Use of Strawberry Genomic Resources in GDR

The cultivated strawberry, Fragaria x ananassa, has a 600-800Mbp allo-octoploid genome consisting of four highly similar subgenomes and a high level of heterozygosity, making the assembly of an accurate whole genome sequence technically very challenging. A high quality reference genome for this valuable fruit crop is highly desirable and would facilitate enhanced methods for gene and SNP discovery, marker-assisted breeding, genomic selection, genome-wide association studies, pedigree based analyses and genotyping-by-sequencing to a far greater extent than the closest currently available high quality genome, that of the diploid F. vesca.

We are currently undertaking a research program with the backing of a consortium of industry partners to produce a comprehensive octoploid genome sequence of the cultivar Redgauntlet using a range of current Illumina-associated technologies (DISCOVAR, long mate pair) and emerging technologies (10x) to hierarchically scaffold the genome to full chromosome scale, developing polyploid aware algorithms at each stage.

The final stage of genome assembly will utilise a high resolution consensus genetic map constructed using the IStraw90 Affymetrix Axiom(R) genotyping platform, using data from F1 mapping populations totaling approximately 1000 progeny. To facilitate linkage map construction we have developed a new outcross mapping tool, Crosslink (https://github.com/eastmallingresearch/crosslink), which automatically corrects common polyploidy related genotyping and mapping errors, and provides several novel features to allow rapid and robust map construction including graphical quality control checks.

We have also developed a resequencing panel of strawberry lines that are important for genetics studies, again using DISCOVAR compatible libraries and a comprehensive transcriptome survey sample set, using Pacbio Isoseq and stranded illumina libraries.

GDR will be used as the main repository for data deposition (as well as short read archives). This talk will outline the timeline for availability of data in the rosaceae database.