OctoSEQ- Sequencing the octoploid strawberry

该提案汇集了一个跨国学术和工业伙伴关系，使用一套创新的实验和计算方法来生成参考二倍体基因组序列。该团队包括来自英国、荷兰、西班牙、意大利和挪威的行业和学术合作伙伴。草莓基因分型技术的最新进展，例如通过美国领导的Rosbreed计划开发Axiom IStraw 90 k SNP基因分型平台（只有由于早期BBSRC资助的二倍体草莓基因组测序才有可能）导致了多个连锁图谱的创建，其使二倍体草莓遗传图谱的某些区域高度饱和。然而，只有四个“二倍体”祖先亚基因组中的一个测序的不足现在是显而易见的，因为“非vesca”样亚基因组的覆盖率相对较低。利用生物信息学和测序的一些最新进展，结合称为大规模并行BAC测序的技术，拟议的项目团队将首先组装一个单倍体草莓基因组的单倍体版本。然后使用测序方法将其分离到单独的亲本基因组中，该测序方法将使用来自BAC序列的信息与单分子光学作图联合收割机组合。支架的进一步锚定将被部署以将基因组组装成完整的染色体。这种方法以前从未尝试过，并且由于最近在基因组测序和可视化方面的一些创新，在过去的六个月里才成为可能，并且处于基因组技术的前沿。这将把基因组分解成两个“单倍型”，一个来自测序品种的每个亲本，允许跟踪遗传，这是一个重要的创新。草莓生产是英国园艺业最成功的故事之一，国内产量仍在继续扩大，导致超过80%的季节自给自足。该作物对英国的价值最近超过每年5亿英镑，使其成为英国价值最高的水果作物。在全球范围内，生产的主要问题仍然是卵菌和真菌疾病的威胁，目前英国正在通过一项由英国工业、BBSRC和Innovate UK资助的综合研究计划来解决这些问题。该行业通过IPA计划支持这一提议，因为他们认识到标记辅助育种（MAB）和其他育种技术对四倍体基因组序列的需求。MAB是一种利用重要基因的近似位置来提高育种计划选择效率的技术，在世界各地的公共和私营部门的许多草莓育种计划中积极部署。然而，由于缺乏一个二倍体草莓基因组，在确定重要的抗病性和果实品质性状的致病基因的进展是缓慢的。基因功能的鉴定和表征是非常重要的，不仅可以使最新一代的顺基因和靶向诱变方法在研究和育种中得以使用，而且还可以促进对多倍体性状进化的基本科学兴趣问题的研究，这对作物科学家和基础研究人员都非常重要。对基因组和基因组的进化和结构的进一步研究将具有广泛的科学意义。这项研究的影响将是巨大的，因为在这个项目中采取的开放和协作的方法吸引了行业和国家研究领导者，使该项目产生的结果能够迅速采用。同样，该项目的资金价值很高，因为它利用了EMR目前高水平的信息学能力以及TGAC的测序和信息学能力，并为泛欧项目和工业-学术界合作伙伴关系提供了跳板。

This proposal assembles a multinational academic and industry partnership to generate a reference octoploid genome sequence using a set of innovative experimental and computational approaches. This team includes industry and academic partners from the UK, Netherlands, Spain, Italy and Norway.Recent advances in strawberry genotyping technologies, for example the development of the Axiom IStraw90k SNP genotyping platform through the US-led Rosbreed programme (only possible due to the earlier part-BBSRC funded sequencing of the diploid strawberry genome) have led to the creation of multiple linkage maps, which highly saturate some areas of the genetic map for octoploid strawberry. However, the shortfalls of having only one of four of the 'diploid' ancestral subgenomes sequenced is now apparent, as coverage of the 'non-vesca'- like subgenomes is comparatively poor. Using some of the latest advances in bioinformatics and sequencing, combined with a technique termed massively parallel BAC sequencing, the proposed project team will first assemble a haploidised version of the octoploid strawberry genome. This will then be separated into separate parental genomes using a sequencing approach, which will combine using information from BAC sequences with single molecule optical mapping. Further anchoring of scaffolds will be deployed to assemble the genome into whole chromosomes. This approach has never been tried before and has only become possible in the last six months due to a number of recent innovations in genome sequencing and visualisation and is at the cutting edge of genome technology. This will resolve the genome into two 'haplotypes', one from each parent of the sequenced cultivar allowing inheritance to be tracked, which is an important innovation. Strawberry production is one of UK horticulture's greatest success stories and domestic output still continues to expand, leading to over 80% self sufficiency when in season. The value of the crop to the UK recently exceeded £500m per annum, making it the highest value fruit crop in the UK. Globally, the primary problems of production remain the threats of oomycete and fungal diseases, which are now being addressed in the UK through a comprehensive research programme funded by both the UK industry, BBSRC and Innovate UK. The industry are supporting this proposal through the IPA scheme, as they recognize the need for an octoploid genome sequence, for marker assisted breeding (MAB) and other breeding techniques.MAB is a technique that uses the approximate location of important genes to improve the efficiency of selection in breeding programmes, actively deployed in a number of strawberry breeding programmes around the world, both in the public and private sector. However, due to the lack of an octoploid strawberry genome, progress at identifying the causative genes underpinning important disease resistance and fruit quality traits is slow. Identification and characterisation of gene function is important, not only to enable use of the latest generation of tools in cisgenic and targeted mutagenesis approaches in research and breeding, but also facilitates the study of questions of fundamental scientific interest about trait evolution in polyploids, which is of great important to both crop scientists and fundamental researchers. Further research on the evolution and structure of the genome and gene ohnologs will be of broad scientific interest. The impact of this research will be large, as the open and collaborative approach that is being taken in this project engages both industry and national research leaders, allowing rapid adoption of the results arising from this project. Similarly, the value for money of the project is high, as it leverages the currently high level of informatics capability available at EMR and sequencing and informatics capabilities at TGAC and provides a springboard to pan-European projects and industry-academia partnerships.