IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-020-20337-3.html
   My bibliography  Save this article

The patterns of deleterious mutations during the domestication of soybean

Author

Listed:
  • Myung-Shin Kim

    (Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology
    Seoul National University)

  • Roberto Lozano

    (Cornell University)

  • Ji Hong Kim

    (Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology)

  • Dong Nyuk Bae

    (Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology)

  • Sang-Tae Kim

    (The Catholic University of Korea)

  • Jung-Ho Park

    (Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology)

  • Man Soo Choi

    (National Institute of Crop Science, Rural Development Administration)

  • Jaehyun Kim

    (National Institute of Crop Science, Rural Development Administration)

  • Hyun-Choong Ok

    (National Institute of Crop Science, Rural Development Administration)

  • Soo-Kwon Park

    (National Institute of Crop Science, Rural Development Administration)

  • Michael A. Gore

    (Cornell University)

  • Jung-Kyung Moon

    (National Institute of Crop Science, Rural Development Administration
    Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration)

  • Soon-Chun Jeong

    (Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology)

Abstract

Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel.

Suggested Citation

  • Myung-Shin Kim & Roberto Lozano & Ji Hong Kim & Dong Nyuk Bae & Sang-Tae Kim & Jung-Ho Park & Man Soo Choi & Jaehyun Kim & Hyun-Choong Ok & Soo-Kwon Park & Michael A. Gore & Jung-Kyung Moon & Soon-Chu, 2021. "The patterns of deleterious mutations during the domestication of soybean," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20337-3
    DOI: 10.1038/s41467-020-20337-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-20337-3
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-020-20337-3?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Muhammad Awais Zahid & Nam Phuong Kieu & Frida Meijer Carlsen & Marit Lenman & Naga Charan Konakalla & Huanjie Yang & Sunmoon Jyakhwa & Jozef Mravec & Ramesh Vetukuri & Bent Larsen Petersen & Svante R, 2024. "Enhanced stress resilience in potato by deletion of Parakletos," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Hai Anh Tran & Hyun Jo & Thi Cuc Nguyen & Jeong-Dong Lee & Hak Soo Seo & Jong Tae Song, 2024. "Genome-Wide Association Analysis for Submergence Tolerance at the Early Vegetative and Germination Stages in Wild Soybean ( Glycine soja )," Agriculture, MDPI, vol. 14(9), pages 1-17, September.
    3. Mitchell J. Feldmann & Dominique D. A. Pincot & Glenn S. Cole & Steven J. Knapp, 2024. "Genetic gains underpinning a little-known strawberry Green Revolution," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    4. Jiantao Guan & Jintao Zhang & Dan Gong & Zhengquan Zhang & Yang Yu & Gaoling Luo & Prakit Somta & Zheng Hu & Suhua Wang & Xingxing Yuan & Yaowen Zhang & Yanlan Wang & Yanhua Chen & Kularb Laosatit & X, 2022. "Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20337-3. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.