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The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice

Author

Listed:
  • Huiying He

    (Chinese Academy of Agricultural Sciences)

  • Yue Leng

    (Chinese Academy of Agricultural Sciences)

  • Xinglan Cao

    (Chinese Academy of Agricultural Sciences
    Henan University
    Shenzhen Research Institute of Henan university)

  • Yiwang Zhu

    (Chinese Academy of Agricultural Sciences
    Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture)

  • Xiaoxia Li

    (Chinese Academy of Agricultural Sciences)

  • Qiaoling Yuan

    (Chinese Academy of Agricultural Sciences)

  • Bin Zhang

    (Chinese Academy of Agricultural Sciences
    Yazhouwan National Laboratory)

  • Wenchuang He

    (Chinese Academy of Agricultural Sciences)

  • Hua Wei

    (Chinese Academy of Agricultural Sciences)

  • Xiangpei Liu

    (Chinese Academy of Agricultural Sciences)

  • Qiang Xu

    (Chinese Academy of Agricultural Sciences)

  • Mingliang Guo

    (Chinese Academy of Agricultural Sciences)

  • Hong Zhang

    (Chinese Academy of Agricultural Sciences)

  • Longbo Yang

    (Chinese Academy of Agricultural Sciences)

  • Yang Lv

    (Chinese Academy of Agricultural Sciences)

  • Xianmeng Wang

    (Chinese Academy of Agricultural Sciences)

  • Chuanlin Shi

    (Chinese Academy of Agricultural Sciences)

  • Zhipeng Zhang

    (Chinese Academy of Agricultural Sciences)

  • Wu Chen

    (Chinese Academy of Agricultural Sciences)

  • Bintao Zhang

    (Chinese Academy of Agricultural Sciences)

  • Tianyi Wang

    (Chinese Academy of Agricultural Sciences)

  • Xiaoman Yu

    (Chinese Academy of Agricultural Sciences)

  • Hongge Qian

    (Chinese Academy of Agricultural Sciences)

  • Qianqian Zhang

    (Chinese Academy of Agricultural Sciences)

  • Xiaofan Dai

    (Chinese Academy of Agricultural Sciences)

  • Congcong Liu

    (Chinese Academy of Agricultural Sciences)

  • Yan Cui

    (Chinese Academy of Agricultural Sciences)

  • Yuexing Wang

    (China National Rice Research Institute)

  • Xiaoming Zheng

    (Chinese Academy of Agricultural Sciences)

  • Guosheng Xiong

    (Nanjing Agricultural University)

  • Yongfeng Zhou

    (Chinese Academy of Agricultural Sciences)

  • Qian Qian

    (Chinese Academy of Agricultural Sciences
    Yazhouwan National Laboratory
    China National Rice Research Institute)

  • Lianguang Shang

    (Chinese Academy of Agricultural Sciences
    Yazhouwan National Laboratory)

Abstract

Tandem repeats (TRs) are genomic regions that tandemly change in repeat number, which are often multiallelic. Their characteristics and contributions to gene expression and quantitative traits in rice are largely unknown. Here, we survey rice TR variations based on 231 genome assemblies and the rice pan-genome graph. We identify 227,391 multiallelic TR loci, including 54,416 TR variations that are absent from the Nipponbare reference genome. Only 1/3 TR variations show strong linkage with nearby bi-allelic variants (SNPs, Indels and PAVs). Using 193 panicle and 202 leaf transcriptomic data, we reveal 485 and 511 TRs act as QTLs independently of other bi-allelic variations to nearby gene expression, respectively. Using plant height and grain width as examples, we identify and validate TRs contributions to rice agronomic trait variations. These findings would enhance our understanding of the functions of multiallelic variants and facilitate rice molecular breeding.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51854-0
    DOI: 10.1038/s41467-024-51854-0
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    References listed on IDEAS

    as
    1. 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.
    2. Daniel C. Jeffares & Clemency Jolly & Mimoza Hoti & Doug Speed & Liam Shaw & Charalampos Rallis & Francois Balloux & Christophe Dessimoz & Jürg Bähler & Fritz J. Sedlazeck, 2017. "Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
    3. Andrew C. Elden & Hyung-Jun Kim & Michael P. Hart & Alice S. Chen-Plotkin & Brian S. Johnson & Xiaodong Fang & Maria Armakola & Felix Geser & Robert Greene & Min Min Lu & Arun Padmanabhan & Dana Clay-, 2010. "Ataxin-2 intermediate-length polyglutamine expansions are associated with increased risk for ALS," Nature, Nature, vol. 466(7310), pages 1069-1075, August.
    4. Gao Wang & Abhishek Sarkar & Peter Carbonetto & Matthew Stephens, 2020. "A simple new approach to variable selection in regression, with application to genetic fine mapping," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 82(5), pages 1273-1300, December.
    5. 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.
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