STRONG3 promotes lignin biosynthesis and culm strength in rice.

Lodging severely reduces rice yield and quality. Culm strength, mainly determined by lignin biosynthesis and secondary cell wall (SCW) formation, is core to lodging resistance. We identified an ethylene response factor (ERF) transcription factor STRONG3 via genome-wide association study (GWAS) of 405 rice accessions based on lignin content. Functional validation demonstrated that STRONG3 positively regulates lignin accumulation, culm diameter, and mechanical strength by promoting sclerenchyma tissue development, vascular bundle enlargement, and SCW thickening. Molecular analyses revealed that STRONG3 directly binds to the GCC-box motif in the promoter of 4CL4, a rate-limiting enzyme in the phenylpropanoid pathway, to activate its transcription. Genetic complementation confirmed that 4CL4 acts downstream of STRONG3 to mediate lignin biosynthesis and culm development. Haplotype analysis identified subspecies-specific favorable alleles: STRONG3G in Geng rice, caused by a single nucleotide polymorphism (4349512) leading to an Ala289Thr substitution in the activation domain that enhances STRONG3's transcriptional activation of 4CL4, and 4CL4TC in Xian rice. Combinatorial analysis showed these alleles synergistically improve culm traits in their respective subspecies. Overexpression of STRONG3 enhanced lodging resistance without compromising grain yield. Our findings uncover a critical regulatory pathway for rice culm development and provide valuable genetic resources and molecular markers for breeding high-yield, lodging-resistant rice varieties.