Development and Preliminary Evaluation of the IStraw90 Axiom® Array in the Cultivated Strawberry (Fragaria ×ananassa)

The RosBREED project has focused on developing high-throughput genome scans for apple, cherry, peach and strawberry to facilitate quantitative trait locus (QTL) discovery and develop the infrastructure for enabling marker-assisted breeding.  This goal was met by the public release of three Illumina® Infinium® arrays for apple, peach, and cherry (8K, 9K, and 6K, respectively) and now by the availability of the International Strawberry 90K (IStraw90^TM) genotyping array developed using the Affymetrix Axiom® platform. Strategies to address the allo-octoploidy challenges posed by the cultivated strawberry included a large number of SNPs (>90,000) to compensate for potential low conversion of candidate to functional SNPs, and targeting genic regions of reduced ploidy. Thus, reduction of effective ploidy levels was achieved intentionally by targeting of probes to subgenome-specific sites, but also occurred due to fortuitous probe placement. The array was evaluated using 384 strawberry samples that consisted of individuals from four mapping populations, numerous pedigreed breeding populations, and several genetically unusual strawberry individuals. New filters and octoploid-specific thresholds were used to identify potentially well-resolved SNPs and eliminate SNPs that produced complicated genotype plot patterns associated with higher error rates for automated genotype clustering. A total of 12,609 well-resolved SNPs were identified and progress in evaluating their performance through inheritance patterns will be presented. This array will enable genome-wide scanning in the cultivated octoploid strawberry and will facilitate QTL discovery for many traits of economic significance in this important fruit crop.