Catalase (CAT) Gene Family in Rapeseed (Brassica napus L.): Genome-Wide Analysis, Identification, and Expression Pattern in Response to Multiple Hormones and Abiotic Stress Conditions

Metal and metal oxide nanoparticles-induced reactive oxygen species: Phytotoxicity and detoxification mechanisms in plant cell

Nanotechnology is advancing rapidly in this century and the industrial use of nanoparticles for new applications in the modernization of different industries such as agriculture, electronic, food, energy, environment, healthcare and medicine is growing exponentially. Despite applications of several nanoparticles in different industries, they show harmful effects on biological systems, especially in plants. Various mechanisms for the toxic effects of nanoparticles have already been proposed; however, elevated levels of reactive oxygen species (ROS) molecules including radicals [(e.g., superoxide (O2•‒), peroxyl (HOO•), and hydroxyl (HO•) and non-radicals [(e.g., hydrogen peroxide (H2O2) and singlet oxygen (1O2) is more important. Excessive production/and accumulation of ROS in cells and subsequent induction of oxidative stress disrupts the normal functioning of physiological processes and cellular redox reactions. Some of the consequences of ROS overproduction include peroxidation of lipids, changes in protein structure, DNA strand breaks, mitochondrial damage, and cell death. Key enzymatic antioxidants with ROS scavenging ability comprised of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), peroxidase (POD), and glutathione reductase (GR), and non-enzymatic antioxidant systems including alpha-tocopherol, flavonoids, phenolic compounds, carotenoids, ascorbate, and glutathione play vital role in detoxification and maintaining plant health by balancing redox reactions and reducing the level of ROS. This review provides compelling evidence that phytotoxicity of nanoparticles, is mainly caused by overproduction of ROS after exposure. In addition, the present review also summarizes the intrinsic detoxification mechanisms in plants in response to nanoparticles accumulation within plant cells.

High Concentrations of Se Inhibited the Growth of Rice Seedlings

Selenium (Se) is crucial for both plants and humans, with plants acting as the main source for human Se intake. In plants, moderate Se enhances growth and increases stress resistance, whereas excessive Se leads to toxicity. The physiological mechanisms by which Se influences rice seedlings' growth are poorly understood and require additional research. In order to study the effects of selenium stress on rice seedlings, plant phenotype analysis, root scanning, metal ion content determination, physiological response index determination, hormone level determination, quantitative PCR (qPCR), and other methods were used. Our findings indicated that sodium selenite had dual effects on rice seedling growth under hydroponic conditions. At low concentrations, Se treatment promotes rice seedling growth by enhancing biomass, root length, and antioxidant capacity. Conversely, high concentrations of sodium selenite impair and damage rice, as evidenced by leaf yellowing, reduced chlorophyll content, decreased biomass, and stunted growth. Elevated Se levels also significantly affect antioxidase activities and the levels of proline, malondialdehyde, metal ions, and various phytohormones and selenium metabolism, ion transport, and antioxidant genes in rice. The adverse effects of high Se concentrations may directly disrupt protein synthesis or indirectly induce oxidative stress by altering the absorption and synthesis of other compounds. This study aims to elucidate the physiological responses of rice to Se toxicity stress and lay the groundwork for the development of Se-enriched rice varieties.

Osmolyte-producing microbial biostimulants regulate the growth of Arachis hypogaea L. under drought stress

Globally, drought stress poses a significant threat to crop productivity. Improving the drought tolerance of crops with microbial biostimulants is a sustainable strategy to meet a growing population's demands. This research aimed to elucidate microbial biostimulants' (Plant Growth Promoting Rhizobacteria) role in alleviating drought stress in oil-seed crops. In total, 15 bacterial isolates were selected for drought tolerance and screened for plant growth-promoting (PGP) attributes like phosphate solubilization and production of indole-3-acetic acid, siderophore, hydrogen cyanide, ammonia, and exopolysaccharide. This research describes two PGPR strains: Acinetobacter calcoaceticus AC06 and Bacillus amyloliquefaciens BA01. The present study demonstrated that these strains (AC06 and BA01) produced abundant osmolytes under osmotic stress, including proline (2.21 and 1.75 µg ml- 1), salicylic acid (18.59 and 14.21 µg ml- 1), trehalose (28.35 and 22.74 µg mg- 1 FW) and glycine betaine (11.35 and 7.74 mg g- 1) respectively. AC06 and BA01 strains were further evaluated for their multifunctional performance by inoculating in Arachis hypogaea L. (Groundnut) under mild and severe drought regimes (60 and 40% Field Capacity). Inoculation with microbial biostimulants displayed distinct osmotic-adjustment abilities of the groundnut, such as growth parameters, plant biomass, photosynthetic pigments, relative water content, proline, and soluble sugar in respective to control during drought. On the other hand, plant sensitivity indexes such as electrolyte leakage and malondialdehyde (MDA) contents were decreased as well as cooperatively conferred plant drought tolerance by induced alterations in stress indicators such as catalase (CAT), ascorbate peroxidase (APX), and superoxide dismutase (SOD). Thus, Acinetobacter sp. AC06 and Bacillus sp. BA01 can be considered as osmolyte producing microbial biostimulants to simultaneously induce osmotic tolerance and metabolic changes in groundnuts under drought stress.

