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Review

Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance

by
İbrahim Erdoğan
1,2,
Birsen Cevher-Keskin
3,
Özlem Bilir
2,4,
Yiguo Hong
2,5 and
Mahmut Tör
2,*
1
Department of Agricultural Biotechnology, Faculty of Agriculture, Kirsehir Ahi Evran University, Kırşehir 40100, Türkiye
2
Department of Biological Sciences, School of Science and the Environment, University of Worcester, Henwick Grove, Worcester WR2 6AJ, UK
3
Genetic Engineering and Biotechnology Institute, TÜBİTAK Marmara Research Center, Kocaeli 41470, Türkiye
4
Trakya Agricultural Research Institute, Atatürk Bulvarı 167/A, Edirne 22100, Türkiye
5
Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
*
Author to whom correspondence should be addressed.
Biology 2023, 12(7), 1037; https://doi.org/10.3390/biology12071037
Submission received: 14 June 2023 / Revised: 17 July 2023 / Accepted: 19 July 2023 / Published: 22 July 2023
(This article belongs to the Section Plant Science)
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Abstract

:

Simple Summary

Pests and diseases, along with environmental factors, significantly contribute to yield losses in crop production. Considering the detrimental impact of pesticides on both the economy and the environment, it is crucial to urgently develop methods that can prevent such damage. Additionally, it is imperative to address challenges posed by the growing world population, climate change, and the emergence of new pathogens. In this century, one of the most important advancements in terms of crop improvement lies in faster and more effective genome editing than is possible via traditional plant breeding, resulting in the production of transgene-free plant lines. The CRISPR/Cas9 genome-editing technique has emerged as the most widely used tool for creating plants with desirable traits, such as disease resistance and tolerance to abiotic stresses. These technologies enable the cultivation of crop plants capable of adapting to these new conditions, offering novel opportunities and solutions.

Abstract

The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions.

1. Introduction

Global food security faces multiple threats, including the challenges posed by a growing population, climate change, and the constant evolution and emergence of plant diseases [1,2,3]. By 2050, the world population is projected to exceed nine and a half billion, leading to a substantial increase in food consumption of 100–110%. However, current agricultural capacities suggest that crop yields for essential crops like wheat, corn, rice, and soybean will only witness a modest rise of 38–67% [4]. It is evident that global climatic changes, including escalating droughts, floods, and harmful micro-organisms, will adversely impact agricultural productivity [5,6]. Biologic stress on plants alone is anticipated to cause yield losses exceeding 40%, resulting in a 15% decline in the overall global food supply [7,8,9]. To address these challenges, pesticides, fertilizers, and other chemicals have been extensively used in recent years to enhance agricultural yield, promote plant health, and combat plant infections. However, the use of such chemicals poses significant threats to the environment, causing damage to soil, water, and vegetation. Additionally, they indirectly affect animals such as birds, fish, beneficial insects, and non-target plants [9,10,11,12,13,14].
Plant genomes have been modified using traditional plant breeding techniques or through physical (such as gamma radiation), chemical (such as ethyl methanesulfonate, EMS), and the biological (including T-DNA and transposon insertion) methods, resulting in point mutations, deletions, and gene duplications. While these approaches have led to crop improvement, they are time consuming, expensive, and often face challenges related to conventional breeding. Moreover, they can cause unintended rearrangements in the genome. Therefore, it is crucial to enhance the development of high-yielding crops that are disease-free and tolerant to abiotic stresses, enabling them to adapt to future challenges. Recognizing these challenges, the scientific community has long been committed to cultivating ideal crops. Genetically modified (GM) crops have been created by transferring beneficial genes to crops through a trans-kingdom approach. Consequently, scientists have directed their efforts toward developing genome-editing tools that can modify the genome without introducing transgenes [2,15,16,17].
The era of genome editing began with the introduction of zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), though it reached new heights following the discovery of CRISPR/Cas technology. The development of CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated nuclease 9) has revolutionized genome editing in plants, enabling significant advancements beyond the outcomes that conventional breeding techniques can achieve [18]. The type II CRISPR/Cas9 system, which was initially found in Streptococcus pyogenes, has become the most widely adopted and extensively utilized system [19,20,21]. The importance of genome-engineering technologies in modern plant development and improvement cannot be overstated. The field of genome engineering has undergone a transformative revolution, which was largely driven by the development and widespread acceptance of CRISPR, which is recognized as one of the most potent gene-editing techniques available [22,23]. The CRISPR system functions by incorporating sequences from foreign elements into a small RNA-based memory, which serves as an inherited resistance mechanism. These short RNAs recognize the foreign invader and employ Cas proteins, which act as enzymatic units, to cut and eliminate the invader’s genetic material. In many aspects, the CRISPR system bears resemblance to the RNA-based defense mechanisms found in animal germ cells, which protect against mobile genetic material [24]. The CRISPR-Cas9 system has been simplified into two key components: a single chimeric RNA known as guide RNA (gRNA) and the enzyme Cas9. Together, these elements enable the editing of specific genomes and facilitate desired modifications in genome engineering [19]. The gRNA consists of CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA) sequences, which guide the sequence-specific cleavage of genomic DNA by Cas9 through a straightforward base-pairing process. Notably, gRNAs can be easily designed to recognize a target sequence of 20 nucleotides in length and induce precise Cas9-dependent cleavage of both DNA strands at a pre-defined location within the target, underscoring the utility of this technology.
The development of genome-edited plants using CRISPR/Cas9 technology consists of five steps: (i) selection of the target gene, (ii) designing a targeted gene-specific sgRNA, (iii) assembling Cas9 and sgRNA, (iv) transformation to the target plant, and (v) regeneration and screening of plant lines (see Figure 1). Here, we describe the usage and benefits of CRISPR genome-editing technology for developing plant lines that are resistant to disease and abiotic stress and provide examples of genes edited to enable crop improvement.

2. Genome Editing Tools and Their Comparison

Genome editing techniques rely on three main sequence-specific nuclease systems: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein (CRISPR/Cas). Mega-nucleases, such as ZFNs and TALENs, have recently enabled the targeted modification of specific genome sequences [25,26]. Until 2013, ZFNs were the most commonly used genome editing technique, followed by TALENs [27,28]. These methods involve engineered fusion proteins, in which a DNA binding domain is fused to the non-specific nuclease domain of the restriction enzyme FokI. They have been successfully applied in various species, including plants [29,30]. However, ZFNs and TALENs face challenges as they require the introduction of a new protein after target verification, making their application more complex [9]. Consequently, these methods have not been widely adopted in plant genome editing, prompting scientists to explore alternative approaches [31,32]. Unlike ZFNs and TALENs, which require specific proteins and sequences, the CRISPR/Cas system only requires a guide RNA (gRNA), which offers a significant advantage (refer to Table 1). The CRISPR/Cas system has emerged as a superior gene-editing technique due to its simplified requirements. In the ZFN and TALEN systems, the restriction endonuclease FokI contains a catalytic domain that generates double-strand breaks with sticky ends of varying lengths, which depend on the linker and spacer used. On the other hand, the Cas9 system of CRISPR/Cas comprises two cut site—RuvC and HNH—that generate blunt ends by cleaving the target DNA three nucleotides upstream of the protospacer adjacent motif (PAM) [19]. The CRISPR target site requires a 3-base pair protospacer adjacent motif (PAM) situated at the 3′ NGG end of the 20-nucleotide recognition sequence. When the Cas9 enzyme generates double-strand breaks (DSBs), initiating the DNA repair mechanism, two biological mechanisms can be employed for genome editing. The first mechanism—non-homologous end joining (NHEJ)—is an error-prone process that leads to small insertions and deletions, compromising the functionality of the cut sites. The second approach is homology-directed repair (HDR), which utilizes templates created via homologous DNA sequences for repair purposes. This repair mechanism can be harnessed to precisely modify the genome or introduce foreign DNA using an externally constructed template donor [33]. The CRISPR/Cas9 method overcomes challenges associated with complex construction of DNA-binding domain expression cassettes, reduced target sensitivity, and lower cutting efficiency encountered in ZFN and TALEN gene-editing technologies. Furthermore, the CRISPR/Cas9 system is easier and more practical to implement [34,35]. In contrast, gRNA-guided cutting in the CRISPR/Cas system relies on a simple base-pairing mechanism, eliminating the need for complex and labor-intensive protein engineering for each target. Instead, a 20-nucleotide gRNA sequence can be designed to specifically recognize and bind to the desired target DNA sequence [3]. However, it should be noted that the CRISPR/Cas system’s requirement for a protospacer adjacent motif (PAM) at the target recognition site may impose limitations on its applicability in certain gene-editing scenarios [36]. In light of the potential drawbacks of a PAM-free nuclease, there are several avenues along which this field can proceed. One approach is to focus on other Cas nucleases, such as Cas9, Cas12a, and remaining Cas nucleases, which still have room to relax PAM recognition without completely eliminating it. By combining ortholog mining and PAM engineering, researchers can expedite the development of these nucleases. The abundance of characterized Cas9 nucleases suggests that there is a wide diversity of PAM sequences in nature that has yet to be fully explored. For example, Type V-C nucleases recognize PAMs with as little as a single base, making them promising candidates for PAM relaxation. Determining the structures of nucleases that naturally recognize only one nucleotide could reveal new insights into PAM recognition and guide future engineering efforts [37]. Type I CRISPR-Cas10 is a CRISPR system that has been shown to induce small insertions and deletions (indels), as well as bi-directional long-range deletions, in tomatoes (Solanum lycopersicum L.). This system allows precise modifications in the tomato genome, with deletions spanning up to 7.2 kb in length. This capability creates the potential for targeted genetic modifications and the development of improved tomato varieties. On the other hand, Type IV CRISPR-Cas13 is a distinct CRISPR system that targets RNA instead of double-stranded DNA. This unique feature enables highly specific knockdown of target genes at the RNA level. By utilizing the RNA-targeting capability of Cas13, researchers can achieve precise regulation of gene expression and potentially develop novel approaches for various applications.
Both Type I CRISPR-Cas10 and Type IV CRISPR-Cas13 demonstrate the versatility and potential of CRISPR technologies for precise genome editing and gene regulation in different organisms, including important crops, such as tomatoes. These advancements open up new possibilities for crop improvement and functional genomics [38,39,40]. In the field of genome engineering in plants, CRISPR activation systems have significantly advanced the capabilities of targeted mutagenesis, base editing, and gene activation. However, these tools are typically used independently, limiting their potential for combined applications. To address this limitation, researchers developed a versatile platform called CRISPR-Combo, which utilizes a single Cas9 protein to enable simultaneous genome editing and gene activation in plants [41]. The CRISPR-Combo platform offers powerful applications to enhance plant genome editing. Firstly, they demonstrate its utility in shortening the plant life cycle and simplifying the screening process for transgene-free genome-edited plants. This outcome is achieved by activating a florigen gene in Arabidopsis, leading to accelerated flowering and seed production. By activating morphogenic genes in poplar, they achieve accelerated plant regeneration and propagation, reducing the time and effort required to generate a large number of edited plants. This novel approach allows the efficient enrichment of heritable targeted mutations, providing a valuable tool for crop breeding. In summary, CRISPR-Combo represents a versatile genome engineering tool that has promising applications in crop breeding [41].

3. Arise of CRISPR/Cas9 Technology

In 1987, the CRISPR/Cas system was discovered in prokaryotes and found to be an adaptive immune system that defends against invading bacteriophages or plasmids. Researchers studying Escherichia coli identified approximately 32 nucleotide non-repeat sequences and tandem repeats downstream of the iap gene. These tandem repeats were later named CRISPR in the year 2000 [42,43]. Studies revealed that the CRISPR spacer sequences showed similarity to sequences from exogenous sources, such as bacterial plasmids and phages. When a bacteriophage infects a bacterium, the endogenous CRISPR system replicates the repeat regions of the phage genome, which are then separated from the protospacer adjacent motif (PAM) through spacer sequences [44,45,46]. The bacterium’s CRISPR/Cas system detects the viral genome and neutralizes it during subsequent phage attacks, functioning as the bacterium’s immune system. The Cas library in the bacterium preserves a record of the invading viral sequences and aids in their destruction upon re-attack.
In traditional crop improvement methods, mutation breeding methods are often employed using chemicals like ethyl methanesulfonate (EMS) or gamma radiation [47]. However, the CRISPR/Cas9 system offers the ability to modify single or multiple target genes. Cas9, which is the enzyme from the type II CRISPR-Cas system of S. pyogenes, is a large monomeric DNA nuclease. It is guided by two non-coding RNA complexes—CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA)—that cleave the DNA target region next to the PAM sequence motif [19,48,49]. Cas9 possesses two nuclease domains that are similar to the RuvC and HNH nucleases of the Cas9 protein (Figure 2).
Indeed, the Cas9 protein, due to its HNH and RuvC-like nuclease domains, is responsible for cleaving the DNA target site. The HNH domain cleaves the complementary DNA strand, while the RuvC-like domain cleaves the non-complementary strand, resulting in a blunt cut in the target DNA [19]. When the Cas9 protein is combined with a single guide RNA (sgRNA) and targeted to a specific genomic site, it induces site-specific double-strand breaks (DSBs) in the DNA of living cells across various organisms. Following the generation of DSBs, different intracellular repair mechanisms come into play, leading to various genome modifications. The two primary repair pathways are non-homologous end-joining (NHEJ) and homology-directed repair (HDR) in nature. NHEJ is an error-prone repair mechanism that often results in random insertions and deletions (indels) at the target gene site. These indels can disrupt the functioning of the gene, leading to gene knockout or loss-of-function mutations. On the other hand, HDR relies on the use of a template, which is typically a homologous DNA sequence, to repair the DSB with high precision. This repair pathway can be utilized to introduce desired modifications or specific DNA sequences into the genome. It is important to note that the repair outcome depends on the specific repair mechanisms of the organism and the factors influencing repair pathway choice. NHEJ is the predominant pathway in many organisms, while HDR is typically less efficient but can be enhanced by optimizing the experimental conditions.
Base editing and prime editing are two recent advancements in CRISPR/Cas technology that have revolutionized the field of genome editing. These techniques offer the ability to induce precise point mutations in the DNA without the need to induce double-strand breaks (DSBs), which can lead to unintended mutations. Base editing encompasses two main types of editor: cytosine base editors (CBEs) and adenine base editors (ABEs). CBEs utilize a modified Cas9 protein fused with an enzyme that is capable of chemically modifying cytosine to induce specific nucleotide changes. This process allows targeted conversion of cytosine into thymine (C-to-T) or guanine (C-to-G) mutations, depending on the desired outcome. On the other hand, ABEs utilize a modified Cas9 protein fused with an enzyme that can convert adenine to inosine, which is then recognized as guanine during DNA replication. This process enables the induction of adenine to guanine (A-to-G) mutations. Prime editing is a more advanced genome editing technique that expands the scope of modifications that can be achieved. It combines a modified Cas9 protein with a reverse transcriptase enzyme and a prime-editing guide RNA (pegRNA). The pegRNA contains the desired edits in the form of a template, which is reverse transcribed and integrated into the target DNA site, allowing precise changes in the DNA sequence. Prime editing enables a broader range of modifications, including transitions, transversions, insertions, and deletions, providing greater flexibility in genome engineering. These advancements in base editing and prime editing have greatly expanded the toolbox of CRISPR/Cas technology, allowing more precise and versatile genome modifications. They offer exciting possibilities for targeted genetic changes and the development of improved crops [50]. Recent studies have highlighted the significance of utilizing endogenous RNA Pol III promoters, specifically U3 and U6 promoters, in the CRISPR/Cas9 system to enhance genome editing efficiency in various plant systems. These promoters are responsible for transcribing single or multiple guide RNAs that guide the Cas9 nuclease to target specific genomic regions. By utilizing endogenous RNA Pol III promoters, researchers have observed improved editing efficiency and precision in plant genome editing. The use of species-specific U3/U6 promoters holds promise in terms of advancing the field of genome editing by enabling more specific and efficient targeting of desired genomic sequences [51].

