Viral diseases cause significant economic losses and are a great risk for a sustainable agriculture. In tomato production, viral disease outbreaks have frequently occurred and caused by new or reappearing viruses, also termed (re)emerging viruses. In recent years, two DNA viruses, TYLCV (tomato yellow leaf curl virus) and ToLCNDV (tomato leaf curl New Delhi virus), and two RNA viruses, ToBRFV (tomato brown rugose fruit virus) and ToCV (tomato chlorosis virus), have had a huge impact on tomato production. In this project, together with eight breeding companies, we aim to breed tomato (& other crops) with durable resistance to viral diseases by using impaired plant susceptibility (S) genes. Our three objectives are (1) to identify & disable plant S-genes, (2) to study the underlying mechanism of the (disabled) identified S-gene(s) and (3) to evaluate the breeding values of impaired S-genes.
We have chosen the S-gene-based approach since viral genomes encode only a small number of proteins and thus viruses are fully dependent on host proteins encoded by S-genes for their proliferation. This is supported by the fact that more than half of the identified resistance factors to viruses are recessively inherited, indicating that the resistance is conferred by loss-of-function of certain S-genes.
This proposal is a follow-up of our previous TKI project (LWV19106), in which we have worked with 12 breeding companies on the identification of tomato S-genes for the four above-mentioned viruses. We have obtained a number of EMS (Ethyl methanesulfonate) and CRISPR mutants with resistance to different viruses. In this project, we will (1) clone the causal S genes of the EMS mutants; (2) study molecular mechanisms associated with certain S-genes and identify novel S genes by innovative approaches (e.g. Proximity labeling). Also, we will (3) continue to screen our tomato EMS population to identify additional mutants. Meanwhile, (4) uncovering allelic variation of the studied S-genes by mining a sequence library of our EMS population and genetic resources of companies. With the identified mutants, in-gene markers, and knowledge on molecular mechanisms, breeding companies will evaluate the breeding values of the S-gene mutants.
Since plant S-genes are shown to be conserved across plant species, the identified S-genes and the new precompetitive knowledge that will be acquired in this project can be easily transferred to other crops.

We aim to breed tomato (& other crops) with durable resistance to viral diseases by using impaired plant susceptibility (S) genes, with three objectives:
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to identify and disable S-genes by generating mutated alleles of the gene
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to study the underlying mechanism of the (disabled) S-gene(s)
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to evaluate the breeding values of the studied S-genes

Viral diseases cause significant economic losses and are a risk for sustainable agriculture due to the use of pesticides, mainly insecticides. At least 312 viruses, satellite viruses, or viroid species in 22 families and 39 genera are associated with tomatoes. The global production of crops is hampered by viral diseases and especially by (re)emerging viruses. (Re)emerging viruses occur due to genomic variation that arises through recombination or acquisition of extra genomic components. Viruses have small RNA or DNA genomes that encode for only a few proteins (5-14). Hence viral proliferation depends on plant S-genes. In this project, we aim to identify plant S-genes and to exploit the impaired S-genes for breeding crops with durable resistance to viruses. Since the use of pesticides/insecticides is becoming more and more restricted, sustainable crop production is becoming increasingly dependent on the use of resistant cultivars. Therewith, the project fits to ST2 (Biotechnology and molecular Breeding) and contributes to durable resilience and sustainable agriculture.

From this proposed project, we anticipate to obtain the following results:
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Plant materials:
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Tomato mutants, five from the previous project and, ~five additional mutants from this project with resistance to the studied viruses and potentially other pathogens.
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S-gene-edited tomato mutants.
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Tools:
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Improved disease assays for ToCV.
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DNA sequence information of S-gene allele series.
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In-gene markers for specific S-gene alleles to facilitate marker assisted selection.
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Know-how:
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Candidates S-genes for viral diseases.
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Insight into functional protein domains encoded by the S-genes, which can be used to create impaired S-genes without causing negative side-effects on plant development.
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New precompetitive knowledge on the modes-of-action of the identified S-genes.
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A potential Patent application, a PhD thesis and scientific papers to public and scientific community
Collaboration with the eight participating companies in this project will certainly ensure a direct knowledge transfer to support innovation in practical breeding, including the use of the identified tomato mutants in their breeding programs where in-gene markers can be applied for marker-assisted selection. With the tomato mutants and insight into mechanisms of S-gene function, companies can extended the S-gene concept to other crops to breed for durable viral disease resistance.