Gibberellin Positively Regulates Tomato Resistance to Tomato Yellow Leaf Curl Virus (TYLCV)

Tomato yellow leaf curl virus (TYLCV) is a prominent viral pathogen that adversely affects tomato plants. Effective strategies for mitigating the impact of TYLCV include isolating tomato plants from the whitefly, which is the vector of the virus, and utilizing transgenic lines that are resistant to the virus. In our preliminary investigations, we observed that the use of growth retardants increased the rate of TYLCV infection and intensified the damage to the tomato plants, suggesting a potential involvement of gibberellic acid (GA) in the conferring of resistance to TYLCV. In this study, we employed an infectious clone of TYLCV to inoculate tomato plants, which resulted in leaf curling and growth inhibition. Remarkably, this inoculation also led to the accumulation of GA3 and several other phytohormones. Subsequent treatment with GA3 effectively alleviated the TYLCV-induced leaf curling and growth inhibition, reduced TYLCV abundance in the leaves, enhanced the activity of antioxidant enzymes, and lowered the reactive oxygen species (ROS) levels in the leaves. Conversely, the treatment with PP333 exacerbated TYLCV-induced leaf curling and growth suppression, increased TYLCV abundance, decreased antioxidant enzyme activity, and elevated ROS levels in the leaves. The analysis of the gene expression profiles revealed that GA3 up-regulated the genes associated with disease resistance, such as WRKYs, NACs, MYBs, Cyt P450s, and ERFs, while it down-regulated the DELLA protein, a key agent in GA signaling. In contrast, PP333 induced gene expression changes that were the opposite of those caused by the GA3 treatment. These findings suggest that GA plays an essential role in the tomato's defense response against TYLCV and acts as a positive regulator of ROS scavenging and the expression of resistance-related genes.

Cloning of CAT genes in Satsuma mandarin and their expression characteristics in response to environmental stress and arbuscular mycorrhizal fungi

KEY MESSAGE

CitCAT1 and CitCAT2 were cloned and highly expressed in mature leaves. High temperatures up-regulated CitCAT1 expression, while low temperatures and Diversispora versiformis up-regulated CitCAT2 expression, maintaining a low oxidative damage. Catalase (CAT), a tetrameric heme-containing enzyme, removes hydrogen peroxide (H2O2) to maintain low oxidative damage in plants exposed to environmental stress. This study aimed to clone CAT genes from Citrus sinensis cv. "Oita 4" and analyze their expression patterns in response to environmental stress, exogenous abscisic acid (ABA), and arbuscular mycorrhizal fungal inoculation. Two CAT genes, CitCAT1 (NCBI accession: PP067858) and CitCAT2 (NCBI accession: PP061394) were cloned, and the open reading frames of their proteins were 1479 bp and 1539 bp, respectively, each encoding 492 and 512 amino acids predicted to be localized in the peroxisome, with CitCAT1 being a stable hydrophilic protein and CitCAT2 being an unstable hydrophilic protein. The similarity of their amino acid sequences reached 83.24%, and the two genes were distantly related. Both genes were expressed in stems, leaves, flowers, and fruits, accompanied by the highest expression in mature leaves. In addition, CitCAT1 expression was mainly up-regulated by high temperatures (37 °C), exogenous ABA, and PEG stress within a short period of time, whereas CitCAT2 expression was up-regulated by exogenous ABA and low-temperature (4 °C) stress. Low temperatures (0 °C) for 12 h just up-regulated CitCAT2 expression in Diversispora versiformis-inoculated plants, and D. versiformis inoculation up-regulated CitCAT2 expression, along with lower hydrogen peroxide and malondialdehyde levels in mycorrhizal plants at low temperatures. It is concluded that CitCAT2 has an important role in resistance to low temperatures as well as mycorrhizal enhancement of host resistance to low temperatures.

A viral movement protein targets host catalases for 26S proteasome-mediated degradation to facilitate viral infection and aphid transmission in wheat

The infection of host plants by many different viruses causes reactive oxygen species (ROS) accumulation and yellowing symptoms, but the mechanisms through which plant viruses counteract ROS-mediated immunity to facilitate infection and symptom development have not been fully elucidated. Most plant viruses are transmitted by insect vectors in the field, but the molecular mechanisms underlying virus‒host-insect interactions are unclear. In this study, we investigated the interactions among wheat, barley yellow dwarf virus (BYDV), and its aphid vector and found that the BYDV movement protein (MP) interacts with both wheat catalases (CATs) and the 26S proteasome ubiquitin receptor non-ATPase regulatory subunit 2 homolog (PSMD2) to facilitate the 26S proteasome-mediated degradation of CATs, promoting viral infection, disease symptom development, and aphid transmission. Overexpression of the BYDV MP gene in wheat enhanced the degradation of CATs, which leading to increased accumulation of ROS and thereby enhanced viral infection. Interestingly, transgenic wheat lines overexpressing BYDV MP showed significantly reduced proliferation of wingless aphids and an increased number of winged aphids. Consistent with this observation, silencing of CAT genes also enhanced viral accumulation and reduced the proliferation of wingless aphids but increased the occurrence of winged aphids. In contrast, transgenic wheat plants overexpressing TaCAT1 exhibited the opposite changes and showed increases in grain size and weight upon infection with BYDV. Biochemical assays demonstrated that BYDV MP interacts with PSMD2 and promotes 26S proteasome-mediated degradation of TaCAT1 likely in a ubiquitination-independent manner. Collectively, our study reveals a molecular mechanism by which a plant virus manipulates the ROS production system of host plants to facilitate viral infection and transmission, shedding new light on the sophisticated interactions among viruses, host plants, and insect vectors.

