Review of applications of artificial intelligence (AI) methods in crop research

Sophisticated and modern crop improvement techniques can bridge the gap for feeding the ever-increasing population. Artificial intelligence (AI) refers to the simulation of human intelligence in machines, which refers to the application of computational algorithms, machine learning (ML) and deep learning (DL) techniques. This is aimed to generalise patterns and relationships from historical data, employing various mathematical optimisation techniques thus making prediction models for facilitating selection of superior genotypes. These techniques are less resource intensive and can solve the problem based on the analysis of large-scale phenotypic datasets. ML for genomic selection (GS) uses high-throughput genotyping technologies to gather genetic information on a large number of markers across the genome. The prediction of GS models is based on the mathematical relation between genotypic and phenotypic data from the training population. ML techniques have emerged as powerful tools for genome editing through analysing large-scale genomic data and facilitating the development of accurate prediction models. Precise phenotyping is a prerequisite to advance crop breeding for solving agricultural production-related issues. ML algorithms can solve this problem through generating predictive models, based on the analysis of large-scale phenotypic datasets. DL models also have the potential reliability of precise phenotyping. This review provides a comprehensive overview on various ML and DL models, their applications, potential to enhance the efficiency, specificity and safety towards advanced crop improvement protocols such as genomic selection, genome editing, along with phenotypic prediction to promote accelerated breeding.

Drought Stress Amelioration Attributes of Plant-Associated Microbiome on Agricultural Plants

The future global food security depends on the availability of water for agriculture. Yet, the ongoing rise in nonagricultural uses for water, such as urban and industrial uses, and growing environmental quality concerns have increased pressure of irrigation water demand and posed danger to food security. Nevertheless, its severity and duration are predicted to rise shortly. Drought pressure causes stunted growth, severe damage to photosynthesis activity, loss in crop yield, reduced seed germination, and reduced nutrient intake by plants. To overcome the effects of a devastating drought on plants, it is essential to think about the causes, mechanisms of action, and long-term agronomy management and genetics. As a result, there is an urgent need for long-term medication to deal with the harmful effects of drought pressure. The review focuses on the adverse impact of drought on the plant, physiological, and biochemical aspects, and management measures to control the severity of drought conditions. This article reviews the role of genome editing (GE) technologies such as CRISPR 9 (CRISPR-Cas9) related spaces and short palindromic relapse between proteins in reducing the effects of phytohormones, osmolytes, external compounds, proteins, microbes (plant growth-promoting microorganism [PGPM]), approach omics, and drought on plants that support plant growth. This research is to examine the potential of using the microbiome associated with plants for drought resistance and sustainable agriculture. Researchers also advocate using a mix of biotechnology, agronomic, and advanced GE technologies to create drought-tolerant plant varieties.

The Calvin-Benson-Bassham cycle in C4 and Crassulacean acid metabolism species

The Calvin-Benson-Bassham (CBB) cycle is the ancestral CO2 assimilation pathway and is found in all photosynthetic organisms. Biochemical extensions to the CBB cycle have evolved that allow the resulting pathways to act as CO2 concentrating mechanisms, either spatially in the case of C4 photosynthesis or temporally in the case of Crassulacean acid metabolism (CAM). While the biochemical steps in the C4 and CAM pathways are known, questions remain on their integration and regulation with CBB cycle activity. The application of omic and transgenic technologies is providing a more complete understanding of the biochemistry of C4 and CAM species and will also provide insight into the CBB cycle in these plants. As the global population increases, new solutions are required to increase crop yields and meet demands for food and other bioproducts. Previous work in C3 species has shown that increasing carbon assimilation through genetic manipulation of the CBB cycle can increase biomass and yield. There may also be options to improve photosynthesis in species using C4 photosynthesis and CAM through manipulation of the CBB cycle in these plants. This is an underexplored strategy and requires more basic knowledge of CBB cycle operation in these species to enable approaches for increased productivity.

Revolutionizing Agriculture: Harnessing CRISPR/Cas9 for Crop Enhancement

Plant crops serve as essential sources of nutritional sustenance, supplying vital nutrients to human diets. However, their productivity and quality are severely jeopardized by factors such as pests, diseases, and adverse abiotic conditions. Addressing these challenges using innovative biotechnological approaches is imperative for advancing sustainable agriculture. In recent years, genome editing technologies have emerged as pivotal genetic tools, revolutionizing plant molecular biology. Among these, the CRISPR-Cas9 system has gained prominence due to its unparalleled precision, streamlined design, and heightened success rates. This review article highlights the profound impact of CRISPR/Cas9 technology on crop improvement. The article critically examines the breakthroughs, ongoing enhancements, and future prospects associated with this cutting-edge technology. In conclusion, the utilization of CRISPR/Cas9 presents a transformative shift in agricultural biotechnology, holding the potential to mitigate longstanding agricultural challenges.

Harnessing the potential of mutation breeding, CRISPR genome editing, and beyond for sustainable agriculture

By 2050, the global population is projected to exceed 9.5 billion, posing a formidable challenge to ensure food security worldwide. To address this pressing issue, mutation breeding in horticultural crops, utilizing physical or chemical methods, has emerged as a promising biotechnological strategy. However, the efficacy of these mutagens can be influenced by various factors, including biological and environmental variables, as well as targeted plant materials. This review highlights the global challenges related to food security and explores the potential of mutation breeding as an indispensable biotechnological tool in overcoming food insecurity. This review also covers the emergence of CRISPR-Cas9, a breakthrough technology offering precise genome editing for the development of high-yield, stress-tolerant crops. Together, mutation breeding and CRISPR can potentially address future food demands. This review focuses into these biotechnological advancements, emphasizing their combined potential to fortify global food security in the face of a booming population.

Recent advances in plant translational genomics for crop improvement

The growing population, climate change, and limited agricultural resources put enormous pressure on agricultural systems. A plateau in crop yields is occurring and extreme weather events and urbanization threaten the livelihood of farmers. It is imperative that immediate attention is paid to addressing the increasing food demand, ensuring resilience against emerging threats, and meeting the demand for more nutritious, safer food. Under uncertain conditions, it is essential to expand genetic diversity and discover novel crop varieties or variations to develop higher and more stable yields. Genomics plays a significant role in developing abundant and nutrient-dense food crops. An alternative to traditional breeding approach, translational genomics is able to improve breeding programs in a more efficient and precise manner by translating genomic concepts into practical tools. Crop breeding based on genomics offers potential solutions to overcome the limitations of conventional breeding methods, including improved crop varieties that provide more nutritional value and are protected from biotic and abiotic stresses. Genetic markers, such as SNPs and ESTs, contribute to the discovery of QTLs controlling agronomic traits and stress tolerance. In order to meet the growing demand for food, there is a need to incorporate QTLs into breeding programs using marker-assisted selection/breeding and transgenic technologies. This chapter primarily focuses on the recent advances that are made in translational genomics for crop improvement and various omics techniques including transcriptomics, metagenomics, pangenomics, single cell omics etc. Numerous genome editing techniques including CRISPR Cas technology and their applications in crop improvement had been discussed.

