OctoSEQ- Sequencing the octoploid strawberry

这一提议汇集了一个跨国学术和行业合作伙伴关系，以使用一套创新的实验和计算方法来生成参考八倍体基因组序列。该团队包括来自英国、荷兰、西班牙、意大利和挪威的业界和学术合作伙伴。草莓基因分型技术的最新进展，例如通过美国领导的罗斯布赖德计划开发的Axiom IStraw90k SNP基因分型平台(只有由于BBSRC资助的二倍体草莓基因组测序的早期部分才有可能)导致创建了多个连锁图谱，这使得八倍体草莓遗传图谱的某些区域高度饱和。然而，现在只对四个‘二倍体’祖先亚基因组中的一个进行测序的缺陷是显而易见的，因为对‘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方面的一些最新进展，结合一种名为大规模并行BAC测序的技术，拟议的项目团队将首先组装八倍体草莓基因组的单倍体版本。然后将使用测序方法将其分离到单独的亲本基因组中，该方法将使用来自BAC序列的信息与单分子光学作图相结合。进一步的支架锚定将被部署以将基因组组装成完整的染色体。这种方法以前从未被尝试过，只是在过去的六个月里才成为可能，这是由于最近基因组测序和可视化方面的一些创新，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，这是一项重要的创新。草莓生产是英国园艺业最成功的故事之一，国内产量仍在继续增长，导致在季节自给自足超过80%。该作物对英国的价值最近超过了每年5亿GB，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个由英国工业、BBSRC和Innovate UK共同资助的综合研究计划来解决这些问题。业界通过IPA计划支持这一建议，因为他们认识到需要八倍体基因组序列，用于标记辅助育种(MAB)和其他育种技术。MAB是一种利用重要基因的大致位置来提高育种计划中选择效率的技术，在世界各地的一些公共和私营部门的草莓育种计划中积极应用。然而，由于缺乏八倍体草莓基因组，在鉴定支撑重要抗病和果实品质性状的致病基因方面进展缓慢。基因功能的鉴定和表征是重要的，不仅可以在研究和育种中使用最新一代的顺式和定向突变方法，而且还有助于研究多倍体性状进化的基本科学兴趣问题，这对作物科学家和基础研究人员都是非常重要的。进一步研究基因组和基因技术的进化和结构将具有广泛的科学意义。这项研究的影响将是巨大的，因为该项目正在采取的开放和合作的方法吸引了行业和国家研究领先者，使该项目产生的结果得以迅速采用。同样，该项目的性价比很高，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，并为泛欧洲项目和产业界-学术界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.