ArticleFrontiers in genetics2019
TDNAscan: A Software to Identify Complete and Truncated T-DNA Insertions.
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 42 citations in OpenAlex.
- Root developmental zonation is independent of cell wall pH.Nature plants · 2026Article
- DNA repair under heat: DNA polymerase λ modulates heat stress-induced mutagenesis in plants.The Plant cell · 2026Article
- Methylviologen resistance in loss-of-function mutants of the polyamine transporter gene OsLAT5.PloS one · 2026Article
- Ensuring effective removal of transgenes before release of genome-edited crops.Nature biotechnology · 2025Article
- T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data.Genome biology · 2025Article
- Deciphering the complex molecular architecture of the genetically modified soybean FG72 through paired-end whole genome sequencing.Food chemistry. Molecular sciences · 2025Article
- Heat-stable protein PGSL1 enhances pollen germination and tube growth at high temperature.Nature communications · 2025Article
- TTLOC: A Tn5 transposase-based approach to localize T-DNA integration sites.Plant physiology · 2025Article
- Rapid meiotic prophase chromosome movements in Arabidopsis thaliana are linked to essential reorganization at the nuclear envelope.Nature communications · 2024Article
- Application of next-generation sequencing in the detection of transgenic crop.Frontiers in genetics · 2024Review
- T-DNA characterization of genetically modified 3-R-gene late blight-resistant potato events with a novel procedure utilizing the Samplix XdropFrontiers in plant science · 2024Article
- Iterative gene integration mediated by 26S rDNA and non-homologous end joining for the efficient production of lycopene in Yarrowia lipolytica.Bioresources and bioprocessing · 2023Article
- Identifying pathogenicity-related genes in the pathogenFrontiers in microbiology · 2023Article
- Identification of T-DNA structure and insertion site in transgenic crops using targeted capture sequencing.Frontiers in plant science · 2023Article
- T-LOCked in: Identifying T-DNA insertions in plant genomes.Plant physiology · 2022Article
- T-LOC: A comprehensive tool to localize and characterize T-DNA integration sites.Plant physiology · 2022Article
- The Arabidopsis T-DNA mutant SALK_008491 carries a 14-kb deletion on chromosome 3 that provides rare insights into the plant response to dynamic light stress.Plant direct · 2022Article
- Article
- Spatial and temporal localization of SPIRRIG and WAVE/SCAR reveal roles for these proteins in actin-mediated root hair development.The Plant cell · 2021Article
- Transcriptome analysis of gynoecium morphogenesis uncovers the chronology of gene regulatory network activity.Plant physiology · 2021Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transfer (T)-DNA insertions in mutants isolated from forward genetic screens are typically identified through thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR), inverse PCR, or plasmid rescue. Despite the popularity and success of these methods, they have limited capabilities, particularly in situations in which the T-DNA is truncated. Here, we present a next generation sequencing (NGS)-based platform to facilitate the identification of complete and truncated T-DNA insertions. Our method enables the detection of the corresponding T-DNA insertion orientation and zygosity as well as insertion annotation. This method, called TDNAscan, was developed to be an open source software. We expect that TDNAscan will be a valuable addition to forward genetics toolkits because it provides a solution to the problem of causal gene identification, particularly genes disrupted by truncated T-DNA insertions. We present a case study in which TDNAscan was used to determine that the recessive
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