Genome-Wide Investigation of Class III Peroxidase Genes in Brassica napus Reveals Their Responsiveness to Abiotic Stresses

Brassica napus (B. napus) is susceptible to multiple abiotic stresses that can affect plant growth and development, ultimately reducing crop yields. In the past, many genes that provide tolerance to abiotic stresses have been identified and characterized. Peroxidase (POD) proteins, members of the oxidoreductase enzyme family, play a critical role in protecting plants against abiotic stresses. This study demonstrated a comprehensive investigation of the POD gene family in B. napus. As a result, a total of 109 POD genes were identified across the 19 chromosomes and classified into five distinct subgroups. Further, 44 duplicate events were identified; of these, two gene pairs were tandem and 42 were segmental. Synteny analysis revealed that segmental duplication was more prominent than tandem duplication among POD genes. Expression pattern analysis based on the RNA-seq data of B. napus indicated that BnPOD genes were expressed differently in various tissues; most of them were expressed in roots rather than in other tissues. To validate these findings, we performed RT-qPCR analysis on ten genes; these genes showed various expression levels under abiotic stresses. Our findings not only furnish valuable insights into the evolutionary dynamics of the BnPOD gene family but also serve as a foundation for subsequent investigations into the functional roles of POD genes in B. napus.

Catalase (CAT) Gene Family in Oil Palm (Elaeis guineensis Jacq.): Genome-Wide Identification, Analysis, and Expression Profile in Response to Abiotic Stress

Catalases (CATs) play crucial roles in scavenging H2O2 from reactive oxygen species, controlling the growth and development of plants. So far, genome-wide identification and characterization of CAT genes in oil palm have not been reported. In the present study, five EgCAT genes were obtained through a genome-wide identification approach. Phylogenetic analysis divided them into two subfamilies, with closer genes sharing similar structures. Gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the EgCAT genes. Several cis-acting elements related to hormone, stress, and defense responses were identified in the promoter regions of EgCATs. Tissue-specific expression of EgCAT genes in five different tissues of oil palm was also revealed by heatmap analysis using the available transcriptome data. Stress-responsive expression analysis showed that five EgCAT genes were significantly expressed under cold, drought, and salinity stress conditions. Collectively, this study provided valuable information on the oil palm CAT gene family and the validated EgCAT genes can be used as potential candidates for improving abiotic stress tolerance in oil palm and other related crops.

Physiological Mechanism through Which Al Toxicity Inhibits Peanut Root Growth

Al (Aluminum) poisoning is a significant limitation to crop yield in acid soil. However, the physiological process involved in the peanut root response to Al poisoning has not been clarified yet and requires further research. In order to investigate the influence of Al toxicity stress on peanut roots, this study employed various methods, including root phenotype analysis, scanning of the root, measuring the physical response indices of the root, measurement of the hormone level in the root, and quantitative PCR (qPCR). This research aimed to explore the physiological mechanism underlying the reaction of peanut roots to Al toxicity. The findings revealed that Al poisoning inhibits the development of peanut roots, resulting in reduced biomass, length, surface area, and volume. Al also significantly affects antioxidant oxidase activity and proline and malondialdehyde contents in peanut roots. Furthermore, Al toxicity led to increased accumulations of Al and Fe in peanut roots, while the contents of zinc (Zn), cuprum (Cu), manganese (Mn), kalium (K), magnesium (Mg), and calcium (Ca) decreased. The hormone content and related gene expression in peanut roots also exhibited significant changes. High concentrations of Al trigger cellular defense mechanisms, resulting in differentially expressed antioxidase genes and enhanced activity of antioxidases to eliminate excessive ROS (reactive oxygen species). Additionally, the differential expression of hormone-related genes in a high-Al environment affects plant hormones, ultimately leading to various negative effects, for example, decreased biomass of roots and hindered root development. The purpose of this study was to explore the physiological response mechanism of peanut roots subjected to aluminum toxicity stress, and the findings of this research will provide a basis for cultivating Al-resistant peanut varieties.

