Natural variation in the GNH1 promoter enhances plant height and grain yield in rice

Plant height and grain number are key factors influencing plant architecture and yield. Although a number of genes regulating rice plant height and grain number have been identified, further elucidation of their regulatory mechanisms remains critical for breeding high-yield rice varieties. In this study, we show that the GRAIN NUMBER AND PLANT HEIGHT 1 (GNH1) gene, which is identical to rice TRYPTOPHAN AMINOTRANSFERASE RELATED 2 (OsTAR2), plays an important role in regulating both rice plant height and grain number. A natural variation located 382 bp upstream of GNH1 impairs the DNA-binding affinity of the C₂H₂-type transcription factor ZFP36, increasing GNH1 transcript abundance and auxin accumulation in the indica cultivar T5 and ultimately leading to increased plant height and grain number. Haplotype analysis revealed that GNH1 has undergone differentiation between indica and japonica subspecies. Increasing the expression level of GNH1 significantly boosts rice yield in two elite rice varieties: Zhonghua 11 and Jigeng 88. Collectively, these findings not only deepen our understanding of the molecular mechanisms underlying plant architecture and yield regulation but also offer a favorable gene for rice genetic improvement.