Natural Negative Feedback Loops Confer Indica-Japonica Differentiation for Grain Size Homeostasis in Rice

Organ size homeostasis plays vital roles in maintaining the normal growth and development in both animals and plants. Grain size is an important agronomic trait for stable yield, quality, domestication, and breeding in crops, but the molecular mechanism underlying final size homeostasis remains unclear. Here, we identified three genes, OsGRX8, OsbZIP47 and OsbZIP08, underlying grain-length variation by genome-wide association study (GWAS) in rice. We confirmed that OsGRX8, OsbZIP47 and OsbZIP08 interact with each other and transcription factors OsbZIP47 negatively and OsbZIP08 positively regulate the expression of the downstream glutaredoxin-encoding gene OsGRX8. The binding ability of OsbZIP08 on the promoter of OsGRX8 in indica is higher than that in japonica, leading the differential expression of OsGRX8 between two subspecies. We further revealed a natural negative feedback regulatory mechanism for grain size homeostasis: OsGRX8 controls the reduction modification of OsbZIP47 thereby increasing OsbZIP47-OsbZIP08 interaction in a redox-dependent way or directly interacts with OsbZIP08 in a redox-independent way to inhibit the transcriptional activity of OsbZIP08 on OsGRX8. Finally, we revealed that two self-regulatory haplotypes (SRHs), caused by co-selected variations of the three genetically unlinked genes which formed the negative feedback loops, showed distinctive indica-japonica differentiation and large genetic contribution to key yield traits. Our findings provided the evolutional OsGRX8-(OsbZIP47)-OsbZIP08-OsGRX8 regulatory loops for synergistically controlling grain size homeostasis by fine-tuning OsGRX8 self-expression, offering a novel case for uncovering QTL interactions underlying genetic diversity of important traits in crops.