ArticleNature protocols2009
A protocol for efficiently retrieving and characterizing flanking sequence tags (FSTs) in Brachypodium distachyon T-DNA insertional mutants.
Article in Nature protocols, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 59 citations in OpenAlex.
- Systematic approach for dissecting promoters and designing transform systems in microalgae.Microbial cell factories · 2025Article
- Genetic modification strategies for enhancing plant resilience to abiotic stresses in the context of climate change.Functional & integrative genomics · 2023Review
- Identification of T-DNA structure and insertion site in transgenic crops using targeted capture sequencing.Frontiers in plant science · 2023Article
- Article
- Development of event-specific detection method for identification of insect resistant NIBGE-1601 cotton harboring double gene Cry1Ac-Cry2Ab construct.Scientific reports · 2021Article
- Using Combined Methods of Genetic Mapping and Nanopore-Based Sequencing Technology to Analyze the Insertion Positions ofFrontiers in plant science · 2021Article
- Cyclic Digestion and Ligation-Mediated PCR Used for Flanking Sequence Walking.Scientific reports · 2020Article
- In Vitro Tissue Culture inInternational journal of molecular sciences · 2020Review
- Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy.Journal of experimental botany · 2019Article
- Genetic Variation for Seed Metabolite Levels inInternational journal of molecular sciences · 2019Article
- CRISPR/Cas9-mediated targeted T-DNA integration in rice.Plant molecular biology · 2019Article
- Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing.Nucleic acids research · 2019Article
- Brachypodium distachyon T-DNA insertion lines: a model pathosystem to study nonhost resistance to wheat stripe rust.Scientific reports · 2016Article
- Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops.Proceedings. Biological sciences · 2015Article
- The Omp85-type outer membrane protein p36 of Arabidopsis thaliana evolved by recent gene duplication.Journal of plant research · 2015Article
- Differential gene expression and metabolomic analyses of Brachypodium distachyon infected by deoxynivalenol producing and non-producing strains of Fusarium graminearum.BMC genomics · 2014Article
- Disturbed local auxin homeostasis enhances cellular anisotropy and reveals alternative wiring of auxin-ethylene crosstalk in Brachypodium distachyon seminal roots.PLoS genetics · 2013Article
- Article
- 40S ribosome biogenesis co-factors are essential for gametophyte and embryo development.PloS one · 2013Article
- An efficient method for transient gene expression in monocots applied to modify the Brachypodium distachyon cell wall.Annals of botany · 2012Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Brachypodium distachyon is emerging as a new model system for bridging research into temperate cereal crops, such as wheat and barley, and for promoting research in novel biomass grasses. Here, we provide an adapter ligation PCR protocol that allows the large-scale characterization of T-DNA insertions into the genome of Brachypodium. The procedure enables the retrieval and mapping of the regions flanking the right and left borders (RB and LB) of the T-DNA inserts and consists of five steps: extraction and restriction digest of genomic DNA; ligation of an adapter to the genomic DNA; PCR amplification of the regions flanking the T-DNA insert(s) using primers specific to the adapter and the T-DNA; sequencing of the PCR products; and identification of the flanking sequence tags (FSTs) characterizing the T-DNA inserts. Analyzing the regions flanking both the LB and RB of the T-DNA inserts significantly improves FST retrieval and the frequency of mutant lines for which at least one FST can be identified. It takes approximately 16 or 10 d for a single person to analyze 96 T-DNA lines using individual or batch procedures, respectively.
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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.