Haitham E. M. Zaki

The Citrus clementina (citrus) plant produces various phytohormones due to the significant involvement of the carotenoid cleavage oxygenase (CCO) gene family in its growth and development. CCO genes can be divided into two main categories: NCED (9-cis-epoxy carotenoid dioxygenase), responsible for abscisic acid (ABA) production, and CCD (carotenoid cleavage dioxygenase), involved in pigment and strigolactone formation. To better understand the roles and positions of CcCCO gene members in relation to these hormones, researchers analyzed the clementine genome. To identify their structural features, they employed phylogenetic analysis, protein interactions, localization, structure, miRNA targets, evolutionary analysis, and transcriptome studies. The study revealed the presence of 15 CcCCO genes, including 11 NCED and 4 CCD genes, scattered across various chromosomes, with the majority located in chloroplasts. Promoter sequencing analysis indicated the presence of different cis-regulatory elements that likely interacted with phytohormones, such as auxin and abscisic acid among others. Notably, two genes, CcNCED1 and CcNCED3, were significantly expressed among the CCO genes, and these were found to be expressed during stress and played a crucial role in enabling optimal plant development. Furthermore, a comprehensive genome-wide comparison of CCO genes in C. Clementine and Arabidopsis thaliana models was conducted to understand their functional characteristics. This research provides a solid foundation for further exploration of the unique attributes of the C. clementina plant, contributing to a deeper understanding of its growth and development processes.

Phytoplasma, a potentially hazardous pathogen associated with witches’ broom, is an economically harmful disease-producing bacteria that damages chilli cultivation. Phytoplasma-infected plants display various symptoms that indicate significant disruptions in normal plant physiology and behaviour. Diseases caused by phytoplasma are widespread and have a major economic impact on crop quality and yield. This work focuses on identifying and examining chilli microRNAs (miRNAs) as potential targets against the 16S rRNA and secA gene of “Candidatus Phytoplasma trifolii” (“Ca. P. trifolii”) through plant miRNA prediction algorithms. Mature chilli miRNAs (CA-miRNAs) were collected and used to hybridise the 16S rRNA and secA genes. A total of four common CA-miRNAs were picked according to genetic consensus. Three algorithms applied in the present study suggested that the physiologically relevant, top-ranked miR169b_2 has a possibly specific site at nucleotide position 1,006 for targeting the ‘Ca. P. trifolii’ 16S rRNA gene. The circos algorithm was then utilised to create the miRNA-mRNA regulatory network. The free energy between the miRNA:mRNA duplex was also computed, and the best value of −17.46 kcal/mol was obtained for CA-miR166c_2. Currently, there are no suitable commercial ‘Ca. P. trifolii’-resistant chilli crops. As a result, the expected biological data provide useful evidence for developing ‘Ca. P. trifolii’-resistant chilli plants.

Ensuring global food security amid mounting challenges, such as population growth, disease infestations, resource limitations, and climate change, is a pressing concern. Anticipated increases in food demand add further complexity to this critical issue. Plant pathogens, responsible for substantial crop losses (up to 41%) in major crops like wheat, rice, maize, soybean, and potato, exacerbate the situation. Timely disease detection is crucial, yet current practices often identify diseases at advanced stages, leading to severe infestations. To address this, remote sensing and Hyperspectral imaging (HSI) have emerged as robust and nondestructive techniques, exhibiting promising results in early disease identification. Integrating machine learning algorithms with image data sets enables precise spatial–temporal disease identification, facilitating timely detection, predictive modeling, and effective disease management without compromising fitness or climate adaptability. By harnessing these cutting-edge technologies and data-driven decision-making, growers can optimize input costs while achieving enhanced yields, making significant strides toward global food security in the face of climate change risks. This review will discuss some of the foundational concepts of remote sensing, several platforms used for remote sensing data collection, successful application of the approach, and its future perspective.

Agriculture plays a fundamental role in ensuring global food security, yet plant diseases remain a significant threat to crop production. Traditional methods to manage plant diseases have been extensively used, but they face significant drawbacks, such as environmental pollution, health risks and pathogen resistance. Similarly, biopesticides are eco-friendly, but are limited by their specificity and stability issues. This has led to the exploration of novel biotechnological approaches, such as the development of synthetic proteins, which aim to mitigate these drawbacks by offering more targeted and sustainable solutions. Similarly, recent advances in genome editing techniques—such as meganucleases (MegNs), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)—are precise approaches in disease management, but are limited by technical challenges and regulatory concerns. In this realm, nanotechnology has emerged as a promising frontier that offers novel solutions for plant disease management. This review examines the role of nanoparticles (NPs), including organic NPs, inorganic NPs, polymeric NPs and carbon NPs, in enhancing disease resistance and improving pesticide delivery, and gives an overview of the current state of nanotechnology in managing plant diseases, including its advantages, practical applications and obstacles that must be overcome to fully harness its potential. By understanding these aspects, we can better appreciate the transformative impact of nanotechnology on modern agriculture and can develop sustainable and effective strategies to mitigate plant diseases, ensuring enhanced agricultural productivity.

