Open AccessIndel Group in Genomes (IGG) Molecular Genetic Markers
Author(s) -
Ted Toal,
Diana BurkartWaco,
T. A. Howell,
M. Ron,
Sundaram Kuppu,
Anne Britt,
Roger T. Chetelat,
Siobhán M. Brady
Publication year - 2016
Publication title -
plant physiology
Language(s) - Uncategorized
Resource type - Journals
SCImago Journal Rank - 3.554
H-Index - 312
eISSN - 1532-2548
pISSN - 0032-0889
DOI - 10.1104/pp.16.00354
Subject(s) - indel , biology , genome , genetics , solanum tuberosum , locus (genetics) , solanum , amplicon , genotyping , genetic marker , primer (cosmetics) , computational biology , gene , genotype , single nucleotide polymorphism , polymerase chain reaction , botany , chemistry , organic chemistry
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.
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