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A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice

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  • Lin Zhang

    (National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of the Chinese Academy of Sciences)

  • Hong Yu

    (State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Bin Ma

    (School of Life Science and Technology, Shanghai Tech University)

  • Guifu Liu

    (State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

  • Jianjun Wang

    (Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences)

  • Junmin Wang

    (Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences)

  • Rongcun Gao

    (Jiaxing Academy of Agricultural Sciences)

  • Jinjun Li

    (Jiaxing Academy of Agricultural Sciences)

  • Jiyun Liu

    (National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Jing Xu

    (National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Yingying Zhang

    (National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Qun Li

    (National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Xuehui Huang

    (National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Jianlong Xu

    (Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences)

  • Jianming Li

    (Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Qian Qian

    (Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences)

  • Bin Han

    (National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences)

  • Zuhua He

    (National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of the Chinese Academy of Sciences)

  • Jiayang Li

    (University of the Chinese Academy of Sciences
    State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences)

Abstract

Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield. The qWS8/ipa1-2D locus is associated with reduced DNA methylation and a more open chromatin state at the IPA1 promoter, thus alleviating the epigenetic repression of IPA1 mediated by nearby heterochromatin. Our findings reveal that IPA traits can be fine-tuned by manipulating IPA1 expression and that an optimal IPA1 expression/dose may lead to an ideal yield, demonstrating a practical approach to efficiently design elite super rice varieties.

Suggested Citation

  • Lin Zhang & Hong Yu & Bin Ma & Guifu Liu & Jianjun Wang & Junmin Wang & Rongcun Gao & Jinjun Li & Jiyun Liu & Jing Xu & Yingying Zhang & Qun Li & Xuehui Huang & Jianlong Xu & Jianming Li & Qian Qian &, 2017. "A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice," Nature Communications, Nature, vol. 8(1), pages 1-10, April.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14789
    DOI: 10.1038/ncomms14789
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    Cited by:

    1. Tao Zhu & Chunjiao Xia & Ranran Yu & Xinkai Zhou & Xingbing Xu & Lin Wang & Zhanxiang Zong & Junjiao Yang & Yinmeng Liu & Luchang Ming & Yuxin You & Dijun Chen & Weibo Xie, 2024. "Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Qianjin Liang & Liyu Chen & Xia Yang & Hui Yang & Shulin Liu & Kun Kou & Lei Fan & Zhifang Zhang & Zongbiao Duan & Yaqin Yuan & Shan Liang & Yucheng Liu & Xingtong Lu & Guoan Zhou & Min Zhang & Fanjia, 2022. "Natural variation of Dt2 determines branching in soybean," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    3. Fuxi Rong & Yusong Lv & Pingchuan Deng & Xia Wu & Yaqi Zhang & Erkui Yue & Yuxin Shen & Sajid Muhammad & Fangrui Ni & Hongwu Bian & Xiangjin Wei & Weijun Zhou & Peisong Hu & Liang Wu, 2024. "Switching action modes of miR408-5p mediates auxin signaling in rice," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Luchang Ming & Debao Fu & Zhaona Wu & Hu Zhao & Xingbing Xu & Tingting Xu & Xiaohu Xiong & Mu Li & Yi Zheng & Ge Li & Ling Yang & Chunjiao Xia & Rongfang Zhou & Keyan Liao & Qian Yu & Wenqi Chai & Sij, 2023. "Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    5. Lunying Wu & Xiaohui Jing & Baolan Zhang & Shoujun Chen & Ran Xu & Penggen Duan & Danni Zou & Shengjian Huang & Tingbo Zhou & Chengcai An & Yuehua Luo & Yunhai Li, 2022. "A natural allele of OsMS1 responds to temperature changes and confers thermosensitive genic male sterility," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    6. Huiying He & Yue Leng & Xinglan Cao & Yiwang Zhu & Xiaoxia Li & Qiaoling Yuan & Bin Zhang & Wenchuang He & Hua Wei & Xiangpei Liu & Qiang Xu & Mingliang Guo & Hong Zhang & Longbo Yang & Yang Lv & Xian, 2024. "The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Hui Shi & Junjie Yin & Zhangjie Zhao & Hong Yu & Hong Yi & Li Xu & Huimin Tong & Min He & Xiaobo Zhu & Xiang Lu & Qing Xiong & Weitao Li & Yongyan Tang & Qingqing Hou & Li Song & Long Wang & Xiaoqiong, 2024. "Fine-tuning of IPA1 transactivation activity by E3 ligase IPI7-mediated non-proteolytic K29-ubiquitination during Magnaporthe oryzae infection," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

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