Natural variation of GNP2 enhances grain number to benefit 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/LAX2T175,262D 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. Grain number per panicle (GNP) is a yield-determining trait of rice. Here, the authors identify a GSK3-like kinase-encoding gene GNP2 and a bZIP transcription factor-encoding gene GNP5, demonstrating their synergistic regulation of GNP and showing that specific allele combinations of these genes enhance rice yield in field conditions.