Shuai Nie^†, Luo Chen^†, Leilei Kong^†, Minhua Zheng, Jingfang Dong, Song Bai, Dilin Liu, Shaohong Zhang, Hao Chen, Haifei Hu, Xin Luan*, Junliang Zhao* and Wu Yang*

Plant Biotechnology Journal

Abstract

Head milled rice rate (HMRR) is a critical trait determining rice yield and economic value, yet its genetic basis remains poorly understood. Here, through genome-wide association study across multiple environments, we identified a major QTL, qHM-RR4-2, and pinpointed OsPUB77, a U- box E3 ubiquitin ligase, as the causal gene. Haplotype analysis and transgenic validation revealed that both knockout and overexpression of OsPUB77 significantly reduce HMRR by disrupting starch accumulation and increasing grain chalkiness. We further demonstrated that OsMADS29 directly binds to the OsPUB77 promoter and represses its transcription. Transcriptomic analysis indicated that OsPUB77 maintains metabolic homeostasis essential for starch biosynthe-sis during grain filling. Our findings establish the OsMADS29-OsPUB77 module as a critical regulator of HMRR and provide a promising target for improving rice milling quality through precision breeding.