Octoseq- sequencing the octoploid strawberry

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.

Principal Investigators: Dr Richard Harrison, Dr Matt Clark

Funder: BBSRC

Duration: 2016-2018

Collaborators: Earlham Institute, Wageningen university, INRA

Industry Partners: AHDB, Freshforward, Graminor, Planasa, Limgroup

Single molecule sequencing is revolutionising the reconstruction of complex plant genomes

The cultivated strawberry is a complex octoploid, derived from two wild octoploid progenitor species.

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