| Literature DB >> 27436831 |
Ted W Toal1, Diana Burkart-Waco1, Tyson Howell1, Mily Ron1, Sundaram Kuppu1, Anne Britt1, Roger Chetelat1, Siobhan M Brady2.
Abstract
Genetic markers are essential when developing or working with genetically variable populations. Indel Group in Genomes (IGG) markers are primer pairs that amplify single-locus sequences that differ in size for two or more alleles. They are attractive for their ease of use for rapid genotyping and their codominant nature. Here, we describe a heuristic algorithm that uses a k-mer-based approach to search two or more genome sequences to locate polymorphic regions suitable for designing candidate IGG marker primers. As input to the IGG pipeline software, the user provides genome sequences and the desired amplicon sizes and size differences. Primer sequences flanking polymorphic insertions/deletions are produced as output. IGG marker files for three sets of genomes, Solanum lycopersicum/Solanum pennellii, Arabidopsis (Arabidopsis thaliana) Columbia-0/Landsberg erecta-0 accessions, and S. lycopersicum/S. pennellii/Solanum tuberosum (three-way polymorphic) are included.Entities:
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Year: 2016 PMID： 27436831 PMCID： PMC5074621 DOI： 10.1104/pp.16.00354
Source DB: PubMed Journal: Plant Physiol ISSN： 0032-0889 Impact factor: 8.340