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Amino acid transporters (AATs) play a crucial role in facilitating the movement of amino acids across cellular membranes, which is vital for the growth and development of plants. Amino acid permease (AAP), which belongs to the AAT family, has been the subject of extensive functional research in plants. Although its importance is recognized, a comprehensive grasp of this family’s dynamics in indica rice remains lacking. In this investigation, a total of 27 AAP genes were identified in the genome of indica rice. Further, the phylogenetic analysis unveiled that the 69 AAP genes from both the model species and other plant species could be classified into 16 distinct subfamilies. The analysis of chromosomal mapping revealed an uneven distribution of the 27 OsAAP genes across the 12 rice chromosomes. Notably, the OsAAP family displayed a total of 10 duplicated gene pairs, along with the identification of numerous conserved motifs. The examination of cis-elements within OsAAP genes unveiled that their promoters contain cis-elements related to phytohormones, plant growth and development, as well as stress responses. Additionally, transcriptome profiling demonstrated that a substantial portion of these genes exhibited responsiveness to various hormones, with their activation spanning multiple tissues and developmental stages in rice. The study identified miRNAs with a specific affinity for OsAAP genes. Out of the 27 OsAAP genes investigated, seventeen were discovered to be targeted by a total of forty-three miRNAs. Furthermore, the aus allele of OsAAP3 that we named OsAAP17 was validated for its effect on productive tillers and yield, and seventeen genetic variants of OsAAP17 were found to be associated with a culm number in indica rice. In addition, indica rice varieties were monomorphic, while aus genotypes displayed polymorphism for OsAAP17 gene-specific in/dels. Moreover, in Season II (rabi season), it was found that the aus allele of OsAAP17 increased the number of productive tillers and the single plant yield by 22.55% and 9.67%, respectively, in a recombinant inbred population created by crossing N22 and JR 201. Remarkably, this enhancement was more pronounced during the dry cultivation season, highlighting the influence of environmental factors in the regulation of tiller numbers mediated by OsAAP17. The discoveries presented here lay a strong foundation for further exploration into the roles of OsAAP family genes across a range of developmental processes. Therefore, the identified allelic variations in the utilization of OsAAP17 has the potential to enhance rice crop production via molecular breeding in the changing climate scenario.

The cytochrome P450 (CYP450) gene family plays a critical role in plant growth and developmental processes, nutrition, and detoxification of xenobiotics in plants. In the present research, a comprehensive set of 105 OsCYP71 family genes was pinpointed within the genome of indica rice. These genes were categorized into twelve distinct subfamilies, where members within the same subgroup exhibited comparable gene structures and conserved motifs. In addition, 105 OsCYP71 genes were distributed across 11 chromosomes, and 36 pairs of OsCYP71 involved in gene duplication events. Within the promoter region of OsCYP71, there exists an extensive array of cis-elements that are associated with light responsiveness, hormonal regulation, and stress-related signaling. Further, transcriptome profiling revealed that a majority of the genes exhibited responsiveness to hormones and were activated across diverse tissues and developmental stages in rice. The OsCYP71P6 gene is involved in insect resistance, senescence, and yield-related traits in rice. Hence, understanding the association between OsCYP71P6 genetic variants and yield-related traits in rice varieties could provide novel insights for rice improvement. Through the utilization of linear regression models, a total of eight promoters were identified, and a specific gene variant (Ser33Leu) within OsCYP71P6 was found to be linked to spikelet fertility. Additionally, different alleles of the OsCYP71P6 gene identified through in/dels polymorphism in 131 rice varieties were validated for their allelic effects on yield-related traits. Furthermore, the single-plant yield, spikelet number, panicle length, panicle weight, and unfilled grain per panicle for the OsCYP71P6-1 promoter insertion variant were found to contribute 20.19%, 13.65%, 5.637%, 8.79%, and 36.86% more than the deletion variant, respectively. These findings establish a robust groundwork for delving deeper into the functions of OsCYP71-family genes across a range of biological processes. Moreover, these findings provide evidence that allelic variation in the promoter and amino acid substitution of Ser33Leu in the OsCYP71P6 gene could potentially impact traits related to rice yield. Therefore, the identified promoter variants in the OsCYP71P6 gene could be harnessed to amplify rice yields.

Salt stress is a severe type of environmental stress. It adversely affects agricultural production worldwide. The overproduction of reactive oxygen species (ROS) is the most frequent phenomenon during salt stress. ROS are extremely reactive and, in high amounts, noxious, leading to destructive processes and causing cellular damage. However, at lower concentrations, ROS function as secondary messengers, playing a critical role as signaling molecules, ensuring regulation of growth and adjustment to multifactorial stresses. Plants contain several enzymatic and non-enzymatic antioxidants that can detoxify ROS. The production of ROS and their scavenging are important aspects of the plant’s normal response to adverse conditions. Recently, this field has attracted immense attention from plant scientists; however, ROS-induced signaling pathways during salt stress remain largely unknown. In this review, we will discuss the critical role of different antioxidants in salt stress tolerance. We also summarize the recent advances on the detrimental effects of ROS, on the antioxidant machinery scavenging ROS under salt stress, and on the crosstalk between ROS and other various signaling molecules, including nitric oxide, hydrogen sulfide, calcium, and phytohormones. Moreover, the utilization of “-omic” approaches to improve the ROS-regulating antioxidant system during the adaptation process to salt stress is also described.