Targeted genome editing technologies are becoming the most important and widely used genetic tools in studies of phytopathology. The “clustered regularly interspaced short palindromic repeats (CRISPR)” and its accompanying proteins (Cas) have been first identified as a natural system associated with the adaptive immunity of prokaryotes that have been successfully used in various genome-editing techniques because of its flexibility, simplicity, and high efficiency in recent years. In this review, we have provided a general idea about different CRISPR/Cas systems and their uses in phytopathology. This review focuses on the benefits of knock-down technologies for targeting important genes involved in the susceptibility and gaining resistance against viral, bacterial, and fungal pathogens by targeting the negative regulators of defense pathways of hosts in crop plants via different CRISPR/Cas systems. Moreover, the possible strategies to employ CRISPR/Cas system for improving pathogen resistance in plants and studying plant–pathogen interactions have been discussed.

Rice bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is responsible for a significant reduction in rice production. Due to the small impact on the environment, biogenic nanomaterials are regarded as a new type of antibacterial agent. In this research, three colloids of silver nanoparticles (AgNPs) were synthesized with different biological materials such as Arctium lappa fruit, Solanum melongena leaves, and Taraxacum mongolicum leaves, and called Al-AgNPs, Sm-AgNPs and Tm-AgNPs, respectively. The appearance of brown colloids and the UV-Visible spectroscopy analysis proved the successful synthesis of the three colloids of AgNPs. Moreover, FTIR and XRD analysis revealed the formation of AgNPs structure. The SEM and TEM analysis indicated that the average diameters of the three synthesized spherical AgNPs were 20.18 nm, 21.00 nm, and 40.08 nm, respectively. The three botanical AgNPs had the strongest bacteriostatic against Xoo strain C2 at 20 μg/mL with the inhibition zone of 16.5 mm, 14.5 mm, and 12.4 mm, while bacterial numbers in a liquid broth (measured by OD₆₀₀) decreased by 72.10%, 68.19%, and 65.60%, respectively. Results showed that the three AgNPs could inhibit biofilm formation and swarming motility of Xoo. The ultrastructural observation showed that Al-AgNPs adhered to the surface of bacteria and broke the bacteria. Overall, the three synthetic AgNPs could be used to inhibit the pathogen Xoo of rice bacterial leaf blight.

Bacteria from the genus Pantoea have been reported to be widely distributed in rice paddy environments with contradictory roles. Some strains promoted rice growth and protected rice from pathogen infection or abiotic stress, but other strain exhibited virulence to rice, even causing severe rice disease. In order to effectively utilize Pantoea in rice production, this paper analyzed the mechanisms underlying beneficial and harmful effects of Pantoea on rice growth. The beneficial effect of Pantoea on rice plants includes growth promotion, abiotic alleviation and disease inhibition. The growth promotion may be mainly attributed to nitrogen-fixation, phosphate solubilization, plant physiological change, the biosynthesis of siderophores, exopolysaccharides, 1-aminocyclopropane-1-carboxylic acid deaminase and phytohormones, including cytokinin, indole-3-acetic acid (IAA), auxins, abscisic acid and gibberellic acid, while the disease inhibition may be mainly due to the induced resistance, nutrient and spatial competition, as well as the production of a variety of antibiotics. The pathogenic mechanism of Pantoea can be mainly attributed to bacterial motility, production of phytohormones such as IAA, quorum sensing-related signal molecules and a series of cell wall-degrading enzymes, while the pathogenicity-related genes of Pantoea include genes encoding plasmids, such as the pPATH plasmid, the hypersensitive response and pathogenicity system, as well as various types of secretion systems, such as T3SS and T6SS. In addition, the existing scientific problems in this field were discussed and future research prospects were proposed.

