A bHLH transcription factor negatively regulates effective panicle number and grain yield by modulating auxin...

Rice yield remains limited by trade-offs between effective panicle number, grain number per panicle, and grain weight. However, the molecular mechanisms linking auxin transport to panicle formation in rice remain largely unknown. In this study, we conducted genome-wide association studies and identified Suppressor of Effective Panicle 1 (SEP1), which encodes a basic helix-loop-helix transcription factor that negatively regulates effective panicle number and yield. SEP1 directly activates OsPIN1a and OsPIN1b, two auxin efflux carriers that modulate auxin transport and distribution in tiller buds. Natural variation in SEP1 alters the transcriptional activation capacity of SEP1, and the SEP1^Hap2 allelic variant exhibits weaker transcriptional activation of OsPIN1a and OsPIN1b, correlating with its prevalence in Xian cultivars with relatively higher panicle numbers. Furthermore, we discovered that Gnp4/LAX PANICLE 2, a RING finger and WD40-associated ubiquitin-like domain-containing protein, destabilizes SEP1 via ubiquitin-proteasome degradation, fine-tuning auxin transport and tiller bud elongation. Notably, knockout of SEP1 in Xian/Geng cultivars significantly increases yield in field trials. Collectively, our study reveals a molecular mechanism for regulating rice yield and provides a practical strategy for breeding high-yield rice.