A genotyping array on the Illumina Infinium platform (Illumina Inc., San Diego, CA, USA) based on 8,784 SNPs. These SNPs represented a highly filtered and selected set, optimized for polymorphism detection among cultivated germplasm and spread throughout the genome. Of these, 7,720 SNPs (88%) passed manufacturing quality control.The scorable SNPs included 501 from candidate genes and 1,307 that were cross-validated with community data sets from TraitGenetics (Gatersleben, Germany), the French National Institute for Agricultural Research (Institut National de la Recherche Agronomique, INRA), and previously published SNPs
SNPs for the array were selected based on a multi-tier strategy that was optimized for polymorphisms within and among cultivated types. Briefly, SNP discovery was based on the Genome Analyzer II-derived transcriptome sequences of four cultivated tomato accessions (NC84173, Fla.7600, OH08-6405, and OH9242), an S. lycopersicum var. cerasiforme accession (PI 114490), and an S. pimpinellifolium accession (PI 128216). SNPs were filtered such that any SNP within 50 bp of an intron/exon junction was removed and SNPs within 50 bp of a second polymorphism were excluded. SNPs were preferentially chosen based on their occurrence in multiple accessions. Genome coverage was assessed, and additional SNPs were selected to improve spacing across the genome. The research community provided a set of candidate genes of interest and 567 SNPs in the high confidence SNP set were located in these genes. Finally, SNPs were cross-validated with data sets from TraitGenetics, INRA, and previously published SNPs