Cowpea, in addition to being a food and feed crop, plays a key role in sustainable farming. The present study’s goal is to develop new high-yielding cowpea varieties. A Field experiment was carried out across 3 summer seasons and the breeding program included 28 distinct cowpea varieties, out of which five potential parents were selected for this investigation. Local cultivars, i.e., Cream 7 ‘Cr7’, Dokki 331 ‘D331’, Commercial 1 ‘Com1’, and introduced cultivars, i.e., Colossus ‘Col’ and Asian Introduction ‘AI’ were utilized to produce six crosses in two generations apart; F₁ and F₂: Col x AI, Col x Com1, Cr7 x AI, Cr7 x Com1, D331 x AI, and D331 x Com1. ‘AI’ and ‘Com1’ were superior in pod length, pod diameter, number of seeds/pod and seeds weight/pod, whereas ‘Col’, ‘Cr7’ and ‘D331’ were superior in seeds yield/plant, number of pods/plant and the least number of aborted ovules/pod. The genotypes/crosses showed greater genotypic variance (GV) than phenotypic variance (PV) for number of pods/plant, pod length, number of seeds/pod, number of aborted ovules/pod, fresh pod weight, seeds weight/pod, and seeds yield/plant. All studied variables showed high heritability (H%) in genotypes/crosses, despite the exception of seeds weight/pod, which ranged from 29.14 in ‘D331’ to 83.7 in F₂ of Col x Com1. F₂ plants and their parents’ genotypes showed greater H%. Cr7 x AI developed the most H%, 99.04% for number of pods/plant. D331 x Com1 and Cr7 x AI exhibited moderate H% for fresh pod weight in F₁, but all other crosses had high H%. F₁ and F₂ crosses yielded moderate to high GCV and PCV for number of seeds/pod. Variations in parental genotypes and crossings reflect genetic diversity and the possibility of selection. Crossing with ‘AI,’ and ‘Com1’ genotypes enhanced the performance of the other varieties, ‘Col’, ‘D331’ and ‘Cr7’. Cr7 x Com1 and D331 x AI were selected as the most promising crosses for cowpea breeding programs.

Plants grow together with microbes that have both negative and positive impacts on the host, while prokaryotes are in turn also hosts for viruses, co-evolving together in a complex interrelationship. Most research focuses on the interaction of either bacterial pathogens interacting with the plant host, or the impact on viruses on their pathogenic bacterial hosts. Few studies have investigated the co-evolution of bacterial pathogens with their host plants as well as with their bacterial viruses. In this work, we aimed to identify the genes that were associated with both phage sensitivity and host pathogenicity of the bacterium Xanthomonas oryzae pv. oryzae (Xoo), which is the most important bacterial rice pathogen. Using the Tn5 transposon mutation technology, we created a library of Xoo strain C2 comprising 4524 mutants, which were subsequently tested for phage infectability. The phage infection tests showed that less than 1% of the mutants (n = 36) were resistant to phage infection, which was attributed to the Tn5 insertion in 19 genes. Interestingly, three out of 19 genes that conveyed resistance to the phage resulted in reduced pathogenicity to rice seedlings compared to the wild type. We identified three genes involved in both phage infection and bacterial virulence, which were studied by knockout mutants and complementation experiments. All of the three knockout mutants were resistant to infection by phage X2, while the complemented strains restored the susceptibility to the bacterial virus. Surprisingly, the genes are also essential for pathogenicity, which we confirmed by single knockout mutants corresponding to the Tn5 mutants. All three genes are involved in lipopolysaccharide synthesis, thus changing the cell envelope surface molecule composition. Our work shows a possible balance in terms of the connection between bacterial virulence and phage resistance, supporting the deployment of phages for the biocontrol of plant pathogens.

Abiotic stresses, such as heavy metals (HMs), drought, salinity and water logging, are the foremost limiting factors that adversely affect the plant growth and crop productivity worldwide. The plants respond to such stresses by activating a series of intricate mechanisms that subsequently alter the morpho-physiological and biochemical processes. Over the past few decades, abiotic stresses in plants have been managed through marker-assisted breeding, conventional breeding, and genetic engineering approaches. With technological advancement, efficient strategies are required to cope with the harmful effects of abiotic environmental constraints to develop sustainable agriculture systems of crop production. Recently, nanotechnology has emerged as an attractive area of study with potential applications in the agricultural science, including mitigating the impacts of climate change, increasing nutrient utilization efficiency and abiotic stress management. Nanoparticles (NPs), as nanofertilizers, have gained significant attention due to their high surface area to volume ratio, eco-friendly nature, low cost, unique physicochemical properties, and improved plant productivity. Several studies have revealed the potential role of NPs in abiotic stress management. This review aims to emphasize the role of NPs in managing abiotic stresses and growth promotion to develop a cost-effective and environment friendly strategy for the future agricultural sustainability.