Application of genome editing techniques to regulate gene expression in crops

BACKGROUND

Enhanced agricultural production is urgently required to meet the food demands of the increasing global population. Abundant genetic diversity is expected to accelerate crop development. In particular, the development of the CRISPR/Cas genome editing technology has greatly enhanced our ability to improve crop's genetic diversity through direct artificial gene modification. However, recent studies have shown that most crop improvement efforts using CRISPR/Cas techniques have mainly focused on the coding regions, and there is a relatively lack of studies on the regulatory regions of gene expression.

RESULTS

This review briefly summarizes the development of CRISPR/Cas system in the beginning. Subsequently, the importance of gene regulatory regions in plants is discussed. The review focuses on recent developments and applications of mutations in regulatory regions via CRISPR/Cas techniques in crop breeding.

CONCLUSION

Finally, an outline of perspectives for future crop breeding using genome editing technologies is provided. This review provides new research insights for crop improvement using genome editing techniques.

Advances in RNA Interference for Plant Functional Genomics: Unveiling Traits, Mechanisms, and Future Directions

RNA interference (RNAi) is a conserved molecular mechanism that plays a critical role in post-transcriptional gene silencing across diverse organisms. This review delves into the role of RNAi in plant functional genomics and its applications in crop improvement, highlighting its mechanistic insights and practical implications. The review begins with the foundational discovery of RNAi's mechanism, tracing its origins from petunias to its widespread presence in various organisms. Various classes of regulatory non-coding small RNAs, including siRNAs, miRNAs, and phasiRNAs, have been uncovered, expanding the scope of RNAi-mediated gene regulation beyond conventional understanding. These RNA classes participate in intricate post-transcriptional and epigenetic processes that influence gene expression. In the context of crop enhancement, RNAi has emerged as a powerful tool for understanding gene functions. It has proven effective in deciphering gene roles related to stress resistance, metabolic pathways, and more. Additionally, RNAi-based approaches hold promise for integrated pest management and sustainable agriculture, contributing to global efforts in food security. This review discusses RNAi's diverse applications, such as modifying plant architecture, extending shelf life, and enhancing nutritional content in crops. The challenges and future prospects of RNAi technology, including delivery methods and biosafety concerns, are also explored. The global landscape of RNAi research is highlighted, with significant contributions from regions such as China, Europe, and North America. In conclusion, RNAi remains a versatile and pivotal tool in modern plant research, offering novel avenues for understanding gene functions and improving crop traits. Its integration with other biotechnological approaches such as gene editing holds the potential to shape the future of agriculture and sustainable food production.

Encapsulated nanopesticides application in plant protection: Quo vadis?

The increased global food insecurity due to the growing population can be addressed with precision and sustainable agricultural practices. To tackle the issues regarding food insecurity, farmers used different agrochemicals that improved plant growth and protection. Among these agrochemicals, synthetic pesticides used for plant protection in the agricultural field have various disadvantages. Conventional applications of synthetic pesticides have drawbacks such as rapid degradation, poor solubility, and non-target effects, as well as increased pesticide runoff that pollutes the environment. Nanotechnology has evolved as a potential solution to increase agricultural productivity through the development of different nanoforms of agrochemicals such as nanopesticides, nano-fabricated fertilizers, nanocapsules, nanospheres, nanogels, nanofibers, nanomicelles, and nano-based growth promoters. Encapsulation of these pesticides inside the nanomaterials has provided good biocompatibility over conventional application by inhibiting the early degradation of active ingredients (AI), increasing the uptake and adhesion of pesticides, improving the stability, solubility, and permeability of the pesticides, and decreasing the environmental impacts due to the pesticide runoff. In this review, different nanoforms of encapsulated pesticides and their smart delivery systems; nanocarriers in RNA interference (RNAi) based pesticides; environmental fate, practical implications, management of nanopesticides; and future perspectives are discussed.

The impact of 'framing' in the adoption of GM crops

Genetically modified (GM) crops offer significant advantages in our crop improvement programs because they are created using a more targeted approach which is not possible in traditional breeding methods. Human benefit is one of the main objectives of crop improvement but the legal framework for the introduction of GM crops and the depiction and portrayal of GM crops in the media create barriers to these benefits. This article attempts to highlight the barriers to GM crop adoption particularly focusing on the idea of "framing" and the way GM technology is framed in the media. The resulting public health, economic, and ecological concerns about genetically modified plants, along with the reality of these misconceptions, are discussed with specific examples. Finally, we propose potential routes toward increased acceptance of GM crops.

Molecular switches in plant stress adaptation

Climate change poses a significant threat to the global ecosystem, prompting plants to use various adaptive mechanisms via molecular switches to combat biotic and abiotic stress factors. These switches activate stress-induced pathways by altering their configuration between stable states. In this review, we investigated the regulation of molecular switches in different plant species in response to stress, including the stress-regulated response of multiple switches in Arabidopsis thaliana. We also discussed techniques for developing stress-resilient crops using molecular switches through advanced biotechnological tools. The literature search, conducted using databases such as PubMed, Google Scholar, Web of Science, and SCOPUS, utilized keywords such as molecular switch, plant adaptation, biotic and abiotic stresses, transcription factors, Arabidopsis thaliana, and crop improvement. Recent studies have shown that a single molecular switch can regulate multiple stress networks, and multiple switches can regulate a single stress condition. This multifactorial understanding provides clarity to the switch regulatory network and highlights the interrelationships of different molecular switches. Advanced breeding techniques, along with genomic and biotechnological tools, have paved the way for further research on molecular switches in crop improvement. The use of synthetic biology in molecular switches will lead to a better understanding of plant stress biology and potentially bring forth a new era of stress-resilient, climate-smart crops worldwide.

