Identification of Chromosome Specific Regions in 8x Cultivated Strawberry by Construction of a SNP Map

The cultivated strawberry, Fragaria x ananassa, is an allo-octoploid (2n = 8x = 56) species, and the complexity of the genome structure has hindered genetic and genomic analysis of this important crop. Although construction for high-density linkage maps with SSR markers and SNPs (Isobe et al. 2013, Bassil et al. 2015, Sargent et al. 2015) and whole-genome sequencing (Hirakawa et al. 2014) have been performed, discrimination of homoeologous chromosomes has never been achieved so far. In the present study, we have identified candidate chromosome specific regions by segregation analysis in a S₁ mapping population of a cultivar, ‘Reikou’ with Axiom IStraw90® SNP array. A total of 8,524 SNPs (6.2 % of tested) showed segregation of AA:AB:BB=1:2:1, which suggested chromosome specific manner. The 8,524 SNPs were mapped onto 39 linkage groups with 3,370 cM in total distance. The mapped SNPs are expected to be seed points for construction of pseudomolecule sequences in the cultivated strawberry.