4. CRISPR/Cas-Mediated Genome Editing for Disease Resistance

Plant diseases caused by biotic factors, such as viruses, fungi, oomycetes, and bacteria, pose a significant threat to crop productivity and global food security. These infections result in substantial yield losses and quality reduction in field crops, fruits, and other edible plant materials. Approximately 20 to 40% of worldwide crop losses are attributed to biotic factors [52]. Traditionally, plant disease resistance has been achieved through the introgression of resistance genes (R-genes) from wild relatives of the cultivated crop. The most common type of resistance mechanism involves nucleotide-binding leucine-rich repeat (NB-LRR) proteins, which recognize specific products of pathogen Avirulence (Avr) genes [53]. Upon recognition, a defensive response is triggered, leading to the host cell’s programmed cell death; this process is known as the hypersensitive reaction (HR) [53]. Another approach to disease resistance is the suppression of susceptibility (S) genes, which are essential for pathogen infection [54]. Many pathogens rely on specific host genes for successful infection and proliferation. Biotrophic fungal pathogens, such as powdery mildews, require prolonged interaction with host cells to achieve effective proliferation [55]. The expression of specific host genes, known as S-genes or susceptibility genes, is necessary for pathogen recognition, penetration, evasion of host defenses, and fulfillment of the pathogen’s metabolic and structural needs [55]. Mutations in S-genes can result in long-term and broad-spectrum recessive heritable resistance [56,57]. Therefore, S-genes play a critical role in plant–pathogen interactions, influencing the host’s susceptibility to infection. The functions of S-genes can be categorized into three major molecular mechanisms: basic compatibility, sustained compatibility, and negative modulation of plant immune signals. Basic compatibility involves host recognition and pathogen penetration, sustained compatibility is necessary for pathogen proliferation and dissemination, and negative modulation of plant immune signals helps to suppress host defense responses [55]. Understanding the molecular mechanisms that underlie S-gene functions and their interactions with pathogens is crucial to the development of effective strategies that enhance plant disease resistance. The barley Mlo (mildew resistance locus) gene is a well-known example of an S-gene mutation that confers resistance to powdery mildew in barley. Deployment of loss-of-function Mlo alleles in barley has resulted in the development of powdery mildew-resistant barley varieties. These resistant plants have been cultivated in the field for many years, demonstrating the durability of S-gene-based resistance against virulent powdery mildew strains [58]. The cloning of the barley Mlo gene revealed that it is conserved across the plant kingdom and exists as a multi-copy gene family in higher plants [59,60,61]. Studies have shown that mutation of the Mlo gene confers resistance to powdery mildew. The Mlo protein is essential for the penetration of powdery mildew fungal spores into host epidermal cells. The Mlo gene encodes a membrane-associated protein with seven transmembrane domains, and its mutation, which uses the CRISPR-Cas9 system, has resulted in the generation of transgene-free and powdery mildew-resistant plants [62,63,64]. Mlo-like genes have also been implicated in powdery mildew susceptibility in various plant species, including Arabidopsis, tomato, pea, pepper, tobacco, bread wheat, and potentially grapevine and peach [63,65,66,67,68,69,70]. These genes are categorized into different classes based on their phylogenetic relationships. Class IV contains Mlo-like genes associated with powdery mildew susceptibility in monocotyledonous species, while class V contains those found in dicotyledonous species. Other classes (I, II, III, and VI) include Mlo-like genes that have not yet been identified as S-genes [61]. The development of next-generation sequencing and CRISPR technologies has facilitated the identification and targeting of S-genes involved in the enhancement of disease resistance in plants. CRISPR/Cas9 has been used to target S-genes, including the Mlo gene, to confer protection against important plant pathogens. Modifying these S-genes can disrupt the compatibility between the host and the pathogen, leading to broad-spectrum and durable disease resistance [71]. Another example is the targeting and alteration of the Enhanced Disease Resistance 1 (EDR1) gene, resulting in a significant decrease in powdery mildew in wheat [35]. One of the notable advantages of CRISPR/Cas9 technology is its ability to target multiple genes simultaneously using a single construct. Studies have shown that a single molecular structure in Arabidopsis can simultaneously induce mutations in 14 different genes [72]. Multiplex genome-editing techniques, through which multiple guide RNAs (gRNAs) are integrated into a single construct under the control of a U3 or U6 promoter, have been successfully applied in crops [73,74,75,76,77]. Previous methods for transgene removal involved either molecular excision or segregation via selfing or backcrossing to the original parent line. The Cas9 system allows transgene-free lines to be selected from segregating populations once a successful mutation in the target genomic region is confirmed [71,78,79].
Viruses pose a significant biotic stress risk to plants and can cause diseases in various commercially important crops. The Eukaryotic Translation Initiation Factor 4E (eIF4E) is a key protein required for the infection cycle of Potyviridae family viruses, which are single-stranded positive-sense RNA viruses. The viral protein genome-linked (VPg) element at the 5′-terminal of potyviruses interacts with eIF4E, and disrupting this interaction has been shown to confer immunity against potyviruses in different plant species [80]. Using CRISPR-Cas9 technology, researchers have successfully disrupted eIF4E genes to generate resistance against potyviruses and ipomoviruses in Arabidopsis and Cucumis sativus (cucumber) in independent studies [18,78]. Importantly, these genome-edited plants did not contain transgenes, demonstrating the potential of CRISPR technology to produce virus-resistant crops without the need to introduce foreign DNA [18,78].
In addition to viral infections, CRISPR-Cas systems are being investigated regarding their potential role in combating bacterial infections in agriculture. One example is citrus canker, which is a devastating disease caused by Xanthomonas citri subsp. citri, which leads to significant yield losses in citrus production worldwide [81]. The CRISPR/Cas9 method has been employed to modify the OsSWEET13 gene, resulting in resistance to bacterial blight caused in rice by the γ-proteobacterium Xanthomonas oryzae pv. oryzae [82]. OsSWEET13 is an S-gene that encodes a sucrose transporter involved in plant–pathogen interactions [73]. Table 2 provides examples of CRISPR-mediated editing of S-genes to generate disease-resistant crops. These studies highlight the potential of CRISPR technologies in addressing various plant diseases caused by viral and bacterial infections.

5. CRISPR/Cas-Mediated Genome Editing for Abiotic Stress Tolerance

Abiotic stresses, such as drought, heat, cold, and salt stress, pose significant challenges to crop production worldwide. Plants have evolved complex mechanisms that allow them to tolerate and respond to these stresses, which involve cellular and transcriptional regulation. Severe stress conditions can lead to membrane damage, cellular injury, and visible symptoms of necrosis in plants [109]. The advent of genome-editing technologies has provided opportunities for researchers to explore the tolerance mechanisms and develop novel traits for abiotic stress resistance. Abiotic stress tolerance is a complex trait controlled by multiple genes, making it challenging to manipulate through traditional breeding methods alone [110]. Numerous regulatory and structural genes are involved in abiotic stress responses. By focusing on “Tolerance (T) genes” that exhibit positive regulatory responses to stress, researchers can enhance stress tolerance through approaches such as gene overexpression, modification of promoter elements, modification of upstream Open Reading Frames (uORFs), or CRISPR activation [111]. Conversely, “Sensitive genes (S)” that are involved in stress susceptibility can also be targeted to study abiotic stress resistance. CRISPR-mediated knockout studies of S-genes have generated plants with enhanced resistance to abiotic stresses [112]. By disrupting these genes, researchers can uncover their functions in stress sensitivity and potentially develop crops with improved stress tolerance. The use of CRISPR technology enables precise and targeted modifications of specific genes involved in abiotic stress responses. By manipulating T-genes or disrupting S-genes, researchers can gain insights into the underlying mechanisms of stress tolerance and develop crop varieties that have enhanced resilience to abiotic stresses.

5.1. Drought Tolerance

Water scarcity and drought stress have become significant global challenges that affect both developing and developed countries. With the increasing impact of global warming, water evaporation from the Earth has intensified, leading to drought stress in plants. Drought stress has adverse effects on plant morphology and biochemistry, resulting in significant crop losses [113,114]. The CRISPR/Cas gene-editing technology has been employed to enhance drought tolerance in various plant species. By targeting specific genes involved in drought-response pathways, researchers have successfully improved the drought tolerance of crops. Here are some examples: Dehydration responsive element binding 2 (TaDREB2) and Ethylene responsive factor 3 (TaERF3) were previously edited using CRISPR/Cas in wheat, resulting in enhanced drought tolerance [115]. A loss-of-function mutation of the SAPK2 gene through CRISPR/Cas editing has improved drought tolerance in Oryza sativa (rice) by affecting ABA signaling, where SAPK2 acts as a primary mediator [116]. CRISPR/Cas9-mediated editing of the SLNPR1 gene in tomato led to enhanced drought tolerance, as evidenced by improved leaf retention under drought stress [117]. The OsDST gene edited using CRISPR/Cas in an O. sativa cultivar MTU1010 improved drought and salt tolerance by promoting leaf retention under drought stress conditions [118,119]. Editing of the OsERF109 gene using the CRISPR/Cas system increased abiotic stress tolerance in O. sativa cultivars [120]. Several ERF family members, including OsBIERF1, OsBIERF3, and OsBIERF4, were edited using CRISPR/Cas in O. sativa, resulting in enhanced abiotic stress tolerance [97]. In maize, CRISPR/Cas9-mediated editing of the ethylene response factor ARGOS8 improved drought tolerance [121]. Knock-out of the ZmWRKY40 gene in Zea mays (maize) using CRISPR/Cas technology led to increased tolerance of drought stress [122]. In tomato, CRISPR/Cas knock-out of the Mitogen-Activated Protein Kinase 3 (SlMAPK3) gene resulted in drought tolerance, which was characterized by increased levels of malondialdehyde, proline, and H2O2 in the mutant lines [123]. Knock-out of the SlNPR1 gene using CRISPR/Cas9 in tomato reduced drought resistance and down-regulated drought-related genes [117]. These examples highlight the potential of CRISPR/Cas gene editing in improving drought tolerance in various crop species by targeting the specific genes involved in drought-response pathways. By modifying these genes, researchers aimed to enhance the ability of plants to withstand drought stress and minimize crop losses.

5.2. Salt Tolerance

Salt stress can have detrimental effects on plant cells, ranging from ion disturbances to necrosis [124]. It triggers various cellular changes, including the production of secondary signal molecules (such as ROS), synthesis of abscisic acid (ABA), alterations in calcium levels and calcium/calmodulin-dependent kinase activation, and the activation of salt overly sensitive (SOS) homeostatic signaling pathways [124]. The CRISPR/Cas gene editing system has been employed to enhance salt stress resistance in several genes. Here are some examples: OsBBS1 (Bilateral Blade Senescence 1) and OsMIR528 (microRNA528) were identified as positive regulators of salt stress and early leaf senescence in O. sativa (rice), respectively. CRISPR/Cas-based targeted mutations in these genes improved salt tolerance in rice [118,125]. Inducing the expression level of the OsRAV2 (related to ABI3/VP1 2 gene) gene through CRISPR/Cas-based targeted mutations enhanced salt tolerance in O. sativa [126]. Loss-of-function mutations of the SnRK2 (SNF1-related protein kinase 2) and SAPK-1 and SAPK-2 (Osmotic Stress/ABA-Activated Protein Kinases) genes using CRISPR in rice resulted in increased salinity resistance [126]. Knockout of the SlMAPK3 (Mitogen-Activated Protein Kinases 3) gene in tomato led to decreased expression levels of SlLOX (Lipoxygenases), SlGST (Glutathione S-transferase), and SlDREB (Dehydration-Responsive Element-Binding ) genes, resulting in improved salt tolerance [123]. Overexpression of GmMYB118 (transcription factors) using CRISPR approaches enhanced drought and salt tolerance in soybeans and Arabidopsis [127]. Editing of the SAPK1 and SAPK2 genes in O. sativa increased salt stress tolerance [128]. Knockout of the SlARF4 (Auxin Response Factors 4) gene, which negatively regulates salt tolerance and osmotic stress, improved salt tolerance in tomato [129]. In Arabidopsis, knockout of the AtC/VIF1 (Cell Wall/Vacuolar Inhibitor) gene, which affects ABA response, conferred salt tolerance [130]. In O. sativa, knockout of the OsDST (Drought and Salt Tolerance) gene, which affects stomata density and leaf thickness, resulted in increased drought and salt tolerance [119]. These examples demonstrate the application of CRISPR/Cas gene editing to the improvement of salt stress tolerance in various plant species by targeting specific genes involved in salt stress response pathways. By manipulating these genes, researchers aim to enhance plants’ ability to cope with salt stress and improve their overall salt tolerance.

