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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #397581

Research Project: Genetics, Epigenetics, Genomics, and Biotechnology for Fruit and Vegetable Quality

Location: Plant, Soil and Nutrition Research

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

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

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.