Tomato Sanger SNP Survey: OPA Design Specifications

SolCAP’s goal is to develop Single Nucleotide Polymorphisms (SNPs) that detect genetic variation within cultivated populations. The SNPs described here were computationally identified within the tomato public Sanger-derived Expressed Sequence Tags by assembling the EST sequences for all tomato varieties to make transcript assemblies (contigs). Putative SNPs were identified by comparison to the emerging tomato genome sequence (Heniz 1706). Putative SNPs were then validated using the Illumina Golden Gate OPA platform ( with 96 tomato lines. The OPA design information and the genotype data for 48 SNP-based markers on the 96 line panel are available below. These data are supplied to help the tomato breeding community assess whether the SNPs are appropriate for different market segments.

Please contact Dave Francis ( for more details.

Tomato OPA design data as an Excel Spreadsheet
Tomato OPA design data a web page

Tomato OPA genotyping data as an Excel Spreadsheet
Tomato OPA genotyping data a web page