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A reference-grade wild soybean genome

Author

Listed:
  • Min Xie

    (The Chinese University of Hong Kong)

  • Claire Yik-Lok Chung

    (The Chinese University of Hong Kong)

  • Man-Wah Li

    (The Chinese University of Hong Kong)

  • Fuk-Ling Wong

    (The Chinese University of Hong Kong)

  • Xin Wang

    (The Chinese University of Hong Kong)

  • Ailin Liu

    (The Chinese University of Hong Kong)

  • Zhili Wang

    (The Chinese University of Hong Kong)

  • Alden King-Yung Leung

    (The Chinese University of Hong Kong)

  • Tin-Hang Wong

    (The Chinese University of Hong Kong)

  • Suk-Wah Tong

    (The Chinese University of Hong Kong)

  • Zhixia Xiao

    (The Chinese University of Hong Kong)

  • Kejing Fan

    (The Chinese University of Hong Kong)

  • Ming-Sin Ng

    (The Chinese University of Hong Kong)

  • Xinpeng Qi

    (The Chinese University of Hong Kong)

  • Linfeng Yang

    (BGI-Shenzhen)

  • Tianquan Deng

    (BGI-Shenzhen)

  • Lijuan He

    (BGI-Shenzhen)

  • Lu Chen

    (BGI-Shenzhen)

  • Aisi Fu

    (Wuhan Institute of Biotechnology)

  • Qiong Ding

    (Wuhan Institute of Biotechnology)

  • Junxian He

    (The Chinese University of Hong Kong)

  • Gyuhwa Chung

    (Chonnam National University)

  • Sachiko Isobe

    (Kazusa-Kamatari)

  • Takanari Tanabata

    (Kazusa-Kamatari)

  • Babu Valliyodan

    (University of Missouri)

  • Henry T. Nguyen

    (University of Missouri)

  • Steven B. Cannon

    (United States Department of Agriculture - Agricultural Research Service (USDA-ARS))

  • Christine H. Foyer

    (University of Leeds)

  • Ting-Fung Chan

    (The Chinese University of Hong Kong)

  • Hon-Ming Lam

    (The Chinese University of Hong Kong)

Abstract

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.

Suggested Citation

  • Min Xie & Claire Yik-Lok Chung & Man-Wah Li & Fuk-Ling Wong & Xin Wang & Ailin Liu & Zhili Wang & Alden King-Yung Leung & Tin-Hang Wong & Suk-Wah Tong & Zhixia Xiao & Kejing Fan & Ming-Sin Ng & Xinpen, 2019. "A reference-grade wild soybean genome," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09142-9
    DOI: 10.1038/s41467-019-09142-9
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    Cited by:

    1. Qingnan Hao & Hongli Yang & Shuilian Chen & Chanjuan Zhang & Limiao Chen & Dong Cao & Songli Yuan & Wei Guo & Zhonglu Yang & Yi Huang & Yanhui Qu & Lucy Qin & Xiaoyan Sheng & Xueyan Wang & Chandrani M, 2024. "A pair of atypical NLR-encoding genes confers Asian soybean rust resistance in soybean," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Weidong Wang & Liyang Chen & Kevin Fengler & Joy Bolar & Victor Llaca & Xutong Wang & Chancelor B. Clark & Tomara J. Fleury & Jon Myrvold & David Oneal & Maria Magdalena Dyk & Ashley Hudson & Jesse Mu, 2021. "A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    3. Isaac Njaci & Bernice Waweru & Nadia Kamal & Meki Shehabu Muktar & David Fisher & Heidrun Gundlach & Collins Muli & Lucy Muthui & Mary Maranga & Davies Kiambi & Brigitte L. Maass & Peter M. F. Emmrich, 2023. "Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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