ArticlePloS one2020
Are the current gRNA ranking prediction algorithms useful for genome editing in plants?
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- DESIGN: a framework for generative AI-enabled crop molecular design-driven breeding.Science China. Life sciences · 2026Review
- Genetic transformation and CRISPR/Cas12a-mediated gene editing of European beech (Fagus sylvatica L.) employing a transient protoplast system.Communications biology · 2026Article
- Evaluation of computational tools for the prediction of CRISPR/SpCas9 gRNA activity in plants.Plant cell reports · 2026Article
- A Rapid Hairy Root-Based Platform for CRISPR/Cas Optimization and Guide RNA Validation in Lettuce.Plants (Basel, Switzerland) · 2026Article
- Optimization of functional genetics tools for a model tetraploid Capsella bursa-pastoris, with focus on homoeolog-aware gene editing.Transgenic research · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Targeted mutagenesis ofaBIOTECH · 2025Article
- Review
- Targeted genome modification in protoplasts of a tea cultivar Kolkhida using RNA-guided Cas9 endonuclease.AoB PLANTS · 2025Article
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Comprehensive benchmarking of genome editing quantification methods for plant applications.iScience · 2025Article
- Highly efficient Agrobacterium rhizogenes-mediated gene editing system in Salvia miltiorrhiza inbred line bh2-7.Plant biotechnology journal · 2025Article
- dCas-Based Tools to Visualize Chromatin or Modify Epigenetic Marks at Specific Plant Genomic Loci.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Single-stranded DNA (ssDNA) donor repair templates and CRISPR/Cas9 enable a high-frequency of targeted insertions in potato.Frontiers in genome editing · 2025Article
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Differential editing efficiencies in cereal crops: a comparative analysis of tRNA and ribozyme multiplexed guide delivery.Frontiers in plant science · 2024Article
- Rare but diverse off-target and somatic mutations found in field and greenhouse grown trees expressing CRISPR/Cas9.Frontiers in bioengineering and biotechnology · 2024Article
- Exploring the source of TYLCV resistance inFrontiers in plant science · 2024Article
- Usefulness of current sgRNA design guidelines and in vitro cleavage assays for plant CRISPR/Cas genome editing: a case targeting the polyphenol oxidase gene family in eggplant (Solanum melongena L.).Transgenic research · 2023Article
- Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Introducing a new trait into a crop through conventional breeding commonly takes decades, but recently developed genome sequence modification technology has the potential to accelerate this process. One of these new breeding technologies relies on an RNA-directed DNA nuclease (CRISPR/Cas9) to cut the genomic DNA, in vivo, to facilitate the deletion or insertion of sequences. This sequence specific targeting is determined by guide RNAs (gRNAs). However, choosing an optimum gRNA sequence has its challenges. Almost all current gRNA design tools for use in plants are based on data from experiments in animals, although many allow the use of plant genomes to identify potential off-target sites. Here, we examine the predictive uniformity and performance of eight different online gRNA-site tools. Unfortunately, there was little consensus among the rankings by the different algorithms, nor a statistically significant correlation between rankings and in vivo effectiveness. This suggests that important factors affecting gRNA performance and/or target site accessibility, in plants, are yet to be elucidated and incorporated into gRNA-site prediction tools.
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Registered trials
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