Molecular evolution and functional modification of plant miRNAs with CRISPR

Deng, Fenglin; Zeng, Fanrong; Shen, Qiufang; Abbas, Asad; Cheng, Jianhui; Jiang, Wei; Chen, Guang; Shah, Adnan Noor; Holford, Paul; Tanveer, Mohsin; Zhang, Dabing; Chen, Zhong‐Hua

doi:10.1016/j.tplants.2022.01.009

Cited by 38 publications

(18 citation statements)

References 151 publications

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“…miRNAs are non-coding small RNAs with a length of 20-24 nt and are encoded by MIR genes which are usually located in intergenic regions with some found in the intronic sequences of protein coding genes ( Song et al., 2019 ; Yu et al., 2019 ). The plant MIR genes may be generated by spontaneous evolution, genic inverted repeats, mutation, MIR family expansion and neofunctionalization, and functional divergence ( Baldrich et al., 2018 ) and mostly originate from chlorophyte algae (e.g., Chlamydomonas reinhardtii ) ( Deng et al., 2022 ). miRNAs are usually formed by Dicer-like protein 1 (DCL1)-mediated cleavage of precursors, possess a stem-loop structure, and mainly regulate the expression of target genes at the post-transcriptional level ( Voinnet, 2009 ; Rogers and Chen, 2013 ).…”

Section: Overview Of Plant Small Rnasmentioning

confidence: 99%

“…Some ncRNA-based technologies have been developed to protect plants from environmental stresses. First, clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) are used for targeted miRNA modification, including knock-out of MIR genes, up- or down-regulation of target genes by CRISPR activation, or CRISPR interference systems ( Deng et al., 2022 ). Secondly, spray-induced gene silencing (SIGS) is an environmentally friendly technique which uses synthesized dsRNA to target pathogenic factors to inhibit diseases ( Wang and Jin, 2017 ).…”

Section: Concluding Remarks and Future Perspectivesmentioning

confidence: 99%

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Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance

et al. 2022

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To survive in adverse environmental conditions, plants have evolved sophisticated genetic and epigenetic regulatory mechanisms to balance their growth and abiotic stress tolerance. An increasing number of non-coding RNAs (ncRNAs), including small RNAs (sRNAs) and long non-coding RNAs (lncRNAs) have been identified as essential regulators which enable plants to coordinate multiple aspects of growth and responses to environmental stresses through modulating the expression of target genes at both the transcriptional and posttranscriptional levels. In this review, we summarize recent advances in understanding ncRNAs-mediated prioritization towards plant growth or tolerance to abiotic stresses, especially to cold, heat, drought and salt stresses. We highlight the diverse roles of evolutionally conserved microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the underlying phytohormone-based signaling crosstalk in regulating the balance between plant growth and abiotic stress tolerance. We also review current discoveries regarding the potential roles of ncRNAs in stress memory in plants, which offer their descendants the potential for better fitness. Future ncRNAs-based breeding strategies are proposed to optimize the balance between growth and stress tolerance to maximize crop yield under the changing climate.

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Section: Overview Of Plant Small Rnasmentioning

confidence: 99%

Section: Concluding Remarks and Future Perspectivesmentioning

confidence: 99%

Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance

et al. 2022

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“…A wide variety of aspects of plant development and stress tolerance are regulated by microribonucleic acids (miRNAs) of 21-24 nucleotides length, which negatively modulate target genes through transcription cleavage and translational inhibition (Deng et al 2022). It has now been demonstrated that drought stress-induced phytohormone signaling and gene expression have a significant influence on miRNA-mediated root growth and branching regulation, and ultimately determine RSA under stressed conditions (Bakhshi et al 2016).…”

Section: Molecular Responsementioning

confidence: 99%

Alleviation of drought and salt stress in vegetables: crop responses and mitigation strategies

