title: Indel Group in Genomes (IGG) Molecular Genetic Markers.
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.
authors.affiliation: Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616.
authors.forename: Ted W
authors.identifier: 0000-0002-0967-4998
authors.initials: TW
authors.lastname: Toal
authors.affiliation: Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616.
authors.forename: Diana
authors.initials: D
authors.lastname: Burkart-Waco
authors.affiliation: Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616.
authors.forename: Tyson
authors.identifier: 0000-0002-6661-9151
authors.initials: T
authors.lastname: Howell
authors.affiliation: Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616.
authors.forename: Mily
authors.identifier: 0000-0003-1682-7275
authors.initials: M
authors.lastname: Ron
authors.affiliation: Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616.
authors.forename: Sundaram
authors.initials: S
authors.lastname: Kuppu
authors.affiliation: Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616.
authors.forename: Anne
authors.initials: A
authors.lastname: Britt
authors.affiliation: Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616.
authors.forename: Roger
authors.initials: R
authors.lastname: Chetelat
authors.affiliation: Department of Biochemistry and Molecular Medicine (T.W.T.), Department of Plant Sciences (D.B.-W., T.H., R.C.), Department of Plant Biology (M.R., S.K., A.B., S.M.B.), and Genome Center (S.M.B.), University of California, Davis, California 95616 sbrady@ucdavis.edu.
authors.forename: Siobhan M
authors.identifier: 0000-0001-9424-8055
authors.initials: SM
authors.lastname: Brady
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D005819:Genetic Markers / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D054643:INDEL Mutation; D018551:Solanum lycopersicum / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D032322:Solanum / Q000235:genetics; D013045:Species Specificity
chemical_list: D005819:Genetic Markers