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

The RosBREED consortium has focused on developing high-throughput genome scans for apple, cherry, peach, and strawberry to facilitate quantitative trait locus (QTL) discovery and further develop the infrastructure for enabling and implementing 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) that are being used by the worldwide scientific community. Development of a high-throughput genome-scanning array in strawberry has lagged behind mostly due to the challenges caused by its allo-octoploid genome. We describe the development of the International Strawberry 90K (IStraw90) Affymetrix Axiom® genotyping array. Approaches to address the allo-octoploidy challenges included a large number of SNPs (> 90,000) to compensate for potential low conversion of candidate to functional SNPs, and bioinformatic extraction of regions of reduced ploidy. This reduction of effective ploidy levels was the direct result of targeting subgenome-specific sites. We also report results of the preliminary evaluation of this array in 384 strawberry samples consisting of mapping populations, breeding populations and their founders, in addition to few diverse strawberry individuals. We expect this array to enable genome-wide scanning in the octoploid strawberry and to facilitate QTL discovery for many traits of economic significance in this important fruit crop.