3Bs of CRISPR-Cas mediated genome editing in plants: exploring the basics, bioinformatics and biosafety landscape

The recent thrust in research has projected the type II clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR-Cas9) system as an avant-garde plant genome editing tool. It facilitates the induction of site-specific double-stranded DNA cleavage by the RNA-guided DNA endonuclease (RGEN), Cas9. Elimination, addition, or alteration of sections in DNA sequence besides the creation of a knockout genotype (CRISPRko) is aided by the CRISPR-Cas9 system in its wild form (wtCas9). The inactivation of the nuclease domain generates a dead Cas9 (dCas9), which is capable of targeting genomic DNA without scissoring it. The dCas9 system can be engineered by fusing it with different effectors to facilitate transcriptional activation (CRISPRa) and transcriptional interference (CRISPRi). CRISPR-Cas thus holds tremendous prospects as a genome-manipulating stratagem for a wide gamut of crops. In this article, we present a brief on the fundamentals and the general workflow of the CRISPR-Cas system followed by an overview of the prospects of bioinformatics in propelling CRISPR-Cas research with a special thrust on the available databases and algorithms/web-accessible applications that have aided in increasing the usage and efficiency of editing. The article also provides an update on the current regulatory landscape in different countries on the CRISPR-Cas edited plants to emphasize the far-reaching impact of the genomic editing technology.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01397-3.

Characterizing patterns of seasonal drought stress for use in common bean breeding in East Africa under present and future climates

Common bean (Phaseolus vulgaris L.) is the second most important source of dietary protein and the third most important source of calories in Africa, especially for the poor. In East Africa, drought is an important constraint to bean production. Therefore, breeding programs in East Africa have been trying to develop drought resistant varieties of common bean. To do this, breeders need information about seasonal drought stress patterns including their onset, intensity, and duration in the target area of the breeding program, so that they can mimic this pattern during field trials. Using the Decision Support for Agrotechnology Transfer (DSSAT) v4.7 model together with historical and future (Coupled Model Inter-comparison Project 6, CMIP6) climate data, this study categorized Ethiopia, Tanzania, and Uganda into different target population of environments (TPEs) based on historical and future seasonal drought stress patterns. We find that stress-free conditions generally dominate across the three countries under historical conditions (50-80% frequency). These conditions are projected to increase in frequency in Ethiopia by 2-10% but the converse is true for Tanzania (2-8% reduction) and Uganda (17-20% reduction) by 2050 depending on the Shared Socioeconomic Pathway (SSP). Accordingly, by 2050, terminal drought stresses of various intensities (moderate, severe, extreme) are prevalent in 34% of Uganda, around a quarter of Ethiopia, and 40% of the bean growing environments in Tanzania. The TPEs identified in each country serve as a basis for prioritizing breeding activities in national programs. However, to optimize resource use in international breeding programs to develop genotypes that are resilient to future projected stress patterns, we argue that common bean breeding programs should focus primarily on identifying genotypes with tolerance to severe terminal drought, with co-benefits in relation to adaptation to moderate and extreme terminal drought. Little to no emphasis on heat stress is warranted by 2050s.

Hormonal involvement in boosting the vegetative vigour underlying caffeine-related improvements in lentil production

Previous studies have shown that caffeine (1,3,7-trimethylxanthine) has some potential for its use as a biostimulant ingredient for boosting lentil production at suboptimal temperatures. However, some limitations to its use include its potential side effects as an emerging contaminant and the current lack of knowledge of its mechanism of action. Here, we aimed to study the mechanisms underlying improved lentil production upon caffeine application. Greenhouse-grown plants treated with caffeine (at 10-5 M, 10-4 M, and 10-3 M) were compared to an untreated, control treatment, and both reproductive and vegetative vigour were evaluated in parallel with endogenous foliar concentrations of phytohormones, including both stress and growth-related hormones. Results showed an enhanced lentil production at the highest caffeine concentration (10-3 M) which might be attributed, at least in part, to a greater vegetative vigour. The hormonal profiling revealed a dual effect. Firstly, there was a specific increase in jasmonoyl-isoleucine (JA-Ile) in the short term, which may provide a priming effect. Secondly, abscisic acid (ABA) content kept at low levels and the active cytokinin (CK) isopentenyl adenine (2-iP) increased and persisted at high levels throughout the reproductive stage. Cytokinin-mediated effects on growth, and more specifically the high CK/ABA ratios in leaves, appeared to mediate caffeine-related effects in boosting vegetative vigour. In conclusion, caffeine emerges as a compelling alkaloid for integration into biostimulant formulations due to its favorable effect in boosting lentil production through an improvement of vegetative vigour. These outcomes appear to be modulated by phytohormones, most notably jasmonates, priming plants for improved performance under suboptimal temperatures, and cytokinins, alongside ABA and its associated ratios, collectively enhancing plant growth and reproductive vigour in challenging conditions.

Assessment of genetic variation among wheat genotypes for drought tolerance utilizing microsatellite markers and morpho-physiological characteristics

Drought is a major abiotic stress that severely limits sustainable wheat (Triticum aestivum L.) productivity via morphological and physio-biochemical alterations of cellular processes. The complex nature and polygenic control of drought tolerance traits make breeding tolerant genotypes quite challenging. However, naturally occurring variabilities among wheat germplasm resources could potentially help combating drought. The present study was conducted to assess the drought tolerance of 18 Bangladeshi hexaploid wheat genotypes, focusing on the identification of potent sources of diversity by combining microsatellite markers, also known as single sequence repeat markers, and morpho-physiological characteristics that might help accelerating wheat crop improvement programs. Initially, the genotypes were evaluated using 25 microsatellite markers followed by an on-field evaluation of 7 morphological traits (plant height, spike number, spike length, grains per spike, 1000-grain weight, grain yield, biological yield) and 6 physiological traits (SPAD value, membrane stability index, leaf relative water content, proline content, canopy temperature depression, and leaf K+ ion content). The field-trial was conducted in a factorial fashion of 18 wheat genotypes and two water regimes (control and drought) following a split-plot randomized complete block design. Regardless of genotype, drought was significantly damaging for all the tested traits; however, substantial variability in drought stress tolerance was evident among the genotypes. Spike length, 1000-grain weight, SPAD value, leaf relative water content, canopy temperature depression, proline content, and potassium (K+) ion content were the most representative of drought-induced growth and yield impairments and also correlated well with the contrasting ability of genotypic tolerance. Microsatellite markers amplified 244 alleles exhibiting 79% genetic diversity. Out of 25 markers, 23 was highly polymorphic showing 77% average polymorphism. Morpho-physiological trait-based hierarchical clustering and microsatellite marker-based neighbor-jointing clustering both revealed three genotypic clusters with 71% co-linearity between them. In both cases, the genotypes Kanchan, BAW-1147, BINA Gom 1, BARI Gom 22, BARI Gom 26, and BARI Gom 33 were found to be comparatively more tolerant than the other tested genotypes, showing potential for cultivation in water-deficit environments. The findings of this study would contribute to the present understanding of drought tolerance in wheat and would provide a basis for future genotype selection for drought-tolerant wheat breeding programs.

