A review on CRISPR/Cas-based epigenetic regulation in plants

Unlocking plant resilience: Advanced epigenetic strategies against heavy metal and metalloid stress

The escalating threat of heavy metal and metalloid stress on plant ecosystems requires innovative strategies to strengthen plant resilience and ensure agricultural sustainability. This review provides important insights into the advanced epigenetic pathways to improve plant tolerance to toxic heavy metals and metalloid stress. Epigenetic modifications, including deoxyribonucleic acid (DNA) methylation, histone modifications, and small ribonucleic acid (RNA) engineering, offer innovative avenues for tailoring plant responses to mitigate the impact of heavy metal and metalloid stress. Technological advancements in high-throughput genome sequencing and functional genomics have unraveled the complexities of epigenetic regulation in response to heavy metal and metalloid contamination. Recent strides in this field encompass identifying specific epigenetic markers associated with stress resilience, developing tools for editing the epigenome, and integrating epigenetic data into breeding programs for stress-resistant crops. Understanding the dynamic interaction between epigenetics and stress responses holds immense potential to engineer resilient crops that thrive in environments contaminated with heavy metals and metalloids. Eventually, harnessing epigenetic strategies presents a promising trajectory toward sustainable agriculture in the face of escalating environmental challenges. Plant epigenomics expands, the potential for sustainable agriculture by implementing advanced epigenetic approaches becomes increasingly evident. These developments lay the foundation for understanding the growing significance of epigenetics in plant stress biology and its potential to mitigate the detrimental effects of heavy metal and metalloid pollution on global agriculture.

CRISPR/Cas9 mediated genome editing for crop improvement against Abiotic stresses: current trends and prospects

Abiotic stresses associated with climate change, such as heat, cold, salinity, and drought, represent a serious threat to crop health. To mitigate the risks posed by these environmental challenges, both transgenic technology and conventional breeding methods have been extensively utilized. However, these methods have faced numerous limitations. The development of synthetic nucleases as precise genetic tools allows for the targeted alteration of stress-responsive genes in crop improvement. The clustered regularly interspaced short palindromic repeats (CRISPR/Cas) genome-editing technique has transformed gene editing with its broad applicability, accessibility, adaptability, flexibility, and simplicity. Its application shows promise for the development of crop types that are more able to survive abiotic stress conditions. The present study presents recent scenario and application of CRISPR/Cas genome-editing technology in enhancing crop tolerance to a variety of abiotic stresses.

KRAS mutations detection methodology: from RFLP to CRISPR/Cas based methods

In personalized cancer medicine, the identification of KRAS mutations is essential for making treatment decisions and improving patient outcomes. This work presents a comprehensive review of the current approaches for detection of KRAS mutations in different cancers. We highlight the value of fast and reliable KRAS mutations discovery and the effectiveness of molecular testing for selecting individuals who might benefit from targeted therapy. We provide an overview of various methods and tools available for detecting KRAS mutations, such as digital droplet PCR, next-generation sequencing (NGS), and polymerase chain reaction (PCR). We also address the difficulties and limitations in the identification of KRAS mutations, namely tumor heterogeneity and the emergence of resistance mechanisms. This article aims to guide clinicians in KRAS mutation identification.

CRISPR/Cas: a powerful tool for designing and improving oil crops

Improving oil yield and quality is a major goal for crop breeding, and CRISPR/Cas-mediated genome editing has opened a new era for designing oil crops with enhanced yield and quality. CRISPR/Cas technology can not only increase oil production but also enhance oil quality, including enhancing pharmaceutical and health components, improving oil nutrients, and removing allergic and toxic components. As new molecular targets for oil biosynthesis are discovered and the CRISPR/Cas system is further improved, CRISPR/Cas will become a better molecular tool for designing new oil crops with higher oil production, enhanced nutrients, and improved health components. 'CRISPRized' oil crops will have broad applications both in industry (e.g., as biofuels) and in daily human life.

Recent advances of CRISPR-based genome editing for enhancing staple crops

An increasing population, climate change, and diminishing natural resources present severe threats to global food security, with traditional breeding and genetic engineering methods often falling short in addressing these rapidly evolving challenges. CRISPR/Cas systems have emerged as revolutionary tools for precise genetic modifications in crops, offering significant advancements in resilience, yield, and nutritional value, particularly in staple crops like rice and maize. This review highlights the transformative potential of CRISPR/Cas technology, emphasizing recent innovations such as prime and base editing, and the development of novel CRISPR-associated proteins, which have significantly improved the specificity, efficiency, and scope of genome editing in agriculture. These advancements enable targeted genetic modifications that enhance tolerance to abiotic stresses as well as biotic stresses. Additionally, CRISPR/Cas plays a crucial role in improving crop yield and quality by enhancing photosynthetic efficiency, nutrient uptake, and resistance to lodging, while also improving taste, texture, shelf life, and nutritional content through biofortification. Despite challenges such as off-target effects, the need for more efficient delivery methods, and ethical and regulatory concerns, the review underscores the importance of CRISPR/Cas in addressing global food security and sustainability challenges. It calls for continued research and integration of CRISPR with other emerging technologies like nanotechnology, synthetic biology, and machine learning to fully realize its potential in developing resilient, productive, and sustainable agricultural systems.