Comprehensive Analysis of the Catalase (CAT) Gene Family and Expression Patterns in Rubber Tree (Hevea brasiliensis) under Various Abiotic Stresses and Multiple Hormone Treatments

Catalase (CAT) is one of the key enzymes involved in antioxidant defense systems and mainly scavenges H2O2 and plays a vital role in plant growth, development, and various adverse stresses. To date, a systematic study of the CAT gene family in rubber tree has not been reported. In this study, five HbCAT gene family members were identified from the rubber tree genome, and these were mainly clustered into two subfamilies. Gene structure and motif analysis showed that exon-intron and motif patterns were conserved across different plant species. Sequence analysis revealed that HbCAT proteins contain one active catalytic site, one heme-ligand signature sequence, three conserved amino acid residues (His, Tyr, and Asn), and one peroxisome-targeting signal 1 (PTS1) sequence. Fragment duplication is a selection pressure for the evolution of the HbCAT family based on Ka/Ks values. Analysis of cis-acting elements in the promoters indicated that HbCAT gene expression might be regulated by abscisic acid (ABA), salicylic acid (SA), and MYB transcription factors; furthermore, these genes might be involved in plant growth, development, and abiotic stress responses. A tissue-specific expression analysis showed that HbCATs gradually increased with leaf development and were highly expressed in mature leaves. Gene expression profiling exhibited the differential expression of the HbCATs under cold, heat, drought, and NaCl stresses. Our results provide comprehensive information about the HbCAT gene family, laying the foundation for further research on its function in rubber tree.

Genome-Wide Identification of Catalase Gene Family and the Function of SmCAT4 in Eggplant Response to Salt Stress

Salinity is an important abiotic stress, damaging plant tissues by causing a burst of reactive oxygen species (ROS). Catalase (CAT) enzyme coded by Catalase (CAT) genes are potent in reducing harmful ROS and hydrogen peroxide (H2O2) produced. Herein, we performed bioinformatics and functional characterization of four SmCAT genes, retrieved from the eggplant genome database. Evolutionary analysis CAT genes revealed that they are divided into subgroups I and II. The RT-qPCR analysis of SmCAT displayed a differential expression pattern in response to abiotic stresses. All the CAT proteins of eggplant were localized in the peroxisome, except for SmCAT4, which localized in the cytomembrane and nucleus. Silencing of SmCAT4 compromised the tolerance of eggplant to salt stress. Suppressed expression levels of salt stress defense related genes SmTAS14 and SmDHN1, as well as increase of H2O2 content and decrease of CAT enzyme activity was observed in the SmCAT4 silenced eggplants. Our data provided insightful knowledge of CAT gene family in eggplant. Positive regulation of eggplant response to salinity by SmCAT4 provides resource for future breeding programs.

Genome-Wide Investigation and Expression Analysis of the Catalase Gene Family in Oat Plants (Avena sativa L.)

Through the degradation of reactive oxygen species (ROS), different antioxidant enzymes, such as catalase (CAT), defend organisms against oxidative stress. These enzymes are crucial to numerous biological functions, like plant development and defense against several biotic and abiotic stresses. However, despite the major economic importance of Avena sativa around the globe, little is known about the CAT gene's structure and organization in this crop. Thus, a genome-wide investigation of the CAT gene family in oat plants has been carried out to characterize the potential roles of those genes under different stressors. Bioinformatic approaches were used in this study to predict the AvCAT gene's structure, secondary and tertiary protein structures, physicochemical properties, phylogenetic tree, and expression profiling under diverse developmental and biological conditions. A local Saudi oat variety (AlShinen) was used in this work. Here, ten AvCAT genes that belong to three groups (Groups I-III) were identified. All identified CATs harbor the two conserved domains (pfam00199 and pfam06628), a heme-binding domain, and a catalase activity motif. Moreover, identified AvCAT proteins were located in different compartments in the cell, such as the peroxisome, mitochondrion, and cytoplasm. By analyzing their promoters, different cis-elements were identified as being related to plant development, maturation, and response to different environmental stresses. Gene expression analysis revealed that three different AvCAT genes belonging to three different subgroups showed noticeable modifications in response to various stresses, such as mannitol, salt, and ABA. As far as we know, this is the first report describing the genome-wide analysis of the oat catalase gene family, and these data will help further study the roles of catalase genes during stress responses, leading to crop improvement.

Uncovering the Role of Hormones in Enhancing Antioxidant Defense Systems in Stressed Tomato (Solanum lycopersicum) Plants

Tomato is one of the most important fruits worldwide. It is widely consumed due to its sensory and nutritional attributes. However, like many other industrial crops, it is affected by biotic and abiotic stress factors, reducing its metabolic and physiological processes. Tomato plants possess different mechanisms of stress responses in which hormones have a pivotal role. They are responsible for a complex signaling network, where the antioxidant system (enzymatic and non-enzymatic antioxidants) is crucial for avoiding the excessive damage caused by stress factors. In this sense, it seems that hormones such as ethylene, auxins, brassinosteroids, and salicylic, jasmonic, abscisic, and gibberellic acids, play important roles in increasing antioxidant system and reducing oxidative damage caused by different stressors. Although several studies have been conducted on the stress factors, hormones, and primary metabolites of tomato plants, the effect of endogenous and/or exogenous hormones on the secondary metabolism is still poorly studied, which is paramount for tomato growing management and secondary metabolites production. Thus, this review offers an updated overview of both endogenous biosynthesis and exogenous hormone application in the antioxidant system of tomato plants as a response to biotic and abiotic stress factors.