5.3. Cold Tolerance

The C-repeat Binding Factor 1 (CBF1) plays a crucial role in protecting plants from cold/chilling injury and preventing electrolyte leakage [131]. Mutant tomato lines with altered CBF1 expression exhibited increased accumulation of hydrogen peroxide and indole acetic acid, which contributed to enhanced cold tolerance [131]. Annexin (OsANN3), which is a gene that encodes a calcium-dependent phospholipid binding protein, has been identified as a contributor to cold stress tolerance in rice. CRISPR/Cas9 editing of the OsANN3 gene resulted in increased relative electrical conductivity and improved cold tolerance [132]. The Stress/ABA-Activated Protein Kinase 2 (SAPK2) gene-edited rice, which was generated using CRISPR/Cas9, showed resistance to cold stress [116]. In O. sativa (rice), the OsMYB30 mutant created through CRISPR/Cas gene editing exhibited enhanced cold tolerance, with an efficiency of approximately 63% [133]. These studies demonstrate the potential of CRISPR/Cas gene editing in improving cold stress tolerance in plants by targeting genes such as CBF1, OsANN3, SAPK2, and OsMYB30. Manipulating these genes can enhance plants’ ability to withstand low temperature conditions and minimize the damage caused by cold stress.

5.4. Heat Tolerance

Heat stress triggers various responses in plants, including alterations to heat shock proteins, enzymes involved in reactive oxygen species (ROS) synthesis, and genes that encode scavenger proteins [134]. Through CRISPR/Cas gene editing, several heat stress-related genes have been targeted to understand their roles in heat tolerance and improve thermotolerance in plants. Deletion mutants of Heat Stress-Sensitive Albino 1 (HSA1) generated using CRISPR/Cas exhibited increased sensitivity to heat stress compared to wild-type tomato plants, indicating the involvement of HSA1 in heat tolerance [135]. In tomato, thermotolerance was achieved by editing BZR1 (Brassinazole-Resistant 1) expression using CRISPR technology. Mutant BZR1 tomato lines displayed impaired hydrogen peroxide (H2O2) production in the apoplast and a reduction in the stimulation of Respiratory Burst Oxidase Homolog 1 (RBOH1), indicating the importance of BZR1 in influencing heat stress response [136]. CRISPR/Cas-mediated editing of the Agamous-Like 6 (AGL6) gene in tomato resulted in the development of heat-tolerant plants that exhibited parthenocarpic fruit formation [137]. In maize, the mutation of the Thermosensitive Genic Male Sterile 5 (TGMS5) gene using CRISPR/Cas technology allowed the production of thermosensitive male sterile plants [138]. These examples highlight the potential application of CRISPR/Cas gene editing to help us understand the function of heat stress-related genes and develop heat-tolerant traits in plants. By manipulating these genes, researchers aim to enhance the ability of plants to withstand high-temperature conditions and minimize the negative effects of heat stress on crop productivity. Table 3 provides further information about abiotic stress-related genes editing performed using CRISPR/Cas technology.

6. Conclusions

Mutation breeding based on physical radiation and chemically induced random mutagenesis has been widely used in the past for genome engineering. However, the emergence of CRISPR/Cas9 genome-editing technology has opened new possibilities and revitalized this field. With the integration of next-generation sequencing technologies, CRISPR/Cas9 has the potential to contribute to the development of future crops and mitigate the negative impacts of climate change on global food production. One of the primary concerns of genome-editing research is off-target effects. Despite being designed for specific genomic regions, genome modification tools can sometimes bind to unintended locations, resulting in undesired alterations. Off-target mutations are typically caused by the presence of other sequences in the genome that are identical or similar to the target gene’s sequence. Various computational methods have been developed to predict potential off-target sites in the genome [180,181]. While some studies have reported off-target effects and questioned the specificity of the CRISPR/Cas9 system, other studies have shown no off-target effects [182,183]. To address off-target activity, different strategies have been employed. Examples include using shorter guide RNAs (sgRNAs) of less than 20 nucleotides and dual Cas9 nickases, which create single-strand breaks, reducing the likelihood of off-target effects [184,185,186]. One of the most significant advantages of the CRISPR/Cas9 system is its ability to simultaneously target homologous genes with a single sgRNA [180,186]. Additionally, the Cas9/sgRNA expression vectors can contain multiple sgRNAs, enabling the study of gene families and their pathways [75,180]. Efforts have been made to deliver Cas9 and sgRNA into cells as protein and RNA to prevent the integration of foreign DNA into the genome. Studies have successfully delivered Cas9 protein and sgRNA directly to plant protoplasts using polyethylene glycol (PEG), as well as biolistically delivered the Cas9-sgRNA ribonucleoprotein complex to maize embryos, resulting in targeted mutations in regenerated plants [187,188]. By avoiding the use of recombinant DNA that can integrate into the genome, plants generated through these methods can be exempt from GMO regulations. These genome-editing techniques offer the potential to introduce desired modifications at the nucleotide level, such as improving yield and quality and providing resistance to diseases, pests, and abiotic stresses without the need for gene transfer. They also have the advantage of saving time and resources compared to labor-intensive processes like traditional selection and backcrossing. In the field of genome editing, there has been a shift from early approaches that relied on mutagenic repair of induced double-strand breaks to more precise and pre-defined modifications. This progress has been achieved through constant optimization of the tools used in genome editing. One area of advancement is the development of base editors, which are more efficient in inducing specific base changes in the genome. These base editors have been improved to have enlarged editing windows, allowing a broader range of targeted modifications. Additionally, advancements in base-editing techniques have enabled the previously challenging C-G transversions, expanding the repertoire of possible genetic modifications. Another significant development is the introduction of prime editors, which have been optimized for applications in plants. Prime editors offer greater precision by allowing the induction of specific substitutions, insertions, and deletions into the genome. This precise control over genetic modifications enhances the potential for targeted improvements in crops. Furthermore, recent breakthroughs have focused on precise restructuring of chromosomes. This approach enables not only the breakage or formation of genetic linkages, but also the swapping of promoters. By manipulating chromosomal structures, researchers can achieve more intricate modifications in the genome, opening up new possibilities for gene regulation and functional genomics. Overall, the ongoing optimization and refinement of genome editing tools have led to significant progress in achieving precise and pre-defined modifications in plant genomes. These advancements hold great promise for crop improvement, enabling the development of plants with desired traits, enhanced productivity, and improved resistance to biotic and abiotic stresses [189]. Considering the relatively short history of next-generation genome-editing techniques, it is evident that they have a high developmental capacity and significant innovation potential in the fields of breeding and plant health. Plants developed using CRISPR/Cas9 genome-editing technology may be more readily accepted by society, as they do not contain foreign genetic material transferred from other organisms. These genome-editing technologies will continue to be used as they are valuable tools in terms of crop improvement, disease resistance, and tolerance of abiotic conditions due to their ability to generate desired mutations in targeted gene regions.

Author Contributions

İ.E., B.C.-K., Ö.B., Y.H. and M.T. wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

Financial supports provided by the Scientific and Technological Research Council of Türkiye (TÜBİTAK) to İ. Erdoğan and Ö. Bilir, as well as that provided by Manier Seeds to M. Tör, are gratefully acknowledged.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

