Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Using genome-wide association study (GWAS), we identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions, including one SD1 structural variant that is not normally detected in standard GWAS analyses. We also found a further 85 QTL/genes for PH in subgroups harbouring distinct SD1 haplotypes. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1NIP subgroup. Furthermore, we found that DTHx, a heading date gene, regulates the expression of SD1, thus, regulating PH in rice. Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.

rice,genetic