Emerging roles of long non-coding RNAs in regulating agriculturally important seed traits

Seeds have enormous economic importance as source of calories, nutrition, edible oil, and biofuels. Therefore, seed traits like seed size and shape, weight, micronutrient content, oil content, quality, post-harvest sprouting, etc., are some of the main targets in crop improvement. Designing the strategies for their improvement benefits heavily from understanding the regulatory aspects of seed development. Recent studies indicate that long non-coding RNAs (lncRNAs) are one of the important regulators of seed development. They played a significant role in crop domestication by influencing seed traits. LncRNAs are conventionally defined as non-coding RNAs greater than 200 bp in length but lacking protein coding potential. Here we highlight the emerging pieces of evidence of lncRNA-mediated regulation of seed development through diverse mechanisms, for instance, by acting as target mimics or precursors of regulatory small RNAs or through chromatin remodeling and post-transcriptional repression. We also enumerate the insights from high-throughput transcriptomic studies from developing seeds of cereal, oilseed, biofuel, and pulse crops. We highlight the lncRNA candidates and lncRNA-mediated regulatory networks regulating seed development and related agronomic traits. Further, we discuss the potential of lncRNAs for improvement of agriculturally important seed traits through marker-assisted breeding and/or transgenic approaches.

Shining in the dark: the big world of small peptides in plants

Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding. We review the biological functions and molecular mechanisms of small peptides in plants, discuss current problems in small peptide research and highlight future research directions in this field. Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.

Genetic modification strategies for enhancing plant resilience to abiotic stresses in the context of climate change

Enhancing the resilience of plants to abiotic stresses, such as drought, salinity, heat, and cold, is crucial for ensuring global food security challenge in the context of climate change. The adverse effects of climate change, characterized by rising temperatures, shifting rainfall patterns, and increased frequency of extreme weather events, pose significant threats to agricultural systems worldwide. Genetic modification strategies offer promising approaches to develop crops with improved abiotic stress tolerance. This review article provides a comprehensive overview of various genetic modification techniques employed to enhance plant resilience. These strategies include the introduction of stress-responsive genes, transcription factors, and regulatory elements to enhance stress signaling pathways. Additionally, the manipulation of hormone signaling pathways, osmoprotectant accumulation, and antioxidant defense mechanisms is discussed. The use of genome editing tools, such as CRISPR-Cas9, for precise modification of target genes related to stress tolerance is also explored. Furthermore, the challenges and future prospects of genetic modification for abiotic stress tolerance are highlighted. Understanding and harnessing the potential of genetic modification strategies can contribute to the development of resilient crop varieties capable of withstanding adverse environmental conditions caused by climate change, thereby ensuring sustainable agricultural productivity and food security.

The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement

Plant breeding has made a significant contribution to increasing agricultural production. Conventional breeding based on phenotypic selection is not effective for crop improvement. Because phenotype is considerably influenced by environmental factors, which will affect the selection of breeding materials for crop improvement. The past two decades have seen tremendous progress in plant breeding research. Especially the availability of high-throughput molecular markers followed by genomic-assisted approaches significantly contributed to advancing plant breeding. Integration of speed breeding with genomic and phenomic facilities allowed rapid quantitative trait loci (QTL)/gene identifications and ultimately accelerated crop improvement programs. The advances in sequencing technology helps to understand the genome organization of many crops and helped with genomic selection in crop breeding. Plant breeding has gradually changed from phenotype-to-genotype-based to genotype-to-phenotype-based selection. High-throughput phenomic platforms have played a significant role in the modern breeding program and are considered an essential part of precision breeding. In this review, we discuss the rapid advance in plant breeding technology for efficient crop improvements and provide details on various approaches/platforms that are helpful for crop improvement. This review will help researchers understand the recent developments in crop breeding and improvements.

Plant lectins: Classical molecules with emerging roles in stress tolerance

Biotic and abiotic stresses impose adverse effects on plant's development, growth, and production. For the past many years, researchers are trying to understand the stress induced responses in plants and decipher strategies to produce stress tolerant crops. It has been demonstrated that molecular networks encompassing an array of genes and functional proteins play a key role in generating responses to combat different stresses. Newly, there has been a resurgence of interest to explore the role of lectins in modulating various biological responses in plants. Lectins are naturally occurring proteins that form reversible linkages with their respective glycoconjugates. To date, several plant lectins have been recognized and functionally characterized. However, their involvement in stress tolerance is yet to be comprehensively analyzed in greater detail. The availability of biological resources, modern experimental tools, and assay systems has provided a fresh impetus for plant lectin research. Against this backdrop, the present review provides background information on plant lectins and recent knowledge on their crosstalks with other regulatory mechanisms, which play a remarkable role in plant stress amelioration. It also highlights their versatile role and suggests that adding more information to this under-explored area will usher in a new era of crop improvement.

Understanding the genomic selection for crop improvement: current progress and future prospects

Although increased use of modern breeding techniques and technology has resulted in long-term genetic gain, the pace of genetic gain must be sped up to satisfy global agricultural demand. However, marker-assisted selection has proven its potential for improving qualitative traits with large effects regulated by one to few genes. Its contribution to the improvement of the quantitative traits regulated by a number of small-effect genes is modest. In this context, genomic selection (GS) has been regarded as the most promising method for genetically enhancing complicated features that are regulated by several genes, each of which has minor effects. By examining a population's phenotypes and high-density marker scores, genomic selection can forecast the breeding potential of individual lines. The fact that GS uses all marker data in the prediction model prevents skewed marker effect estimations and maximizes the amount of variation caused by small-effect QTL. It has the ability to speed up the breeding cycle and as a consequence of which superior genotypes are selected rapidly. Developing the best GS models while taking into account non-additive effects, genotype-by-environment interaction, and cost-effectiveness will enable the widespread implementation of GS in plants. These steps will also increase heritability estimation and prediction accuracy. This review focuses on the shift from conventional selection methods to GS, underlying statistical tools and methodologies, the state of GS research in agricultural plants, and prospects for its effective use in the creation of climate-resilient crops.

Divergent structures and functions of the Cupin proteins in plants

Cupin superfamily proteins have extensive functions. Their members are not only involved in the development of plants but also responded to various stresses. Whereas, the research on the Cupin members has not attracted enough attention. In this article, we summarized the research progress on these family genes in recent years and explored their evolution, structural characteristics, and biological functions. The significance of members of the Cupin family in the development of plant cell walls, roots, leaves, flowers, fruits, and seeds and their role in stress response are highlighted. Simultaneously, the prospective application of Cupin protein in crop enhancement was introduced. Some members can enhance plant growth, development, and resistance to adversity, thereby increasing crop yield. It will be as a foundation for future effective crop research and breeding.

