Ghd7‑triggered transcriptional regulation for synergistically improving rice eating quality and yield

Improving both eating quality and yield remains a major challenge in rice breeding. Here, we identify Ghd7 as the causal gene underlying the grain amylose content QTL qAC7 and reveal Ghd7–triggered transcriptional regulation that balances starch and protein to coordinate yield and quality. Ghd7 transcriptionally activates PCF3 and exhibits dominant epistasis over it. A natural TA/T variant in PCF3 determines its DNA-binding affinity: the PCF3‑T allele strongly represses OsNF-YC4, increasing starch and reducing protein in grain, whereas PCF3‑TA fails to exert this repressive effect. Haplotype and evolutionary analyses show that the favorable allele PCF3‑T has not been selected. Combining Ghd7‑1/4 with PCF3‑T further enhances both yield and eating quality. Our findings uncover a possible transcriptional cascade and highlight Ghd7‑1/4 and PCF3‑T as promising targets for simultaneously improving rice yield and quality. Rice breeders struggle to boost yield and eating quality simultaneously as the two traits often work against each other. Here, the authors identify a CCT domain transcription regulator encoding gene Ghd7 in determining rice grain amylose content and functioning in balancing starch and protein to coordinate yield and quality.