Global warming is a serious threat to food security and severely affects plant growth, developmental processes, and, eventually, crop productivity. Respiratory metabolism plays a critical role in the adaptation of diverse stress in plants. Aconitase (ACO) is the main enzyme, which catalyzes the revocable isomerization of citrate to isocitrate in the Krebs cycle. The function of ACO gene family members has been extensively studied in model plants, for instance Arabidopsis. However, their role in plant developmental processes and various stress conditions largely remained unknown in other plant species. Thus, we identified 15 ACO genes in wheat to elucidate their function in plant developmental processes and different stress environments. The phylogenetic tree revealed that TaACO genes were classified into six groups. Further, gene structure analysis of TaACOs has shown a distinctive evolutionary path. Synteny analysis showed the 84 orthologous gene pairs in Brachypodium distachyon, Aegilops tauschii, Triticum dicoccoides, Oryza sativa, and Arabidopsis thaliana. Furthermore, Ka/Ks ratio revealed that most TaACO genes experienced strong purifying selection during evolution. Numerous cis-acting regulatory elements were detected in the TaACO promoters, which play a crucial role in plant development processes, phytohormone signaling, and are related to defense and stress. To understand the function of TaACO genes, the expression profiling of TaACO genes were investigated in different tissues, developmental stages, and stress conditions. The transcript per million values of TaACOs genes were retrieved from the Wheat Expression Browser Database. We noticed the differential expression of the TaACO genes in different tissues and various stress conditions. Moreover, gene ontology analysis has shown enrichment in the tricarboxylic acid metabolic process (GO:0072350), citrate metabolic process (GO:0006101), isocitrate metabolic process GO:0006102, carbohydrate metabolic (GO:0005975), and glyoxylate metabolic process (GO:0046487). Therefore, this study provided valuable insight into the ACO gene family in wheat and contributed to the further functional characterization of TaACO during different plant development processes and various stress conditions.

Proline-rich extensin-like receptor kinases (PERKs) are a class of receptor kinases implicated in multiple cellular processes in plants. However, there is a lack of information on the PERK gene family in wheat. Therefore, we identified 37 PERK genes in wheat to understand their role in various developmental processes and stress conditions. Phylogenetic analysis of PERK genes from Arabidopsis thaliana, Oryza sativa, Glycine max, and T. aestivum grouped them into eight well-defined classes. Furthermore, synteny analysis revealed 275 orthologous gene pairs in B. distachyon, Ae. tauschii, T. dicoccoides, O. sativa and A. thaliana. Ka/Ks values showed that most TaPERK genes, except TaPERK1, TaPERK2, TaPERK17, and TaPERK26, underwent strong purifying selection during evolutionary processes. Several cis-acting regulatory elements, essential for plant growth and development and the response to light, phytohormones, and diverse biotic and abiotic stresses, were predicted in the promoter regions of TaPERK genes. In addition, the expression profile of the TaPERK gene family revealed differential expression of TaPERK genes in various tissues and developmental stages. Furthermore, TaPERK gene expression was induced by various biotic and abiotic stresses. The RT-qPCR analysis also revealed similar results with slight variation. Therefore, this study’s outcome provides valuable information for elucidating the precise functions of TaPERK in developmental processes and diverse stress conditions in wheat.

The world has faced the challenges of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for the last two years, first diagnosed at the end of 2019 in Wuhan and widely distributed worldwide. As a result, the WHO has proclaimed the illness brought on by this virus to be a global pandemic. To combat COVID-19, researcher communities continuously develop and implement rapid diagnoses, safe and effective vaccinations and other alternative therapeutic procedures. However, synthetic drug-related side effects and high costs have piqued scientists’ interest in natural product-based therapies and medicines. In this regard, antiviral substances derived from natural resources and some medicines have seen a boom in popularity. For instance, algae are a rich source of compounds such as lectins and sulfated polysaccharides, which have potent antiviral and immunity-boosting properties. Moreover, Algae-derived compounds or metabolites can be used as antibodies and vaccine raw materials against COVID-19. Furthermore, some algal species can boost immunity, reduce viral activity in humans and be recommended for usage as a COVID-19 preventative measure. However, this field of study is still in its early stages of development. Therefore, this review addresses critical characteristics of algal metabolites, their antioxidant potential and therapeutic potential in COVID-19.

