Novel Plant Breeding Techniques Shake Hands with Cereals to Increase Production

Breakthrough in CRISPR/Cas system: Current and future directions and challenges

Targeted genome editing (GE) technology has brought a significant revolution in fictional genomic research and given hope to plant scientists to develop desirable varieties. This technology involves inducing site-specific DNA perturbations that can be repaired through DNA repair pathways. GE products currently include CRISPR-associated nuclease DNA breaks, prime editors generated DNA flaps, single nucleotide-modifications, transposases, and recombinases. The discovery of double-strand breaks, site-specific nucleases (SSNs), and repair mechanisms paved the way for targeted GE, and the first-generation GE tools, ZFNs and TALENs, were successfully utilized in plant GE. However, CRISPR-Cas has now become the preferred tool for GE due to its speed, reliability, and cost-effectiveness. Plant functional genomics has benefited significantly from the widespread use of CRISPR technology for advancements and developments. This review highlights the progress made in CRISPR technology, including multiplex editing, base editing (BE), and prime editing (PE), as well as the challenges and potential delivery mechanisms.

Overview and Management of the Most Common Eukaryotic Diseases of Flax (Linum usitatissimum)

Flax is an important crop cultivated for its seeds and fibers. It is widely grown in temperate regions, with an increase in cultivation areas for seed production (linseed) in the past 50 years and for fiber production (fiber flax) in the last decade. Among fiber-producing crops, fiber flax is the most valuable species. Linseed is the highest omega-3 oleaginous crop, and its consumption provides several benefits for animal and human health. However, flax production is impacted by various abiotic and biotic factors that affect yield and quality. Among biotic factors, eukaryotic diseases pose a significant threat to both seed production and fiber quality, which highlights the economic importance of controlling these diseases. This review focuses on the major eukaryotic diseases that affect flax in the field, describing the pathogens, their transmission modes and the associated plant symptoms. Moreover, this article aims to identify the challenges in disease management and provide future perspectives to overcome these biotic stresses in flax cultivation. By emphasizing the key diseases and their management, this review can aid in promoting sustainable and profitable flax production.

Genomic Dynamics and Functional Insights under Salt Stress in Gossypium hirsutum L

The changing climate is intensifying salt stress globally. Salt stress is a menace to cotton crop quality and yield. The seedling, germination, and emergence phases are more prone to the effects of salt stress than other stages. Higher levels of salt can lead to delayed flowering, a reduced number of fruiting positions, shedding of fruits, decreased boll weight, and yellowing of fiber, all of which have an adverse effect on the yield and quality of the seed cotton. However, sensitivity toward salt stress is dependent on the salt type, cotton growth phase, and genotype. As the threat of salt stress continues to grow, it is crucial to gain a comprehensive understanding of the mechanisms underlying salt tolerance in plants and to identify potential avenues for enhancing the salt tolerance of cotton. The emergence of marker-assisted selection, in conjunction with next-generation sequencing technologies, has streamlined cotton breeding efforts. This review begins by providing an overview of the causes of salt stress in cotton, as well as the underlying theory of salt tolerance. Subsequently, it summarizes the breeding methods that utilize marker-assisted selection, genomic selection, and techniques for identifying elite salt-tolerant markers in wild species or mutated materials. Finally, novel cotton breeding possibilities based on the approaches stated above are presented and debated.

Mechanisms of salinity tolerance and their possible application in the breeding of vegetables

BACKGROUND

In dry and semi-arid areas, salinity is the most serious hazard to agriculture, which can affect plant growth and development adversely. Over-accumulation of Na⁺ in plant organs can cause an osmotic effect and an imbalance in nutrient uptake. However, its harmful impact can vary depending on genotype, period of exposure to stress, plant development stage, and concentration and content of salt. To overcome the unfavorable effect of salinity, plants have developed two kinds of tolerance strategies based on either minimizing the entrance of salts by the roots or administering their concentration and diffusion.

RESULTS

Having sufficient knowledge of Na⁺ accumulation mechanisms and an understanding of the function of genes involved in transport activity will present a new option to enhance the salinity tolerance of vegetables related to food security in arid regions. Considerable improvements in tolerance mechanisms can be employed for breeding vegetables with boosted yield performance under salt stress. A conventional breeding method demands exhaustive research work in crops, while new techniques of molecular breeding, such as cutting-edge molecular tools and CRISPR technology are now available in economically important vegetables and give a fair chance for the development of genetically modified organisms.

