A solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity

Authors: POWELL, ADRIEN - Boyce Thompson Institute; FEDER, ARI - Boyce Thompson Institute; LI, JIE - Boyce Thompson Institute; SCHMIDT, MAXIMILLION - Aachen University; COURTNEY, LANCE - Cornell University; ALSEEKH, SALEH - Max Planck Institute For Biogeochemistry; JOBSON, EMMA - Boyce Thompson Institute; VOGEL, ALEXANDER - Aachen University; XU, YIMIN - Boyce Thompson Institute; LYON, DAVID - Lawrence Berkeley National Laboratory; DUMSCHOTT, KATHRYN - Ibg-4 Bioinformatics; MCHALE, MARCUS - National University Of Ireland; SUPLICE, RONAN - National University Of Ireland; BAO, KAN - Boyce Thompson Institute; LAL, ROHIT - Boyce Thompson Institute; DUNHAN, ASHA - Boyce Thompson Institute; HALAB, ASIS - Ibg-4 Bioinformatics; DENTON, ALISANDRA - Aachen University; BOLGER, MARIE - Ibg-4 Bioinformatics; FERNIE, ALISDAIR - Max Planck Institute For Biogeochemistry; HIND, SARA - University Of Illinois; MUELLER, LUKAS - Boyce Thompson Institute; MARTIN, GREGORY - Boyce Thompson Institute; FEI, ZHANGJUN - Boyce Thompson Institute; MARTIN, CATHIE - John Innes Center; Giovannoni, James; STICKLER, SUSAN - Boyce Thompson Institute; USEDAL, BJORN - Aachen University

Submitted to: The Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/27/2022
Publication Date: 4/12/2022
Citation: Powell, A., Feder, A., Li, J., Schmidt, M., Courtney, L., Alseekh, S., Jobson, E., Vogel, A., Xu, Y., Lyon, D., Dumschott, K., Mchale, M., Suplice, R., Bao, K., Lal, R., Dunhan, A., Halab, A., Denton, A., Bolger, M., Fernie, A., Hind, S., Mueller, L., Martin, G., Fei, Z., Martin, C., Giovannoni, J.J., Stickler, S., Usedal, B. 2022. A solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. The Plant Journal. 110(6):1791-1810. https://doi.org/10.1111/tpj.15770.
DOI: https://doi.org/10.1111/tpj.15770

Interpretive Summary: Tomato is one of the most widely consumed fruit crops with great worldwide value. It is rich in essential nutrients, particularly provitamin A, folate, vitamin C, vitamin E and vitamin K, and calcium. Tomato yield, however, is often reduced significantly by losses caused by adverse environmental conditions, disease, pest damage, and post-harvest processes. The narrow collections deployed in most breeding programs limits the potential for tomato improvement. Fortunately, close wild relatives present opportunities to add enormous genetic diversity to tomato breeding programs and the means to identify and study genes that underpin useful traits. At least 14 wild relatives can be crossed to the cultivated tomato including Solanum lycopersicoides. In addition, this wild tomato has been shown to exhibit enhanced tolerance to cold, heat, drought and salt. To improve understanding of the genes responsible for these agriculturally important traits and increase the utility of this wild tomato relative in tomato breeding, a full genome sequence was generated. We compared the genome to that of tomato to identify unique features that may be key to the understanding important characteristics that could be used to improve tomato.

Technical Abstract: Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37'938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36'×'LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene B-cyclase whose function we demonstrate.