The role of invasive plant species in drought resilience in agriculture: the case of sweet briar (Rosa rubiginosa L.)

Sweet briar (Rosa rubiginosa) belongs to the group of wild roses. Under natural conditions it grows throughout Europe, and was introduced also into the southern hemisphere, where it has efficiently adapted to dry lands. This review focuses on the high adaptation potential of sweet briar to soil drought in the context of global climatic changes, especially considering steppe formation and desertification of agricultural, orchard, and horticultural areas. We provide a comprehensive overview of current knowledge on sweet briar traits associated with drought tolerance and particularly water use efficiency, sugar accumulation, accumulation of CO2 in intercellular spaces, stomatal conductance, gibberellin level, effective electron transport between photosystem II and photosystem I, and protein content. We discuss the genetics and potential applications in plant breeding and suggest future directions of study concerning invasive populations of R. rubiginosa. Finally, we point out that sweet briar can provide new genes for breeding in the context of depleting gene pools of the crop plants.

Silicon nanoparticles: Synthesis, uptake and their role in mitigation of biotic stress

In the current scenario of global warming and climate change, plants face many biotic stresses, which restrain growth, development and productivity. Nanotechnology is gaining precedence over other means to deal with biotic and abiotic constraints for sustainable agriculture. One of nature's most beneficial metalloids, silicon (Si) shows ameliorative effect against environmental challenges. Silicon/Silica nanoparticles (Si/SiO₂NPs) have gained special attention due to their significant chemical and optoelectronic capabilities. Its mesoporous nature, easy availability and least biological toxicity has made it very attractive to researchers. Si/SiO₂NPs can be synthesised by chemical, physical and biological methods and supplied to plants by foliar, soil, or seed priming. Upon uptake and translocation, Si/SiO₂NPs reach their destined cells and cause optimum growth, development and tolerance against environmental stresses as well as pest attack and pathogen infection. Using Si/SiO₂NPs as a supplement can be an eco-friendly and cost-effective option for sustainable agriculture as they facilitate the delivery of nutrients, assist plants to mitigate biotic stress and enhances plant resistance. This review aims to present an overview of the methods of formulation of Si/SiO₂NPs, their application, uptake, translocation and emphasize the role of Si/SiO₂NPs in boosting growth and development of plants as well as their conventional advantage as fertilizers with special consideration on their mitigating effects towards biotic stress.

An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges

Genome editing is a useful, adaptable, and favored technique for both functional genomics and crop enhancement. Over the years, rapidly evolving genome editing technologies, including clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas), transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs), have shown broad application prospects in gene function research and improvement of critical agronomic traits in many crops. These technologies have also opened up opportunities for plant breeding. These techniques provide excellent chances for the quick modification of crops and the advancement of plant science in the future. The current review describes various genome editing techniques and how they function, particularly CRISPR/Cas9 systems, which can contribute significantly to the most accurate characterization of genomic rearrangement and plant gene functions as well as the enhancement of critical traits in field crops. To accelerate the use of gene-editing technologies for crop enhancement, the speed editing strategy of gene-family members was designed. As it permits genome editing in numerous biological systems, the CRISPR technology provides a valuable edge in this regard that particularly captures the attention of scientists.

Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis

The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.

Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways

Plants are the most important sources of food for humans, as well as supplying many ingredients that are of great importance for human health. Developing an understanding of the functional components of plant metabolism has attracted considerable attention. The rapid development of liquid chromatography and gas chromatography, coupled with mass spectrometry, has allowed the detection and characterization of many thousands of metabolites of plant origin. Nowadays, elucidating the detailed biosynthesis and degradation pathways of these metabolites represents a major bottleneck in our understanding. Recently, the decreased cost of genome and transcriptome sequencing rendered it possible to identify the genes involving in metabolic pathways. Here, we review the recent research which integrates metabolomic with different omics methods, to comprehensively identify structural and regulatory genes of the primary and secondary metabolic pathways. Finally, we discuss other novel methods that can accelerate the process of identification of metabolic pathways and, ultimately, identify metabolite function(s).

Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution

BACKGROUND

Mitochondria are organelles within eukaryotic cells that are central to the metabolic processes of cellular respiration and ATP production. However, the evolution of mitochondrial genomes (mitogenomes) in plants is virtually unknown compared to animal mitogenomes or plant plastids, due to complex structural variation and long stretches of repetitive DNA making accurate genome assembly more challenging. Comparing the structural and sequence differences of organellar genomes within and between sorghum species is an essential step in understanding evolutionary processes such as organellar sequence transfer to the nuclear genome as well as improving agronomic traits in sorghum related to cellular metabolism.

RESULTS

Here, we assembled seven sorghum mitochondrial and plastid genomes and resolved reticulated mitogenome structures with multilinked relationships that could be grouped into three structural conformations that differ in the content of repeats and genes by contig. The grouping of these mitogenome structural types reflects the two domestication events for sorghum in east and west Africa.

CONCLUSIONS

We report seven mitogenomes of sorghum from different cultivars and wild sources. The assembly method used here will be helpful in resolving complex genomic structures in other plant species. Our findings give new insights into the structure of sorghum mitogenomes that provides an important foundation for future research into the improvement of sorghum traits related to cellular respiration, cytonuclear incompatibly, and disease resistance.

High-Throughput Base Editing-Mediated Artificial Evolution Streamlines Trait Gene Identification in Rice

Base Editing-Mediated Gene Evolution (BEMGE) method develops novel rice germplasms with mutations in any endogenous gene through employing both Cas9n-based cytosine and adenine base editors combined with an sgRNA library tiling the full-length coding region, for obtaining unknown functional SNPs. Here we describe the process of artificial evolution of OsALS1 in rice cells using BEMGE through Agrobacterium-mediated transformation. BEMGE method has the potential to generate numerous nucleotide changes to screen pivotal amino acids (AAs) and to accelerate crop improvement.

The Role of Membrane Transporters in the Biofortification of Zinc and Iron in Plants

Over three billion people suffer from various health issues due to the low supply of zinc (Zn) and iron (Fe) in their food. Low supply of micronutrients is the main cause of malnutrition and biofortification could help to solve this issue. Understanding the molecular mechanisms of biofortification is challenging. The membrane transporters are involved in the uptake, transport, storage, and redistribution of Zn and Fe in plants. These transporters are also involved in biofortification and help to load the Zn and Fe into the endosperm of the seeds. Very little knowledge is available on the role and functions of membrane transporters involved in seed biofortification. Understanding the mechanism and role of membrane transporters could be helpful to improve biofortification. In this review, we provide the details on membrane transporters involved in the uptake, transport, storage, and redistribution of Zn and Fe. We also discuss available information on transporters involved in seed biofortification. This review will help plant breeders and molecular biologists understand the importance and implications of membrane transporters for seed biofortification.

