ArticlePlant biotechnology journal2022
Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa.
Article in Plant biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 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
40 citing papers in PubMed, 80 citations in OpenAlex.
- Integrated Comparative Genomics and Population Genomics Reveal the Genomic and Epigenomic Basis of Barley (Plants (Basel, Switzerland) · 2026Article
- panHiTE: A comprehensive and accurate pipeline for TE detection in large-scale population genomes.Plant communications · 2026Article
- The jujube pan-TE map identifies transposable element insertions associated with domestication and pericarp development.Horticulture research · 2026Article
- A Pan-TE Map Reveals the Important Role of Transposable Elements in Gene Expression and Phenotypic Diversity in 2,311 Rapeseed Accessions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Factors determining chromosomal localization of transposable elements in plants.Plant biology (Stuttgart, Germany) · 2025Review
- Identification of PpTHE1, a cell wall integrity sensor regulating the increased duration of harvest window in slow-melting flesh peach, through the assembly of a chromosome-level reference genome of Prunus persica.Plant biotechnology journal · 2025Article
- Genome-wide identification and evolutionary analysis of disease resistance genes in Brassica carinata.The plant genome · 2025Article
- Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression.aBIOTECH · 2025Article
- Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.The Plant journal : for cell and molecular biology · 2025Article
- A haplotype-resolved reference genome for Eucalyptus grandis.G3 (Bethesda, Md.) · 2025Article
- A pangenome reference of wild and cultivated rice.Nature · 2025Article
- DNA Methylation and Alternative Splicing Safeguard Genome and Transcriptome After a Retrotransposition Burst inInternational journal of molecular sciences · 2025Article
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- Graphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
- Genome sequencing of 'Fuji' apple clonal varieties reveals genetic mechanism of the spur-type morphology.Nature communications · 2024Article
- Lactuca super-pangenome reduces bias towards reference genes in lettuce research.BMC plant biology · 2024Article
- Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants.Molecular biology and evolution · 2024Article
- Impact of Chromosomal Fusion and Transposable Elements on the Genomic Evolution and Genetic Diversity ofPlants (Basel, Switzerland) · 2024Article
- Characterization of active transposable elements and their new insertions in tuber propagated greater yam (Dioscorea alata).BMC genomics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu-401-42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP-containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.
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.