No new data were created or analyzed in this study. Data sharing is not applicable to this article.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Anderson, P.K.; Cunningham, A.A.; Patel, N.G.; Morales, F.J.; Epstein, P.R.; Daszak, P. Emerging Infectious Diseases of Plants: Pathogen Pollution, Climate Change and Agrotechnology Drivers. Trends Ecol. Evol. 2004, 19, 535–544. [Google Scholar] [CrossRef]
  2. Tilman, D.; Balzer, C.; Hill, J.; Befort, B.L. Global Food Demand and the Sustainable Intensification of Agriculture. Proc. Natl. Acad. Sci. USA 2011, 108, 20260–20264. [Google Scholar] [CrossRef] [PubMed]
  3. Bebber, D.P.; Gurr, S.J. Crop-Destroying Fungal and Oomycete Pathogens Challenge Food Security. Fungal Genet. Biol. 2015, 74, 62–64. [Google Scholar] [CrossRef]
  4. Ray, D.K.; Mueller, N.D.; West, P.C.; Foley, J.A. Yield Trends Are Insufficient to Double Global Crop Production by 2050. PLoS ONE 2013, 8, e66428. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  5. Field, C.B.; Barros, V.R. (Eds.) Climate Change 2014–Impacts, Adaptation and Vulnerability: Regional Aspects; Cambridge University Press: Cambridge, UK, 2014. [Google Scholar]
  6. Scheben, A.; Wolter, F.; Batley, J.; Puchta, H.; Edwards, D. Towards CRISPR/Cas Crops–Bringing Together Genomics and Genome Editing. New Phytol. 2017, 216, 682–698. [Google Scholar] [CrossRef] [Green Version]
  7. Chen, K.; Wang, Y.; Zhang, R.; Zhang, H.; Gao, C. CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. Annu. Rev. Plant Biol. 2019, 70, 667–697. [Google Scholar] [CrossRef] [PubMed]
  8. Mushtaq, M.; Sakina, A.; Wani, S.H.; Shikari, A.B.; Tripathi, P.; Zaid, A.; Salgotra, R.K. Harnessing genome editing techniques to engineer disease resistance in plants. Front. Plant Sci. 2019, 10, 550. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  9. Tyagi, S.; Kumar, R.; Kumar, V.; Won, S.Y.; Shukla, P. Engineering disease resistant plants through CRISPR-Cas9 technology. GM Crops Food 2021, 12, 125–144. [Google Scholar] [CrossRef] [PubMed]
  10. Tyagi, S.; Mulla, S.I.; Lee, K.J.; Chae, J.C.; Shukla, P. VOCs-Mediated Hormonal Signaling and Crosstalk with Plant Growth Promoting Microbes. Crit. Rev. Biotechnol. 2018, 38, 1277–1296. [Google Scholar] [CrossRef] [PubMed]
  11. Vannier, N.; Agler, M.; Hacquard, S. Microbiota-mediated disease resistance in plants. PLoS Pathog. 2019, 15, e1007740. [Google Scholar] [CrossRef] [Green Version]
  12. Yin, K.; Qiu, J.L. Genome Editing for Plant Disease Resistance: Applications and Perspectives. Philos. Trans. R. Soc. B 2019, 374, 20180322. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  13. Ahmad, S.; Wei, X.; Sheng, Z.; Hu, P.; Tang, S. CRISPR/Cas9 for development of disease resistance in plants: Recent progress, limitations and future prospects. Brief. Funct. Genom. 2020, 19, 26–39. [Google Scholar] [CrossRef] [PubMed]
  14. Kaiser, N.; Douches, D.; Dhingra, A.; Glenn, K.C.; Herzig, P.R.; Stowe, E.C.; Swarup, S. The Role of Conventional Plant Breeding in Ensuring Safe Levels of Naturally Occurring Toxins in Food Crops. Trends Food Sci. Technol. 2020, 100, 51–66. [Google Scholar] [CrossRef]
  15. Foley, J.A.; Ramankutty, N.; Brauman, K.A.; Cassidy, E.S.; Gerber, J.S.; Johnston, M.; Zaks, D.P. Solutions for a Cultivated Planet. Nature 2011, 478, 337–342. [Google Scholar] [CrossRef] [Green Version]
  16. Zhang, Y.; Massel, K.; Godwin, I.D.; Gao, C. Applications and Potential of Genome Editing in Crop Improvement. Genome Biol. 2018, 19, 210. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  17. Prado, J.R.; Segers, G.; Voelker, T.; Carson, D.; Dobert, R.; Phillips, J.; Martino-Catt, S. Genetically Engineered Crops: From Idea to Product. Annu. Rev. Plant Biol. 2014, 65, 769–790. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  18. Chandrasekaran, J.; Brumin, M.; Wolf, D.; Leibman, D.; Klap, C.; Pearlsman, M.; Gal-On, A. Development of Broad Virus Resistance in Non-transgenic Cucumber Using CRISPR/Cas9 Technology. Mol. Plant Pathol. 2016, 17, 1140–1153. [Google Scholar] [CrossRef] [Green Version]
  19. Jinek, M.; Chylinski, K.; Fonfara, I.; Hauer, M.; Doudna, J.A.; Charpentier, E. A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science 2012, 337, 816–821. [Google Scholar] [CrossRef]
  20. Bortesi, L.; Fischer, R. The CRISPR/Cas9 System for Plant Genome Editing and Beyond. Biotechnol. Adv. 2015, 33, 41–52. [Google Scholar] [CrossRef]
  21. Pallarès Masmitjà, M.; Knödlseder, N.; Güell, M. CRISPR-GRNA Design. In CRISPR Gene Editing: Methods and Protocols; Humana: New York, NY, USA, 2019; pp. 3–11. [Google Scholar]
  22. Mojica, F.J.; Díez-Villaseñor, C.; García-Martínez, J.; Almendros, C. Short Motif Sequences Determine the Targets of the Prokaryotic CRISPR Defence System. Microbiology 2009, 155, 733–740. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  23. Zhang, F.; Wen, Y.; Guo, X. CRISPR/Cas9 for Genome Editing: Progress, Implications and Challenges. Hum. Mol. Genet. 2014, 23, 40–46. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  24. Karginov, F.V.; Hannon, G.J. The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea. Mol. Cell 2010, 37, 7–19. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Ma, X.; Zhu, Q.; Chen, Y.; Liu, Y.G. CRISPR/Cas9 Platforms for Genome Editing in Plants: Developments and Applications. Mol. Plant 2016, 9, 961–974. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  26. Kamburova, V.S.; Nikitina, E.V.; Shermatov, S.E.; Buriev, Z.T.; Kumpatla, S.P.; Emani, C.; Abdurakhmonov, I.Y. Genome Editing in Plants: An Overview of Tools and Applications. Int. J. Agron. 2017, 2017, 7315351. [Google Scholar] [CrossRef] [Green Version]
  27. Kim, Y.G.; Cha, J.; Chandrasegaran, S. Hybrid Restriction Enzymes: Zinc Finger Fusions to Fok I Cleavage Domain. Proc. Natl. Acad. Sci. USA 1996, 93, 1156–1160. [Google Scholar] [CrossRef]
  28. Christian, M.; Cermak, T.; Doyle, E.L.; Schmidt, C.; Zhang, F.; Hummel, A.; Voytas, D.F. Targeting DNA Double-Strand Breaks with TAL Effector Nucleases. Genetics 2010, 186, 757–761. [Google Scholar] [CrossRef] [Green Version]
  29. Jankele, R.; Svoboda, P. TAL Effectors: Tools for DNA Targeting. Brief. Funct. Genom. 2014, 13, 409–419. [Google Scholar] [CrossRef]
  30. Palpant, N.J.; Dudzinski, D. Zinc Finger Nucleases: Looking toward Translation. Gene Ther. 2013, 20, 121–127. [Google Scholar] [CrossRef] [Green Version]
  31. Khandagale, K.; Nadaf, A. Genome Editing for Targeted Improvement of Plants. Plant Biotechnol. Rep. 2016, 10, 327–343. [Google Scholar] [CrossRef]
  32. Shah, T.; Andleeb, T.; Lateef, S.; Noor, M.A. Genome Editing in Plants: Advancing Crop Transformation and Overview of Tools. Plant Physiol. Biochem. 2018, 131, 12–21. [Google Scholar] [CrossRef]
  33. Gratz, S.J.; Harrison, M.M.; Wildonger, J.; O’Connor-Giles, K.M. Precise Genome Editing of Drosophila with CRISPR RNA-Guided Cas9. Methods Mol Biol. 2015, 1311, 335–348. [Google Scholar]
  34. Ledford, H. CRISPR, the Disruptor. Nature 2015, 522, 20–25. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  35. Zhang, Y.; Bai, Y.; Wu, G.; Zou, S.; Chen, Y.; Gao, C.; Tang, D. Simultaneous Modification of Three Homoeologs of Ta EDR 1 by Genome Editing Enhances Powdery Mildew Resistance in Wheat. Plant J. 2017, 91, 714–724. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  36. Liu, X.; Wu, S.; Xu, J.; Sui, C.; Wei, J. Application of CRISPR/Cas9 in plant biology. Acta Pharm. Sin. B 2017, 7, 292–302. [Google Scholar] [CrossRef]
  37. Collias, D.; Beisel, C.L. CRISPR technologies and the search for the PAM-free nuclease. Nat. Commun. 2021, 12, 555. [Google Scholar] [CrossRef] [PubMed]
  38. Wada, N.; Osakabe, K.; Osakabe, Y. Expanding the plant genome editing toolbox with recently developed CRISPR–Cas systems. Plant Physiol. 2022, 188, 1825–1837. [Google Scholar] [CrossRef] [PubMed]
  39. Nayeemul Bari, S.M.; Hatoum-Aslan, A. CRISPR-Cas10 assisted editing of virulent staphylococcal phages. Methods Enzymol. 2019, 616, 385–409. [Google Scholar]
  40. Hillary, V.E.; Ceasar, S.A. A Review on the Mechanism and Applications of CRISPR/Cas9/Cas12/Cas13/Cas14 Proteins Utilized for Genome Engineering. Mol. Biotechnol. 2023, 65, 311–325. [Google Scholar] [CrossRef]
  41. Pan, C.; Li, G.; Malzahn, A.A.; Cheng, Y.; Leyson, B.; Sretenovic, S.; Gurel, F.; Coleman, G.D.; Qi, Y. Boosting plant genome editing with a versatile CRISPR-Combo system. Nat. Plants 2022, 8, 513–525. [Google Scholar] [CrossRef] [PubMed]
  42. Mojica, F.J.; Díez-Villaseñor, C.; Soria, E.; Juez, G. Biological Significance of a Family of Regularly Spaced Repeats in the Genomes of Archaea, Bacteria and Mitochondria. Mol. Microbiol. 2000, 36, 244–246. [Google Scholar] [CrossRef]
  43. Jansen, R.; Embden, J.D.V.; Gaastra, W.; Schouls, L.M. Identification of Genes That Are Associated with DNA Repeats in Prokaryotes. Mol. Microbiol. 2002, 43, 1565–1575. [Google Scholar] [CrossRef] [PubMed]
  44. Mojica, F.J.; Díez-Villaseñor, C.; García-Martínez, J.; Soria, E. Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements. J. Mol. Evol. 2005, 60, 174–182. [Google Scholar] [CrossRef] [PubMed]
  45. Bolotin, A.; Quinquis, B.; Sorokin, A.; Ehrlich, S.D. Clustered Regularly Interspaced Short Palindrome Repeats (CRISPRs) Have Spacers of Extrachromosomal Origin. Microbiology 2005, 151, 2551–2561. [Google Scholar] [CrossRef] [Green Version]
  46. Pourcel, C.; Salvignol, G.; Vergnaud, G. CRISPR Elements in Yersinia Pestis Acquire New Repeats by Preferential Uptake of Bacteriophage DNA, and Provide Additional Tools for Evolutionary Studies. Microbiology 2005, 151, 653–663. [Google Scholar] [CrossRef] [Green Version]
  47. Belhaj, K.; Chaparro-Garcia, A.; Kamoun, S.; Patron, N.J.; Nekrasov, V. Editing Plant Genomes with CRISPR/Cas9. Curr. Opin. Biotechnol. 2015, 32, 76–84. [Google Scholar] [CrossRef] [PubMed]
  48. Deltcheva, E.; Chylinski, K.; Sharma, C.M.; Gonzales, K.; Chao, Y.; Pirzada, Z.A.; Charpentier, E. CRISPR RNA Maturation by Trans-Encoded Small RNA and Host Factor RNase III. Nature 2011, 471, 602–607. [Google Scholar] [CrossRef] [Green Version]
  49. Sorek, R.; Lawrence, C.M.; Wiedenheft, B. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu. Rev. Biochem. 2013, 82, 237–266. [Google Scholar] [CrossRef] [Green Version]
  50. Deb, S.; Choudhury, A.; Kharbyngar, B.; Satyawada, R.R. Applications of CRISPR/Cas9 technology for modification of the plant genome. Genetica 2022, 150, 1–12. [Google Scholar] [CrossRef]
  51. Kor, S.D.; Chowdhury, N.; Keot, A.K.; Yogendra, K.; Chikkaputtaiah, C.; Sudhakar Reddy, P. RNA Pol III promoters—Key players in precisely targeted plant genome editing. Front. Genet. 2023, 13, 989199. [Google Scholar] [CrossRef]
  52. Savary, S.; Ficke, A.; Aubertot, J.N.; Hollier, C. Crop Losses Due to Diseases and Their Implications for Global Food Production Losses and Food Security. Food Secur. 2012, 4, 519–537. [Google Scholar] [CrossRef]
  53. Jones, J.D.; Dangl, J.L. The plant immune system. Nature 2006, 444, 323–329. [Google Scholar] [CrossRef] [Green Version]
  54. de Almeida Engler, J.; Favery, B.; Engler, G.; Abad, P. Loss of Susceptibility as an Alternative for Nematode Resistance. Curr. Opin. Biotechnol. 2005, 16, 112–117. [Google Scholar] [CrossRef]
  55. Schie, C.C.; Takken, F.L. Susceptibility Genes 101: How to Be a Good Host. Annu. Rev. Phytopathol. 2014, 52, 551–581. [Google Scholar] [CrossRef]
  56. Pavan, S.; Jacobsen, E.; Visser, R.G.; Bai, Y. Loss of Susceptibility as a Novel Breeding Strategy for Durable and Broad-Spectrum Resistance. Mol. Breed. 2010, 25, 1–12. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  57. Eckardt, N.A. Plant Disease Susceptibility Genes? Plant Cell 2002, 14, 1983–1986. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  58. Jørgensen, I.H. Discovery, characterization and exploitation of Mlo powdery mildew resistance in barley. Euphytica 1992, 63, 141–152. [Google Scholar] [CrossRef]