The Plant Metabolic Changes and the Physiological and Signaling Functions in the Responses to Abiotic Stress

Global climate change has altered, and will further alter, rainfall patterns and temperatures likely causing more frequent drought and heat waves, which will consequently exacerbate abiotic stresses of plants and significantly decrease the yield and quality of crops. On the one hand, the global demand for food is ever-increasing owing to the rapid increase of the human population. On the other hand, metabolic responses are one of the most important mechanisms by which plants adapt to and survive to abiotic stresses. Here we therefore summarize recent progresses including the plant primary and secondary metabolic responses to abiotic stresses and their function in plant resistance acting as antioxidants, osmoregulatory, and signaling factors, which enrich our knowledge concerning commonalities of plant metabolic responses to abiotic stresses, including their involvement in signaling processes. Finally, we discuss potential methods of metabolic fortification of crops in order to improve their abiotic stress tolerance.

Metabolite-Based Genome-Wide Association Studies of Large-Scale Metabolome Analysis to Illustrate Alterations in the Metabolite Landscape of Plants upon Responses to Stresses

Given that anthropogenic activities are evoking a profound effect on the climate resulting in more extreme events such as severe drought and heat waves while global demand for food is ever-increasing, understanding plant responses to stresses is critical. As metabolites are fundamental for plant growth regulation and plant lifespan and an important component of yield, illustrating how the metabolite landscape of plant changes following stress will supply important clues as to how to improve the plant resistance to stress. Recently, billions of single-nucleotide polymorphisms (SNPs) have been obtained and used to identify the associations between genetic variants of genomes and relevant crop agronomic traits through different genetic methods such as genome-wide association studies (GWAS). Therefore, in this chapter, we provide comprehensive guidelines concerning the experimental design, metabolite profiling, and metabolite-based genome-wide association studies (mGWAS) of large-scale metabolome analysis to accelerate the future identification of the valuable stress-resistant genes and metabolites.

Prospects of Feral Crop De Novo Redomestication

Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to the adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case 'redomestication'. Feral crops are plants that have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e. neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.

CRISPR/Cas-mediated editing of cis-regulatory elements for crop improvement

To improve future agricultural production, major technological advances are required to increase crop production and yield. Targeting the coding region of genes via the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated Protein (CRISPR/Cas) system has been well established and has enabled the rapid generation of transgene-free plants, which can lead to crop improvement. The emergence of the CRISPR/Cas system has also enabled scientists to achieve cis-regulatory element (CRE) editing and, consequently, engineering endogenous critical CREs to modulate the expression of target genes. Recent genome-wide association studies have identified the domestication of natural CRE variants to regulate complex agronomic quantitative traits and have allowed for their engineering via the CRISPR/Cas system. Although engineering plant CREs can be advantageous to drive gene expression, there are still many limitations to its practical application. Here, we review the current progress in CRE editing and propose future strategies to effectively target CREs for transcriptional regulation for crop improvement.

Autophagy: a game changer for plant development and crop improvement

Manipulation of autophagic pathway represents a tremendous opportunity for designing climate-smart crops with improved yield and better adaptability to changing environment. For exploiting autophagy to its full potential, identification and comprehensive characterization of adapters/receptor complex and elucidation of its regulatory network in crop plants is highly warranted.  Autophagy is a major intracellular trafficking pathway in eukaryotes involved in vacuolar degradation of cytoplasmic constituents, mis-folded proteins, and defective organelles. Under optimum conditions, autophagy operates at a basal level to maintain cellular homeostasis, but under stressed conditions, it is induced further to provide temporal stress relief. Our understanding of this highly dynamic process has evolved exponentially in the past few years with special reference to several plant-specific roles of autophagy. Here, we review the most recent advances in the field of autophagy in plants and discuss its potential implications in designing crops with improved stress and disease-tolerance, enhanced yield potential, and improved capabilities for producing metabolites of high economic value. We also assess the current knowledge gaps and the possible strategies to develop a robust module for biotechnological application of autophagy to enhance bioeconomy and sustainability of agriculture.

A detailed landscape of CRISPR-Cas-mediated plant disease and pest management

Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.

Application of RNAi technology: a novel approach to navigate abiotic stresses

BACKGROUND

Due to the rising population globally, and the demand for food, it is critical to significantly increase crop production by 2050. However, climate change estimates show that droughts and heatwaves will become more prevalent in many parts of the world, posing a severe danger to food output.

METHODS

Selective breeding based on genetic diversity is falling short of meeting the expanding need for food and feed. However, the advent of modern plant genetic engineering, genome editing, and synthetic biology provides precise techniques for producing crops capable of sustaining yield under stress situations.

RESULTS

As a result, crop varieties with built-in genetic tolerance to environmental challenges are desperately needed. In the recent years, small RNA (sRNA) data has progressed to become one of the most effective approaches for the improvement of crops. So many sRNAs (18-30nt) have been found with the use of hi-tech bioinformatics and sequencing techniques which are involved in the regulation of sequence specific gene noncoding RNAs (short ncRNAs) i.e., microRNA (miRNA) and small interfering RNA (siRNA). Such research outcomes may advance our understanding of the genetic basis of adaptability of plants to various environmental challenges and the genetic variation of plant's tolerance to a number of abiotic stresses.

CONCLUSION

The review article highlights current trends and advances in sRNAs' critical role in responses of plants to drought, heat, cold, and salinity, and also the potential technology that identifies the abiotic stress-regulated sRNAs, and techniques for analyzing and validating the target genes.

Fungi-derived agriculturally important nanoparticles and their application in crop stress management - Prospects and environmental risks

Nanotechnology has a wide range of agricultural applications, with emphasize on the development of novel nano-agrochemicals such as, nano-fertilizer and nano-pesticides. It has a significant impact on sustainable agriculture by increasing agricultural productivity, while reducing the use of inorganic fertilizers, pesticides, and herbicides. Nano-coating delivery methods for agrochemicals have improved agrochemical effectiveness, safety, and consistency. Biosynthesis of nanoparticles (NPs) has recently been recognized as an effective tool, contrary to chemically derived NPs, for plant abiotic and biotic stress control, and crop improvement. In this regard, fungi have tremendous scope and importance for producing biogenic NPs of various sizes, shapes, and characteristics. Fungi are potential candidates for synthesis of biogenic NPs due to their enhanced bioavailability, biological activity, and higher metal tolerance. However, their biomimetic properties and high capacity for dispersion in soil, water environments, and foods may have negative environmental consequences. Furthermore, their bioaccumulation raises significant concerns about the novel properties of nanomaterials potentially causing adverse biological effects, including toxicity. This review provides a concise outline of the growing role of fungal-mediated metal NPs synthesis, its potential applications in crop field, and associated issues of nano-pollution in soil and its future implications.