Molecular Mechanism of Response and Adaptation of Antioxidant Enzyme System to Salt Stress in Leaves of Gymnocarpos przewalskii

The antioxidant enzyme system is the main defense system responsible for maintaining cellular reactive oxygen species (ROS) homeostasis and normal plant growth and development after saline stress. In this study, we identified and characterized the members of the SOD, APX and CAT gene families of the antioxidant enzyme system in Gymnocarpos przewalskii, using plant physiology and molecular biology methods, and analyzed the pattern of enzyme activity in response to NaCl stress. It was found that seven, six and two genes of SOD, APX and CAT gene families, respectively, were expressed in the leaf tissue of G. przewalskii, in which most of the genes were significantly upregulated under NaCl stress, and the enzymatic activities were in accordance with the gene expression. Three positive selection sites in the GpCAT1 gene can increase the hydrophilicity of the GpCAT1 protein, increase the volume of the active site and increase the affinity for H2O2, thus improving the catalytic efficiency of GpCAT1. The results of the present study provide new insights for further investigations of the evolution and function of the SOD, APX and CAT gene families in G. przewalskii and their essential roles under salt stress, and the findings will be useful for revealing the molecular mechanism of salt tolerance and breeding of salt-tolerant plants.

Farmyard manure, a potential organic additive to reclaim copper and Macrophomina phaseolina stress responses in mash bean plants

In the era of global warming, stress combinations instead of individual stress are realistic threats faced by plants that can alter or trigger a wide range of plant responses. In the current study, the cumulative effect of charcoal rot disease caused by notorious fungal pathogen viz., Macrophomina phaseolina was investigated under toxic levels of copper (Cu) in mash bean, and farmyard manure (FYM) was employed to manage stress. Therefore, Cu-spiked soil (50 and 100 mg/kg) was inoculated with the pathogen, and amended with 2% FYM, to assess the effect of intricate interactions on mash bean plants through pot experiments. Results demonstrated that the individual stress of the pathogen or Cu was more severe for morpho-growth, physio-biochemical, and expression profiles of stress-related genes and total protein in mash bean plants as compared to stress combinations. Under single Cu stress, a significant amount of Cu accumulated in plant tissues, particularly in roots than in upper ground tissues, while, under stress combination less Cu accumulated in the plants. Nonetheless, 2% FYM in soil encountered the negative effect of stress responses provoked by the pathogen, Cu, or both by improving health markers (photosynthetic pigments, reducing sugar, total phenolics) and oxidative stress markers (catalase, peroxidase, and polyphenol oxidase), together with regulating the expression of stress-related genes (catalase, ascorbate peroxidase, and cytokinin-resistant genes), and proteins, besides decreasing Cu uptake in the plants. FYM worked better at lower concentrations (50 mg/kg) of Cu than at higher ones (100 mg/kg), hence could be used as a suitable option for better growth, yield, and crop performance under charcoal rot disease stress in Cu-contaminated soils.

Catalase Gene Family in Durum Wheat: Genome-Wide Analysis and Expression Profiling in Response to Multiple Abiotic Stress Conditions

Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. In fact, the CAT enzyme modulates the hydrogen peroxide (H₂O₂) contents in cells by translating this toxic compound into water (H₂O) and O₂^- to reduce reactive oxygen species (ROS) contents in cells. ROS are produced as a result of biotic and abiotic environmental stressors. To avoid ROS toxicity, plants are armed with different enzymatic and non-enzymatic systems to decompose ROS. Among the enzymatic system, CAT proteins are well studied. CAT not only controls growth and development in plants but is also involved in plant defense against different stresses. So far, the CAT gene family has not been reported in durum wheat (Triticum turgidum ssp. durum L.). Therefore, a genome-wide comprehensive analysis was conducted to classify the CAT genes in the durum wheat genome. Here, six TdCAT genes were identified. Based on phylogenetics, the TdCAT genes belong to three groups (Groups I-III) which is explainable by their comparable structural characteristics. Using bio-informatic analysis, we found that the secondary and tertiary structures were conserved among plants and present similar structures among durum wheat CATs. Two conserved domains (pfam00199 and pfam06628) are also present in all identified proteins, which have different subcellular localizations: peroxisome and mitochondrion. By analyzing their promoters, different cis-elements were identified, such as hormone-correlated response and stress-related responsive elements. Finally, we studied the expression pattern of two catalase genes belonging to two different sub-classes under different abiotic stresses. Expression profiling revealed that TdCAT2 and TdCAT3 presented a constitutive expression pattern. Moreover, both genes are induced in response to salt, mannitol, cold, heat and ABA. Thus, we speculate that those genes are activated by different stresses, such as oxygen deficiency, light, cold, abscisic acid and methyl jasmonate. Further, this study will help in understanding the behavior of CAT genes during environmental stress in durum wheat and in Triticeae species in general.

Comprehensive identification of glutathione peroxidase (GPX) gene family in response to abiotic stress in pepper (Capsicum annuum L.)

