Favorable alleles of GRAIN-FILLING RATE 1 increase the grain-filling rate and yield of rice

Hybrid rice (Oryza sativa) has been cultivated commercially for 42 years in China. However, poor grain filling still limits the development of hybrid japonica rice. We report here the map-based cloning and characterization of the GRAIN-FILLING RATE 1 (GFR1) gene present at a major-effect quantitative trait locus (QTL). We elucidated and confirmed the function of GFR1 via genetic complementation experiments and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing in combination with genetic and molecular biological analyses. In addition, we conducted haplotype association analysis to mine the elite alleles of GFR1 among 117 rice accessions. We observed that GFR1 was constitutively expressed and encoded a membrane-localized protein. The allele of the rice accession Ludao (GFR1Ludao) improved the grain-filling rate of rice by increasing rubisco initial activity in the Calvin cycle. Moreover, the increased expression of the cell wall invertase (CIN) gene OsCIN1 in near isogenic line NIL-GFR1Ludao promoted the unloading of sucrose during the rice grain-filling stage. A yeast two-hybrid assay indicated that the rubisco small subunit (OsRbcS) interacts with GFR1, possibly in the regulation of the rice grain-filling rate. Evaluation of the grain-filling rate and grain yield of F1 plants harboring GFR1Ludao and the alleles of 20 hybrids widely cultivated commercially confirmed that favorable alleles of GFR1 can be used to further improve the grain-filling rate of hybrid japonica rice.