Understanding of the various aspects of gene regulatory networks related to crop improvement

The hierarchical relationship between transcription factors, associated proteins, and their target genes is defined by a gene regulatory network (GRN). GRNs allow us to understand how the genotype and environment of a plant are incorporated to control the downstream physiological responses. During plant growth or environmental acclimatization, GRNs are diverse and can be differently regulated across tissue types and organs. An overview of recent advances in the development of GRN that speed up basic and applied plant research is given here. Furthermore, the overview of genome and transcriptome involving GRN research along with the exciting advancement and application are discussed. In addition, different approaches to GRN predictions were elucidated. In this review, we also describe the role of GRN in crop improvement, crop plant manipulation, stress responses, speed breeding and identifying genetic variations/locus. Finally, the challenges and prospects of GRN in plant biology are discussed.

Current status and impending progress for cassava structural genomics

We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.

Advancing designer crops for climate resilience through an integrated genomics approach

Climate change and exponential population growth are exposing an immediate need for developing future crops that are highly resilient and adaptable to changing environments to maintain global food security in the next decade. Rigorous selection from long domestication history has rendered cultivated crops genetically disadvantaged, raising concerns in their ability to adapt to these new challenges and limiting their usefulness in breeding programmes. As a result, future crop improvement efforts must rely on integrating various genomic strategies ranging from high-throughput sequencing to machine learning, in order to exploit germplasm diversity and overcome bottlenecks created by domestication, expansive multi-dimensional phenotypes, arduous breeding processes, complex traits and big data.

CRISPR/Cas technology for improving nutritional values in the agricultural sector: an update

BACKGROUND

The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system was initially identified in bacteria and archaea as a defense mechanism to confer immunity against phages. Later on, it was developed as a gene editing tool for both prokaryotic and eukaryotic cells including plant cells.

METHODS AND RESULTS

CRISPR/Cas9 approach has wider applications in reverse genetics as well as in crop improvement. Various characters involved in enhancing economic value and crop sustainability against biotic/abiotic stresses can be targeted through this tool. Currently, CRISPR/Cas9 gene editing mechanism has been applied on around 20 crop species for improvement in several traits including yield enhancement and resistance against biotic and abiotic stresses. In the last five years, maximum genome editing research has been validated in rice, wheat, maize and soybean. Genes targeted in these plants has been involved in causing male sterility, conferring resistance against pathogens or having certain nutritional value.

CONCLUSIONS

Current review summarizes various applications of CRISPR/Cas system and its future prospects in plant biotechnology targeting crop improvement with higher yield, disease tolerance and enhanced nutritional value.

Chloroplast Engineering: Fundamental Insights and Its Application in Amelioration of Environmental Stress

Chloroplasts are specialized organelle that are responsible for converting light energy to chemical energy, thereby driving the carbon dioxide fixation. Apart from photosynthesis, chloroplast is the site for essential cellular processes that determine the plant adaptation to changing environment. Owing to the presence of their own expression system, it provides an optimum platform for engineering valued traits as well as site for synthesis of bio-compounds. Advancements in technology have further enhanced the scope of using chloroplast as a multifaceted tool for the biotechnologist to develop stress-tolerant plants and ameliorate environmental stress. Focusing on chloroplast biotechnology, this review discusses the advances in chloroplast engineering and its application in enhancing plant adaptation and resistance to environmental stress and the development of new bioproducts and processes. This is accomplished through analysis of its biogenesis and physiological processes, highlighting the chloroplast engineering and recent developments in chloroplast biotechnology. In the first part of the review, the evolution and principles of structural organization and physiology of chloroplast are discussed. In the second part, the chief methods and mechanisms involved in chloroplast transformation are analyzed. The last part represents an updated analysis of the application of chloroplast engineering in crop improvement and bioproduction of industrial and health compounds.

Recent advancements in CRISPR/Cas technology for accelerated crop improvement

Precise genome engineering approaches could be perceived as a second paradigm for targeted trait improvement in crop plants, with the potential to overcome the constraints imposed by conventional CRISPR/Cas technology. The likelihood of reduced agricultural production due to highly turbulent climatic conditions increases as the global population expands. The second paradigm of stress-resilient crops with enhanced tolerance and increased productivity against various stresses is paramount to support global production and consumption equilibrium. Although traditional breeding approaches have substantially increased crop production and yield, effective strategies are anticipated to restore crop productivity even further in meeting the world's increasing food demands. CRISPR/Cas, which originated in prokaryotes, has surfaced as a coveted genome editing tool in recent decades, reshaping plant molecular biology in unprecedented ways and paving the way for engineering stress-tolerant crops. CRISPR/Cas is distinguished by its efficiency, high target specificity, and modularity, enables precise genetic modification of crop plants, allowing for the creation of allelic variations in the germplasm and the development of novel and more productive agricultural practices. Additionally, a slew of advanced biotechnologies premised on the CRISPR/Cas methodologies have augmented fundamental research and plant synthetic biology toolkits. Here, we describe gene editing tools, including CRISPR/Cas and its imitative tools, such as base and prime editing, multiplex genome editing, chromosome engineering followed by their implications in crop genetic improvement. Further, we comprehensively discuss the latest developments of CRISPR/Cas technology including CRISPR-mediated gene drive, tissue-specific genome editing, dCas9 mediated epigenetic modification and programmed self-elimination of transgenes in plants. Finally, we highlight the applicability and scope of advanced CRISPR-based techniques in crop genetic improvement.

Genome Editing and Designer Crops for the Future

Domestication spanning over thousands of years led to the evolution of crops that are being cultivated in recent times. Later, selective breeding methods were practiced by human to produce improved cultivars/germplasm. Classical breeding was further transformed into molecular- and genomics-assisted breeding strategies, however, these approaches are labor-intensive and time-consuming. The advent of omics technologies has facilitated the identification of genes and genetic determinants that regulate particular traits allowing the direct manipulation of target genes and genomic regions to achieve desirable phenotype. Recently, genome editing technologies such as meganucleases (MN), zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-Associated protein 9 (Cas9) have gained popularity for precise editing of genes to develop crop varieties with superior agronomic, physiological, climate-resilient, and nutritional traits. Owing to the efficiency and precision, genome editing approaches have been widely used to design the crops that can survive the challenges posed by changing climate, and also cater the food and nutritional requirements for ever-growing population. Here, we briefly review different genome editing technologies deployed for crop improvement, and the fundamental differences between GE technology and transgene-based approach. We also summarize the recent advances in genome editing and how this radical expansion can complement the previously established technologies along with breeding for creating designer crops.

