Together with two pioneering academic labs with respective expertise in genome editing and disease resistance and two of the largest vegetable breeding companies with strong expertise in tomato breeding, Computomics contributes with a proprietary foundational AI model for gene regulation and pangenome expertise to the project "INNO-TOM - Using pangenomes and gene targeting approaches to breed disease-resistant and nutrient-enriched cis- and intragenic INNOvative TOMato varieties" funded by the German BMBF.
Research topics:
INNO-TOM aims at creating novel tomato cis- and intragenic varieties with traits that will provide benefits for the growers as well as for the consumers. With 186 million tons of fresh fruit produced in 2022 (FAOSTAT), tomato is the second most important vegetable crop worldwide next to potato. Tomato is grown in a wide range of countries, including Germany, either in the field, e.g. for processing tomatoes, or in greenhouses for the fresh market. The tomato seed market is highly competitive and time to market is a key factor in the development of novel varieties.
The traits we will target are bacterial and virus resistance as well as biofortification. We will introduce these traits using a highly efficient genome editing technology (Cas-Exo) which IPB Halle developed during a previously funded BMBF project (Genereplace, Crop Plants of the Future). Cas-Exo is based on homology directed repair (HDR) and allows the direct replacement of alleles or variants from the breeder’s pool into the genome of breeding cultivars. This leads to two critical advantages to efficiently breed climate resilient plant varieties:
Thus, INNO-TOM will provide solutions to breeders who need to rapidly develop novel varieties adapted to climate change, contributing to a more sustainable agriculture with reduced use of pesticides and satisfying consumer needs. We will target two major diseases of tomato cultivation: bacterial spot (caused by Xanthomonas sp.) and viral diseases caused by Tobamoviruses, such as the Tomato Mosaic Virus (ToMV) and Tomato Brown Rugose Fruit Virus (ToBRFV). Both these diseases can cause major yield loss and see the emergence of novel strains that overcome current resistance genes, requiring rapid breeding to avoid pandemics. The second type of trait we will target is biofortification to create cis-genic purple tomatoes that accumulate anthocyanins, which has been previously achieved by a transgenic approach. A diet rich in anthocyanins has disease-preventing benefits and tomato, as the most widely consumed fresh vegetable, is ideally suited for this purpose. Furthermore, anthocyanin-rich tomatoes have an extended shelf life and reduced susceptibility to gray mold.
All the traits we will develop satisfy the criteria of Annex I of the recently proposed change in the EU regulation of genome edited crops, which was recently approved by the EU Committee on Environment, Food Safety and Public Health, and are therefore anticipated to be brought to the market without the need for deregulation in the near future in the EU. In both cases (disease resistance and biofortification), the identification of the alleles or promoter enhancers to be introduced will be supported by bioinformatics, in particular the development of a tomato pangenome browser (Computomics GmbH).
At the end of the initial four years of this project, we will produce tomato lines with cumulated disease resistance and biofortification traits in elite breeding material provided by the tomato breeding partners. These lines will then be ready for testing. The concept can then be extended to other traits for the second funding period. The INNO-TOM consortium consists of two academic labs with respective expertise in genome engineering and disease resistance, a bioinformatics SME (Computomics GmbH) and two tomato breeding companies (KWS and Rijk Zwaan), thus covering the whole value chain from initial research to development and commercialization. INNO-TOM will serve as a blueprint for the use of Homology-Based Genome Editing (HBGE) in plant breeding for other crops.
Partners involved are:
Project duration is four years (Nov 2024 – Oct 2028), with the option to extend for another four years.
The project is supported by funds of the German Federal Ministry of Education and Research (FKZ 031B1538C).
Share on