independently from other bradyrhizobia, depending on biological and/or geological events. For functional analyses, the
rhcJ
genes of ORS3257, SUTN9‐2, DOA9, and USDA110 were disrupted. These mutations had cultivar‐specific effects on nodulation properties. The T3SSs of ORS3257 and DOA9 showed negative effects on
V. radiata
nodulation, while the T3SS of SUTN9‐2 showed no effect on
V. radiata
symbiosis. In the roots of
V. radiata
CN72, the expression levels of the
PR1
gene after inoculation with ORS3257 and DOA9 were significantly higher than those after inoculation with ORS3257
ΩT3SS
, DOA9
ΩT3SS,
and SUTN9‐2. The T3Es from ORS3257 and DOA9 could trigger
PR1
expression, which ultimately leads to abort nodulation. In contrast, the T3E from SUTN9‐2 reduced
PR1
expression. It seems that the mutualistic relationship between SUTN9‐2 and
V. radiata
may have led to the selection of the most well‐adapted combination of T3SS and symbiotic bradyrhizobial genotype.