A New Approach for CRISPR/Cas9 Editing and Selection of Pathogen-Resistant Plant Cells of Wine Grape cv. 'Merlot'

Grape is one of the most economically significant berry crops. Owing to the biological characteristics of grapes, such as the long juvenile period (5-8 years), high degree of genome heterozygosity, and the frequent occurrence of inbreeding depression, homozygosity during crossbreeding leads to loss of varietal characteristics and viability. CRISPR/Cas editing has become the tool of choice for improving elite technical grape varieties. This study provides the first evidence of a decrease in the total fraction of phenolic compounds and an increase in the concentration of peroxide compounds in grape callus cells upon the addition of chitosan to the culture medium. These previously unreported metabolic features of the grape response to chitosan have been described and used for the first time to increase the probability of selecting plant cells with MLO7 knockout characterised by an oxidative burst in response to the presence of a pathogen modulated by chitosan in the high-metabolite black grape variety 'Merlot'. This was achieved by using a CRISPR/Cas9 editing vector construction with the peroxide sensor HyPer as a reporter. This research represents the first CRISPR/Cas9 editing of 'Merlot', one of the most economically important elite technical grape varieties.

Revolutionizing soybean genomics: How CRISPR and advanced sequencing are unlocking new potential

Soybean Glycine max L., paleopolyploid genome, poses challenges to its genetic improvement. However, the development of reference genome assemblies and genome sequencing has completely changed the field of soybean genomics, allowing for more accurate and successful breeding techniques as well as research. During the single-cell revolution, one of the most advanced sequencing tools for examining the transcriptome landscape is single-cell RNA sequencing (scRNA-seq). Comprehensive resources for genetic improvement of soybeans may be found in the SoyBase and other genomics databases. CRISPR-Cas9 genome editing technology provides promising prospects for precise genetic modifications in soybean. This method has enhanced several soybean traits, including as yield, nutritional value, and resistance to both biotic and abiotic stresses. With base editing techniques that allow for precise DNA modifications, the use of CRISPR-Cas9 is further increased. With the availability of the reference genome for soybeans and the following assembly of wild and cultivated soybeans, significant chromosomal rearrangements and gene duplication events have been identified, offering new perspectives on the complex genomic structure of soybeans. Furthermore, major single nucleotide polymorphisms (SNPs) linked to stachyose and sucrose content have been found through genome-wide association studies (GWAS), providing important tools for enhancing soybean carbohydrate profiles. In order to open up new avenues for soybean genetic improvement, future research approaches include investigating transcriptional divergence processes, enhancing genetic resources, and incorporating CRISPR-Cas9 technologies.

iJAZ: the next breakthrough for engineering pest-resistance in plants?

Although transgenic Bacillus thuringiensis (Bt) crops have brought various ecological and socioeconomic benefits, there is evidence suggesting that pests will eventually develop resistance to Bt crops. Thus, additional genes are urgently needed to engineer pest resistance in plants. A recent study by Mo et al. indicates that iJAZ maybe the next breakthrough for engineering pest resistance in plants.

An epigenetic toolbox for conservation biologists

Ongoing climatic shifts and increasing anthropogenic pressures demand an efficient delineation of conservation units and accurate predictions of populations' resilience and adaptive potential. Molecular tools involving DNA sequencing are nowadays routinely used for these purposes. Yet, most of the existing tools focusing on sequence-level information have shortcomings in detecting signals of short-term ecological relevance. Epigenetic modifications carry valuable information to better link individuals, populations, and species to their environment. Here, we discuss a series of epigenetic monitoring tools that can be directly applied to various conservation contexts, complementing already existing molecular monitoring frameworks. Focusing on DNA sequence-based methods (e.g. DNA methylation, for which the applications are readily available), we demonstrate how (a) the identification of epi-biomarkers associated with age or infection can facilitate the determination of an individual's health status in wild populations; (b) whole epigenome analyses can identify signatures of selection linked to environmental conditions and facilitate estimating the adaptive potential of populations; and (c) epi-eDNA (epigenetic environmental DNA), an epigenetic-based conservation tool, presents a non-invasive sampling method to monitor biological information beyond the mere presence of individuals. Overall, our framework refines conservation strategies, ensuring a comprehensive understanding of species' adaptive potential and persistence on ecologically relevant timescales.