  59. Büschges, R.; Hollricher, K.; Panstruga, R.; Simons, G.; Wolter, M.; Frijters, A.; Schulze-Lefert, P. The barley Mlo gene: A novel control element of plant pathogen resistance. Cell 1997, 88, 695–705. [Google Scholar] [CrossRef] [Green Version]
  60. Devoto, A.; Piffanelli, P.; Nilsson, I.; Wallin, E.; Panstruga, R.; Heijne, G.; Schulze-Lefert, P. Topology, Subcellular Localization, and Sequence Diversity of the Mlo Family in Plants. J. Biol. Chem. 1999, 274, 34993–35004. [Google Scholar] [CrossRef] [Green Version]
  61. Devoto, A.; Hartmann, H.A.; Piffanelli, P.; Elliott, C.; Simmons, C.; Taramino, G.; Panstruga, R. Molecular Phylogeny and Evolution of the Plant-Specific Seven-Transmembrane MLO Family. J. Mol. Evol. 2003, 56, 77–88. [Google Scholar] [CrossRef] [PubMed]
  62. Shan, Q.; Wang, Y.; Li, J.; Zhang, Y.; Chen, K.; Liang, Z.; Gao, C. Targeted Genome Modification of Crop Plants Using a CRISPR-Cas System. Nat. Biotechnol. 2013, 31, 686–688. [Google Scholar] [CrossRef]
  63. Wang, Y.; Cheng, X.; Shan, Q.; Zhang, Y.; Liu, J.; Gao, C.; Qiu, J.L. Simultaneous Editing of Three Homoeoalleles in Hexaploid Bread Wheat Confers Heritable Resistance to Powdery Mildew. Nat. Biotechnol. 2014, 32, 947–951. [Google Scholar] [CrossRef]
  64. Nekrasov, V.; Wang, C.; Win, J.; Lanz, C.; Weigel, D.; Kamoun, S. Rapid Generation of a Transgene-Free Powdery Mildew Resistant Tomato by Genome Deletion. Sci. Rep. 2017, 7, 482. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  65. Consonni, C.; Humphry, M.E.; Hartmann, H.A.; Livaja, M.; Durner, J.; Westphal, L.; Panstruga, R. Conserved requirement for a plant host cell protein in powdery mildew pathogenesis. Nat. Genet. 2006, 38, 716–720. [Google Scholar] [CrossRef] [PubMed]
  66. Bai, Y.; Pavan, S.; Zheng, Z.; Zappel, N.F.; Reinstädler, A.; Lotti, C.; Panstruga, R. Naturally Occurring Broad-Spectrum Powdery Mildew Resistance in a Central American Tomato Accession Is Caused by Loss of Mlo Function. Mol. Plant-Microbe Interact. 2008, 21, 30–39. [Google Scholar] [CrossRef] [Green Version]
  67. Humphry, M.; Reinstaedler, A.; Ivanov, S.; Bisseling, T.O.N.; Panstruga, R. Durable Broad-spectrum Powdery Mildew Resistance in Pea Er1 Plants Is Conferred by Natural Loss-of-function Mutations in PsMLO1. Mol. Plant Pathol. 2011, 12, 866–878. [Google Scholar] [CrossRef] [PubMed]
  68. Zheng, Z.; Nonomura, T.; Appiano, M.; Pavan, S.; Matsuda, Y.; Toyoda, H.; Bai, Y. Loss of Function in Mlo Orthologs Reduces Susceptibility of Pepper and Tomato to Powdery Mildew Disease Caused by Leveillula Taurica. PLoS ONE 2013, 8, e70723. [Google Scholar] [CrossRef]
  69. Appiano, M.; Pavan, S.; Catalano, D.; Zheng, Z.; Bracuto, V.; Lotti, C.; Bai, Y. Identification of Candidate MLO Powdery Mildew Susceptibility Genes in Cultivated Solanaceae and Functional Characterization of Tobacco NtMLO1. Transgenic Res. 2015, 24, 847–858. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  70. Feechan, A.; Jermakow, A.M.; Torregrosa, L.; Panstruga, R.; Dry, I.B. Identification of Grapevine MLO Gene Candidates Involved in Susceptibility to Powdery Mildew. Funct. Plant Biol. 2008, 35, 1255–1266. [Google Scholar] [CrossRef]
  71. Zaidi, S.S.E.A.; Mukhtar, M.S.; Mansoor, S. Genome Editing: Targeting Susceptibility Genes for Plant Disease Resistance. Trends Biotechnol. 2018, 36, 898–906. [Google Scholar] [CrossRef]
  72. Peterson, B.A.; Haak, D.C.; Nishimura, M.T.; Teixeira, P.J.; James, S.R.; Dangl, J.L.; Nimchuk, Z.L. Genome-Wide Assessment of Efficiency and Specificity in CRISPR/Cas9 Mediated Multiple Site Targeting in Arabidopsis. PLoS ONE 2016, 11, e0162169. [Google Scholar] [CrossRef] [Green Version]
  73. Borrelli, V.M.; Brambilla, V.; Rogowsky, P.; Marocco, A.; Lanubile, A. The enhancement of plant disease resistance using CRISPR/Cas9 technology. Front. Plant Sci. 2018, 9, 1245. [Google Scholar] [CrossRef] [PubMed]
  74. Ma, Y.; Zhang, L.; Huang, X. Genome Modification by CRISPR/Cas9. FEBS J. 2014, 281, 5186–5193. [Google Scholar] [CrossRef]
  75. Xing, H.L.; Dong, L.; Wang, Z.P.; Zhang, H.Y.; Han, C.Y.; Liu, B.; Chen, Q.J. A CRISPR/Cas9 Toolkit for Multiplex Genome Editing in Plants. BMC Plant Biol. 2014, 14, 327. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  76. Zhou, H.; Liu, B.; Weeks, D.P.; Spalding, M.H.; Yang, B. Large Chromosomal Deletions and Heritable Small Genetic Changes Induced by CRISPR/Cas9 in Rice. Nucleic Acids Res. 2014, 42, 10903–10914. [Google Scholar] [CrossRef] [PubMed]
  77. Xu, R.; Yang, Y.; Qin, R.; Li, H.; Qiu, C.; Li, L.; Yang, J. Rapid Improvement of Grain Weight via Highly Efficient CRISPR/Cas9-Mediated Multiplex Genome Editing in Rice. J. Genet. Genom. = Yi Chuan Xue Bao 2016, 43, 529–532. [Google Scholar] [CrossRef] [PubMed]
  78. Pyott, D.E.; Sheehan, E.; Molnar, A. Engineering of CRISPR/Cas9-mediated Potyvirus Resistance in Transgene-free Arabidopsis Plants. Mol. Plant Pathol. 2016, 17, 1276–1288. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  79. Gao, X.; Chen, J.; Dai, X.; Zhang, D.; Zhao, Y. An Effective Strategy for Reliably Isolating Heritable and Cas9-Free Arabidopsis Mutants Generated by CRISPR/Cas9-Mediated Genome Editing. Plant Physiol. 2016, 171, 1794–1800. [Google Scholar] [CrossRef] [Green Version]
  80. Bastet, A.; Robaglia, C.; Gallois, J.L. eIF4E Resistance: Natural Variation Should Guide Gene Editing. Trends Plant Sci. 2017, 22, 411–419. [Google Scholar] [CrossRef]
  81. Stover, E.D.; Driggers, R.; Richardson, M.L.; Hall, D.G.; Duan, Y.; Lee, R.F. Incidence and Severity of Asiatic Citrus Canker on Diverse Citrus and Citrus-Related Germplasm in a Florida Field Planting. HortScience 2014, 49, 4–9. [Google Scholar] [CrossRef] [Green Version]
  82. Zhou, J.; Peng, Z.; Long, J.; Sosso, D.; Liu, B.O.; Eom, J.S.; Yang, B. Gene Targeting by the TAL Effector PthXo2 Reveals Cryptic Resistance Gene for Bacterial Blight of Rice. Plant J. 2015, 82, 632–643. [Google Scholar] [CrossRef]
  83. Malnoy, M.; Viola, R.; Jung, M.H.; Koo, O.J.; Kim, S.; Kim, J.S.; Nagamangala Kanchiswamy, C. DNA-Free Genetically Edited Grapevine and Apple Protoplast Using CRISPR/Cas9 Ribonucleoproteins. Front. Plant Sci. 2016, 7, 1904. [Google Scholar] [CrossRef]
  84. Santillán Martínez, M.I.; Bracuto, V.; Koseoglou, E.; Appiano, M.; Jacobsen, E.; Visser, R.G.F.; Wolters, A.A.; Bai, Y. CRISPR/Cas9-targeted mutagenesis of the tomato susceptibility gene PMR4 for resistance against powdery mildew. BMC Plant Biol. 2020, 20, 284. [Google Scholar] [CrossRef] [PubMed]
  85. Ji, X.; Zhang, H.; Zhang, Y.; Wang, Y.; Gao, C. Establishing a CRISPR–Cas-like immune system conferring DNA virus resistance in plants. Nat. Plants 2015, 1, 15144. [Google Scholar] [CrossRef] [PubMed]
  86. Tripathi, J.N.; Ntui, V.O.; Ron, M.; Muiruri, S.K.; Britt, A.; Tripathi, L. CRISPR/Cas9 Editing of Endogenous Banana Streak Virus in the B Genome of Musa spp. Overcomes a Major Challenge in Banana Breeding. Commun. Biol. 2019, 2, 46. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  87. Kis, A.; Hamar, É.; Tholt, G.; Bán, R.; Havelda, Z. Creating Highly Efficient Resistance against Wheat Dwarf Virus in Barley by Employing CRISPR/Cas9 System. Plant Biotechnol. J. 2019, 17, 1004. [Google Scholar] [CrossRef]
  88. Fister, A.S.; Landherr, L.; Maximova, S.N.; Guiltinan, M.J. Transient Expression of CRISPR/Cas9 Machinery Targeting TcNPR3 Enhances Defense Response in Theobroma cacao. Front. Plant Sci. 2018, 9, 268. [Google Scholar] [CrossRef] [Green Version]
  89. Jia, H.; Zhang, Y.; Orbović, V.; Xu, J.; White, F.F.; Jones, J.B.; Wang, N. Genome Editing of the Disease Susceptibility Gene Cs LOB 1 in Citrus Confers Resistance to Citrus Canker. Plant Biotechnol. J. 2017, 15, 817–823. [Google Scholar] [CrossRef] [Green Version]
  90. Peng, A.; Chen, S.; Lei, T.; Xu, L.; He, Y.; Wu, L.; Zou, X. Engineering Canker-resistant Plants through CRISPR/Cas9-targeted Editing of the Susceptibility Gene Cs LOB 1 Promoter in Citrus. Plant Biotechnol. J. 2017, 15, 1509–1519. [Google Scholar] [CrossRef] [Green Version]
  91. Wang, X.; Tu, M.; Wang, D.; Liu, J.; Li, Y.; Li, Z.; Wang, X. CRISPR/Cas9-mediated Efficient Targeted Mutagenesis in Grape in the First Generation. Plant Biotechnol. J. 2018, 16, 844–855. [Google Scholar] [CrossRef] [Green Version]
  92. Gumtow, R.; Wu, D.; Uchida, J.; Tian, M. A Phytophthora Palmivora Extracellular Cystatin-like Protease Inhibitor Targets Papain to Contribute to Virulence on Papaya. Mol. Plant-Microbe Interact. 2018, 31, 363–373. [Google Scholar] [CrossRef] [Green Version]
  93. Oliva, R.; Ji, C.; Atienza-Grande, G.; Huguet-Tapia, J.C.; Perez-Quintero, A.; Li, T.; Yang, B. Broad-Spectrum Resistance to Bacterial Blight in Rice Using Genome Editing. Nat. Biotechnol. 2019, 37, 1344–1350. [Google Scholar] [CrossRef] [Green Version]
  94. Kim, Y.A.; Moon, H.; Park, C.J. CRISPR/Cas9-Targeted Mutagenesis of Os8N3 in Rice to Confer Resistance to Xanthomonas oryzae pv. oryzae. Rice 2019, 12, 67. [Google Scholar] [CrossRef]
  95. Xu, Z.; Xu, X.; Gong, Q.; Li, Z.; Li, Y.; Wang, S.; Chen, G. Engineering Broad-Spectrum Bacterial Blight Resistance by Simultaneously Disrupting Variable TALE-Binding Elements of Multiple Susceptibility Genes in Rice. Mol. Plant 2019, 12, 1434–1446. [Google Scholar] [CrossRef] [Green Version]
  96. Li, S.; Shen, L.; Hu, P.; Liu, Q.; Zhu, X.; Qian, Q.; Wang, Y. Developing Disease-resistant Thermosensitive Male Sterile Rice by Multiplex Gene Editing. J. Integr. Plant Biol. 2019, 61, 1201–1205. [Google Scholar] [CrossRef]
  97. Wang, F.; Wang, C.; Liu, P.; Lei, C.; Hao, W.; Gao, Y.; Zhao, K. Enhanced Rice Blast Resistance by CRISPR/Cas9-Targeted Mutagenesis of the ERF Transcription Factor Gene OsERF922. PLoS ONE 2016, 11, e0154027. [Google Scholar] [CrossRef] [Green Version]
  98. Xie, K.; Yang, Y. RNA-Guided Genome Editing in Plants Using a CRISPR–Cas System. Mol. Plant 2013, 6, 1975–1983. [Google Scholar] [CrossRef] [Green Version]
  99. Macovei, A.; Sevilla, N.R.; Cantos, C.; Jonson, G.B.; Slamet-Loedin, I.; Čermák, T.; Chadha-Mohanty, P. Novel Alleles of Rice EIF4G Generated by CRISPR/Cas9-targeted Mutagenesis Confer Resistance to Rice Tungro Spherical Virus. Plant Biotechnol. J. 2018, 16, 1918–1927. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  100. Yin, K.; Han, T.; Xie, K.; Zhao, J.; Song, J.; Liu, Y. Engineer Complete Resistance to Cotton Leaf Curl Multan Virus by the CRISPR/Cas9 System in Nicotiana benthamiana. Phytopathol. Res. 2019, 1, 9. [Google Scholar] [CrossRef] [Green Version]
  101. Ali, Z.; Abulfaraj, A.; Idris, A.; Ali, S.; Tashkandi, M.; Mahfouz, M.M. CRISPR/Cas9-Mediated Viral Interference in Plants. Genome Biol. 2015, 16, 238. [Google Scholar] [CrossRef] [Green Version]
  102. Baltes, N.J.; Hummel, A.W.; Konecna, E.; Cegan, R.; Bruns, A.N.; Bisaro, D.M.; Voytas, D.F. Conferring Resistance to Geminiviruses with the CRISPR–Cas Prokaryotic Immune System. Nat. Plants 2015, 1, 15145. [Google Scholar] [CrossRef] [PubMed]
  103. Tashkandi, M.; Ali, Z.; Aljedaani, F.; Shami, A.; Mahfouz, M.M. Engineering Resistance against Tomato Yellow Leaf Curl Virus via the CRISPR/Cas9 System in Tomato. Plant Signal. Behav. 2018, 13, 1525996. [Google Scholar] [CrossRef] [Green Version]
  104. Thomazella, D.P.T.; Seong, K.; Mackelprang, R.; Dahlbeck, D.; Geng, Y.; Gill, U.S.; Qi, T.; Pham, J.; Giuseppe, P.; Lee, C.Y.; et al. Loss of function of a DMR6 ortholog in tomato confers broad-spectrum disease resistance. Proc. Natl. Acad. Sci. USA 2021, 6, 118. [Google Scholar] [CrossRef]
