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Natural variation of GNP2 enhances grain number to benefit rice yield

Author

Listed:
  • Qianfeng Hu

    (China Agricultural University)

  • Zhikun Zhao

    (China Agricultural University)

  • Lingling Ma

    (China Agricultural University)

  • Haijian Xia

    (China Agricultural University)

  • Zhiqi Ma

    (China Agricultural University)

  • Penghui Xu

    (China Agricultural University)

  • Xianpeng Wang

    (China Agricultural University)

  • Rui Zhu

    (China Agricultural University)

  • Yong Zhao

    (China Agricultural University)

  • Haifeng Guo

    (China Agricultural University)

  • Xiaoyang Zhu

    (China Agricultural University)

  • Yawen Zeng

    (Yunnan Academy of Agricultural Sciences)

  • Yinghua Pan

    (Guangxi Academy of Agricultural Sciences)

  • Danting Li

    (Guangxi Academy of Agricultural Sciences)

  • Xingming Sun

    (China Agricultural University
    Sanya Institute of China Agricultural University)

  • Jinjie Li

    (China Agricultural University
    Sanya Institute of China Agricultural University)

  • Hongliang Zhang

    (China Agricultural University
    Sanya Institute of China Agricultural University)

  • Zichao Li

    (China Agricultural University
    Sanya Institute of China Agricultural University)

  • Zhanying Zhang

    (China Agricultural University
    Sanya Institute of China Agricultural University)

Abstract

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.

Suggested Citation

  • Qianfeng Hu & Zhikun Zhao & Lingling Ma & Haijian Xia & Zhiqi Ma & Penghui Xu & Xianpeng Wang & Rui Zhu & Yong Zhao & Haifeng Guo & Xiaoyang Zhu & Yawen Zeng & Yinghua Pan & Danting Li & Xingming Sun , 2025. "Natural variation of GNP2 enhances grain number to benefit rice yield," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-64564-y
    DOI: 10.1038/s41467-025-64564-y
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