Haplotype-resolved assembly of cultivated tetraploid potato

栽培四倍体马铃薯的单倍型解析组装

• 批准号: 514146394
• 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
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/514146394?language=en
• 关键词: Haplotype; resolved; assembly; cultivated; tetraploid

Potato is one of the most important staple foods and is among the five most produced crops in the world. Globally more than 350 billion kilograms of potato are produced per year with an increasing trend particularly in developing countries in Asia. But despite this social and economic importance, our knowledge of the genomic makeup modern potato cultivars is negligibly small as the highly divergent and autotetraploid genome challenges the commonly applied genome resequencing methods. In this project, we propose to use our newly developed assembly method to generate haplotype-resolved, chromosome-scale assemblies of ten carefully chosen potatoes. For this we have selected cultivars which were introduced in the beginning of modern potato breeding and were repeatedly used in various different breeding programs. The 40 haplotypes we propose to assemble are therefore segregating in many of the contemporary potato cultivars and knowing their sequence can support functional annotation of many of these contemporary potatoes. To show how these newly generated haplotypes can actually be used in practice, we will combine the 40 haplotypes assemblies to a complex reference sequence (using genome-graph based alignment algorithms) and use them for a broad-scale genomic diversity analysis of more than 100 publicly available potato genomes (sequenced with short reads). This will allow us to showcase how the resource can be used and at the same time untangle the genomic impact of modern potato breeding. Besides these insights, the assembled haplotypes and the means how to make use of them will be an unprecedented tool for the potato community and specifically support genomic-assisted breeding efforts.

马铃薯是最重要的主粮之一，也是世界上产量最多的五种作物之一。全球马铃薯年产量超过 3500 亿公斤，并且呈增长趋势，特别是在亚洲发展中国家。但是，尽管具有如此重要的社会和经济重要性，我们对现代马铃薯品种的基因组构成的了解却微乎其微，因为高度分化的同源四倍体基因组对常用的基因组重测序方法提出了挑战。在这个项目中，我们建议使用我们新开发的组装方法来生成十个精心挑选的马铃薯的单倍型解析的染色体规模组装。为此，我们选择了在现代马铃薯育种之初引入的品种，并在各种不同的育种计划中反复使用。因此，我们建议组装的 40 个单倍型在许多当代马铃薯品种中是分离的，了解它们的序列可以支持许多这些当代马铃薯的功能注释。为了展示如何在实践中实际使用这些新生成的单倍型，我们将把 40 个单倍型组件组合成一个复杂的参考序列（使用基于基因组图的比对算法），并使用它们对 100 多个公开可用的马铃薯基因组（使用短读长测序）进行大规模基因组多样性分析。这将使我们能够展示如何利用资源，同时阐明现代马铃薯育种的基因组影响。除了这些见解之外，组装的单倍型以及如何利用它们的方法将成为马铃薯界前所未有的工具，并特别支持基因组辅助育种工作。