The evolution of the RLP gene family in wild tomato species

为了在不断变化的气候条件下培育出抗病原菌的作物，了解野生作物近缘自然种群的抗病原菌机制是很重要的。然而，在这类作物近亲中，抗性相关基因的遗传多样性和进化仍然知之甚少。本文主要研究野生番茄RLP （Receptor Like Protein，受体样蛋白）基因家族的多样性、进化和功能。RLP基因家族是一个庞大而复杂的基因家族，其成员在发育过程中发挥着多种作用，最重要的是在抗性中发挥作用。在真菌黄枝霉与番茄茄的相互作用中，rlp得到了最好的研究。植物-病原体相互作用的最好理解的分子模型系统之一。在野生番茄亲缘种中已经发现了大量作为枝孢杆菌抗性基因的rlp，称为Cf基因，一些研究也表明单个Cf基因在一个或多个野生番茄物种中存在等位基因变异和重组变异体。然而，对RLP的多样性、演化和功能缺乏系统的认识。近年来，长读序列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RLP基因的长读和靶向重测序相结合的方法。我将利用这些序列数据1)编录不同野生番茄品种的所有rlp，研究不同品种是否含有抗性基因，以及这些差异是否与气候等因素有关。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在抗性中的作用。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，将了解基因的进化史，并将能够将其置于功能的背景下，在抵抗主要病原体方面，如C. fulvum。因此，该项目将为基因家族进化提供有价值的基础知识。它还将为寻找新的遗传资源以产生更好的抗性品种的番茄育种者提供有用的信息。

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.