Khalid

Huda²,

Yong³

et al. 2022

Plant Growth Regul

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In recent decades, the demand for vegetables has increased significantly due to the blooming global population. Climate change has affected vegetable production by increasing the frequencies and severity of abiotic and biotic stresses. Among the abiotic stresses, drought and salinity are the major issues that possess severe threats on vegetable production. Many vegetables (e.g., carrot, tomato, okra, pea, eggplant, lettuce, potato) are usually sensitive to drought and salt stress. The defence mechanisms of plants against salt and drought stress have been extensively studied in model plant species and field crops. Better understanding of the mechanisms of susceptibility of vegetables to drought and salt stresses will help towards the development of more tolerant genotypes as a long-term strategy against these stresses. However, the intensity of the challenges also warrants more immediate approaches to mitigate these stresses and enhance vegetable production in the short term. Therefore, this review enlightens the updated knowledge of responses (physiological and molecular) against drought and salinity in vegetables and potentially effective strategies to enhance production. Moreover, we summarized different technologies such as seed priming, genetic transformation, biostimulants, nanotechnology, and cultural practices adopted to enhance vegetable production under drought and salinity stress. We propose that approaches of conventional breeding, genetic engineering, and crop management should be combined to generate drought and salt resistance cultivars and adopt smart cultivation practices for sustainable vegetable production in a changing climate.

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“…Owing to its versatility, efficiency, and accuracy at targeted genome modification, CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/Cas9)‐mediated gene editing has increasingly been adopted by the plant community to mutagenise single gene and gene family for functional genomics and to create novel germplasm of diverse crops for designed and precision crop breeding (Zhang et al, 2019 ). The functions of several miRNAs have also been investigated using CRISPR/Cas9‐based approaches (Deng et al, 2022 ). For example, functional specificity of all five Arabidopsis MIR172 genes in regulating shoot apex development and flowering time are elegantly distinguished using mutant alleles created by CRISPR/Cas9‐mediated gene editing (Lian et al, 2021 ; O'Maoileidigh et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

CRISPR/Cas9‐mediated saturated mutagenesis of the cotton MIR482 family for dissecting the functionality of individual members in disease response

et al. 2022

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Many genes encoding nucleotide‐binding leucine‐rich repeat receptors (NLRs) are regulated and fine‐tuned by miR482 to balance the trade‐off between disease resistance and growth. Dicotyledonous plants, including cotton, usually have multiple miR482 isoforms. Each miR482 isoform can regulate several NLRs that in turn can be regulated by several different miR482 isoforms. Dissecting the functionality of individual miR482 isoforms in disease response and in balancing the disease resistance and growth trade‐off demands a collection of mutants mutated in individual miR482 members (single or multiple). In this study, we generated such a collection of cotton miR482 mutants using CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/Cas9) genome editing and transformation of pooled guide RNAs (gRNAs). In total, 84 T 0 plants representing 40 independent transgenic events and harboring mutation in each of the 10 miR482 isoforms were generated. The average editing efficiency of the 18 transformed gRNAs is 75%, ranging from 0 (3 gRNAs) to 100% (8 gRNAs). Most miR482 isoforms have a diverse range of mutations, including small indels (1–44 bp) and substitutions, which are expected to impair biogenesis of miR482. All nine mutant populations used in Verticillium dahliae infection experiments showed a disease index lower than the control, with four being significantly lower. The disease assay also suggests a different role of different miR482 isoforms in disease response and a potential dosage effect of miR482l. The study demonstrates the feasibility of saturation mutagenesis of plant miRNA families with dozens of genetic loci using CRISPR/Cas9 and provides the cotton community a valuable resource for uncovering the miR482‐ NLR module(s) underlying the interaction between cotton and different pathogens.

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Molecular evolution and functional modification of plant miRNAs with CRISPR

Cited by 38 publications

References 151 publications

Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance

Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance

Alleviation of drought and salt stress in vegetables: crop responses and mitigation strategies

CRISPR/Cas9‐mediated saturated mutagenesis of the cotton MIR482 family for dissecting the functionality of individual members in disease response

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