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Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

Author

Listed:
  • Xin Wang

    (Boyce Thompson Institute)

  • Lei Gao

    (Boyce Thompson Institute
    CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences)

  • Chen Jiao

    (Boyce Thompson Institute)

  • Stefanos Stravoravdis

    (Boyce Thompson Institute)

  • Prashant S. Hosmani

    (Boyce Thompson Institute)

  • Surya Saha

    (Boyce Thompson Institute)

  • Jing Zhang

    (Boyce Thompson Institute)

  • Samantha Mainiero

    (Boyce Thompson Institute)

  • Susan R. Strickler

    (Boyce Thompson Institute)

  • Carmen Catala

    (Boyce Thompson Institute)

  • Gregory B. Martin

    (Boyce Thompson Institute
    Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University)

  • Lukas A. Mueller

    (Boyce Thompson Institute)

  • Julia Vrebalov

    (Boyce Thompson Institute)

  • James J. Giovannoni

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

  • Shan Wu

    (Boyce Thompson Institute)

  • Zhangjun Fei

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

Abstract

Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.

Suggested Citation

  • Xin Wang & Lei Gao & Chen Jiao & Stefanos Stravoravdis & Prashant S. Hosmani & Surya Saha & Jing Zhang & Samantha Mainiero & Susan R. Strickler & Carmen Catala & Gregory B. Martin & Lukas A. Mueller &, 2020. "Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19682-0
    DOI: 10.1038/s41467-020-19682-0
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    Cited by:

    1. Alessandro Natalini & Nazzareno Acciarri & Teodoro Cardi, 2021. "Breeding for Nutritional and Organoleptic Quality in Vegetable Crops: The Case of Tomato and Cauliflower," Agriculture, MDPI, vol. 11(7), pages 1-21, June.
    2. Felix Homma & Jie Huang & Renier A. L. van der Hoorn, 2023. "AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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