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Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa

Author

Listed:
  • Haitao Chen

    (Chinese Academy of Sciences
    Guangdong Sanjie Forage Biotechnology Co., Ltd.
    Sanjie Institute of Forage
    University of Chinese Academy of Sciences)

  • Yan Zeng

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yongzhi Yang

    (Lanzhou University)

  • Lingli Huang

    (Guangdong Sanjie Forage Biotechnology Co., Ltd.
    Sanjie Institute of Forage
    Northwestern Polytechnical University)

  • Bolin Tang

    (Guangdong Sanjie Forage Biotechnology Co., Ltd.
    Sanjie Institute of Forage
    Lanzhou University)

  • He Zhang

    (BGI-Qingdao)

  • Fei Hao

    (Northwestern Polytechnical University)

  • Wei Liu

    (Chinese Academy of Sciences
    Guangdong Sanjie Forage Biotechnology Co., Ltd.
    Sanjie Institute of Forage
    University of Chinese Academy of Sciences)

  • Youhan Li

    (Xishuangbanna Tropical Botanical Garden)

  • Yanbin Liu

    (Lanzhou University)

  • Xiaoshuang Zhang

    (Guangdong Sanjie Forage Biotechnology Co., Ltd.
    Sanjie Institute of Forage)

  • Ru Zhang

    (Northwestern Polytechnical University)

  • Yesheng Zhang

    (Chinese Academy of Sciences)

  • Yongxin Li

    (Northwestern Polytechnical University)

  • Kun Wang

    (Northwestern Polytechnical University)

  • Hua He

    (Xishuangbanna Tropical Botanical Garden)

  • Zhongkai Wang

    (Northwestern Polytechnical University)

  • Guangyi Fan

    (BGI-Qingdao)

  • Hui Yang

    (Northwestern Polytechnical University)

  • Aike Bao

    (Lanzhou University)

  • Zhanhuan Shang

    (Lanzhou University)

  • Jianghua Chen

    (Xishuangbanna Tropical Botanical Garden)

  • Wen Wang

    (Chinese Academy of Sciences
    Northwestern Polytechnical University)

  • Qiang Qiu

    (Northwestern Polytechnical University)

Abstract

Artificially improving traits of cultivated alfalfa (Medicago sativa L.), one of the most important forage crops, is challenging due to the lack of a reference genome and an efficient genome editing protocol, which mainly result from its autotetraploidy and self-incompatibility. Here, we generate an allele-aware chromosome-level genome assembly for the cultivated alfalfa consisting of 32 allelic chromosomes by integrating high-fidelity single-molecule sequencing and Hi-C data. We further establish an efficient CRISPR/Cas9-based genome editing protocol on the basis of this genome assembly and precisely introduce tetra-allelic mutations into null mutants that display obvious phenotype changes. The mutated alleles and phenotypes of null mutants can be stably inherited in generations in a transgene-free manner by cross pollination, which may help in bypassing the debate about transgenic plants. The presented genome and CRISPR/Cas9-based transgene-free genome editing protocol provide key foundations for accelerating research and molecular breeding of this important forage crop.

Suggested Citation

  • Haitao Chen & Yan Zeng & Yongzhi Yang & Lingli Huang & Bolin Tang & He Zhang & Fei Hao & Wei Liu & Youhan Li & Yanbin Liu & Xiaoshuang Zhang & Ru Zhang & Yesheng Zhang & Yongxin Li & Kun Wang & Hua He, 2020. "Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16338-x
    DOI: 10.1038/s41467-020-16338-x
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    Cited by:

    1. Yanting Shen & Wanying Li & Ying Zeng & Zhipeng Li & Yiqiong Chen & Jixiang Zhang & Hong Zhao & Lingfang Feng & Dongming Ma & Xiaolu Mo & Puyue Ouyang & Lili Huang & Zheng Wang & Yuannian Jiao & Hong-, 2022. "Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Aiping Song & Jiangshuo Su & Haibin Wang & Zhongren Zhang & Xingtan Zhang & Yves Peer & Fei Chen & Weimin Fang & Zhiyong Guan & Fei Zhang & Zhenxing Wang & Likai Wang & Baoqing Ding & Shuang Zhao & Li, 2023. "Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Botong Zhou & Ping Hu & Guichun Liu & Zhou Chang & Zhiwei Dong & Zihe Li & Yuan Yin & Zunzhe Tian & Ge Han & Wen Wang & Xueyan Li, 2024. "Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangements," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    4. Hao Liu & Ming Xu & Yuhan Guo & Zhencuo Dan & Xin Liu & Jiayi Zhang & Cong Li & Shizhen Jia & Lei Jia & Ailing Yu & Lili Cong, 2024. "Combined Transcriptome and Metabolome Analysis of Alfalfa Responses to Aphid Infestation," Agriculture, MDPI, vol. 14(9), pages 1-17, September.

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