  105. Ortigosa, A.; Gimenez-Ibanez, S.; Leonhardt, N.; Solano, R. Design of a Bacterial Speck Resistant Tomato by CRISPR/Cas9-mediated Editing of Sl JAZ 2. Plant Biotechnol. J. 2019, 17, 665–673. [Google Scholar] [CrossRef] [Green Version]
  106. Prihatna, C.; Barbetti, M.J.; Barker, S.J. A Novel Tomato Fusarium Wilt Tolerance Gene. Front. Microbiol. 2018, 9, 1226. [Google Scholar] [CrossRef]
  107. Zhang, S.; Wang, L.; Zhao, R.; Yu, W.; Li, R.; Li, Y.; Shen, L. Knockout of SlMAPK3 Reduced Disease Resistance to Botrytis cinerea in Tomato Plants. J. Agric. Food Chem. 2018, 66, 8949–8956. [Google Scholar] [CrossRef]
  108. Wang, Z.; Hardcastle, T.J.; Pastor, A.C.; Yip, W.H.; Tang, S.; Baulcombe, D.C. A Novel DCL2-Dependent MiRNA Pathway in Tomato Affects Susceptibility to RNA Viruses. Genes Dev. 2018, 32, 1155–1160. [Google Scholar] [CrossRef] [Green Version]
  109. Polle, A. Dissecting the Superoxide Dismutase-Ascorbate-Glutathione-Pathway in Chloroplasts by Metabolic Modeling. Computer Simulations as a Step towards Flux Analysis. Plant Physiol. 2001, 126, 445–462. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  110. Fang, Y.; Xiong, L. General mechanisms of drought response and their application in drought resistance improvement in plants. Cell. Mol. Life Sci. 2015, 72, 673–689. [Google Scholar] [CrossRef] [PubMed]
  111. Ma, L.; Liang, Z. CRISPR Technology for Abiotic Stress Resistant Crop Breeding. Plant Growth Regul. 2021, 94, 115–129. [Google Scholar] [CrossRef]
  112. Zafar, S.A.; Zaidi, S.S.E.A.; Gaba, Y.; Singla-Pareek, S.L.; Dhankher, O.P.; Li, X.; Pareek, A. Engineering Abiotic Stress Tolerance via CRISPR/Cas-Mediated Genome Editing. J. Exp. Bot. 2020, 71, 470–479. [Google Scholar] [CrossRef]
  113. Ilyas, M.; Nisar, M.; Khan, N.; Hazrat, A.; Khan, A.H.; Hayat, K.; Fahad, S.; Khan, A.; Ullah, A. Drought Tolerance Strategies in Plants: A Mechanistic Approach. J. Plant Growth Regul. 2021, 40, 926–944. [Google Scholar] [CrossRef]
  114. Hanna, S.H.S.; Osborne-Lee, I.W.; Cesaretti, G.P.; Misso, R.; Khalil, M.T. Ecological Agro-Ecosystem Sustainable Development in Relationship to Other Sectors in the Economic System, and Human Ecological Footprint and Imprint. Agric. Agric. Sci. Procedia 2016, 8, 17–30. [Google Scholar] [CrossRef] [Green Version]
  115. Kim, D.; Alptekin, B.; Budak, H. CRISPR/Cas9 Genome Editing in Wheat. Funct. Integr. Genom. 2018, 18, 31–41. [Google Scholar] [CrossRef] [Green Version]
  116. Lou, D.; Wang, H.; Liang, G.; Yu, D. OsSAPK2 Confers Abscisic Acid Sensitivity and Tolerance to Drought Stress in Rice. Front. Plant Sci. 2017, 8, 993. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  117. Li, R.; Liu, C.; Zhao, R.; Wang, L.; Chen, L.; Yu, W.; Shen, L. CRISPR/Cas9-Mediated SlNPR1 Mutagenesis Reduces Tomato Plant Drought Tolerance. BMC Plant Biol. 2019, 19, 38. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  118. Ganie, S.A.; Wani, S.H.; Henry, R.; Hensel, G. Improving Rice Salt Tolerance by Precision Breeding in a New Era. Curr. Opin. Plant Biol. 2021, 60, 101996. [Google Scholar] [CrossRef]
  119. Santosh Kumar, V.V.; Verma, R.K.; Yadav, S.K.; Yadav, P.; Watts, A.; Rao, M.V.; Chinnusamy, V. CRISPR-Cas9 Mediated Genome Editing of Drought and Salt Tolerance (OsDST) Gene in Indica Mega Rice Cultivar MTU1010. Physiol. Mol. Biol. Plants 2020, 26, 1099–1110. [Google Scholar] [CrossRef]
  120. Mishra, R.; Joshi, R.K.; Zhao, K. Genome editing in rice: Recent advances, challenges, and future implications. Front. Plant Sci. 2018, 9, 1361. [Google Scholar] [CrossRef]
  121. Shi, J.; Gao, H.; Wang, H.; Lafitte, H.R.; Archibald, R.L.; Yang, M.; Habben, J.E. ARGOS 8 Variants Generated by CRISPR-Cas9 Improve Maize Grain Yield under Field Drought Stress Conditions. Plant Biotechnol. J. 2017, 15, 207–216. [Google Scholar] [CrossRef] [Green Version]
  122. Wang, C.T.; Ru, J.N.; Liu, Y.W.; Yang, J.F.; Li, M.; Xu, Z.S.; Fu, J.D. The Maize WRKY Transcription Factor ZmWRKY40 Confers Drought Resistance in Transgenic Arabidopsis. Int. J. Mol. Sci. 2018, 19, 2580. [Google Scholar] [CrossRef] [Green Version]
  123. Wang, L.; Chen, L.; Li, R.; Zhao, R.; Yang, M.; Sheng, J.; Shen, L. Reduced Drought Tolerance by CRISPR/Cas9-Mediated SlMAPK3 Mutagenesis in Tomato Plants. J. Agric. Food Chem. 2017, 65, 8674–8682. [Google Scholar] [CrossRef]
  124. Julkowska, M.M.; Testerink, C. Tuning Plant Signaling and Growth to Survive Salt. Trends Plant Sci. 2015, 20, 586–594. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  125. Sun, B.R.; Fu, C.Y.; Fan, Z.L.; Chen, Y.; Chen, W.F.; Zhang, J.; Li, C. Genomic and Transcriptomic Analysis Reveal Molecular Basis of Salinity Tolerance in a Novel Strong Salt-Tolerant Rice Landrace Changmaogu. Rice 2019, 12, 99. [Google Scholar] [CrossRef] [PubMed]
  126. Duan, Y.B.; Li, J.; Qin, R.Y.; Xu, R.F.; Li, H.; Yang, Y.C.; Yang, J.B. Identification of a Regulatory Element Responsible for Salt Induction of Rice OsRAV2 through Ex Situ and in Situ Promoter Analysis. Plant Mol. Biol. 2016, 90, 49–62. [Google Scholar] [CrossRef] [PubMed]
  127. Du, Y.T.; Zhao, M.J.; Wang, C.T.; Gao, Y.; Wang, Y.X.; Liu, Y.W.; Ma, Y.Z. Identification and Characterization of GmMYB118 Responses to Drought and Salt Stress. BMC Plant Biol. 2018, 18, 320. [Google Scholar] [CrossRef] [Green Version]
  128. Lou, D.; Wang, H.; Yu, D. The Sucrose Non-Fermenting-1-Related Protein Kinases SAPK1 and SAPK2 Function Collaboratively as Positive Regulators of Salt Stress Tolerance in Rice. BMC Plant Biol. 2018, 18, 203. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  129. Bouzroud, S.; Gasparini, K.; Hu, G.; Barbosa, M.A.M.; Rosa, B.L.; Fahr, M.; Zouine, M. Down Regulation and Loss of Auxin Response Factor 4 Function Using CRISPR/Cas9 Alters Plant Growth, Stomatal Function and Improves Tomato Tolerance to Salinity and Osmotic Stress. Genes 2020, 11, 272. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  130. Yang, W.; Chen, S.; Cheng, Y.; Zhang, N.; Ma, Y.; Wang, W.; Wang, S. Cell Wall/Vacuolar Inhibitor of Fructosidase 1 Regulates ABA Response and Salt Tolerance in Arabidopsis. Plant Signal. Behav. 2020, 15, 1744293. [Google Scholar] [CrossRef]
  131. Li, R.; Zhang, L.; Wang, L.; Chen, L.; Zhao, R.; Sheng, J.; Shen, L. Reduction of Tomato-Plant Chilling Tolerance by CRISPR–Cas9-Mediated SlCBF1 Mutagenesis. J. Agric. Food Chem. 2018, 66, 9042–9051. [Google Scholar] [CrossRef]
  132. Shen, C.; Que, Z.; Xia, Y.; Tang, N.; Li, D.; He, R.; Cao, M. Knock out of the Annexin Gene OsAnn3 via CRISPR/Cas9-Mediated Genome Editing Decreased Cold Tolerance in Rice. J. Plant Biol. 2017, 60, 539–547. [Google Scholar] [CrossRef]
  133. Zeng, Y.; Wen, J.; Zhao, W.; Wang, Q.; Huang, W. Rational Improvement of Rice Yield and Cold Tolerance by Editing the Three Genes OsPIN5b, GS3, and OsMYB30 with the CRISPR–Cas9 System. Front. Plant Sci. 2020, 10, 1663. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  134. Shah, K.; Singh, M.; Rai, A.C. Effect of Heat-Shock Induced Oxidative Stress Is Suppressed in BcZAT12 Expressing Drought Tolerant Tomato. Phytochemistry 2013, 95, 109–117. [Google Scholar] [CrossRef] [PubMed]
  135. Qiu, Z.; Kang, S.; He, L.; Zhao, J.; Zhang, S.; Hu, J.; Zhu, L. The Newly Identified Heat-Stress Sensitive Albino 1 Gene Affects Chloroplast Development in Rice. Plant Sci. 2018, 267, 168–179. [Google Scholar] [CrossRef] [PubMed]
  136. Yin, Y.; Qin, K.; Song, X.; Zhang, Q.; Zhou, Y.; Xia, X.; Yu, J. BZR1 Transcription Factor Regulates Heat Stress Tolerance through FERONIA Receptor-like Kinase-Mediated Reactive Oxygen Species Signaling in Tomato. Plant Cell Physiol. 2018, 59, 2239–2254. [Google Scholar] [CrossRef] [PubMed]
  137. Klap, C.; Yeshayahou, E.; Bolger, A.M.; Arazi, T.; Gupta, S.K.; Shabtai, S.; Barg, R. Tomato Facultative Parthenocarpy Results from Sl AGAMOUS-LIKE 6 Loss of Function. Plant Biotechnol. J. 2017, 15, 634–647. [Google Scholar] [CrossRef]
  138. Li, J.; Zhang, H.; Si, X.; Tian, Y.; Chen, K.; Liu, J.; Gao, C. Generation of Thermosensitive Male-Sterile Maize by Targeted Knockout of the ZmTMS5 Gene. J. Genet. Genom. = Yi Chuan Xue Bao 2017, 44, 465–468. [Google Scholar] [CrossRef] [PubMed]
  139. Wang, B.; Zhong, Z.; Wang, X.; Han, X.; Yu, D.; Wang, C.; Zhang, Y. Knockout of the OsNAC006 Transcription Factor Causes Drought and Heat Sensitivity in Rice. Int. J. Mol. Sci. 2020, 21, 2288. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  140. Wu, J.; Yan, G.; Duan, Z.; Wang, Z.; Kang, C.; Guo, L.; Dai, C. Roles of the Brassica napus DELLA Protein BnaA6.RGA, in Modulating Drought Tolerance by Interacting with the ABA Signaling Component BnaA10.ABF2. Front. Plant Sci. 2020, 11, 577. [Google Scholar] [CrossRef]
  141. Liao, S.; Qin, X.; Luo, L.; Han, Y.; Wang, X.; Usman, B.; Li, R. CRISPR/Cas9-Induced Mutagenesis of Semi-Rolled Leaf1, 2 Confers Curled Leaf Phenotype and Drought Tolerance by Influencing Protein Expression Patterns and ROS Scavenging in Rice (Oryza sativa L.). Agronomy 2019, 9, 728. [Google Scholar] [CrossRef] [Green Version]
  142. Shim, J.S.; Oh, N.; Chung, P.J.; Kim, Y.S.; Choi, Y.D.; Kim, J.K. Overexpression of OsNAC14 Improves Drought Tolerance in Rice. Front. Plant Sci. 2018, 9, 310. [Google Scholar]
  143. Zhang, H.; Zhang, J.; Wei, P.; Zhang, B.; Gou, F.; Feng, Z.; Zhu, J.K. The CRISPR/C As9 System Produces Specific and Homozygous Targeted Gene Editing in Rice in One Generation. Plant Biotechnol. J. 2014, 12, 797–807. [Google Scholar] [CrossRef]
  144. Roca Paixão, J.F.; Gillet, F.X.; Ribeiro, T.P.; Bournaud, C.; Lourenço-Tessutti, I.T.; Noriega, D.D.; Grossi-de-Sa, M.F. Improved Drought Stress Tolerance in Arabidopsis by CRISPR/DCas9 Fusion with a Histone AcetylTransferase. Sci. Rep. 2019, 9, 8080. [Google Scholar] [CrossRef] [Green Version]
  145. Park, J.J.; Dempewolf, E.; Zhang, W.; Wang, Z.Y. RNA-Guided Transcriptional Activation via CRISPR/DCas9 Mimics Overexpression Phenotypes in Arabidopsis. PLoS ONE 2017, 12, e0179410. [Google Scholar] [CrossRef] [Green Version]
  146. Osakabe, Y.; Watanabe, T.; Sugano, S.S.; Ueta, R.; Ishihara, R.; Shinozaki, K.; Osakabe, K. Optimization of CRISPR/Cas9 Genome Editing to Modify Abiotic Stress Responses in Plants. Sci. Rep. 2016, 6, 26685. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  147. Zhao, C.; Zhang, Z.; Xie, S.; Si, T.; Li, Y.; Zhu, J.K. Mutational Evidence for the Critical Role of CBF Transcription Factors in Cold Acclimation in Arabidopsis. Plant Physiol. 2016, 171, 2744–2759. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  148. Zhou, Y.; Zhang, Y.; Wang, X.; Han, X.; An, Y.; Lin, S.; Xia, X. Root-specific NF-Y Family Transcription Factor, PdNF-YB21, Positively Regulates Root Growth and Drought Resistance by Abscisic Acid-mediated Indoylacetic Acid Transport in Populus. New Phytol. 2020, 227, 407–426. [Google Scholar] [CrossRef] [PubMed]
  149. Li, P.; Li, Y.J.; Zhang, F.J.; Zhang, G.Z.; Jiang, X.Y.; Yu, H.M.; Hou, B.K. The Arabidopsis UDP-glycosyltransferases UGT79B2 and UGT79B3, Contribute to Cold, Salt and Drought Stress Tolerance via Modulating Anthocyanin Accumulation. Plant J. 2017, 89, 85–103. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  150. Nawaz, G.; Han, Y.; Usman, B.; Liu, F.; Qin, B.; Li, R. Knockout of OsPRP1, a Gene Encoding Proline-Rich Protein, Confers Enhanced Cold Sensitivity in Rice (Oryza sativa L.) at the Seedling Stage. 3 Biotech 2019, 9, 254. [Google Scholar] [CrossRef] [PubMed]
  151. Sanderson, B.J.; Park, S.; Jameel, M.I.; Kraft, J.C.; Thomashow, M.F.; Schemske, D.W.; Oakley, C.G. Genetic and Physiological Mechanisms of Freezing Tolerance in Locally Adapted Populations of a Winter Annual. Am. J. Bot. 2020, 107, 250–261. [Google Scholar] [CrossRef] [Green Version]