Plant glutathione peroxidase (GPX) plays an important role in the maintenance of cell homeostasis and in the antioxidant response in plants. In this study, the peroxidase (GPX) gene family was identified in the whole genome of pepper using bioinformatic method. As a result, a total of 5 CaGPX genes were identified, which were unevenly distributed on 3 of the 12 chromosomes of pepper genome. Based on phylogenetic analysis, 89 GPX genes in 17 species from lower plants to higher plants can be divided into 4 groups GroupⅠ, Group Ⅱ, Group Ⅲ, Group Ⅳ). The MEME Suite analysis of GPX proteins shows that all these proteins contain four highly conserved motifs, as well as other conserved sequences and amino acid residues. Gene structure analysis revealed the conservative exon-intron organization pattern of these genes. In the promoter region of CaGPX genes, many cis elements of plant hormone and abiotic stress response were identified in each of CaGPX proteins. In addition, expression patterns of CaGPX genes in different tissues, developmental stages and responses to abiotic stress were also performed. The results of qRT-PCR showed that the transcripts of CaGPX genes varied greatly under abiotic stress at different time points. There results suggest that the GPX gene family of pepper may play a role in plant development andstress response. In conclusion, our research provides new insights into the evolution of pepper GPX gene family, and understanding for functional of these genes in response to abiotic stresses.

Genome-Wide Identification and Analysis of the Plant Cysteine Oxidase (PCO) Gene Family in Brassica napus and Its Role in Abiotic Stress Response

Plant Cysteine Oxidase (PCO) is a plant O₂-sensing enzyme catalyzing the oxidation of cysteine to Cys-sulfinic acid at the N-termini of target proteins. To better understand the Brassica napus PCO gene family, PCO genes in B. napus and related species were analyzed. In this study, 20, 7 and 8 PCO genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the PCOs were divided into five groups: PCO1, PCO2, PCO3, PCO4 and PCO5. Gene organization and motif distribution analysis suggested that the PCO gene family was relatively conserved during evolution. According to the public expression data, PCO genes were expressed in different tissues at different developmental stages. Moreover, qRT-PCR data showed that most of the Bna/Bra/BoPCO5 members were expressed in leaves, roots, flowers and siliques, suggesting an important role in both vegetative and reproductive development. Expression of BnaPCO was induced by various abiotic stress, especially waterlogging stress, which was consistent with the result of cis-element analysis. In this study, the PCO gene family of Brassicaceae was analyzed for the first time, which contributes to a comprehensive understanding of the origin and evolution of PCO genes in Brassicaceae and the function of BnaPCO in abiotic stress responses.

Genome-wide analysis of Catalase gene family reveal insights into abiotic stress response mechanism in Brassica juncea and B. rapa

Environmental stresses affect the yield and productivity of Brassica crops. Catalases are important antioxidant enzymes involved in reducing excess hydrogen peroxide produced by environmental stresses. In the present study, nine and seven CAT family members in two oilseed Brassica species (B. juncea and B. rapa) were identified with complete characterization based on gene and protein structure. Phylogenetic classification categorized CAT proteins into three classes and differentiated the monocot and dicot-specific CAT proteins. Further, the gene and protein characterizations revealed a high degree of conservation across the CAT family members. Differences were observed in the CAT-HEME binding affinity in CAT1, CAT2, and CAT3 isozymes, which could suggest their differential enzyme activities in different conditions. Furthermore, protein-protein interaction with other antioxidant proteins suggested their coordinated role in ROS scavenging mechanisms. Notably, the differential gene expression of BjuCATs and BraCATs and CAT enzyme activities suggested their crucial roles in major abiotic stresses faced by Brassica species. Promoter analysis in BjuCATs and BraCATs suggested the presence of abiotic-stress responsive cis-regulatory elements. Gene regulatory network analysis suggested miRNA and TF mediated stress response in BjuCATs and BraCATs. CAT family screening and characterization in Brassica sp. has established a basic ground for further functional validation in abiotic and heavy-metal stresses which can help in developing stress tolerant crops.

In-silico identification and characterization of O-methyltransferase gene family in peanut (Arachis hypogaea L.) reveals their putative roles in development and stress tolerance

Cultivated peanut (Arachis hypogaea) is a leading protein and oil-providing crop and food source in many countries. At the same time, it is affected by a number of biotic and abiotic stresses. O-methyltransferases (OMTs) play important roles in secondary metabolism, biotic and abiotic stress tolerance. However, the OMT genes have not been comprehensively analyzed in peanut. In this study, we performed a genome-wide investigation of A. hypogaea OMT genes (AhOMTs). Gene structure, motifs distribution, phylogenetic history, genome collinearity and duplication of AhOMTs were studied in detail. Promoter cis-elements, protein-protein interactions, and micro-RNAs targeting AhOMTs were also predicted. We also comprehensively studied their expression in different tissues and under different stresses. We identified 116 OMT genes in the genome of cultivated peanut. Phylogenetically, AhOMTs were divided into three groups. Tandem and segmental duplication events played a role in the evolution of AhOMTs, and purifying selection pressure drove the duplication process. AhOMT promoters were enriched in several key cis-elements involved in growth and development, hormones, light, and defense-related activities. Micro-RNAs from 12 different families targeted 35 AhOMTs. GO enrichment analysis indicated that AhOMTs are highly enriched in transferase and catalytic activities, cellular metabolic and biosynthesis processes. Transcriptome datasets revealed that AhOMTs possessed varying expression levels in different tissues and under hormones, water, and temperature stress. Expression profiling based on qRT-PCR results also supported the transcriptome results. This study provides the theoretical basis for further work on the biological roles of AhOMT genes for developmental and stress responses.

