Towards a large sized Axiom SNP array for the allooctoploid strawberry

A central goal of the RosBREED consortium has been to establish SNP arrays for peach, cherry, apple, and strawberry, to facilitate QTL discovery and marker‐assisted breeding. This goal has been advanced by the release of three Illumina® Infinium® arrays for apple, peach, and cherry (8K, 9K and 6K, respectively). Here, we report on the development of a 90K Strawberry Affymetrix Axiom® genotyping array. The cultivated strawberry is an allo‐octoploid. This level and type of ploidy creates challenges to overcome, which we address in several ways. First, the large size of the array permits success despite a lower conversion rate of candidate to functional SNPs than for diploid crops. Second, we exploit site‐specific, biological reductions in ploidy resulting from subgenome‐specific deletions. Third, we exploit designed reductions in ploidy by targeting probes to sites of subgenome‐specific sequence motifs. Fourth, we include SNPs and/or probes specific to one sub‐genome. We are using a diverse germplasm discovery panel of 19 octoploids. The array will target several polymorphism types, including indels and di‐ and multi‐allelic SNPs. Here we describe our approaches to reduce the effective ploidy level so as to choose subgenome‐specific SNPs. We also report on a new bioinformatics pipeline, which includes local re‐alignment around indels and polymorphism type‐specific filtering strategies. Production of the array starts in September 2012 and it will become commercially available.