The RosBREED project aimed to enhance the infrastructure for marker-assisted breeding, including platform development for high throughput genome scans. For the allo-octoploid, cultivated strawberry, this goal was met by the public release of the International Strawberry 90K (IStraw90TM) Axiom® genotyping array developed in collaboration with Affymetrix. Array design mainly exploited polymorphisms identified in the cultivated strawberry. The challenges of allo-octoploidy were addressed by maximizing the number of SNP targets to compensate for potential low conversion of candidate to functional SNPs, and sub-genome-specific probe targeting. Additionally, some reduced ploidy genomic sites were targeted via fortuitous probe placement. The array was evaluated on four mapping populations, numerous pedigreed breeding populations, various cultivars and selections, and several genetically unusual strawberry genotypes. New filters were developed and octoploid-specific thresholds were used in the genotyping procedure to identify potentially well-resolved and more complex SNP markers. A total of 12,609 well-resolved SNPs were obtained and evaluated through the generation of a genetic linkage map for ‘Holiday’ × ‘Korona’ (HK), where 6,689 of the 8,084 polymorphic HK-SNPs were successfully mapped. These mapped SNPs were also checked for marker consistency in the pedigreed cultivars and breeding selections using FlexQTLTM. Results of the SNP development strategies, improved gridding algorithm and automated genotype scoring will be presented. This array is the first high throughput genotyping platform in an octoploid organism and we expect it to enable genome-wide scanning in the cultivated octoploid strawberry and facilitate QTL discovery for many traits of economic significance in this important Rosaceous fruit crop.
