Extent and side effects of wild introgressions in cultivated tomato

在过去的一个世纪里，将野生等位基因导入栽培番茄是育种中的一种常见做法，它已经改善了重要的性状，如病原菌抗性或果实品质。因此，即使不是全部，也是大多数现代番茄品种都含有来自各种野生番茄品种的导入基因。虽然每个导入的基因和功能都得到了很好的描述，但关于这些导入的确切大小、其中包含的基因数量，或者由于不完全回交方案而散布在整个基因组中的额外的意外野生片段的存在，人们知之甚少。这些特征在唯一可用的栽培番茄参考基因组序列中变得明显，其中可以检测到四个导入，其中一个不包含任何已知的有益基因。由于它们的跨度很大，来自野生物种的导入可能会产生与最初设计导入时不同的重大意想不到的后果。已有文献记载的负面影响包括由于导入区域的基因组重排而抑制重组，或由于不利的基因沿着导入中的有利等位基因拖拽而产生的多效性效应。在这里，我们建议利用已公布的涵盖13个不同物种的600多个番茄种质的全基因组信息来建立第一个400多个番茄品种的野生导入的综合目录。为此，我们建议首先从一个不包含任何导入的品种中构建一个番茄参考基因组组件。这一新的高质量参考基因组将极大地简化非栽培片段的鉴定，并使基于上述重新测序数据生成栽培番茄野生导入的全面目录成为可能。由此产生的目录将允许我们选择另外五个品种，显示现代番茄中最常见的导入分离。然后，选定的材料将被用来产生它们的导入组装，从而极大地扩展了我们对制造现代番茄的基因库的了解。最后，我们将结合新的技术和经典的遗传方法来研究最常见的导入对携带它们的材料的减数分裂重组的抑制和转录图谱的修改的影响。本项目的研究成果不仅将为今后番茄的研究提供重要资源，还将直接指导通过导入精准育种改良番茄品种。我们的联盟将两个具有互补优势的团队结合在一起，包括在番茄遗传和进化方面的长期专业知识，以及在高通量基因组数据分析和基因组组装方面的经验。

Introgression of wild alleles into cultivated tomato has been a common practice in breeding programs over the last century that has improved important traits like pathogen resistance or fruit quality. As a result, most if not all modern tomato varieties contain introgressions from a variety of wild tomato species. While the genes and functions that motivated each of the introgressions are well described, little known is known about the exact size of these introgressions, the number of genes included in them, or the existence of additional unexpected wild segments scattered throughout the genome due to incomplete backcrossing schemes. These features became evident in the only cultivated tomato reference genome sequence available, where four introgressions could be detected and one of them does not contain any known beneficial gene. Due to their large spans, introgressions from wild species can have significant unexpected consequences different from those intended when the introgressions were originally designed. Documented negative effects include suppression of recombination due to genomic rearrangements in the introgressed region or pleiotropic effects due to unfavorable genes dragged along the beneficial alleles included in the introgression.Here we propose to utilize published whole-genome information of more than 600 tomato accessions encompassing 13 different species to establish the first comprehensive catalog of wild introgressions in more than 400 tomato cultivars. To do this, we propose to first construct a tomato reference genome assembly from a cultivar that does not contain any introgressions. This new high-quality reference genome will greatly simplify the identification of non-cultivated fragments and enable the generation of a comprehensive catalog of wild introgressions in cultivated tomato based on the re-sequencing data mentioned above. The resulting catalog will allow us to select five additional cultivars displaying the most common introgressions segregating in modern tomatoes. The selected accessions will be then used to generate assemblies of their introgressions, thus greatly expanding our knowledge on the gene pool that makes modern tomatoes. Finally, we will combine novel techniques with classic genetic approaches to study the effect of the most common introgressions on the suppression of meiotic recombination and modification of transcriptional landscape of the accessions that carry them. The results of this project will not only generate major resources for future research in tomato, but will also serve as direct guidance to improve tomato cultivars by precision breeding of introgressions. Our consortium combines two groups with complementary strength including long lasting expertise in tomato genetics and evolution with experiences in high-throughput genomic data analysis and genome assembly.