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

Authors: WANG, XIN - Boyce Thompson Institute; GAO, LEI - Boyce Thompson Institute; JIAO, CHEN - Boyce Thompson Institute; STRAVORAVDIS, STEFANOS - Boyce Thompson Institute; HOSMANI, PRASHANT - Boyce Thompson Institute; SAHA, SURYA - Boyce Thompson Institute; ZHANG, JING - Boyce Thompson Institute; MAINIERO, SAMANTHA - Boyce Thompson Institute; STRICKLER, SUSAN - Boyce Thompson Institute; CATALA, CARMEN - Boyce Thompson Institute; MARTIN, GREGORY - Boyce Thompson Institute; MULLER, LUKAS - Boyce Thompson Institute; VREBALOV, JULIA - Cornell University; Giovannoni, James; WU, SHAN - Boyce Thompson Institute; FEI, ZHANGJUN - Boyce Thompson Institute

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/27/2020
Publication Date: 11/16/2020
Citation: Wang, X., Gao, L., Jiao, C., Stravoravdis, S., Hosmani, P., Saha, S., Zhang, J., Mainiero, S., Strickler, S., Catala, C., Martin, G., Muller, L., Vrebalov, J., Giovannoni, J.J., Wu, S., Fei, Z. 2020. Genome of Solanum pimpinelifolium provides insights into structural variants during tomato breeding. Nature Communications. 11:5817. https://doi.org/10.1038/s41467-020-19682-0.
DOI: https://doi.org/10.1038/s41467-020-19682-0

Interpretive Summary: Tomato (Solanum lycopersicum) is the world’s leading vegetable crop with a total production of 182 million tons and a worth over US $60 billion in 2018 . S. pimpinellifolium (SP) carrying red, small, and round fruits is the wild progenitor of the cultivated tomato. It was domesticated in South America to give rise to S. lycopersicum var. cerasiforme (SLC), which was later improved into the big-fruited tomato S. lycopersicum var. lycopersicum (SLL) in Mesoamerica. The fact that SP can freely cross with SLL has enabled the breeding of modern tomato cultivars to improve disease resistance, abiotic stress tolerance, and other fruit quality traits derived from the wild species. Due to the importance of SP, draft genome assemblies have been generated. Here we present a high quality genome sequence of SP that will enable research and breeding using this ancestral genome.

Technical 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.