Combining two main functional alleles can increase rice yield.

() is one of the key genes in regulating photosynthesis and plant architecture. As the antagonistic effects of have concurrent impacts on photosynthesis and yield component traits, how we can effectively utilize the gene to further increase rice yield is not clear. In this study, we used two different main functional alleles, each of which has previously been proven to have specifically advantageous traits, and tested whether the combined alleles have a higher yield than the homozygous alleles. Our results exhibited that the combined alleles had better parent heterosis (BPH) for panicle number and the total filled grain number per plant, and had middle parent heterosis (MPH) for spikelet number per panicle without affecting thousand-grain weight when compared with the homozygous alleles. In consequence, the hybrid plants displayed highly increased grain yield compared with both homozygous parents. The hybrid plants also had better plant architecture and higher canopy photosynthesis. Western blot and proteomics results showed the hybrid plants had a middle abundant NAL1 protein level, and the upregulated proteins were mainly involved in the nucleus and DNA binding process but the downregulated proteins were mainly involved in the oxidation-reduction process, single-organism metabolic process, and fatty acid biosynthetic process. Furthermore, the hybrid vigor effect of was confirmed by substituting the mutual male parent 9311 with 9311-NIL in two super hybrid rice varieties (LYP9 and YLY1). This study demonstrates that we can achieve a higher level of grain production in hybrid rice by using the heterosis of .