Implementation of the IStraw90 Axiom® SNP Array Genotyping Platform for Genetic Linkage Map Construction in the Diploid Strawberry Model Species, Fragaria vesca

The wild strawberry species, Fragaria vesca (L.), is recognized as a diploid (2n = 2x = 14) ancestor of the cultivated octoploid (2n = 8x = 56) strawberry, F. ×ananassa, a valuable fruit crop in the United States. Although the F. vesca ‘Hawaii 4’ genome assembly was used as the reference for SNP discovery in designing the Affymetrix IStraw90 Axiom^® SNP array, none of the array markers were specifically designed for genotyping in F. vesca, being targeted instead to detect variants discovered in octoploid germplasm (85,663 SNPs) or in ancestral diploid F. iinumae (3,751 SNPs). Our aim was to evaluate the performance of the IStraw90 Array as a tool for linkage mapping in F. vesca, a strawberry species outside its intended range. This study relied on the F₂ mapping population from an existing cross between the yellow-fruited strawberry F. vesca ssp. vesca f. semperflorens, ‘Yellow Wonder' (Y) and red-fruited F. vesca ssp. americana ‘Pawtuckaway’ (P), and utilized 60 individuals of this YPF2 population as the source of marker segregation data. After filtering the array data, 1,637 SNP markers were subjected to mapping analysis using JoinMap v4.1. The resultant YPF2 linkage map consists of 1,377 SNP markers with 324 unique loci across seven linkage groups, spanning 470.9 cM, with a mapping density of 1.45 cM/locus. Thus, our result indicates that the IStraw90 Array may be an effective genotyping tool for Fragaria species other than those for which it was designed, given a sufficiently wide mapping cross.