  152. Park, S.; Gilmour, S.J.; Grumet, R.; Thomashow, M.F. CBF-Dependent and CBF-Independent Regulatory Pathways Contribute to the Differences in Freezing Tolerance and Cold-Regulated Gene Expression of Two Arabidopsis Ecotypes Locally Adapted to Sites in Sweden and Italy. PLoS ONE 2018, 13, e0207723. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  153. Shi, Y.; Huang, J.; Sun, T.; Wang, X.; Zhu, C.; Ai, Y.; Gu, H. The Precise Regulation of Different COR Genes by Individual CBF Transcription Factors in Arabidopsis thaliana. J. Integr. Plant Biol. 2017, 59, 118–133. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  154. Jia, Y.; Ding, Y.; Shi, Y.; Zhang, X.; Gong, Z.; Yang, S. The Cbfs Triple Mutants Reveal the Essential Functions of CBF s in Cold Acclimation and Allow the Definition of CBF Regulons in Arabidopsis. New Phytol. 2016, 212, 345–353. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  155. Liu, X.; Wu, D.; Shan, T.; Xu, S.; Qin, R.; Li, H.; Li, J. The Trihelix Transcription Factor OsGTγ-2 Is Involved Adaption to Salt Stress in Rice. Plant Mol. Biol. 2020, 103, 545–560. [Google Scholar] [CrossRef]
  156. Mo, W.; Tang, W.; Du, Y.; Jing, Y.; Bu, Q.; Lin, R. PHYTOCHROME-INTERACTING FACTOR-LIKE14 and SLENDER RICE1 Interaction Controls Seedling Growth under Salt Stress. Plant Physiol. 2020, 184, 506–517. [Google Scholar] [CrossRef]
  157. Alfatih, A.; Wu, J.; Jan, S.U.; Zhang, Z.S.; Xia, J.Q.; Xiang, C.B. Loss of Rice PARAQUAT TOLERANCE 3 Confers Enhanced Resistance to Abiotic Stresses and Increases Grain Yield in Field. Plant Cell Environ. 2020, 43, 2743–2754. [Google Scholar] [CrossRef]
  158. Yin, W.; Xiao, Y.; Niu, M.; Meng, W.; Li, L.; Zhang, X.; Tong, H. ARGONAUTE2 Enhances Grain Length and Salt Tolerance by Activating BIG GRAIN3 to Modulate Cytokinin Distribution in Rice. Plant Cell 2020, 32, 2292–2306. [Google Scholar] [CrossRef] [PubMed]
  159. Chen, G.; Hu, J.; Dong, L.; Zeng, D.; Guo, L.; Zhang, G.; Qian, Q. The Tolerance of Salinity in Rice Requires the Presence of a Functional Copy of FLN2. Biomolecules 2019, 10, 17. [Google Scholar] [CrossRef] [Green Version]
  160. Wang, W.C.; Lin, T.C.; Kieber, J.; Tsai, Y.C. Response Regulators 9 and 10 Negatively Regulate Salinity Tolerance in Rice. Plant Cell Physiol. 2019, 60, 2549–2563. [Google Scholar] [CrossRef]
  161. Qin, H.; Wang, J.; Chen, X.; Wang, F.; Peng, P.; Zhou, Y.; Huang, R. Rice Os DOF 15 Contributes to Ethylene-inhibited Primary Root Elongation under Salt Stress. New Phytol. 2019, 223, 798–813. [Google Scholar] [CrossRef]
  162. Lan, T.; Zheng, Y.; Su, Z.; Yu, S.; Song, H.; Zheng, X.; Wu, W. OsSPL10, a SBP-Box Gene, Plays a Dual Role in Salt Tolerance and Trichome Formation in Rice (Oryza sativa L.). G3 Genes Genomes Genet. 2019, 9, 4107–4114. [Google Scholar] [CrossRef] [Green Version]
  163. Liu, J.; Cui, L.; Xie, Z.; Zhang, Z.; Liu, E.; Peng, X. Two NCA1 Isoforms Interact with Catalase in a Mutually Exclusive Manner to Redundantly Regulate Its Activity in Rice. BMC Plant Biol. 2019, 19, 105. [Google Scholar] [CrossRef] [PubMed]
  164. Zhang, A.; Liu, Y.; Wang, F.; Li, T.; Chen, Z.; Kong, D.; Luo, L. Enhanced Rice Salinity Tolerance via CRISPR/Cas9-Targeted Mutagenesis of the OsRR22 Gene. Mol. Breed. 2019, 39, 47. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  165. Wang, B.; Zhong, Z.; Zhang, H.; Wang, X.; Liu, B.; Yang, L.; Han, X.; Yu, D.; Zheng, X.; Wang, C.; et al. Targeted Mutagenesis of NAC Transcription Factor Gene, OsNAC041, Leading to Salt Sensitivity in Rice. Rice Sci. 2019, 26, 98–108. [Google Scholar]
  166. Zhang, C.; Srivastava, A.K.; Sadanandom, A. Targeted Mutagenesis of the SUMO Protease, Overly Tolerant to Salt1 in Rice through CRISPR/Cas9-Mediated Genome Editing Reveals a Major Role of This SUMO Protease in Salt Tolerance. BioRxiv 2019, 555706. [Google Scholar] [CrossRef] [Green Version]
  167. Zeng, D.D.; Yang, C.C.; Qin, R.; Alamin, M.; Yue, E.K.; Jin, X.L.; Shi, C.H. A Guanine Insert in OsBBS1 Leads to Early Leaf Senescence and Salt Stress Sensitivity in Rice (Oryza sativa L.). Plant Cell Rep. 2018, 37, 933–946. [Google Scholar] [CrossRef] [PubMed]
  168. Zhao, C.; Qiu, J.; Agarwal, G.; Wang, J.; Ren, X.; Xia, H.; Wang, X. Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea). Front. Plant Sci. 2017, 8, 1209. [Google Scholar] [CrossRef] [Green Version]
  169. Zhang, M.; Cao, Y.; Wang, Z.; Wang, Z.Q.; Shi, J.; Liang, X.; Jiang, C. A Retrotransposon in an HKT1 Family Sodium Transporter Causes Variation of Leaf Na+ Exclusion and Salt Tolerance in Maize. New Phytol. 2018, 217, 1161–1176. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  170. Qiu, T.; Qi, M.; Ding, X.; Zheng, Y.; Zhou, T.; Chen, Y.; Wang, J. The SAUR41 Subfamily of SMALL AUXIN UP RNA Genes Is Abscisic Acid Inducible to Modulate Cell Expansion and Salt Tolerance in Arabidopsis thaliana Seedlings. Ann. Bot. 2020, 125, 805–819. [Google Scholar] [CrossRef] [Green Version]
  171. Huang, Y.; Cao, H.; Yang, L.; Chen, C.; Shabala, L.; Xiong, M.; Shabala, S. Tissue-Specific Respiratory Burst Oxidase Homolog-Dependent H2O2 Signaling to the Plasma Membrane H+-ATPase Confers Potassium Uptake and Salinity Tolerance in Cucurbitaceae. J. Exp. Bot. 2019, 70, 5879–5893. [Google Scholar] [CrossRef]
  172. Vlcko, T.; Ohnoutkova, L. Allelic Variants of CRISPR/Cas9 Induced Mutation in an Inositol Trisphosphate 5/6 Kinase Gene Manifest Different Phenotypes in Barley. Plants 2020, 9, 195. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  173. Wang, T.; Xun, H.; Wang, W.; Ding, X.; Tian, H.; Hussain, S.; Wang, S. Mutation of GmAITR Genes by CRISPR/Cas9 Genome Editing Results in Enhanced Salinity Stress Tolerance in Soybean. Front. Plant Sci. 2021, 12, 779598. [Google Scholar] [CrossRef]
  174. Dubiel, M.; Beeckman, T.; Smagghe, G.; Damme, E.J. Arabidopsis Lectin EULS3 Is Involved in ABA Signaling in Roots. Front. Plant Sci. 2020, 11, 437. [Google Scholar] [CrossRef] [PubMed]
  175. Nandy, S.; Pathak, B.; Zhao, S.; Srivastava, V. Heat-shock-inducible CRISPR/Cas9 System Generates Heritable Mutations in Rice. Plant Direct 2019, 3, 00145. [Google Scholar] [CrossRef] [PubMed]
  176. Huang, Y.; Xuan, H.; Yang, C.; Guo, N.; Wang, H.; Zhao, J.; Xing, H. GmHsp90A2 Is Involved in Soybean Heat Stress as a Positive Regulator. Plant Sci. 2019, 285, 26–33. [Google Scholar] [CrossRef] [PubMed]
  177. Hu, Z.; Li, J.; Ding, S.; Cheng, F.; Li, X.; Jiang, Y.; Shi, K. The Protein Kinase CPK28 Phosphorylates Ascorbate Peroxidase and Enhances Thermotolerance in Tomato. Plant Physiol. 2021, 186, 1302–1317. [Google Scholar] [CrossRef] [PubMed]
  178. Bertier, L.D.; Ron, M.; Huo, H.; Bradford, K.J.; Britt, A.B.; Michelmore, R.W. High-Resolution Analysis of the Efficiency, Heritability, and Editing Outcomes of CRISPR/Cas9-Induced Modifications of NCED4 in Lettuce (Lactuca sativa). G3 Genes Genomes Genet. 2018, 8, 1513–1521. [Google Scholar] [CrossRef] [Green Version]
  179. Miao, C.; Xiao, L.; Hua, K.; Zou, C.; Zhao, Y.; Bressan, R.A.; Zhu, J.K. Mutations in a Subfamily of Abscisic Acid Receptor Genes Promote Rice Growth and Productivity. Proc. Natl. Acad. Sci. USA 2018, 115, 6058–6063. [Google Scholar] [CrossRef] [Green Version]
  180. Zhang, D.; Li, Z.; Li, J.F. Targeted Gene Manipulation in Plants Using the CRISPR/Cas Technology. J. Genet. Genom. 2016, 43, 251–262. [Google Scholar] [CrossRef]
  181. Zhang, Y.; Liang, Z.; Zong, Y.; Wang, Y.; Liu, J.; Chen, K.; Gao, C. Efficient and Transgene-Free Genome Editing in Wheat through Transient Expression of CRISPR/Cas9 DNA or RNA. Nat. Commun. 2016, 7, 12617. [Google Scholar] [CrossRef] [Green Version]
  182. Ceasar, S.A.; Rajan, V.; Prykhozhij, S.V.; Berman, J.N.; Ignacimuthu, S. Insert, Remove or Replace: A Highly Advanced Genome Editing System Using CRISPR/Cas9. Biochim. Biophys. Acta (BBA)-Mol. Cell Res. 2016, 1863, 2333–2344. [Google Scholar] [CrossRef]
  183. Pan, C.; Ye, L.; Qin, L.; Liu, X.; He, Y.; Wang, J.; Lu, G. CRISPR/Cas9-Mediated Efficient and Heritable Targeted Mutagenesis in Tomato Plants in the First and Later Generations. Sci. Rep. 2016, 6, 24765. [Google Scholar] [CrossRef] [Green Version]
  184. Lawrenson, T.; Shorinola, O.; Stacey, N.; Li, C.; Østergaard, L.; Patron, N.; Harwood, W. Induction of Targeted, Heritable Mutations in Barley and Brassica Oleracea Using RNA-Guided Cas9 Nuclease. Genome Biol. 2015, 16, 258. [Google Scholar] [CrossRef] [Green Version]
  185. Paul, J.W.; Qi, Y. CRISPR/Cas9 for Plant Genome Editing: Accomplishments, Problems and Prospects. Plant Cell Rep. 2016, 35, 1417–1427. [Google Scholar] [CrossRef]
  186. Rani, R.; Yadav, P.; Barbadikar, K.M.; Baliyan, N.; Malhotra, E.V.; Singh, B.K.; Singh, D. CRISPR/Cas9: A Promising Way to Exploit Genetic Variation in Plants. Biotechnol. Lett. 2016, 38, 1991–2006. [Google Scholar] [CrossRef]
  187. Woo, J.W.; Kim, J.; Kwon, S.I.; Corvalán, C.; Cho, S.W.; Kim, H.; Kim, J.S. DNA-Free Genome Editing in Plants with Preassembled CRISPR-Cas9 Ribonucleoproteins. Nat. Biotechnol. 2015, 33, 1162–1164. [Google Scholar] [CrossRef] [PubMed]
  188. Svitashev, S.; Schwartz, C.; Lenderts, B.; Young, J.K.; Mark Cigan, A. Genome Editing in Maize Directed by CRISPR–Cas9 Ribonucleoprotein Complexes. Nat. Commun. 2016, 7, 13274. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  189. Capdeville, N.; Schindele, P.; Puchta, H. Getting better all the time—Recent progress in the development of CRISPR/Cas-based tools for plant genome engineering. Curr. Opin. Biotechnol. 2023, 79, 102854. [Google Scholar] [CrossRef] [PubMed]
Biology 12 01037 g001 550
Figure 1. The basic flow of CRISPR/Cas9 technology used to edit target genes.
Figure 1. The basic flow of CRISPR/Cas9 technology used to edit target genes.
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Figure 2. RNA-guided cleavage by the Cas9 protein.
Figure 2. RNA-guided cleavage by the Cas9 protein.
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Table
Table 1. Specifications of genome editing (GE) tools.
Table 1. Specifications of genome editing (GE) tools.
Genome Editing ToolsTarget Site (bp)Off TargetingEnzymeDNA Binding MediatorBinding SpecifityDNA CleavageUsageOrigin
CRISPR/Cas920VariableCas9crRNA/
sgRNA		1:1 nucleotide pairingRNA-dependentEasyBacteria/Archaea
ZFNs18–36HighFokIZinc-finger protein3 nucleotidesProtein-dependentHighly difficultEukaryotes
TALENs30–40LowFokITranscription activator-like effector1 nucleotideProtein-dependentDifficultBacteria
Table
Table 2. Genes targeted by CRISPR-based genome editing techniques for imparting resistance against diseases.
Table 2. Genes targeted by CRISPR-based genome editing techniques for imparting resistance against diseases.
Host PlantPathogenDiseaseTargeted GeneDelivery MethodTransgene-FreeResultReferences
AppleErwinia amylovoraFire blightDIPM-1, DIPM-2 and
DIPM-4		Agrobacterium-mediated transformationYesEnhanced disease resistance[83]
ArabidopsisOidium neolycopersiciPowdery mildewPMR4Agrobacterium-mediated transformationNoEnhanced disease resistance[84]
Beet Severe Curly Top Virus (BSCTV)DNA viral
disease		IR, CP, RepAgrobacterium-mediated transformationNoGeminivirus-resistant plants[85]
Turnip Mosaic Virus (TuMV)RNA viral
disease		Elf(iso)4EAgrobacterium-mediated transformationYesPotyvirus-resistant plants[78]
BananaBanana Streak Virus (BSV)DNA viral
disease		eBSVAgrobacterium-mediated transformationNot definedInactivation of eBSV caused
asymptomatic plants		[86]
BarleyWheat Dwarf Virus (WDV)DNA viral
disease		MP, CP, Rep/Rep, IRAgrobacterium-mediated transformationNoNo disease symptoms and
