Crop bioengineering via gene editing: reshaping the future of agriculture

Atia, Mohamed; Jiang, Wenjun; Sedeek, Khalid; Butt, Haroon; Mahfouz, Magdy

doi:10.1007/s00299-024-03183-1

Cited by 6 publications

(3 citation statements)

References 161 publications

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“…Moreover, CRISPR technology, which was initially used for plant genome editing in 2013, has been exploited to improve crop traits. Progress in the related research has resulted in enhanced breeding practices, but it has also simplified the classification of lncRNA functions, thereby enabling researchers to functionally validate lncRNAs in crops ( Atia et al., 2024 ; Chovatiya et al., 2024 ). In this context, lncRNAs are also expected to play a more essential role in the genetic breeding of crops, the development of biological resource, the engineering of plant cells, and other areas.…”

Section: Discussion and Prospectsmentioning

confidence: 99%

Update on functional analysis of long non-coding RNAs in common crops

Zhang,

Pi,

Wang

et al. 2024

Front. Plant Sci.

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With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.

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Section: Discussion and Prospectsmentioning

confidence: 99%

Update on functional analysis of long non-coding RNAs in common crops

Zhang,

Pi,

Wang

et al. 2024

Front. Plant Sci.

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“…Thus, a yearround production system is desirable. Genome editing technology has been utilized to improve crop yield, nutrient, stress tolerance (Atia et al 2024) and many countries adapted guidelines that permit the cultivation of non-transgenic gene-edited lines similar to conventionally bred lines (Buchholzer and Frommer. 2023).…”

Section: Discussionmentioning

confidence: 99%

CRISPR-Cas9-mediated mutagenesis of the flowering repressor gene VcCENTRORADIALIS (VcCEN) induces early flowering in tetraploid highbush blueberry

Omori,

Yamane,

Osakabe

et al. 2024

Preprint

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Flowering marks the vegetative-to-reproductive growth transition and is the most important event in the plant life cycle. Unlike annual plants, perennial fruit trees flower and set fruits only after an extended juvenile phase (i.e., several years), which is an impediment to efficient breeding and gene function analyses. In this study, we generated an early flowering blueberry line via the CRISPR-Cas9-mediated mutagenesis of VcCENTRORADIALIS (VcCEN). The expression of VcCEN in the apical bud was negatively correlated with flower bud formation. Moreover, in the cultivar that flowers in both autumn and spring, the VcCEN expression level was lower and decreased earlier than in the normal cultivar that flowers in only spring. The expression data suggested that VcCEN functions as a flowering repressor. The CRISPR-Cas9 vector harboring a gRNA targeting VcCENwas introduced into the blueberry genome via Agrobacterium-mediated transformation. Mutations (e.g., 1–10 bp indels) were detected in the stable transformants, with all VcCEN alleles of the tetraploid genome mutated in some lines. Compared with the wild-type (WT), the cen mutants exhibited repressed vegetative growth. Additionally, in the mutants, first flowering occurred within 1 year after the Agrobacterium infection, which was approximately 1–2 years earlier than in WT. The mutants set a single terminal flower without entering dormancy, whereas WT produced an apical flower and multiple axillary flowers that bloomed after an exposure to chilling conditions and then warm temperatures. This early flowering trait is conducive to efficient breeding and gene functional analyses, especially in fruit crops with a long juvenile phase.

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“…Starting with the use of natural and "designer" endonucleases to cleave specific chromosomal targets, this work has been tremendously accelerated in recent years by the availability of CRISPR/Cas endonucleases. Following on from earlier work using transgenic tester loci, Zinc-finger and TALE nucleases , the application of CRISPR/Cas tools to plant models over the last decade has enabled exciting new experimental approaches, and resulted in major advances in the understanding and application of DNA repair and recombination in model and crop plants (Atia et al, 2024;Fauser et al, 2014;Gao, 2021;Jiang et al, 2013;Kamoen et al, 2024;Li et al, 2013;Nekrasov et al, 2013;Přibylová and Fischer, 2024;Schiml et al, 2016;Shan et al, 2013;Vu et al, 2017;Wolter et al, 2021;Xue and Greene, 2021).…”

Section: Introductionmentioning

confidence: 99%

Context effects on repair of 5’-overhang DSB induced by Cas12a in Arabidopsis

Lageix,

Sanchez-Rebato,

Gallego

et al. 2024

Preprint

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Sequence-specific endonucleases have been key to the study of the mechanisms and control of DNA double-strand break (DSB) repair and recombination and the availability of CRISPR-Cas nucleases over the last decade has driven rapid progress in understanding and application of targeted recombination in many organisms, including plants. We present here an analysis of recombination at targeted chromosomal 5’overhang DSB generated by the FnCas12a endonuclease in the plant,Arabidopsis thaliana. The much-studied Cas9 nuclease cleaves DNA to generate blunt-ended, double-strand breaks (DSB), but relatively less is known about the repair of other types of breaks, such as those with 5’-overhanging ends. Sequencing the repaired breaks clearly shows that the majority of repaired DSB carry small deletions and are thus repaired locally by End-Joining recombination, confirmed by Nanopore sequencing of larger amplicons. Paired DSB generate deletions at one or both cut-sites, as well as deletions and reinsertions of the deleted segment between the two cuts, visible as inversions. While differences are seen in the details, overall the deletion patterns are similar between repair at single-cut and double-cut events, notwithstanding the fact that only the former involve cohesive DNA overhangs. A strikingly different repair pattern is however observed at breaks flanked by direct repeats. This change in sequence context results in the presence of an alternative class of repair events, corresponding to highly efficient repair by Single-strand Annealing recombination.

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Crop bioengineering via gene editing: reshaping the future of agriculture

Cited by 6 publications

References 161 publications

Update on functional analysis of long non-coding RNAs in common crops

Update on functional analysis of long non-coding RNAs in common crops

CRISPR-Cas9-mediated mutagenesis of the flowering repressor gene VcCENTRORADIALIS (VcCEN) induces early flowering in tetraploid highbush blueberry

Context effects on repair of 5’-overhang DSB induced by Cas12a in Arabidopsis

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