The Rhizobial Type III Effector NopD Regulates the GmPP2C-ENOD93 Axis to Control Symbiotic Nodulation and Yield in Soybean

Type III effector proteins (T3Es) are pivotal orchestrators of host–microbe interactions and essential for establishing symbiosis, thereby influencing soybean growth and productivity through modulation of symbiotic nitrogen fixation (SNF). While the central role of the T3E NopD in soybean SNF is recognized, its mechanistic underpinnings have remained elusive. In this study, we determined that GmPP2C, whose expression is regulated by NopD, serves as a regulator of nodulation. Overexpression of GmPP2C suppressed infection-thread formation and markedly reduced nodule number, whereas CRISPR/Cas9-mediated disruption enhanced infection events and partially rescued nodulation defects of NopD deficiency. Transcriptome profiling and complementation assays indicate GmPP2C inhibits nodulation by repressing ENOD93. Loss of GmPP2C increased per-plant yield without altering plant architecture or seed quality. These findings delineate the NopD–GmPP2C–ENOD93 regulatory module governing soybean nodulation and pinpoint GmPP2C as a compelling target for molecular breeding to enhance nitrogen-fixation efficiency and bolster crop yields.