CONCLUSIONS

Therefore, this review highlights the molecular mechanisms of salinity tolerance, various molecular methods of breeding, and many sources of genetic variation for inducing tolerance to salinity stress.

Applications and Prospects of CRISPR/Cas9-Mediated Base Editing in Plant Breeding

The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 system (Cas9) has been used at length to optimize multiple aspects of germplasm resources. However, large-scale genomic research has indicated that novel variations in crop plants are attributed to single-nucleotide polymorphisms (SNPs). Therefore, substituting single bases into a plant genome may produce desirable traits. Gene editing by CRISPR/Cas9 techniques frequently results in insertions-deletions (indels). Base editing allows precise single-nucleotide changes in the genome in the absence of double-strand breaks (DSBs) and donor repair templates (DRTs). Therefore, BEs have provided a new way of thinking about genome editing, and base editing techniques are currently being utilized to edit the genomes of many different organisms. As traditional breeding techniques and modern molecular breeding technologies complement each other, various genome editing technologies have emerged. How to realize the greater potential of BE applications is the question we need to consider. Here, we explain various base editings such as CBEs, ABEs, and CGBEs. In addition, the latest applications of base editing technologies in agriculture are summarized, including crop yield, quality, disease, and herbicide resistance. Finally, the challenges and future prospects of base editing technologies are presented. The aim is to provide a comprehensive overview of the application of BE in crop breeding to further improve BE and make the most of its value.

A CRISPR way for accelerating cereal crop improvement: Progress and challenges

Humans rely heavily on cereal grains as a key source of nutrients, hence regular improvement of cereal crops is essential for ensuring food security. The current food crisis at the global level is due to the rising population and harsh climatic conditions which prompts scientists to develop smart resilient cereal crops to attain food security. Cereal crop improvement in the past generally depended on imprecise methods like random mutagenesis and conventional genetic recombination which results in high off targeting risks. In this context, we have witnessed the application of targeted mutagenesis using versatile CRISPR-Cas systems for cereal crop improvement in sustainable agriculture. Accelerated crop improvement using molecular breeding methods based on CRISPR-Cas genome editing (GE) is an unprecedented tool for plant biotechnology and agriculture. The last decade has shown the fidelity, accuracy, low levels of off-target effects, and the high efficacy of CRISPR technology to induce targeted mutagenesis for the improvement of cereal crops such as wheat, rice, maize, barley, and millets. Since the genomic databases of these cereal crops are available, several modifications using GE technologies have been performed to attain desirable results. This review provides a brief overview of GE technologies and includes an elaborate account of the mechanisms and applications of CRISPR-Cas editing systems to induce targeted mutagenesis in cereal crops for improving the desired traits. Further, we describe recent developments in CRISPR-Cas-based targeted mutagenesis through base editing and prime editing to develop resilient cereal crop plants, possibly providing new dimensions in the field of cereal crop genome editing.

Application of CRISPR/Cas system in cereal improvement for biotic and abiotic stress tolerance

Application of the recently developed CRISPR/Cas tools might help enhance cereals' growth and yield under biotic and abiotic stresses. Cereals are the most important food crops for human life and an essential source of nutrients for people in developed and developing countries. The growth and yield of all major cereals are affected by both biotic and abiotic stresses. To date, molecular breeding and functional genomic studies have contributed to the understanding and improving cereals' growth and yield under biotic and abiotic stresses. Clustered, regularly inter-spaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been predicted to play a major role in precision plant breeding and developing non-transgenic cereals that can tolerate adverse effects of climate change. Variants of next-generation CRISPR/Cas tools, such as prime editor, base editor, CRISPR activator and repressor, chromatin imager, Cas12a, and Cas12b, are currently used in various fields, including plant science. However, few studies have been reported on applying the CRISPR/Cas system to understand the mechanism of biotic and abiotic stress tolerance in cereals. Rice is the only plant used frequently for such studies. Genes responsible for biotic and abiotic stress tolerance have not yet been studied by CRISPR/Cas system in other major cereals (sorghum, barley, maize and small millets). Examining the role of genes that respond to biotic and abiotic stresses using the CRISPR/Cas system may help enhance cereals' growth and yield under biotic and abiotic stresses. It will help to develop new and improved cultivars with biotic- and abiotic-tolerant traits for better yields to strengthen food security. This review provides information for cereal researchers on the current status of the CRISPR/Cas system for improving biotic and abiotic stress tolerance in cereals.

Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response

DUF966 genes are widely found in monocotyledons, dicotyledons, mosses, and other species. Current evidence strongly suggests that they are involved in growth regulation and stress tolerance in crops. However, their functions in cucumbers remain unexplored. Here, cucumber CsDUF966 was systemically identified and characterized using bioinformatics. Eight CsDUF966 genes were identified in the cucumber genome. These were phylogenetically separated into three groups. All CsDUF966 proteins were hydrophilic and localized to the nucleus. Moreover, three acidic and five basic proteins were identified. Evolutionary analysis of DUF966 between cucumber and 33 other Cucurbitaceae species/cultivars revealed that most CsDUF966 genes were conserved, whereas CsDUF966_4.c and CsDUF966_7.c were positively selected among the five cucumber cultivars. Expression profiling analysis showed that CsDUF966 had variable expression patterns, and that miRNA164, miRNA166, and Csa-novel-35 were involved in the post-transcriptional regulation of CsDUF966_4.c and CsDUF966_7.c. The expression of CsDUF966_4.c and CsDUF966_7.c, which were under strong neofunctionalization selection, was strictly regulated in fruit and tissues, including seeds, pericarps, peels, and spines, suggesting that these genes are fruit growth regulators and were strongly selected during the cucumber breeding program. In conclusion, the results reveal the roles of CsDUF966s in regulating cucumber fruit development and lay the foundation for further functional studies.

Cleome gynandra: A wonder climate-smart plant for nutritional security for millions in semi-arid areas

Spider plant (Cleome gynandra) is predominantly used as a traditional leafy vegetable throughout Africa and is considered a rich natural source of essential nutrients such as vitamins, minerals and proteins. With the increase in malnutrition, diet related non-communicable diseases and poverty across the continent of Africa, the spider plant is a bona fide alternative healthy food crop to alleviate these challenges. Spider plant is an erect annual herb that could grow up to 150 cm tall, strongly branched, with a long taproot and few secondary roots. It is commonly consumed in resource-poor communities especially during times of major food scarcity. It is a drought-tolerant and resilient annual vegetable crop capable of growing well in a wide range of climatic and edaphic conditions. Despite the potential benefits and wide adaptability, progressive attempts towards the development of C. gynandra as a crop have been impeded by issues like low investment in research and development resulting in poor seed quality, relatively low yields and susceptibility to pests and diseases. In this paper, we reviewed the research that has been done regarding its morphology, growing conditions, production and utilisation (i.e., nutrition). The current review highlighted the status of the science in advancing the domestication of C. gynandra as a potential power crop for several African countries. The review concluded that with the advancement of modern biotechnology techniques and genome sequencing, there is a compelling case for investment and development in C. gynandra as a candidate for managing micronutrient deficiencies during the post-pandemic era. Finally, the existing knowledge gaps (e.g., breeding) that necessitate explorations were identified and recommendations that could enhance its development and potential commercialisation were made.

Ribonomics Approaches to Identify RBPome in Plants and Other Eukaryotes: Current Progress and Future Prospects

RNA-binding proteins (RBPs) form complex interactions with RNA to regulate the cell’s activities including cell development and disease resistance. RNA-binding proteome (RBPome) aims to profile and characterize the RNAs and proteins that interact with each other to carry out biological functions. Generally, RNA-centric and protein-centric ribonomic approaches have been successfully developed to profile RBPome in different organisms including plants and animals. Further, more and more novel methods that were firstly devised and applied in mammalians have shown great potential to unravel RBPome in plants such as RNA-interactome capture (RIC) and orthogonal organic phase separation (OOPS). Despise the development of various robust and state-of-the-art ribonomics techniques, genome-wide RBP identifications and characterizations in plants are relatively fewer than those in other eukaryotes, indicating that ribonomics techniques have great opportunities in unraveling and characterizing the RNA–protein interactions in plant species. Here, we review all the available approaches for analyzing RBPs in living organisms. Additionally, we summarize the transcriptome-wide approaches to characterize both the coding and non-coding RBPs in plants and the promising use of RBPome for booming agriculture.