Use of Pentaploid Surrogates for Assembly and Anchoring of Octoploid Strawberry Genomes

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 have found that pentaploid hybrids and progeny populations generated from certain diploid x octoploid crosses can be used as “surrogate haploids”. These pentaploids offer many potential advantages for genomic research in strawberry. We describe initial progress in the use of a pentaploid progeny population to construct a linkage map. The mapping population derived from a cross between F. vesca (H4) and octoploid Fragaria LB48, where LB48 is a F1 hybrid between F. virginiana accessions L1 and BC6. A subpopulation of 30 pentaploid individuals was interrogated by the Axiom Istraw90 strawberry SNP array. A total of 5261 markers were used for map construction using JoinMap 4.1.  4289 markers were allocated to 41 linkage groups, covering a total map distance of 1998.5 centimorgan (CM). Our results validate the use of a pentaploid progeny population for genetic linkage map construction, and indicate that a higher resolution pentaploid-based map could be used for anchoring the assembly of a pentaploid-derived octoploid strawberry genome.