ArticlePlant communications2022
Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.
Article in Plant communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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
18 citing papers in PubMed, 38 citations in OpenAlex.
- Ancient Transposable Elements Sustain Global Ecological Adaptation Despite Chronically Low Nucleotide Diversity.Molecular ecology · 2026Article
- From night hormone to green signal: The journey of melatonin.Protoplasma · 2026Review
- Large-Scale Identification of Transposon Insertion Polymorphisms in Leguminous Plants from Paired-End WGS Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Investigating the role of transposable elements in shaping abdominal fat and egg production phenotypic traits in geese.BMC genomics · 2025Article
- Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.Nature communications · 2025Article
- A Genome-Wide Association Screen for Genes Affecting Leaf Trichome Development and Epidermal Metal Accumulation in Arabidopsis.Plant, cell & environment · 2025Article
- Uncovering the breeding contribution of transposable elements from landraces to improved varieties through pan-genome-wide analysis in rice.Frontiers in plant science · 2025Article
- Genomic selection for agronomical phenotypes using genome-wide SNPs and SVs in pearl millet.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice.National science review · 2024Article
- Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels.International journal of molecular sciences · 2023Article
- Taming transposable elements in livestock and poultry: a review of their roles and applications.Genetics, selection, evolution : GSE · 2023Review
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.Mobile DNA · 2023Article
- Recent Advances in Antibiotic-Free Markers; Novel Technologies to Enhance Safe Human Food Production in the World.Molecular biotechnology · 2023Review
- A graph-based genome and pan-genome variation of the model plant Setaria.Nature genetics · 2023Article
- CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes.Genome research · 2023Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.bioRxiv : the preprint server for biology · 2023Article
- A pangenome analysis pipeline provides insights into functional gene identification in rice.Genome biology · 2023Article
- Predicting phenotypes from novel genomic markers using deep learning.Bioinformatics advances · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) are a major force in the production of new alleles during domestication; nevertheless, their use in association studies has been limited because of their complexity. We have developed a TE genotyping pipeline (TEmarker) and applied it to whole-genome genome-wide association study (GWAS) data from 176 Oryza sativa subsp. japonica accessions to identify genetic elements associated with specific agronomic traits. TE markers recovered a large proportion (69%) of single-nucleotide polymorphism (SNP)-based GWAS peaks, and these TE peaks retained ca. 25% of the SNPs. The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium (LD) among SNP markers. A genome scan revealed positive selection on TEs associated with agronomic traits. We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs, including an allele of LOC_Os11g08410 associated with plant height and panicle length traits. Together, these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.
Indexed as
Identifiers
What Socratic 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 Socratic graph.