Tomato Yellow Leaf Curl Virus Disease incited by Tomato yellow leaf curl virus (TYLCV) causes huge losses in tomato production worldwide and is caused by different related begomovirus species. Breeding for TYLCV resistance has been based on the introgression of multiple resistance genes originating from several wild tomato species. In this study we have fine-mapped the widely used Solanum chilense–derived Ty-1 and Ty-3 genes by screening nearly 12,000 plants for recombination events and generating recombinant inbred lines. Multiple molecular markers were developed and used in combination with disease tests to fine-map the genes to a small genomic region (approximately 70 kb). Using a Tobacco Rattle Virus–Virus Induced Gene Silencing approach, the resistance gene was identified. It is shown that Ty-1 and Ty-3 are allelic and that they code for a RNA–dependent RNA polymerase (RDR) belonging to the RDRγ type, which has an atypical DFDGD motif in the catalytic domain. In contrast to the RDRα type, characterized by a catalytic DLDGD motif, no clear function has yet been described for the RDRγ type, and thus the Ty-1/Ty-3 gene unveils a completely new class of resistance gene. Although speculative, the resistance mechanism of Ty-1/Ty-3 and its specificity towards TYLCV are discussed in light of the function of the related RDRα class in the amplification of the RNAi response in plants and transcriptional silencing of geminiviruses in plants.

Tomato mosaic virus (ToMV) is an important Tobamovirus that causes significant crop losses. Resistance to the ToMV is conferred by the genes Tm1, Tm2 and Tm2a. Among these three genes, Tm2a confers resistance to most strains of the ToMV. Screening of genetic lines under field conditions based on phenotype is time‐consuming and challenging due to concerns associated with stability of the virus and its potential transmission to other plants. Tightly linked molecular markers associated with resistance genes can improve selection efficiency and avoid these problems. This study developed a PCR‐based marker based on restriction site differences from Tm2a locus‐specific sequences, which was found to be useful in identifying the resistant and susceptible genotypes and was consistent with phenotypic data. The marker is a codominant cleaved amplified polymorphic sequence (CAPS) marker producing 270‐ and 600‐bp DNA fragments from resistant genotypes and an 870‐bp fragment from susceptible genotypes when digested with HaeIII restriction enzyme. This novel marker can be useful for tomato breeders to screen progeny from segregating populations for ToMV resistance.

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Late blight (LB), caused by the oomycete Phytophthora infestans, is one of the most devastating diseases of tomato. Three major genes Ph-1, Ph-2 and Ph-3 conferring resistance to LB have been identified and mapped to the chromosomes 7, 10 and 9, respectively. However, PCR-based molecular markers associated with these genes are limited. Molecular markers are extremely useful in the screening and selection of tomato lines for the development of LB resistant genotypes. The objective of this study was to identify molecular markers associated with Ph-3 gene conferring LB resistance in tomato. Four co-dominant markers were found to be associated with Ph-3, all of which were sequence characterized amplified region (SCAR) type. Breeding lines and cultivars were inoculated with a field isolate of Phytophthora infestans to collect phenotypic data on disease resistance. Genotypic data from molecular markers associated with Ph-3 were in close agreement with the phenotypic data for the lines tested. With the verification of genotypic data from novel molecular markers in known genotypes supported by phenotypic data, the novel molecular markers may be useful in screening tomato populations aiming to develop LB resistant genotypes or cloning the LB resistant genes.