ArticleBMC genetics2012
Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean.
Article in BMC genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled 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.
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.
Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Combination of meta-analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean.The plant genome · 2023Pooled it
- Unveiling Adulteration in Herbal Markets: MassARRAY iPLEX Assay for Accurate Identification ofInternational journal of molecular sciences · 2025Article
- Mapping yield and yield-related traits using diverse common bean germplasm.Frontiers in genetics · 2023Article
- Plant mitochondrial introns as genetic markers - conservation and variation.Frontiers in plant science · 2023Article
- QTL mapping and identification of genes associated with the resistance to Acanthoscelides obtectus in cultivated common bean using a high-density genetic linkage map.BMC plant biology · 2022Article
- Review
- Review
- Article
- Association Mapping for Yield Attributing Traits and Yellow Mosaic Disease Resistance in Mung Bean [Frontiers in plant science · 2021Article
- Genome-Wide Association Study and Genomic Prediction for Soybean Cyst Nematode Resistance in USDA Common Bean (Frontiers in plant science · 2021Article
- Genome-Wide Association Studies of Mineral Content in Common Bean.Frontiers in plant science · 2021Article
- Marker association study of yield attributing traits in common bean (Phaseolus vulgaris L.).Molecular biology reports · 2020Article
- Article
- Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Frontiers in genetics · 2020Article
- Marker-Trait Association Analysis of Seed Traits in Accessions of Common Bean (Frontiers in genetics · 2020Article
- Predicting Thermal Adaptation by Looking Into Populations' Genomic Past.Frontiers in genetics · 2020Review
- Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate.Frontiers in plant science · 2020Review
- Inheritance of Rootstock Effects in Avocado (Frontiers in plant science · 2020Article
- Diversification and genetic structure of the western-to-eastern progression of European Phaseolus vulgaris L. germplasm.BMC plant biology · 2019Article
- Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans.Genes · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies.
resultsIn this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings.
conclusionsIn short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.