Genome-wide characterization of sugarcane catalase gene family identifies a ScCAT1 gene associated disease resistance

In plants, catalase (CAT) mainly scavenges H₂O₂ from reactive oxygen species (ROS) and regulates the growth and development. So far, genome-wide identification of CAT gene family in Saccharum has not yet been reported. Here, 16 SsCAT genes were identified based on a Saccharum spontaneum genome. They were clustered into three subfamilies, with closer genes sharing similar structures. Most SsCAT proteins contained three conserved amino acids, one active catalytic site, one heme-ligand signature, and three peroxisomal targeting signal 1 (PTS1) sequences. The cis-regulatory element prediction revealed that SsCAT genes were involved in growth and development, and in response to various hormones and stresses. RNA-Seq databases showed that SsCAT genes were differentially expressed in Saccharum tissues and under cold, drought, and Sporisorium scitamineum stresses. The ScCAT1 gene transcript (GenBank accession number KF664183) and relevant CAT activity were up-regulated under S. scitamineum stress. Overexpression of ScCAT1 gene in Nicotiana benthamiana could enhance its resistance to pathogen infection through scavenging of excessive toxic ROS and up-regulated expressions of genes related to hypersensitive response (HR), ROS and salicylic acid (SA) pathways. This study provides comprehensive information for the CAT gene family and sets up a basis for its function identification in sugarcane.

Moschus exerted protective activity against H2O2-induced cell injury in PC12 cells through regulating Nrf-2/ARE signaling pathways

The pivotal characteristics of Alzheimer's disease (AD) are irreversible memory loss and progressive cognitive decline, eventually causing death from brain failure. In the various proposed hypotheses of AD, oxidative stress is also regarded as a symbolic pathophysiologic cascade contributing to brain diseases. Using Chinese herbal medicine may be beneficial for treating and preventing AD. As a rare and valuable animal medicine, Moschus possesses antioxidant and antiapoptotic efficacy and is extensively applied for treating unconsciousness, stroke, coma, and cerebrovascular diseases. We aim to evaluate whether Moschus protects PC12 cells from hydrogen peroxide (H₂O₂)-induced cellular injury. The chemical constituents of Moschus are analyzed by GC-MS assay. The cell viability, reactive oxygen species (ROS) levels, mitochondrial membrane potential (MMP) levels, oxidative stress-related indicators, and apoptotic proteins are determined. Through GC-MS analysis, nineteen active contents were identified. The cell viability loss, lactate dehydrogenase releases, MMP levels, ROS productions, and Malondialdehyde (MDA) activities decreased, and BAX, Caspase-3, and Kelch-like ECH-associated protein 1 expression also significantly down-regulated and heme oxygenase 1, nuclear factor erythroid-2-related factor 2 (Nrf-2), and quinine oxidoreductase 1 expression upregulated after pretreatment of Moschus. The result indicated Moschus has neuroprotective activity in relieving H₂O₂-induced cellular damage, and the potential mechanism might be associated with regulating the Nrf-2/ARE signaling pathway. A more in-depth and comprehensive understanding of Moschus in the pathogenesis of AD will provide a fundamental basis for in vivo AD animal model research, which may be able to provide further insights and new targets for AD therapy.

Identification and Phylogenetic Analysis of the R2R3-MYB Subfamily in Brassica napus

The R2R3-MYB sub-family proteins are composed of most members of MYB (v-Myb avian myeloblastosis viral oncogene homolog) protein, a plant-specific transcription factor (TF) that is classified into four classes depending on the number of MYB repeats. R2R3-MYB TFs are involved in physiological and biochemical processes. However, the functions of the Brassica napus R2R3-MYB genes are still mainly unknown. In this study, 35 Brassica napus MYB (BnaMYB) genes were screened in the genome of Brassica napus, and details about their physical and chemical characteristics, evolutionary relationships, chromosome locations, gene structures, three-dimensional protein structures, cis-acting promoter elements, and gene duplications were uncovered. The BnaMYB genes have undergone segmental duplications and positive selection pressure, according to evolutionary studies. The same subfamilies have similar intron-exon patterns and motifs, according to the genes' structure and conserved motifs. Additionally, through cis-element analysis, many drought-responsive and other stress-responsive cis-elements have been found in the promoter regions of the BnaMYB genes. The expression of the BnaMYB gene displays a variety of tissue-specific patterns. Ten lignin-related genes were chosen for drought treatment. Our research screened four genes that showed significant upregulation under drought stress, and thus may be important drought-responsive genes. The findings lay a new foundation for understanding the complex mechanisms of BnaMYB in multiple developmental stages and pathways related to drought stress in rapeseed.

Developing future heat-resilient vegetable crops

Climate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants' biochemical and molecular processes; having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.

