Abstract

Establishing the symbiosis between legumes and nitrogen-fixing rhizobia requires the precise modulation of auxin levels. However, our understanding of auxin’s regulatory roles, particularly rhizobia-derived auxins, remains limited. Our study reveals that the auxin biosynthesis gene YUC2a is essential for the spatiotemporal control of nodule development in soybean (Glycine max). This process is orchestrated by three transcription factors: Nuclear Factor-YA9 (NF-YA9), Lateral Organ Boundaries Domain 41 (LBD41), and Nodule Inception 1a (NIN1a). In the early stages of nodulation, rhizobial auxin stimulates NF-YA9 expression, NF-YA9 then activates YUC2a expression in the cortical cell layer, establishing optimal auxin levels for nodule initiation. In the middle stages, rhizobial auxin elevates LBD41 expression, and LBD41 suppresses YUC2a to control auxin levels, ensuring proper rhizobia colonization. In the late stages, rhizobial auxin inhibits NIN1a expression, which increases YUC2a expression in nitrogen-fixing symbiosomes, fine-tuning optimal auxin levels for nodule maturation. Disruption of YUC2a and its homologs impairs cell division in nodule primordia, reducing nodule density and nitrogen fixation capacity. Conversely, cortex-specific overexpression of YUC2a promotes nodule formation but inhibits rhizobia colonization. This dynamic auxin regulation optimizes nodule development in soybean, revealing rhizobia-derived auxin's critical role in nitrogen-fixing symbiosis.