The evolution of the RLP gene family in wild tomato species

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In order to generate pathogen resistant crops, also under changing climate conditions, it is important to understand the mechanisms that govern pathogen resistance in natural populations of wild crop relatives. However, the genetic diversity and evolution of resistance-associated genes in such crop relatives remains poorly understood. Here I want to study the diversity, evolution and function of the RLP (Receptor Like Protein) gene family in wild tomato. The RLP gene family is large and complex, and the members fulfill various roles in development and most importantly in resistance. RLPs are best studied in the context of the interaction between the fungus Cladosporium fulvum and tomato, Solanum lycopersicum. One of the best understood molecular model systems for plant-pathogen interactions. A large number of RLPs that function as Cladosporium resistance genes, called Cf genes, have been described in wild tomato relative and several studies also show allelic variation and recombinant variants of single Cf genes in one or more wild tomato species. However, systematic understanding of RLP diversity, evolution and functionality is lacking. Recent years have seen a tremendous improvement in quality for long read sequencing. New approaches like targeted resequencing make it possible to extensively mine genomes and enrich for large and complex gene families such as the RLP gene family. In this project, I will use a combination of long read and targeted resequencing of RLP genes. I will use these sequence data to 1) catalog all RLPs in different wild tomato species and study whether different species contain resistance genes and whether these differences are for example climate related. 2) Study the underlying evolutionary mechanisms in relation to the different hypothesized roles of RLPs in defence and development and 3) perform functional studies on a subset of RLPs, in order to validate the implications of the observed genetic diversity in the gene family and to provide insights in how RLPs function in resistance in general. At the end of the project we will have a complete overview of the RLP family in wild tomatoes, will know the evolutionary history of the genes and will be able to place this in the context of functionality, in terms of resistance against major pathogens like C. fulvum. Thus, this project will provide valuable basic knowledge on gene family evolution. It will also provide useful information for tomato breeders looking for new genetic resources to generate better resistant varieties.