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Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation

Author

Listed:
  • Feng Liu

    (Hunan Agricultural University)

  • Jiantao Zhao

    (Hunan Agricultural University
    Boyce Thompson Institute)

  • Honghe Sun

    (Boyce Thompson Institute
    Cornell University)

  • Cheng Xiong

    (Hunan Agricultural University)

  • Xuepeng Sun

    (Boyce Thompson Institute
    Zhejiang A&F University)

  • Xin Wang

    (Boyce Thompson Institute
    Huazhong Agricultural University)

  • Zhongyi Wang

    (Hunan Agricultural University)

  • Robert Jarret

    (Plant Genetic Resources Conservation Unit)

  • Jin Wang

    (Hunan Agricultural University)

  • Bingqian Tang

    (Hunan Agricultural University)

  • Hao Xu

    (Hunan Agricultural University)

  • Bowen Hu

    (Hunan Agricultural University)

  • Huan Suo

    (Hunan Agricultural University)

  • Bozhi Yang

    (Hunan Agricultural University)

  • Lijun Ou

    (Hunan Agricultural University)

  • Xuefeng Li

    (Institute of Vegetable Research, Hunan Academy of Agricultural Science)

  • Shudong Zhou

    (Institute of Vegetable Research, Hunan Academy of Agricultural Science)

  • Sha Yang

    (Institute of Vegetable Research, Hunan Academy of Agricultural Science)

  • Zhoubing Liu

    (Hunan Agricultural University)

  • Fang Yuan

    (Hunan Agricultural University)

  • Zhenming Pei

    (Hunan Agricultural University)

  • Yanqing Ma

    (Hunan Agricultural University)

  • Xiongze Dai

    (Hunan Agricultural University)

  • Shan Wu

    (Boyce Thompson Institute)

  • Zhangjun Fei

    (Boyce Thompson Institute
    U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health)

  • Xuexiao Zou

    (Hunan Agricultural University)

Abstract

Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.

Suggested Citation

  • Feng Liu & Jiantao Zhao & Honghe Sun & Cheng Xiong & Xuepeng Sun & Xin Wang & Zhongyi Wang & Robert Jarret & Jin Wang & Bingqian Tang & Hao Xu & Bowen Hu & Huan Suo & Bozhi Yang & Lijun Ou & Xuefeng L, 2023. "Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41251-4
    DOI: 10.1038/s41467-023-41251-4
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    References listed on IDEAS

    as
    1. Catherine Parry & Yen-Wei Wang & Shih-wen Lin & Derek W Barchenger, 2021. "Reproductive compatibility in Capsicum is not necessarily reflected in genetic or phenotypic similarity between species complexes," PLOS ONE, Public Library of Science, vol. 16(3), pages 1-17, March.
    2. Shan Wu & Biyao Zhang & Neda Keyhaninejad & Gustavo R. Rodríguez & Hyun Jung Kim & Manohar Chakrabarti & Eudald Illa-Berenguer & Nathan K. Taitano & M. J Gonzalo & Aurora Díaz & Yupeng Pan & Courtney , 2018. "A common genetic mechanism underlies morphological diversity in fruits and other plant organs," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    3. Yi Liao & Juntao Wang & Zhangsheng Zhu & Yuanlong Liu & Jinfeng Chen & Yongfeng Zhou & Feng Liu & Jianjun Lei & Brandon S. Gaut & Bihao Cao & J. J. Emerson & Changming Chen, 2022. "The 3D architecture of the pepper genome and its relationship to function and evolution," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    4. Joseph K Pickrell & Jonathan K Pritchard, 2012. "Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data," PLOS Genetics, Public Library of Science, vol. 8(11), pages 1-17, November.
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    Cited by:

    1. Weikai Chen & Xiangfeng Wang & Jie Sun & Xinrui Wang & Zhangsheng Zhu & Dilay Hazal Ayhan & Shu Yi & Ming Yan & Lili Zhang & Tan Meng & Yu Mu & Jun Li & Dian Meng & Jianxin Bian & Ke Wang & Lu Wang & , 2024. "Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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