ABR-PG: The Use of Pentaploid Surrogates for Assembly and Anchoring of Octoploid Strawberry Genomes

ABR-PG：使用五倍体替代物组装和锚定八倍体草莓基因组

• 批准号: 1444585
• 负责人: Thomas Davis
• 金额: $ 41.14万
• 依托单位: University of New Hampshire
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-02-15 至 2018-01-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1444585&HistoricalAwards=false
• 关键词: ABR; PG; Use; Pentaploid; Surrogates

The cultivated strawberry (Fragaria x ananassa) and its immediate ancestors, F. chiloensis and F. virginiana, are an important and intriguing crop plant system from evolutionary, genomic and horticultural perspectives. Having originated from a cross between its two immediate ancestors in the mid-1700s, the cultivated strawberry is one of the youngest crop species. It has four genomes, each present in two copies, making a total of eight genomes. These were passed down from as many as four ancestors, thus making the cultivated strawberry among the most genomically complex crop plants. As yet, it has not been possible to get a genome sequence for the cultivated strawberry, primarily because of the great complexity of having eight genomes. This challenge is addressed in this project by implementation of a new strategy that reduces the number of genomes to be sequenced from eight to four. The approach is to get a hybrid with five genomes - called a pentaploid - by first crossing a well-studied variety with two genomes (termed a diploid) to one with eight. After sequencing the pentaploid, the genome of the diploid is subtracted out bioinformatically, leaving only four genomes to be assembled. The result will be the first assembled genome sequence for one of the immediate ancestors of the cultivated strawberry, which will be a resource of immense value to strawberry researchers and breeders interested in further improving this economically important and healthful fruit crop.No reference genome has yet been established for an octoploid strawberry. Challenges facing such efforts include those inherent to polyploidy, as well as those associated with heterozygosity. The octoploid strawberry species, including the cultivated Fragaria x ananassa and its immediate ancestors F. chiloensis and F. virginiana, are subject to inbreeding depression, and doubled haploid clones as used for genome assembly in the peach and apple genome projects have not been an available option in strawberry. A bold approach will be implemented to solve this problem by using pentaploid hybrids as "modified haploid" subjects for whole genome sequencing and linkage mapping. The project goals are to construct a high resolution, pentaploid-based linkage map and use it to anchor a pentaploid-based genome assembly, from which the known diploid genome copy has been digitally subtracted out. Linkage mapping will be accomplished using markers from the Axiom IStraw90 SNP array. The specific project objectives are to: 1) construct a high resolution, octoploid linkage map based upon a novel, pentaploid mapping population; 2) construct an octoploid genome assembly based upon newly generated DNA sequence and optical mapping data derived from a single pentaploid plant; 3) anchor the genome assembly to the linkage map; and, 4) compare the utility of the newly assembled octoploid genome to that of the existing diploid genome as references in relation to an expanded program of SNP discovery in octoploid germplasm. The project will establish a needed knowledge foundation for subsequent research aimed at defining the subgenome composition(s) of the octoploid Fragaria species. Only within this knowledge framework will it be possible to define the homoeologues and subgenomic specificities of genes of economic and basic scientific interest. The employment of a pentaploid progeny population for linkage map construction will provide detailed insight into patterns of allele segregation that might otherwise be obscured by the challenges of genotype calling in an octoploid, thereby offering the potential to differentiate disomic and polysomic inheritance patterns and to finally establish whether the latter do in fact occur at the octoploid level in strawberry. The genomic resources to be developed, including the first octoploid reference genome, will be rapidly disseminated via the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) and Genome Database for Rosaceae (http://www.rosaceae.org/) public databases. The research products will advance both basic and applied research in strawberry, and will reinforce efforts to implement marker-assisted breeding in strawberry.

从进化、基因组和园艺的角度来看，栽培草莓（Fragaria x ananassa）及其直接祖先 F. chiloensis 和 F. virginiana 是一种重要且有趣的农作物系统。 栽培草莓起源于 1700 年代中期其两个直系祖先之间的杂交，是最年轻的作物品种之一。 它有四个基因组，每个基因组有两个拷贝，总共有八个基因组。 它们是从多达四个祖先那里传承下来的，从而使栽培草莓成为基因组最复杂的农作物之一。 迄今为止，还不可能获得栽培草莓的基因组序列，主要是因为八个基因组非常复杂。 该项目通过实施一项新策略来解决这一挑战，该策略将待测序的基因组数量从八个减少到四个。该方法是通过首先将经过充分研究的具有两个基因组的品种（称为二倍体）与一个具有八个基因组的品种杂交，获得具有五个基因组的杂交体（称为五倍体）。 对五倍体进行测序后，从生物信息学角度减去二倍体的基因组，只留下四个基因组进行组装。 结果将是第一个组装的栽培草莓直系祖先之一的基因组序列，这对于有兴趣进一步改善这种经济上重要且健康的水果作物的草莓研究人员和育种者来说将是具有巨大价值的资源。尚未有参考基因组已为八倍体草莓建立。 这些努力面临的挑战包括多倍体固有的挑战以及与杂合性相关的挑战。八倍体草莓品种，包括栽培的 Fragaria x ananassa 及其直接祖先 F. chiloensis 和 F. virginiana，都受到近交衰退的影响，并且用于桃子和苹果基因组计划中基因组组装的双单倍体克隆尚未可用草莓的选项。将采用一种大胆的方法来解决这个问题，即使用五倍体杂种作为“修饰单倍体”对象进行全基因组测序和连锁图谱。该项目的目标是构建高分辨率、基于五倍体的连锁图，并用它来锚定基于五倍体的基因组组装，其中已知的二倍体基因组副本已被数字减去。将使用 Axiom IStraw90 SNP 阵列中的标记来完成连锁图谱。具体项目目标是： 1) 基于新型五倍体作图群体构建高分辨率八倍体连锁图谱； 2) 基于新生成的 DNA 序列和来自单个五倍体植物的光学图谱数据构建八倍体基因组组装； 3) 将基因组组装锚定到连锁图上； 4) 比较新组装的八倍体基因组与现有二倍体基因组的效用，作为与八倍体种质中 SNP 发现的扩展程序相关的参考。该项目将为后续研究建立所需的知识基础，旨在定义八倍体草莓物种的亚基因组组成。只有在这个知识框架内，才有可能定义具有经济和基础科学意义的基因的同源物和亚基因组特异性。使用五倍体后代群体进行连锁图谱构建将提供对等位基因分离模式的详细了解，否则这些模式可能会被八倍体中基因型调用的挑战所掩盖，从而提供区分二体性和多体性遗传模式并最终建立等位基因分离模式的潜力。后者是否确实发生在草莓的八倍体水平上。待开发的基因组资源，包括第一个八倍体参考基因组，将通过国家生物技术信息中心（http://www.ncbi.nlm.nih.gov/）和蔷薇科基因组数据库（http://www.ncbi.nlm.nih.gov/）快速传播/www.rosaceae.org/）公共数据库。该研究产品将推动草莓的基础和应用研究，并加强草莓标记辅助育种的实施力度。