TY - JOUR T1 - Genome of <em>Solanum pimpinellifolium</em> provides insights into structural variants during tomato breeding JF - bioRxiv DO - 10.1101/2020.06.17.157859 SP - 2020.06.17.157859 AU - Xin Wang AU - Lei Gao AU - Chen Jiao AU - Stefanos Stravoravdis AU - Prashant S. Hosmani AU - Surya Saha AU - Jing Zhang AU - Samantha Mainiero AU - Susan R. Strickler AU - Carmen Catala AU - Gregory B. Martin AU - Lukas A. Mueller AU - Julia Vrebalov AU - James J. Giovannoni AU - Shan Wu AU - Zhangjun Fei Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/06/18/2020.06.17.157859.abstract N2 - 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 breeding of tomato. Here we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 high-confidence structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions unravels alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous novel SVs underlying 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 novel 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.Competing Interest StatementThe authors have declared no competing interest. ER -