Natural variation of GNP2 enhances grain number to benefit rice yield

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, Jinjie Li, Hongliang Zhang, Zichao Li and Zhanying Zhang ()
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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
Jinjie Li: China Agricultural University
Hongliang Zhang: China Agricultural University
Zichao Li: China Agricultural University
Zhanying Zhang: China Agricultural University

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-64564-y

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