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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
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    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. 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.
    3. 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.

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