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

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, Julia Vrebalov, James J. Giovannoni, Shan Wu () and Zhangjun Fei ()
Additional contact information
Xin Wang: Boyce Thompson Institute
Lei Gao: Boyce Thompson Institute
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
Lukas A. Mueller: Boyce Thompson Institute
Julia Vrebalov: Boyce Thompson Institute
James J. Giovannoni: Boyce Thompson Institute
Shan Wu: Boyce Thompson Institute
Zhangjun Fei: Boyce Thompson Institute

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-19682-0

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