Suppressors of Cytokinin Receptor Mutant pal1/ohk4 Confer Favorable Alleles of Grain Number 1a (Gn1a) for Improving Grain Yield in japonica Rice

The number of panicles per plant, grain number per panicle, and grain weight are three key factors influencing rice grain yield. Gn1a , a major quantitative trait locus (QTL) for grain number per panicle, encodes the cytokinin oxidase/dehydrogenase (CKX) OsCKX2. While the use of elite Gn1a alleles has been well documented in indica rice cultivars, their potential in japonica rice remains largely unexplored. In this study, we characterized three suppressor mutants of the rice cytokinin receptor mutant pal1/ohk4 and found that all causal genes are novel alleles of Gn1a through MutMap approach. These three suppressor mutants caused single amino acid substitution in the FAD-binding domain (G556D and G156D) and cytokinin-binding domain (Y357C), respectively, resulting in significantly reduced enzymatic activity of OsCKX2 and elevated cytokinin levels in the panicle. Haplotypes analysis of Gn1a using natural population from the 3K Rice Genomes Project showed that G556D, G156D, and Y357C are novel alleles of Gn1a . G556, G156, and Y357 are highly conserved, whereas four natural variants G54A, A105V, H116R, and N535K identified in different haplotypes of Gn1a show extremely low conservation. By backcrossing the suppressor mutants with its original wild type Huaidao 5, an elite japonica rice variety, we developed improved lines carrying only the gn1a mutation. The improved lines showed a significant increase in grain number per panicle, grain weight, as well as panicle number per plant, plant height and stem thickness, leading to 25.7%–28.7% increase in grain yield per plot compared with Huaidao 5. This study provides valuable Gn1a alleles for synergistic improvement of the three key yield factors and germplasm resources for high-yielding breeding in japonica rice.