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Suppressors of the Cytokinin Receptor Mutant pal1/ohk4 Confer Favorable Alleles of Grain Number1a (Gn1a) for Improving Grain Yield in japonica Rice

  1. State Key Laboratory of Crop Gene Resources and Breeding / National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Biobreeding Institute, Xianghu Laboratory, Hangzhou 311231, China; College of Agriculture, Fisheries and Forestry, Fiji National University, Nausori 1544, Fiji Islands; Institute of Wetland Agriculture and Ecology, Shandong Academy of Agricultural Sciences, Ji’nan 250100, China; #These authors contributed equally to this article
  • Contact: LI Xueyong
  • Supported by:

    This work was supported by the Biological Breeding-National Science and Technology Major Project, China (Grant No. 2023ZD0406801), National Natural Science Foundation of China (Grant No. 32300278), the Key R&D Plan of Shandong Province (Grant No. 2024LZGC009), Innovation Program of Chinese Academy of Agricultural Sciences (Grant No. CAAS-CSCB-202402), and Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences (Grant No. CXGC2025B09). We thank the Key Facility Platform of the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences for their technical support in the Next-generation sequencing of the MutMap DNA samples.

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Abstract: 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.

Key words: grain number, panicle size, cytokinin, Gn1a, OsCKX2, OHK4, suppressor, Oryza sativa