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; 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，基因组和园艺观点来看，栽培的草莓（Fragaria X Ananassa）及其直系祖先F. chiloensis和F. Virginiana是一个重要而有趣的作物植物系统。 栽培的草莓起源于1700年代中期的两个直接祖先之间的十字架，是最年轻的农作物之一。 它有四个基因组，每个基因组分为两个拷贝，总共八个基因组。 这些是从多达四个祖先中传给的，因此使种植的草莓成为了最复杂的农作物植物。 到目前为止，还不可能获得栽培草莓的基因组序列，这主要是因为拥有八个基因组的复杂性。 该项目通过实施一种新策略来解决该挑战，该策略将要测序的基因组数减少到四个。该方法是通过首先将良好的品种与两个基因组（称为二倍体）越过八个基因组（称为五倍体），从而获得五个基因组的混合体，称为五倍体。 测序五倍体形成后，二倍体的基因组会从生物信息上减去，只剩下四个基因组要组装。 结果将是耕种草莓的直接祖先之一的第一个组装基因组序列，这将是对有兴趣进一步改善这种经济重要和健康的水果作物感兴趣的草莓研究人员和育种者的巨大价值的资源。尚未建立章鱼草莓的参考基因组。 这种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。章鱼草莓物种，包括栽培的Fragaria X Ananassa及其直接祖先F. chiloensis和F. Virginiana，受到近交抑郁症的约束，在桃子和Apple基因组项目中使用的基因组组装使用了两倍的单倍体克隆，在草莓中不可用。通过将五足动物杂种作为整个基因组测序和链接映射的“修改单倍体”主题，将实现一种大胆的方法来解决此问题。项目目标是构建一个高分辨率，基于五匹匹匹酯的链接图，并使用它来锚定基于五倍体的基因组组件，从中可以从中减去已知的二倍体基因组副本。链接映射将使用来自ISTRAW90 SNP数组的标记来完成。特定的项目目标是：1）基于新颖的五角足映射种群来构建高分辨率的章鱼链接图； 2）基于新产生的DNA序列和来自单个五型植物的光学映射数据构建章鱼基因组组装； 3）将基因组组件固定到链接图；和，4）将新组装的章鱼基因组与现有二倍体基因组的效用作为与章鱼种质中SNP发现扩展程序有关的参考。该项目将为后续研究建立一个必要的知识基础，旨在定义章鱼Fragaria物种的亚基因组组成。只有在这个知识框架内，才有可能定义经济和基本科学利益基因基因的同种词和亚基因组特异性。使用五培养基后代人口进行连锁图构造将提供对等位基因隔离模式的详细见解，否则可能会因章鱼中呼叫的基因型的挑战所掩盖，从而提供区分疾病和多性性遗传模式的潜力，并最终确定后者是否在octopplo级别上发生在Strapperry中。要开发的基因组资源，包括第一个章鱼参考基因组，将通过国家生物技术信息中心（http://www.ncbi.nlm.nih.gov/）迅速传播。研究产品将推进草莓的基础研究和应用研究，并将加强在草莓中实施标记辅助育种的努力。