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The identification of grain size genes by RapMap reveals directional selection during rice domestication

Author

Listed:
  • Juncheng Zhang

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Dejian Zhang

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Yawei Fan

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Cuicui Li

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Pengkun Xu

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Wei Li

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Qi Sun

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Xiaodong Huang

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Chunyu Zhang

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Linyue Wu

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Huaizhou Yang

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Shiyu Wang

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Xiaomin Su

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Xingxing Li

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Yingying Song

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Meng-en Wu

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

  • Xingming Lian

    (Huazhong Agricultural University)

  • Yibo Li

    (Huazhong Agricultural University
    Hubei Hongshan Laboratory)

Abstract

Cloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity. Here, we introduce RapMap, a method for rapid multi-QTL mapping by employing F2 gradient populations (F2GPs) constructed by minor-phenotypic-difference accessions. The co-segregation standard of the single-locus genetic models ensures simultaneous integration of a three-in-one framework in RapMap i.e. detecting a real QTL, confirming its effect, and obtaining its near-isogenic line-like line (NIL-LL). We demonstrate the feasibility of RapMap by cloning eight rice grain-size genes using 15 F2GPs in three years. These genes explain a total of 75% of grain shape variation. Allele frequency analysis of these genes using a large germplasm collection reveals directional selection of the slender and long grains in indica rice domestication. In addition, major grain-size genes have been strongly selected during rice domestication. We think application of RapMap in crops will accelerate gene discovery and genomic breeding.

Suggested Citation

  • Juncheng Zhang & Dejian Zhang & Yawei Fan & Cuicui Li & Pengkun Xu & Wei Li & Qi Sun & Xiaodong Huang & Chunyu Zhang & Linyue Wu & Huaizhou Yang & Shiyu Wang & Xiaomin Su & Xingxing Li & Yingying Song, 2021. "The identification of grain size genes by RapMap reveals directional selection during rice domestication," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25961-1
    DOI: 10.1038/s41467-021-25961-1
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    Cited by:

    1. Md Babul Akter & Azad Mosab-Bin & Mohammad Kamruzzaman & Reflinur Reflinur & Nazmun Nahar & Md Sohel Rana & Md Imdadul Hoque & Md Shahidul Islam, 2022. "Morpho-molecular diversity study of rice cultivars in Bangladesh," Czech Journal of Genetics and Plant Breeding, Czech Academy of Agricultural Sciences, vol. 58(2), pages 64-72.

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