Here we present a collection markers based on single nucleotide polymorphisms (SNPs) mined from expressed sequence tags (EST) available at The SOL Genomics Network,SGN(Unigene set version 200607). These markers are designed to detect inter-specific SNPs among three tomato species: Solanum lycopersicum, Solanum habrochaites and Solanum pennellii. Indels have not been included in the database but are available on the downloads page.

For each SNP we designed a set of primers that take into account predicted intron positions and provide restriction endonucleases that can be used to detect the polymorphism. Please note that for certain SNPs that are close to introns or to the end of the sequences our pipeline fails to design primers. In those cases we recommend manual development of primers based on the given estimated allele sequences and intron positions.

If you plan to use any of the molecular markers made available through this website please cite our publication. More information at How to cite us

  • To search for markers in a specific unigene, please enter an ID in the box below:

    • Unigene search:
                               Example: SGN-U316477 or 316477

  • To browse only those SNPs and markers that have been experimentally verified use the following links:

    • browse tested lxh SNPs - Markers for polymorphisms between Solanum lycopersicum and Solanum habrochaites that were verified by PCR and digestion with the corresponding restriction enzyme.

    • browse tested lxp SNPs - Markers for polymorphisms between Solanum lycopersicum and Solanum pennellii that were verified by PCR and digestion with the corresponding restriction enzyme.

  • To browse the complete list of SNPs and markers mined click on the following links:

    • browse all lxh SNPs - All markers (tested and untested) for polymorphisms between Solanum lycopersicum and Solanum habrochaites

    • browse all lxp SNPs - Markers (tested and untested) for polymorphisms between Solanum lycopersicum and Solanum pennellii



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