virus presence		[87]
CacaoPhytophthora tropicalisBlack pod rotTcNPR3Agrobacterium-mediated transformationNoEnhanced disease resistance[88]
CitrusXanthomonas citri subsp. citriCitrus cankerCsLOB1Agrobacterium-mediated transformationNoEnhanced disease resistance[89]
X. citri subsp. citriCitrus cankerCsLOB1/promoterAgrobacterium-mediated transformationNoEnhanced disease resistance[90]
CucumberCucumber Vein Yellowing Virus (CVYV), Zucchini Yellow Mosaic Virus (ZYMV), and Papaya Ring Spot Mosaic Virus-W (PRSV-W)RNA viral
disease		elf4EAgrobacterium-mediated transformationYesResistance to viruses[18]
GrapevineErysiphe necatorPowdery mildewMlo-7Polyethylene glycol-mediated (PEG) protoplast transformationYesEnhanced disease resistance[83]
Botrytis cinereaGray moldVvWRKY52Agrobacterium-mediated transformationNoEnhanced disease resistance[91]
PapayaP. palmivoraRoot, stem, and fruit rotalEPIC8Agrobacterium-mediated transformationNot definedEnhanced disease resistance[92]
RiceX. oryzae pv. OryzaeBacterial BlightSWEET11, SWEET13 and
SWEET14/promoter		Agrobacterium-mediated transformationNot definedEnhanced broad-spectrum disease resistance[93]
X. oryzae pv. OryzaeBacterial BlightOs8N3/promoterAgrobacterium-mediated transformationYesEnhanced disease resistance[94]
X. oryzae pv. OryzaeBacterial BlightOsSWEET11 and
OsSWEET14/promoter		Agrobacterium-mediated transformationNoEnhanced broad-spectrum disease resistance[95]
X. oryzae pv. OryzaeBacterial Blight and Rice BlastXa13Not definedYesEnhanced disease resistance[96]
X. oryzae pv. OryzaeBacterial BlightOsSWEET13Agrobacterium-mediated transformationNoEnhanced disease resistance[82]
Magnaporthe oryzaeRice blastOsERF922Agrobacterium-mediated transformationYesEnhanced disease resistance[97]
M. oryzaeRice blastTMS5, Pi21, and Xa13Not definedYesEnhanced disease resistance[96]
M. griseaRice blastOsMPK5Protoplast transformationNoResistance not confirmed[98]
Rice tungro bacilliform virusRice tungro diseaseeIF4GAgrobacterium-mediated transformationYesEnhanced disease resistance[99]
TobaccoCotton Leaf Curl Multan Virus (CLCuMuV)DNA viral
disease		IR and C1Agrobacterium-mediated transformationNoComplete resistance to virus infection[100]
Tomato Yellow
Leaf Curly Virus (TYLCV), Beet Curly
Top Virus (BCTV), and Merremia Mosaic Virus (MeMV)		DNA viral
disease		IR, CP, RCRIIAgrobacterium-mediated transformationNoNo disease symptoms and
reduced virus
accumulation		[101]
Bean Yellow Dwarf Virus (BeYDV)DNA viral
disease		LIR, RepAgrobacterium-mediated transformationNoReduced symptoms and virus load[102]
Beet Severe Curly Top Virus (BSCTV)DNA viral
disease		IR, CP, RepAgrobacterium-mediated transformationNoGeminivirus-resistant plants[85]
Tomato Yellow Leaf Curl Virus (TYLCV) DNA viral
disease		CP, RepAgrobacterium-mediated transformationNoEnhanced disease resistance[103]
TomatoPseudomonas syringaeBacterial speckSIDMR6–1Agrobacterium-mediated transformationNoEnhanced disease resistance[104]
P. capsiciPhytophthora
blight		SIDMR6–1Agrobacterium-mediated transformationNoEnhanced disease resistance[104]
Xanthomonas spp.Bacterial spotSIDMR6–1Agrobacterium-mediated transformationNoEnhanced disease resistance[104]
P. syringae pv. tomato
(Pto) DC3000		Bacterial speckSlJAZ2Agrobacterium-mediated transformationNot definedEnhanced disease resistance and
defence trade-off solved		[105]
O. neolycopersiciPowdery mildewSlMlo1Agrobacterium-mediated transformationNoEnhanced disease resistance[64]
O. neolycopersiciPowdery mildewSIPMR4Agrobacterium-mediated transformationNoEnhanced disease resistance[84]
Fusarium oxysporum f. sp.
lycopersici		Fusarium wiltSolyc08g075770Agrobacterium-mediated transformationNoEnhanced disease susceptibility[106]
B. cinereaGray moldSlMAPK3Agrobacterium-mediated transformationNoEnhanced disease susceptibility[107]
PVX, TMVRNA viral
disease		DCL2Agrobacterium-mediated transformationNoResistance to PVX and TMV[108]
Tomato Yellow Leaf Curl Virus (TYLCV) DNA viral
disease		CP, RepAgrobacterium-mediated transformationNoEnhanced disease resistance[103]
WheatBlumeria graminis f. sp. triticiPowdery mildewTaMloProtoplast and Biolistic transformationYesEnhanced disease resistance[63]
B. graminis f. sp. triticiPowdery mildewTaEDR1Biolistic transformationNoEnhanced disease resistance[35]
Table
Table 3. Genes targeted using CRISPR-based genome editing techniques to impart tolerance of abiotic stress.
Table 3. Genes targeted using CRISPR-based genome editing techniques to impart tolerance of abiotic stress.
Abiotic StressesPlant SpeciesTargeted GeneDelivery MethodRegulating Direction of Response to Stress FunctionReferences
DroughtOryza sativaOsNAC006Agrobacterium -mediated transformationTranscription factor[139]
Brassica napusBnaA6.RGAAgrobacterium-mediated transformationTranscription factor[140]
O. sativaSRL1, SRL2Agrobacterium-mediated transformationRolling of leaf[141]
O. sativa subsp. indicaOsDSTAgrobacterium-mediated transformationDrought and salt tolerance (DST) gene[119]
O. sativaOsNAC14Agrobacterium-mediated transformationTranscription factor[142]
O. sativaOsSAPK2Agrobacterium-mediated transformationABA signaling[116]
O. sativaOsMYB1, OsYSA, OsROC5, OsDERF1, OsPDS, OsPMS3, OsEPSPS, OsMSH1, OsMYB5, OsSPPAgrobacterium-mediated transformationAmino acid synthesis[143]
Solanum lycopersicum L.SlNPR1Agrobacterium-mediated transformationDrought tolerance[117]
S. lycopersicum L.MAPK3Agrobacterium-mediated transformationGrowth and development[123]
Triticum aestivumTaDREB2, TaERF3PEG-mediated transformationDehydration-responsive element-binding protein[115]
Zea maysARGOS8Particle bombardmentEthylene-responsive gene family regulator[121]
Arabidopsis thalianaAREB1Agrobacterium-mediated transformationABA signaling[144]
A. thalianaAtAVP1, AtPAP1Agrobacterium-mediated transformationTranscription factor[145]
A. thalianaAtOST2Agrobacterium-mediated transformationStomatal movement[146]
A. thalianaAtMIR169a, AtMIR827a, TFL1Agrobacterium-mediated transformationNegative factor of drought tolerance[147]
Glycine maxGmMYB118Agrobacterium-mediated transformationTranscription factor[127]
Populus clone NE-19PdNF-YB21Agrobacterium-mediated leaf disc methodTranscription factor ABA-mediated indoylacetic acid transport[148]
ColdO. sativaOsMYB30, OsPIN5b, GS3Agrobacterium-mediated transformationCold tolerance[133]
A. thalianaUGT79B2, UGT79B3Agrobacterium-mediated transformationUDP-glycosyltransferases[149]
O. sativa subsp. indicaOsPRP1Agrobacterium-mediated transformationPlant growth and stress response[150]
A. thalianaAtCBF2Agrobacterium-mediated transformationEncodes AP2/ERF (APETALA2/Ethylene-Responsive Factor)-type transcription factors)[151]
A. thalianaAtCBF1, AtCBF2, AtCBF3Agrobacterium-mediated transformationEncodes AP2/ERF (APETALA2/Ethylene-Responsive Factor)-type transcription factors)[147,152,153]
S. lycopersicum L.SlCBF1Agrobacterium-mediated transformationTranscription factor[131]
O. sativaOsAnn3Agrobacterium-mediated transformationPlant development and protection from environmental stresses[132]
A. thalianaCBFsAgrobacterium-mediated transformationTranscription factor[154]
SalinityO. sativaOsGTg-2Agrobacterium-mediated transformationTranscription factor[155]
O. sativaPIL14Agrobacterium-mediated transformationPhytochrome-Interacting Factor[156]
O. sativaOstPQT3Agrobacterium-mediated transformationE3 ubiquitin ligase (enhances resistance to abiotic stresses)[157]
O. sativaOsAGO2Agrobacterium-mediated transformationTranscriptional transactivator (growth and development, stress and defense responses, alternative splicing, and DNA repair)[158]
O. sativaOsDSTAgrobacterium-mediated transformationZinc-finger transcription factor[119]
O. sativaFLN2Agrobacterium-mediated transformationSucrose metabolism fructokinase-like protein2[159]
O. sativaOsRR9 and OsRR10Agrobacterium-mediated transformationCytokinin signaling[160]
O. sativaOsDOF15Agrobacterium-mediated transformationTranscription factor (regulates cell proliferation in the root)[161]
O. sativaOsSPL10Agrobacterium-mediated transformationTranscription factor[162]
O. sativaNCA1a, NCA1bAgrobacterium-mediated transformationRegulation of catalase activity [163]
O. sativaRR22Agrobacterium-mediated transformationTranscription factor (cytokinin signal transduction and metabolism)[164]
O. sativaOsNAC041Agrobacterium-mediated transformationTranscription factor[165]
O. sativaOsOTS1Agrobacterium-mediated transformationSalt stress response regulation[166]
O. sativaOsSAPK1, OsSAPK2Agrobacterium-mediated transformationABA pathway regulator[129]
O. sativaOsBBS1Agrobacterium-mediated transformationReceptor-like cytoplasmic kinase[167]
O. sativaOsMIR408, OsMIR528Agrobacterium -mediated transformationSalt stress response regulation[168]
O. sativaOsRAV2Agrobacterium-mediated transformationTranscription factor[126]
Z. maysHKT1Agrobacterium-mediated transformationHigh-affinity potassium transporter[169]
A. thalianaAtSAUR41Agrobacterium-mediated transformationAuxin response gene[170]
Cucurbita moschataRBOHDAgrobacterium-mediated transformationNADPH oxidase is a key member for H2O2 production[171]
A. thalianaAtC/VIF1Agrobacterium-mediated transformationCell wall/vacuolar inhibitor of fructosidases[130]
Hordeum vulgareHvITPK5/6Agrobacterium-mediated transformationSequential phosphorylation of inositol phosphate to inositol hexakisphosphate[172]
G. max L.GmAITRAgrobacterium-mediated transformationTranscription factors that are involved in the regulation of ABA signaling[173]
S. lycopersicum L.SlARF4Agrobacterium-mediated transformationARFs play a key role in regulating the expression of auxin response genes[129]
A. thalianaArathEULS3Agrobacterium-mediated transformationStress-responsive protein, stomatal closure[174]
Heat StressS. lycopersicum L.BZR1Agrobacterium-mediated transformationBrassinosteroid regulation[136]
O sativaOsPDSGene gunPhytoene Desaturase gene encodes one of the important enzymes in the carotenoid biosynthesis pathway[175]
G. max L.GmHsp90A2Agrobacterium-mediated transformationMolecular chaperone and heat shock protein[176]
O. sativaOsHSA1Agrobacterium-mediated transformationChloroplast development at early stages and functions can protect chloroplasts under heat stress at later stages[135]
S. lycopersicum L.Slcpk28Agrobacterium-mediated transformationDecreases the activity of antioxidant enzymes[177]
O. sativaOsNAC006PEG-mediatedMediates the process of photosynthesis and limits the activity of antioxidant enzymes[139]
Z. maysTMS5Particle bombardmentThermosensitive genic male sterile 5[138]
Lactuca sativaLsNCED4Agrobacterium-mediated transformationKey regulatory enzyme in the biosynthesis of abscisic acid (ABA)[178]
O. sativaOsPYL1/4/6Agrobacterium-mediated transformationABA receptor[179]
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Erdoğan, İ.; Cevher-Keskin, B.; Bilir, Ö.; Hong, Y.; Tör, M. Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance. Biology 2023, 12, 1037. https://doi.org/10.3390/biology12071037

AMA Style

Erdoğan İ, Cevher-Keskin B, Bilir Ö, Hong Y, Tör M. Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance. Biology. 2023; 12(7):1037. https://doi.org/10.3390/biology12071037

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Erdoğan, İbrahim, Birsen Cevher-Keskin, Özlem Bilir, Yiguo Hong, and Mahmut Tör. 2023. "Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance" Biology 12, no. 7: 1037. https://doi.org/10.3390/biology12071037

APA Style

Erdoğan, İ., Cevher-Keskin, B., Bilir, Ö., Hong, Y., & Tör, M. (2023). Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance. Biology, 12(7), 1037. https://doi.org/10.3390/biology12071037

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