The evolution of the RLP gene family in wild tomato species

为了产生病原体抗性作物，也在不断变化的气候条件下，重要的是要了解野生作物近缘种的自然群体中控制病原体抗性的机制。然而，这些作物近缘种中抗性相关基因的遗传多样性和进化仍然知之甚少。本论文旨在研究野生番茄中RLP（Receptor Like Protein）基因家族的多样性、进化和功能。RLP基因家族庞大而复杂，其成员在发育中发挥着各种作用，最重要的是在抗性中发挥作用。RLP最好在真菌Cladosporium fulvum和番茄Solanum lycopersicum之间相互作用的背景下进行研究。植物-病原体相互作用的最佳分子模型系统之一。在野生番茄近缘种中已经描述了大量作为枝孢属抗性基因（称为Cf基因）起作用的RLP，并且一些研究还显示了一个或多个野生番茄物种中单个Cf基因的等位基因变异和重组变体。然而，RLP的多样性，进化和功能缺乏系统的了解。近年来，长读段测序的质量有了巨大的提高。靶向重测序等新方法使广泛挖掘基因组和丰富大型复杂基因家族（如RLP基因家族）成为可能。在这个项目中，我将使用长读和RLP基因的靶向重测序的组合。我将使用这些序列数据1）对不同野生番茄物种中的所有RLP进行编目，并研究不同物种是否包含抗性基因，以及这些差异是否与例如气候有关。2)研究与RLP在防御和发育中的不同假设作用相关的潜在进化机制，3）对RLP的一个子集进行功能研究，以验证基因家族中观察到的遗传多样性的含义，并提供RLP如何在抗性中发挥作用的见解。在项目结束时，我们将对野生番茄中的RLP家族有一个完整的概述，将知道基因的进化历史，并将能够将其置于功能性的背景下，在对主要病原体如C的抗性方面。黄腐病菌因此，该项目将为基因家族进化提供有价值的基础知识。它还将为番茄育种者寻找新的遗传资源以培育更好的抗性品种提供有用的信息。

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.