A Comparison of Genome-wide SNP Markers in Octoploid Strawberry Between the Affymetrix IStraw90 Axiom® Array and a Targeted Sequencing Approach

Cultivated strawberry is an allo-octoploid in the Rosaceae. Strawberry breeders are interested in using marker-assisted selection for genetic enrichment of current breeding germplasm, but the complexities of the octoploid genome create various challenges. Single nucleotide polymorphism (SNP) markers are abundantly available in plant genomes, and high-resolution, polymorphic and sub-genome specific SNPs markers are highly desirable to identify allelic variation for robust marker-locus-trait associations. Recent development of the first genome-wide array-based scanning platform, Axiom IStraw90^®, for octoploid strawberry, enabled sub-genome specific genotyping of 25 individuals that were also genotyped by a targeted sequencing (TS) approach at University of Florida  (UF), Gainesville. These individuals included a small F1 mapping population and UF breeding materials (cultivars, selections and founders). A preliminary comparison was made between these two techniques for several parameters including genomic coverage, polymorphism, genotype frequencies, marker density, minor allele frequencies and polymorphism information content (PIC). Sub-genome specific alleles (A/B format) from the IStraw90 Axiom^® array and alleles (A/T/G/C format) from TS approach were present in different combinations among these 25 individuals. Both methods had similar genomic coverage and marker density appeared higher in the TS approach. Future work will use a larger number of array-based SNPs and determine sub-genome specificity of SNP markers of the TS approach using more pedigree-linked individuals and higher genome coverage.