Extent and side effects of wild introgressions in cultivated tomato

栽培番茄野生基因渗入的程度和副作用

• 批准号: 406695473
• 负责人: Professor Dr. Korbinian Schneeberger
• 金额: --
• 依托单位: Institut für Genetik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2018
• 资助国家: 德国
• 起止时间: 2017-12-31 至 2021-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/406695473?language=en
• 关键词: Extent; side; effects; wild; introgressions

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.

在过去的世纪里，将野生等位基因渗入栽培番茄已经成为育种计划中的一种常见做法，其改善了重要性状，如病原体抗性或果实品质。因此，大多数（如果不是所有的话）现代番茄品种含有来自各种野生番茄物种的基因渗入。虽然激发每个基因渗入的基因和功能都有很好的描述，但对这些基因渗入的确切大小、其中包含的基因数量或由于不完全回交方案而分散在整个基因组中的额外的意想不到的野生片段的存在知之甚少。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，其中可以检测到四种基因渗入，其中一种不包含任何已知的有益基因。由于它们的大跨度，来自野生物种的基因渗入可能具有与最初设计基因渗入时预期的那些不同的显著的意想不到的结果。记录的负面影响包括由于渗入区域中的基因组重排而抑制重组，或由于不利基因与渗入中包括的有益等位基因一起被沿着而产生多效性效应。包括13个不同物种的600多个番茄种质的基因组信息，以建立第一个400多个番茄野生渐渗的综合目录个品种要做到这一点，我们建议首先构建一个番茄参考基因组组装从一个品种，不包含任何基因渗入。这种新的高质量参考基因组将大大简化非栽培片段的鉴定，并能够基于上述重测序数据生成栽培番茄中野生基因渗入的综合目录。由此产生的目录将使我们能够选择五个额外的品种显示最常见的基因渗入分离在现代番茄。然后，选择的加入将用于产生它们的基因渗入的组装，从而大大扩展了我们对现代番茄基因库的知识。最后，我们将结合联合收割机新技术与经典的遗传方法，研究最常见的基因渗入对减数分裂重组的抑制和携带它们的加入的转录景观的修改的影响。该项目的结果不仅将为番茄的未来研究提供重要资源，而且还将为通过基因渗入的精确育种来改良番茄品种提供直接指导。我们的联盟结合了两个具有互补优势的团队，包括在番茄遗传学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。