CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation

Cardi, Teodoro; Murovec, Jana; Bakhsh, Allah; Boniecka, Justyna; Brügmann, Tobias; Bull, Simon E.; Eeckhaut, Tom; Fladung, Matthias; Galovic, Vladislava; Linkiewicz, Anna; Lukan, Tjaša; Mafra, Isabel; Michalski, K.; Kavas, Musa; Nicolia, Alessandro; Nowakowska, Justyna A.; Sági, László; Sarmiento, Cecilia; Yıldırım, Kubilay; Zlatković, Milica; Hensel, Goetz; Laere, Katrijn Van

doi:10.1016/j.tplants.2023.05.012

Cited by 67 publications

(26 citation statements)

References 168 publications

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“…The studies mentioned above on maize and wheat illustrate well that transcription‐binding cis elements can be inserted or deleted in drought response genes to strictly optimize their expression under drought stress conditions, and greatly alleviate the negative effects of these genes on plant growth and development under normal conditions (Shi et al, 2017; Xia et al, 2021; Li et al, 2023). Although genome editing has been applied to enhance plant abiotic and biotic stress tolerance (Li et al, 2022b), several issues and challenges limit its broad application in breeding (Cardi et al, 2023). To induce abiotic stress resistance via genome editing, the function annotation of plant tolerance and sensitivity genes is required.…”

Section: Discussionmentioning

confidence: 99%

Integrative regulatory mechanisms of stomatal movements under changing climate

Zhang,

Chen,

Song

et al. 2024

JIPB

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Global climate change‐caused drought stress, high temperatures and other extreme weather profoundly impact plant growth and development, restricting sustainable crop production. To cope with various environmental stimuli, plants can optimize the opening and closing of stomata to balance CO2 uptake for photosynthesis and water loss from leaves. Guard cells perceive and integrate various signals to adjust stomatal pores through turgor pressure regulation. Molecular mechanisms and signaling networks underlying the stomatal movements in response to environmental stresses have been extensively studied and elucidated. This review focuses on the molecular mechanisms of stomatal movements mediated by abscisic acid, light, CO2, reactive oxygen species, pathogens, temperature, and other phytohormones. We discussed the significance of elucidating the integrative mechanisms that regulate stomatal movements in helping design smart crops with enhanced water use efficiency and resilience in a climate‐changing world.

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Section: Discussionmentioning

confidence: 99%

Integrative regulatory mechanisms of stomatal movements under changing climate

Zhang,

Chen,

Song

et al. 2024

JIPB

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“…T he general approach for identifying gene function is based on the analysis of mutants using forward or reverse genetics. Although clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated genome editing has become a widely used tool for targeted mutagenesis, the timeliness and cost of generating mutants for a given target gene can remain a limiting factor (Cardi et al, 2023). Thus, a sequence-indexed mutant library can offer complementary advantages and opportunities for synergy.…”

Section: Introductionmentioning

confidence: 99%

Expansion and improvement of ChinaMu by MuT‐seq and chromosome‐level assembly of theMu‐starter genome

Liang,

Wang,

Han

et al. 2024

JIPB

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ChinaMu is the largest sequence‐indexed Mutator (Mu) transposon insertional library in maize (Zea mays). In this study, we made significant improvements to the size and quality of the ChinaMu library. We developed a new Mu‐tag isolation method Mu‐Tn5‐seq (MuT‐seq). Compared to the previous method used by ChinaMu, MuT‐seq recovered 1/3 more germinal insertions, while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time. Using MuT‐seq, we identified 113,879 germinal insertions from 3,168 Mu‐active F1 families. We also assembled a high‐quality genome for the Mu‐active line Mu‐starter, which harbors the initial active MuDR element and was used as the pollen donor for the mutation population. Using the Mu‐starter genome, we recovered 33,662 (15.6%) additional germinal insertions in 3,244 (7.4%) genes in the Mu‐starter line. The Mu‐starter genome also improved the assignment of 117,689 (54.5%) germinal insertions. The newly upgraded ChinaMu dataset currently contains 215,889 high‐quality germinal insertions. These insertions cover 32,224 pan‐genes in the Mu‐starter and B73Ref5 genomes, including 23,006 (80.4%) core genes shared by the two genomes. As a test model, we investigated Mu insertions in the pentatricopeptide repeat (PPR) superfamily, discovering insertions for 92% (449/487) of PPR genes in ChinaMu, demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.

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“…The Cas protein is then guided to the target locus, inducing a cut that can lead to gene silencing, repair, or the insertion of new genetic material 1 . For more than a decade, CRISPR/Cas has been employed to modify plant genomes, enabling the study of specific genes or biosynthetic pathways, and accelerating breeding efforts in various plant species, including both model and non-model crops (reviewed in 2 ).…”

Section: Introductionmentioning

confidence: 99%

Genome editing in almond: A CRISPR-based approach through hairy root transformation

Jedličková,

Štefková,

Sánchez López

et al. 2024

Preprint

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Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) technology has revolutionized genome manipulation for crop enhancement, providing a powerful toolkit. However, the tissue culture and plant regeneration steps that are critical to the CRISPR/Cas editing framework are often challenging, especially in some woody plant species that exhibit substantial resistance to these procedures. To address this, we have developed an injection-based protocol for inducing hairy roots in almond (Prunus dulcis, syn. Prunus amygdalus), a species known for its recalcitrance to conventional transformation methods. Notably, the hairy root induction method also proved effective in almond x peach hybrids. To evaluate its utility for gene functional analysis, we combined the hairy root transformation system with CRISPR/Cas9 gene editing technology, targeting two transcription factor genes (ERF74 and GAI). Our efforts resulted in transformants with target knock-out, suggesting the potential of this genetic transformation technology as a valuable tool for future routine gene function studies in almond.

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CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation

Cited by 67 publications

References 168 publications

Integrative regulatory mechanisms of stomatal movements under changing climate

Integrative regulatory mechanisms of stomatal movements under changing climate

Expansion and improvement of ChinaMu by MuT‐seq and chromosome‐level assembly of theMu‐starter genome

Genome editing in almond: A CRISPR-based approach through hairy root transformation

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