Toward a Pentaploid-Based Assembly of an Octoploid Strawberry Reference Genome

The assembly of a reference genome for an octoploid Fragaria (strawberry) species remains an elusive goal. Challenges facing such efforts include those inherent to polyploidy, as well as those associated with heterozygosity. In the absence of an available octoploid-derived haploid or doubled haploid, we show that pentaploid hybrids and progeny populations generated from certain diploid x octoploid crosses can serve as “surrogate haploids”. These pentaploids offer many potential advantages for genomic research in strawberry, including linkage map construction.

A mapping population was derived from a cross between F. vesca ‘Hawaii 4’ (2x) and LB48 (8x), where LB48 is the F1 hybrid of a cross between F. virginiana accessions L1 (subsp. virginiana 8x) and BC6 (subsp. glauca 8x). The mapping population of 178 pentaploid individuals was subjected to SNP genotyping using the Axiom IStraw90 SNP array. A total of 6,586 markers were allocated to 29 linkage groups, covering a total map distance of 2,670 cM. In order to assign subgenome affinities to linkage groups, we classified SNP markers by performing phylogenetic analysis of marker flanking sequence and homolog sequences from F. vesca, F. iinumae, and other species. Markers in three subgenome categories (F. vesca- like, F. iinumae-like, and other/unknown) were identified. This study provided promising results of using a pentaploid progeny population for the construction of a high-density linkage map and in the long term for anchoring a genome assembly representative of an octoploid genome. One pentaploid plant has been chosen for sequencing and assembly, now in progress.