Culm diameter directly affects lodging and yield traits in cereal crops. However, the underlying molecular mechanisms of these interrelated, complex agronomic traits remain unclear. Here, we identify a quantitative trait locus for culm diameter in rice (Oryza sativa) and cloned the candidate gene, STRONG1. This gene encodes MICROTUBULE-ASSOCIATED PROTEIN 70 (MAP70), which localizes to cortical microtubules and alters the arrangement of the microtubule skeleton. Knockout or knockdown of STRONG1 enhances grain yield by synchronously improving lodging resistance, panicle architecture, and plant architecture. One single-nucleotide polymorphism, SNP − 1304 (C to A), in a MYB61-binding site within the STRONG1 promoter affects its expression, resulting in changes in cellulose content and sclerenchyma cell wall development. Rice accessions harboring the Hap-STRONG1^C haplotype derived from wild rice, with reduced STRONG1 expression, show enhanced lodging resistance and yield, compared to accessions carrying Hap-STRONG1^A. Knockout of STRONG1 results in a 9.3–15.4% increase in yield, compared to the wild type in a field plot trial. Knockout of STRONG1 also improves panicle and plant architecture, facilitating high-density planting. This study provides a candidate gene for the development of improved rice varieties with stable, high yields.

Grain number per panicle critically determines rice yield. Although many underlying genes have been reported, yet the molecular mechanisms linking ethylene to panicle development remain unclear. Here, we identify GRAIN NUMBER PER PANICLE 3 (GNP3) as a regulator of GNP through genome-wide association study (GWAS) combined with map-based cloning. GNP3 encodes a MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 22 (OsMKKK22) that phosphorylates S-adenosyl-L-methionine synthetase 1 (SAMS1), triggering its degradation to suppress ethylene biosynthesis. Ethylene overaccumulation in gnp3-1 mutants reduces grain number, while GNP3 overexpression enhances panicle branching and grain yield by lowering ethylene levels. We demonstrate that a natural haplotype GNP3^Hap-Tprevalent in indica subspecies strengthens GNP3-SAMS1 interaction, accelerating SAMS1 degradation and improving grain number. Furthermore, overexpressing GNP3 increases grain yield by approximately 20% in field plot conditions. Our findings unveil a MAPK-ethylene regulatory module and highlight GNP3^Hap-T as a valuable genetic resource for breeding high-yield rice.

Grain size substantially influences rice quality and yield. In this study, we identified CONTROL OF SLENDER RICE 1 ( COR1 ), a quantitative trait locus encoding an F-box protein that enhances grain length by promoting cell proliferation. The transcription factor OsbZIP35 represses COR1 expression, while COR1 interacts with OsTCP19, leading to its degradation. Knockout of either OsbZIP35 or OsTCP19 results in increased grain length, confirming their regulatory roles in grain development. The OsbZIP35-COR1-OsTCP19 module controls the expression of the cell cycle gene OsCycB1;4 , thereby modulating cell proliferation and ultimately determining grain size. Five haplotypes of COR1 were identified, with COR1 -Hap1 and COR1 -Hap3 being elite alleles associated with longer grains. Field plot trials demonstrated that the near-isogenic line NIL- COR1 ^SLG increased yield by ~6.6% compared to NIL- COR1 ^Nip . These findings elucidate the genetic mechanisms underlying grain size regulation and offer promising strategies for improving rice yield.

Natural variations provide valuable genetic resources for improving rice grain number per panicle (GNP). Here, our genome-wide association study (GWAS) identifies GNP2 and GNP5 as key regulators of GNP that enhance rice yield. GNP5 encodes a bZIP transcription factor binding to the S5779181 locus in the GNP2 promoter, where natural variation significantly influences GNP. GNP2 encodes a conserved GSK3-like kinase that phosphorylates and stabilizes Gnp4/LAX2. The phosphorylated Gnp4/LAX2^T175,262D promotes yield by modulating transcription factors involved in panicle development. Haplotype analysis reveals an elite allele combination (Type I) of GNP5 and GNP2 that significantly increases GNP. Field trials demonstrate that enhanced GNP2 expression raises yield by approximately 10%. Our findings thus uncover a genetic resource with application potential for enhancing rice yield.