A High Density Linkage Map for the Ancestral Diploid Strawberry Fragaria iinumae using Markers from GBS and the ISTRAW90 Axiom® SNP Array

In recent years, phylogenetic, and other evidence has accumulated implicating diploid (2n=2x=14) F. iinumae as a second subgenome contributor to the octoploid (2n=8x=56) strawberries, including the cultivated strawberry, Fragaria ×ananassa and its ancestors F. chiloensis and F. virginiana. Previously, diploid F. vesca had been identified as an ancestral subgenome donor, and the representative ‘Hawaii4’ genome was published in 2011 as the first Fragaria reference genome. We have developed germplasm and genomic resources for F. iinumae, including high throughput genomic sequence data and a linkage mapping population. We now report construction of two high density linkage maps, constructed using GBS markers and SNPs from the IStraw90 Axiom ® Strawberry array. The maps, each of seven linkage groups, are based on segregation data from an F2 population (F2Ds) derived from a cross between two F. iinumae accessions (CFRA1955 and CFRA1849) collected in Hokkaido, Japan by Tom Davis and Kim Hummer in 2004. The maps differ with regard to the numbers of genotyped individuals and the markers employed. A GBS-only map based on 85 F2 plants defines 220 loci comprising 972 markers, with a map density of 2.1 cM and a map length 457.4 cM. A combined GBS-SNP map of only 21 individuals defines 158 loci comprising 3,181 SNP and 994 GBS markers. We plan to expand the SNP genotyping to include all 85 F2 individuals. The F. iinumae linkage maps will be used to anchor an F. iinumae genome assembly, thereby providing an important new genomic resource for Fragaria.