Exploring the patterns of evolution: Core thoughts and focus on the saltational model

The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.

Epigenetic modification: A novel insight into diabetic wound healing

Wound healing is an intricate and fine regulatory process. In diabetic patients, advanced glycation end products (AGEs), excessive reactive oxygen species (ROS), biofilm formation, persistent inflammation, and angiogenesis regression contribute to delayed wound healing. Epigenetics, the fast-moving science in the 21st century, has been up to date and associated with diabetic wound repair. In this review, we go over the functions of epigenetics in diabetic wound repair in retrospect, covering transcriptional and posttranscriptional regulation. Among these, we found that histone modification is widely involved in inflammation and angiogenesis by affecting macrophages and endothelial cells. DNA methylation is involved in factors regulation in wound repair but also affects the differentiation phenotype of cells in hyperglycemia. In addition, noncodingRNA regulation and RNA modification in diabetic wound repair were also generalized. The future prospects for epigenetic applications are discussed in the end. In conclusion, the study suggests that epigenetics is an integral regulatory mechanism in diabetic wound healing.

Epigenetic regulation and epigenetic memory resetting during plant rejuvenation

Reversal of plant developmental status from the mature to the juvenile phase, thus leading to the restoration of the developmental potential, is referred to as plant rejuvenation. It involves multilayer regulation, including resetting gene expression patterns, chromatin remodeling, and histone modifications, eventually resulting in the restoration of juvenile characteristics. Although plants can be successfully rejuvenated using some forestry practices to restore juvenile morphology, physiology, and reproductive capabilities, studies on the epigenetic mechanisms underlying this process are in the nascent stage. This review provides an overview of the plant rejuvenation process and discusses the key epigenetic mechanisms involved in DNA methylation, histone modification, and chromatin remodeling in the process of rejuvenation, as well as the roles of small RNAs in this process. Additionally, we present new inquiries regarding the epigenetic regulation of plant rejuvenation, aiming to advance our understanding of rejuvenation in sexually and asexually propagated plants. Overall, we highlight the importance of epigenetic mechanisms in the regulation of plant rejuvenation, providing valuable insights into the complexity of this process.

Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities

Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.

Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications

Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.

Epigenetic processes in plant stress priming: Open questions and new approaches

Priming reflects the capacity of plants to memorise environmental stress experience and improve their response to recurring stress. Epigenetic modifications in DNA and associated histone proteins may carry short-term and long-term memory in the same plant or mediate transgenerational effects, but the evidence is still largely circumstantial. New experimental tools now enable scientists to perform targeted manipulations that either prevent or generate a particular epigenetic modification in a particular location of the genome. Such 'reverse epigenetics' approaches allow for the interrogation of causality between individual priming-induced modifications and their role for altering gene expression and plant performance under recurring stress. Furthermore, combining site-directed epigenetic manipulation with conditional and cell-type specific promoters creates novel opportunities to test and engineer spatiotemporal patterns of priming.

Promoter editing for the genetic improvement of crops

Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.

Enhancing Crop Resilience to Drought Stress through CRISPR-Cas9 Genome Editing

With increasing frequency and severity of droughts in various parts of the world, agricultural productivity may suffer major setbacks. Among all the abiotic factors, drought is likely to have one of the most detrimental effects on soil organisms and plants. Drought is a major problem for crops because it limits the availability of water, and consequently nutrients which are crucial for plant growth and survival. This results in reduced crop yields, stunted growth, and even plant death, according to the severity and duration of the drought, the plant's developmental stage, and the plant's genetic background. The ability to withstand drought is a highly complex characteristic that is controlled by multiple genes, making it one of the most challenging attributes to study, classify, and improve. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) technology has opened a new frontier in crop enhancement, revolutionizing plant molecular breeding. The current review provides a general understanding of principles as well as optimization of CRISPR system, and presents applications on genetic enhancement of crops, specifically in terms of drought resistance and yield. Moreover, we discuss how innovative genome editing techniques can aid in the identification and modification of genes conferring drought tolerance.

Epigenomics in stress tolerance of plants under the climate change

BACKGROUND

Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO₂, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence.

EPIGENETIC MECHANISMS AND MARKS

The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles.

EPIGENOMICS IN CROP IMPROVEMENT

To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding.

CONCLUSIONS AND FUTURE PROSPECTUS

A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.