Metabolomics: a systems biology approach for enhancing heat stress tolerance in plants

Comprehensive metabolomic investigations provide a large set of stress-related metabolites and metabolic pathways, advancing crops under heat stress conditions. Metabolomics-assisted breeding, including mQTL and mGWAS boosted our understanding of improving numerous quantitative traits under heat stress. During the past decade, metabolomics has emerged as a fascinating scientific field that includes documentation, evaluation of metabolites, and chemical methods for cell monitoring programs in numerous plant species. A comprehensive metabolome profiling allowed the investigator to handle the comprehensive data groups of metabolites and the equivalent metabolic pathways in an extraordinary manner. Metabolomics, together with transcriptomics, plays an influential role in discovering connections between stress and genes/metabolite, phenotyping, and biomarkers documentation. Further, it helps to decode several metabolic systems connected with heat stress (HS) tolerance in plants. Heat stress is a critical environmental factor that is globally affecting the growth and productivity of plants. Thus, there is an urgent need to exploit modern breeding and biotechnological tools like metabolomics to develop cultivars with improved HS tolerance. Several studies have reported that amino acids, carbohydrates, nitrogen metabolisms, etc. and metabolites involved in the biosynthesis and catalyzing actions play a game-changing role in HS response and help plants to cope with the HS. The use of metabolomics-assisted breeding (MAB) allows a well-organized transmission of higher yield and HS tolerance at the metabolome level with specific properties. Progressive metabolomics systematic techniques have accelerated metabolic profiling. Nonetheless, continuous developments in bioinformatics, statistical tools, and databases are allowing us to produce ever-progressing, comprehensive insights into the biochemical configuration of plants and by what means this is inclined by genetic and environmental cues. Currently, assimilating metabolomics with post-genomic platforms has allowed a significant division of genetic-phenotypic connotation in several plant species. This review highlights the potential of a state-of-the-art plant metabolomics approach for the improvement of crops under HS. The development of plants with specific properties using integrated omics (metabolomics and transcriptomics) and MAB can provide new directions for future research to enhance HS tolerance in plants to achieve a goal of "zero hunger".

Improvement of millets in the post-genomic era

Millets are food and nutrient security crops in the semi-arid tropics of developing countries. Crop improvement using modern tools is one of the priority areas of research in millets. The whole-genome sequence (WGS) of millets provides new insight into understanding and studying the genes, genome organization and genomic-assisted improvement of millets. The WGS of millets helps to carry out genome-wide comparison and co-linearity studies among millets and other cereal crops. This approach might lead to the identification of genes underlying biotic and abiotic stress tolerance in millets. The available genome sequence of millets can be used for SNP identification, allele discovery, association and linkage mapping, identification of valuable candidate genes, and marker-assisted breeding (MAB) programs. Next generation sequencing (NGS) technology provides opportunities for genome-assisted breeding (GAB) through genomic selection (GS) and genome-wide association studies (GAWS) for crop improvement. Clustered, regularly interspaced, short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) genome editing (GE) system provides new opportunities for millet improvement. In this review, we discuss the details on the WGS available for millets and highlight the importance of utilizing such resources in the post-genomic era for millet improvement. We also draw inroads on the utilization of various approaches such as GS, GWAS, functional genomics, gene validation and GE for millet improvement. This review might be helpful for understanding the developments in the post-genomic era of millet improvement.

Salt tolerance mechanisms in the Lycopersicon clade and their trade-offs

Salt stress impairs growth and yield in tomato, which is mostly cultivated in arid and semi-arid areas of the world. A number of wild tomato relatives (Solanum pimpinellifolium, S. pennellii, S. cheesmaniae and S. peruvianum) are endemic to arid coastal areas and able to withstand higher concentration of soil salt concentrations, making them a good genetic resource for breeding efforts aimed at improving salt tolerance and overall crop improvement. However, the complexity of salt stress response makes it difficult to introgress tolerance traits from wild relatives that could effectively increase tomato productivity under high soil salt concentrations. Under commercial production, biomass accumulation is key for high fruit yields, and salt tolerance management strategies should aim to maintain a favourable plant water and nutrient status. In this review, we first compare the effects of salt stress on the physiology of the domesticated tomato and its wild relatives. We then discuss physiological and energetic trade-offs for the different salt tolerance mechanisms found within the Lycopersicon clade, with a focus on the importance of root traits to sustain crop productivity.

Harnessing tissue-specific genome editing in plants through CRISPR/Cas system: current state and future prospects

In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement. CRISPR/Cas is a powerful genome-editing tool with a wide range of applications for the genetic improvement of crops. However, the constitutive genome editing of vital genes is often associated with pleiotropic effects on other genes, needless metabolic burden, or interference in the cellular machinery. Tissue-specific genome editing (TSGE), on the other hand, enables researchers to study those genes in specific cells, tissues, or organs without disturbing neighboring groups of cells. Until recently, there was only limited proof of the TSGE concept, where the CRISPR-TSKO tool was successfully used in Arabidopsis, tomato, and cotton, laying a solid foundation for crop improvement. In this review, we have laid out valuable insights into the concept and application of TSGE on relatively unexplored areas such as grain trait improvement under favorable or unfavorable conditions. We also enlisted some of the prominent tissue-specific promoters and described the procedure of their isolation with several TSGE promoter expression systems in detail. Moreover, we highlighted potential negative regulatory genes that could be targeted through TSGE using tissue-specific promoters. In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement.

Promoter profiling of Arabidopsis amino acid transporters: clues for improving crops

The review describes the importance of amino acid transporters in plant growth, development, stress tolerance, and productivity. The promoter analysis provides valuable insights into their functionality leading to agricultural benefits. Arabidopsis thaliana genome is speculated to possess more than 100 amino acid transporter genes. This large number suggests the functional significance of amino acid transporters in plant growth and development. The current article summarizes the substrate specificity, cellular localization, tissue-specific expression, and expression of the amino acid transporter genes in response to environmental cues. However, till date functionality of a majority of amino acid transporter genes in plant development and stress tolerance is unexplored. Considering, that gene expression is mainly regulated by the regulatory motifs localized in their promoter regions at the transcriptional levels. The promoter regions ( ~ 1-kbp) of these amino acid transporter genes were analysed for the presence of cis-regulatory motifs responsive to developmental and external cues. This analysis can help predict the functionality of known and unexplored amino acid transporters in different tissues, organs, and various growth and development stages and responses to external stimuli. Furthermore, based on the promoter analysis and utilizing the microarray expression data we have attempted to identify plausible candidates (listed below) that might be targeted for agricultural benefits.