Tuberculosis (TB) is a recurrent and progressive disease, with high mortality rates worldwide. The drug-resistance phenomenon of Mycobacterium tuberculosis is a major obstruction of allelopathy treatment. An adverse side effect of allelopathic treatment is that it causes serious health complications. The search for suitable alternatives of conventional regimens is needed, i.e., by considering medicinal plant secondary metabolites to explore anti-TB drugs, targeting the action site of M. tuberculosis. Nowadays, plant-derived secondary metabolites are widely known for their beneficial uses, i.e., as antioxidants, antimicrobial agents, and in the treatment of a wide range of chronic human diseases (e.g., tuberculosis), and are known to “thwart” disease virulence. In this regard, in silico studies can reveal the inhibitory potential of plant-derived secondary metabolites against Mycobacterium at the very early stage of infection. Computational approaches based on different algorithms could play a significant role in screening plant metabolites against disease virulence of tuberculosis for drug designing.

In the current scenario of changing climatic conditions and the rising global population, there is an urgent need to explore novel, efficient, and economical natural products for the benefit of humankind. Biosurfactants are one of the latest explored microbial synthesized biomolecules that have been used in numerous fields, including agriculture, pharmaceuticals, cosmetics, food processing, and environment-cleaning industries, as a source of raw materials, for the lubrication, wetting, foaming, emulsions formulations, and as stabilizing dispersions. The amphiphilic nature of biosurfactants have shown to be a great advantage, distributing themselves into two immiscible surfaces by reducing the interfacial surface tension and increasing the solubility of hydrophobic compounds. Furthermore, their eco-friendly nature, low or even no toxic nature, durability at higher temperatures, and ability to withstand a wide range of pH fluctuations make microbial surfactants preferable compared to their chemical counterparts. Additionally, biosurfactants can obviate the oxidation flow by eliciting antioxidant properties, antimicrobial and anticancer activities, and drug delivery systems, further broadening their applicability in the food and pharmaceutical industries. Nowadays, biosurfactants have been broadly utilized to improve the soil quality by improving the concentration of trace elements and have either been mixed with pesticides or applied singly on the plant surfaces for plant disease management. In the present review, we summarize the latest research on microbial synthesized biosurfactant compounds, the limiting factors of biosurfactant production, their application in improving soil quality and plant disease management, and their use as antioxidant or antimicrobial compounds in the pharmaceutical industries.

Many pathogenic viral pandemics have caused threats to global health; the COVID-19 pandemic is the latest. Its transmission is growing exponentially all around the globe, putting constraints on the health system worldwide. A novel coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causes this pandemic. Many candidate vaccines are available at this time for COVID-19, and there is a massive international race underway to procure as many vaccines as possible for each country. However, due to heavy global demand, there are strains in global vaccine production. The use of a plant biotechnology-based expression system for vaccine production also represents one part of this international effort, which is to develop plant-based heterologous expression systems, virus-like particles (VLPs)-vaccines, antiviral drugs, and a rapid supply of antigen-antibodies for detecting kits and plant origin bioactive compounds that boost the immunity and provide tolerance to fight against the virus infection. This review will look at the plant biotechnology platform that can provide the best fight against this global pandemic.

Genetic diversity analysis and cultivar identification were performed using a core set of single nucleotide polymorphisms (SNPs) in cucumber (Cucumis sativus L.). For the genetic diversity study, 280 cucumber accessions collected from four continents (Asia, Europe, America, and Africa) by the National Agrobiodiversity Center of the Rural Development Administration in South Korea and 20 Korean commercial F1 hybrids were genotyped using 151 Fluidigm SNP assay sets. The heterozygosity of the SNP loci per accession ranged from 4.76 to 82.76%, with an average of 32.1%. Population genetics analysis was performed using population structure analysis and hierarchical clustering (HC), which indicated that these accessions were classified mainly into four subpopulations or clusters according to their geographical origins. The subpopulations for Asian and European accessions were clearly distinguished from each other (FST value = 0.47), while the subpopulations for Korean F1 hybrids and Asian accessions were closely related (FST = 0.34). The highest differentiation was observed between American and European accessions (FST = 0.41). Nei’s genetic distance among the 280 accessions was 0.414 on average. In addition, 95 commercial F1 hybrids of three cultivar groups (Baekdadagi-, Gasi-, and Nakhap-types) were genotyped using 82 Fluidigm SNP assay sets for cultivar identification. These 82 SNPs differentiated all cultivars, except seven. The heterozygosity of the SNP loci per cultivar ranged from 12.20 to 69.14%, with an average of 34.2%. Principal component analysis and HC demonstrated that most cultivars were clustered based on their cultivar groups. The Baekdadagi- and Gasi-types were clearly distinguished, while the Nakhap-type was closely related to the Baekdadagi-type. Our results obtained using core Fluidigm SNP assay sets provide useful information for germplasm assessment and cultivar identification, which are essential for breeding and intellectual right protection in cucumber.