Advances and Challenges in CRISPR/Cas-Based Fungal Genome Engineering for Secondary Metabolite Production: A Review

Fungi represent an important source of bioactive secondary metabolites (SMs), which have wide applications in many fields, including medicine, agriculture, human health, and many other industries. The genes involved in SM biosynthesis are usually clustered adjacent to each other into a region known as a biosynthetic gene cluster (BGC). The recent advent of a diversity of genetic and genomic technologies has facilitated the identification of many cryptic or uncharacterized BGCs and their associated SMs. However, there are still many challenges that hamper the broader exploration of industrially important secondary metabolites. The recent advanced CRISPR/Cas system has revolutionized fungal genetic engineering and enabled the discovery of novel bioactive compounds. In this review, we firstly introduce fungal BGCs and their relationships with associated SMs, followed by a brief summary of the conventional strategies for fungal genetic engineering. Next, we introduce a range of state-of-the-art CRISPR/Cas-based tools that have been developed and review recent applications of these methods in fungi for research on the biosynthesis of SMs. Finally, the challenges and limitations of these CRISPR/Cas-based systems are discussed and directions for future research are proposed in order to expand their applications and improve efficiency for fungal genetic engineering.

Application of CRISPR/Cas9-mediated gene editing for abiotic stress management in crop plants

Abiotic stresses, including drought, salinity, cold, heat, and heavy metals, extensively reducing global agricultural production. Traditional breeding approaches and transgenic technology have been widely used to mitigate the risks of these environmental stresses. The discovery of engineered nucleases as genetic scissors to carry out precise manipulation in crop stress-responsive genes and associated molecular network has paved the way for sustainable management of abiotic stress conditions. In this context, the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas)-based gene-editing tool has revolutionized due to its simplicity, accessibility, adaptability, flexibility, and wide applicability. This system has great potential to build up crop varieties with enhanced tolerance against abiotic stresses. In this review, we summarize the latest findings on understanding the mechanism of abiotic stress response in plants and the application of CRISPR/Cas-mediated gene-editing system towards enhanced tolerance to a multitude of stresses including drought, salinity, cold, heat, and heavy metals. We provide mechanistic insights on the CRISPR/Cas9-based genome editing technology. We also discuss applications of evolving genome editing techniques such as prime editing and base editing, mutant library production, transgene free and multiplexing to rapidly deliver modern crop cultivars adapted to abiotic stress conditions.

Engineering Abiotic Stress Tolerance in Crop Plants through CRISPR Genome Editing

Environmental abiotic stresses challenge food security by depressing crop yields often exceeding 50% of their annual production. Different methods, including conventional as well as genomic-assisted breeding, mutagenesis, and genetic engineering have been utilized to enhance stress resilience in several crop species. Plant breeding has been partly successful in developing crop varieties against abiotic stresses owning to the complex genetics of the traits as well as the narrow genetic base in the germplasm. Irrespective of the fact that genetic engineering can transfer gene(s) from any organism(s), transgenic crops have become controversial mainly due to the potential risk of transgene-outcrossing. Consequently, the cultivation of transgenic crops is banned in certain countries, particularly in European countries. In this scenario, the discovery of the CRISPR tool provides a platform for producing transgene-free genetically edited plants-similar to the mutagenized crops that are not extensively regulated such as genetically modified organisms (GMOs). Thus, the genome-edited plants without a transgene would likely go into the field without any restriction. Here, we focused on the deployment of CRISPR for the successful development of abiotic stress-tolerant crop plants for sustaining crop productivity under changing environments.

Herbicide resistance in grass weeds: Epigenetic regulation matters too

Although herbicides have been successfully used for controlling weeds, their continuous use has developed in the evolution of resistance to all major herbicide modes of action worldwide. Reports suggest that the members of Poaceae family are more prone to developing herbicide resistance than other families. In plants, epigenetic mechanisms play critical roles by increasing their stress-adaptive potential in a rapidly changing environment. Epigenetic mechanisms involve alteration of the expression of genetic elements, but without any changes in the DNA sequence. Although the possible roles of epigenetic mechanisms in contributing to survival and fitness under various stresses are well documented in model plants and crops, their contribution to herbicide resistance in weeds is still in its infancy. A few studies with herbicides have shown differential expression of DNA methyltransferases, histone methyltransferases and DNA demethylases in response to the herbicides; however, no further studies were conducted. In the case of herbicide stress, exploring how these epigenetic processes affect the gene expression pattern in individual plants subjected to recurrent selection would be exciting. Hence, our mini-review will focus on the potential contributions of epigenetic mechanisms to the adaptive responses of grass-weedy species to herbicide stress. A better understanding of these epigenetic changes will add novel perceptions to our knowledge of herbicide resistance evolution in weeds enabling the development of herbicides with novel targets.