ArticlePlant biotechnology journal2019
Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants.
Article in Plant biotechnology journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
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Who cites it
93 citing papers in PubMed.
- Trial
- CRISPR/Cas9-mediated editing of theGM crops & food · 2026Article
- NIR-II biomimetic nanoplatform optogenetic CD274 editing of HNSCC immunogenicity for enhanced photoimmunotherapy.Materials today. Bio · 2026Article
- Review
- MicroRNA-mediated regulation of cell wall dynamics and intercellular communication under stress.Frontiers in plant science · 2026Review
- Development of novel transgene-free high-oleic peanuts through CRISPR-Cas9-mediated gene editing of two AhFAD2 homologues.Plant biotechnology journal · 2025Article
- CRISPR-Cas Gene Editing Technology in Potato.International journal of molecular sciences · 2025Review
- Deciphering the dynamic expression network of fiber elongation and the functional role of the GhTUB5 gene for fiber length in cotton based on an introgression population of upland cotton.Journal of advanced research · 2025Article
- Genome editing in maize and sorghum: A comprehensive review of CRISPR/Cas9 and emerging technologies.The plant genome · 2025Review
- Enhancing quality and climate resilient traits in vegetatively propagated polyploids: transgenic and genome editing advancements, challenges and future directions.Frontiers in genetics · 2025Review
- Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries.Genome research · 2024Article
- Impact of predictive selection of LbCas12a CRISPR RNAs upon on- and off-target editing rates in soybean.Plant direct · 2024Article
- GbPP2C80 Interacts with GbWAKL14 to Negatively Co-Regulate Resistance to Fusarium and Verticillium wilt via MPK3 and ROS Signaling in Sea Island Cotton.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- An Orphan Gene Enhances Male Reproductive Success in Plutella xylostella.Molecular biology and evolution · 2024Article
- CRISPR/Cas9 revolutionizesHorticulture research · 2024Article
- CRISPR/Cas9 as a Mutagenic Factor.International journal of molecular sciences · 2024Review
- Genome-wide evaluation of gene editing outcomes using CRISPR/Cas9 in seed propagatedFrontiers in plant science · 2024Article
- The 4Fs of cotton: genome editing of cotton for fiber, food, feed, and fuel to achieve zero hunger.Frontiers in genome editing · 2024Review
- Transcriptional and proteomic analysis.GM crops & food · 2023Article
- A comprehensive overview of cotton genomics, biotechnology and molecular biological studies.Science China. Life sciences · 2023Review
33 more citing papers are in PubMed but not listed here.
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15 authors.
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Abstract
The CRISPR/Cas9 system has been extensively applied for crop improvement. However, our understanding of Cas9 specificity is very limited in Cas9-edited plants. To identify on- and off-target mutation in an edited crop, we described whole genome sequencing (WGS) of 14 Cas9-edited cotton plants targeted to three genes, and three negative (Ne) control and three wild-type (WT) plants. In total, 4188-6404 unique single-nucleotide polymorphisms (SNPs) and 312-745 insertions/deletions (indels) were detected in 14 Cas9-edited plants compared to WT, negative and cotton reference genome sequences. Since the majority of these variations lack a protospacer-adjacent motif (PAM), we demonstrated that the most variations following Cas9-edited are due either to somaclonal variation or/and pre-existing/inherent variation from maternal plants, but not off-target effects. Of a total of 4413 potential off-target sites (allowing ≤5 mismatches within the 20-bp sgRNA and 3-bp PAM sequences), the WGS data revealed that only four are bona fide off-target indel mutations, validated by Sanger sequencing. Moreover, inherent genetic variation of WT can generate novel off-target sites and destroy PAMs, which suggested great care should be taken to design sgRNA for the minimizing of off-target effect. These findings suggested that CRISPR/Cas9 system is highly specific for cotton plants.
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