Evidence map›Paper›PMID 27436831›Full record

ArticlePlant physiology2016

Indel Group in Genomes (IGG) Molecular Genetic Markers.

Ted W Toal, Diana Burkart-Waco, Tyson Howell, Mily Ron, Sundaram Kuppu, Anne Britt, Roger Chetelat, Siobhan M Brady

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Plant physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Tm-1 back in business: an allele from Solanum pennellii accessions plays a major role in ToBRFV resistance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025
    Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Ted W ToalDepartment 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.ORCID 0000-0002-0967-4998
Diana Burkart-WacoDepartment 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.
Tyson HowellDepartment 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.ORCID 0000-0002-6661-9151
Mily RonDepartment 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.ORCID 0000-0003-1682-7275
Sundaram KuppuDepartment 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.
Anne BrittDepartment 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.
Roger ChetelatDepartment 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.
Siobhan M BradyDepartment 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.ORCID 0000-0001-9424-8055

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

INDEL MutationPolymorphism, Single NucleotideAllelesArabidopsisBase SequenceChromosome MappingChromosomes, PlantComputational BiologyGenetic MarkersGenome, PlantGenotypeSolanumSolanum lycopersicumSpecies SpecificityGenetic Markers

Identifiers

PMID27436831
PMCPMC5074621

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.