The Development of New Diploid (F. iinumae) and Polyploid Reference Genomes for Strawberry (Fragaria)

The F. vesca ‘Hawaii 4’ reference genome has proven to be an immensely valuable resource for strawberry genetic/genomic research and resource development, including the IStraw90 SNP array. However, of the four pairs of subgenomes present in octoploid Fragaria, including the cultivated species F. xananassa, only one pair is derived from F. vesca. Here we describe the development of a second diploid strawberry reference genome, that of the ancestral diploid F. iinumae (Fii).  Using germplasm collected in Hokkaido, Japan in 2004, we have developed an F2 generation mapping population which was subjected to SNP array and GBS genotyping, culminating in the construction of a high density linkage map of 4,173 markers at 496 loci spanning 451 cM. This map is now being used to anchor a Fii genome assembly. Comparison of the Fii linkage map to available versions of the ‘Hawaii 4’ genome assembly reveals no large scale genomic rearrangements, but illuminates discrepancies that may be indicative of small scale divergences and/or remaining errors in the latest 'Hawaii 4' assembly. The development of an octoploid reference genome is also being pursued, utilizing a novel strategy in which diploid x octoploid crosses are used to produce pentaploid progeny which can be exploited as “surrogate haploids”.  A preliminary linkage map has been constructed using SNP array data from a pentaploid progeny population, and whole genome sequencing of a specific pentaploid individual has been initiated.