Genome-wide identification of germin-like proteins in peanut (Arachis hypogea L.) and expression analysis under different abiotic stresses

Peanut is an important food and feed crop, providing oil and protein nutrients. Germins and germin-like proteins (GLPs) are ubiquitously present in plants playing numerous roles in defense, growth and development, and different signaling pathways. However, the GLP members have not been comprehensively studied in peanut at the genome-wide scale. We carried out a genome-wide identification of the GLP genes in peanut genome. GLP members were identified comprehensively, and gene structure, genomic positions, motifs/domains distribution patterns, and phylogenetic history were studied in detail. Promoter Cis-elements, gene duplication, collinearity, miRNAs, protein-protein interactions, and expression were determined. A total of 84 GLPs (AhGLPs ) were found in the genome of cultivated peanut. These GLP genes were clustered into six groups. Segmental duplication events played a key role in the evolution of AhGLPs, and purifying selection pressure was underlying the duplication process. Most AhGLPs possessed a well-maintained gene structure and motif organization within the same group. The promoter regions of AhGLPs contained several key cis-elements responsive to 'phytohormones', 'growth and development', defense, and 'light induction'. Seven microRNAs (miRNAs) from six families were found targeting 25 AhGLPs. Gene Ontology (GO) enrichment analysis showed that AhGLPs are highly enriched in nutrient reservoir activity, aleurone grain, external encapsulating structure, multicellular organismal reproductive process, and response to acid chemicals, indicating their important biological roles. AhGLP14, AhGLP38, AhGLP54, and AhGLP76 were expressed in most tissues, while AhGLP26, AhGLP29, and AhGLP62 showed abundant expression in the pericarp. AhGLP7, AhGLP20, and AhGLP21, etc., showed specifically high expression in embryo, while AhGLP12, AhGLP18, AhGLP40, AhGLP78, and AhGLP82 were highly expressed under different hormones, water, and temperature stress. The qRT-PCR results were in accordance with the transcriptome expression data. In short, these findings provided a foundation for future functional investigations on the AhGLPs for peanut breeding programs.

Analysis of CAT Gene Family and Functional Identification of OsCAT3 in Rice

Catalase (CAT) is an important antioxidant enzyme in plants that plays a key role in plant growth and stress responses. CAT is usually encoded by a small gene family that has been cloned and functionally studied in some species, such as Arabidopsis, wheat and cucumber, but its specific roles in rice are not clear at present. In this study, we identified three CAT family genes (OsCAT1, OsCAT2 and OsCAT3) in the rice genome and performed a systematic bioinformatics analysis. RT-PCR analysis revealed that OsCAT1-OsCAT3 was primarily expressed in vegetative tissues such as roots, stems and leaves. Since OsCAT3 showed the highest expression level among the three OsCAT genes, we then focused on its related functions. OsCAT3 prokaryotic expression protein has an obvious ability to remove H2O2. The OsCAT3crispr plant was short and had a low survival rate, the leaves were small with brown lesions, and the activities of the CAT, POD and SOD enzymes were significantly reduced. A microarray analysis showed that differentially expressed genes were primarily enriched in toxin metabolism and photosynthesis. This study laid a foundation for further understanding the function of the rice OsCAT gene.

Seed Myco-priming improves crop yield and herbivory induced defenses in maize by coordinating antioxidants and Jasmonic acid pathway

BACKGROUND

Seed Myco-priming based on consortium of entomopathogenic fungi is very effective seed treatment against Ostrinia furnacalis herbivory. Maize regulates defense responses against herbivory by the production of defense-related enzymatic and non-enzymatic antioxidants, phytohormones, and their corresponding genes. Jasmonic acid (JA) plays a key role in plant-entomopathogenic fungi-herbivore interaction.

RESULTS

To understand how a consortium of the entomopathogenic fungi Beauveria bassiana and Trichoderma asperellum induce changes in the response of maize to herbivory and increase the crop yield, 2-year field experiment, antioxidant enzymes, leaf transcriptome, and phytohormone were performed. Fungal inoculation enhanced the production of antioxidant enzymes and JA signaling pathway more than the normal herbivory. The comparison between single inoculated, consortium inoculated, and non-inoculated plants resulted in distinct transcriptome profiles representing a considerable difference in expression of antioxidant- and JA- responsive genes identified through Weighted gene co-expression network analysis (WGCNA) and expression analysis, respectively. Seed priming with a consortium of B. bassiana and T. asperellum significantly enhanced the expression of genes involved in antioxidants production and JA biosynthesis cascade, with the highest expression recorded at 24-h post O. furnacalis larval infestation. They reduced the larval nutritional indices and survival up to 87% and enhancing crop yield and gross return up to 82-96% over the year 2018 and 2019.

CONCLUSION

From our results we suggest that a consortium of B. bassiana and T. asperellum can be used synergistically against O. furnacalis in maize under field condition and can mediate antioxidants- and JA- associated maize defense response by boosting up the expression of their responsive genes, thereby enhancing crop yield.

Genome-Scale Investigation of GARP Family Genes Reveals Their Pivotal Roles in Nutrient Stress Resistance in Allotetraploid Rapeseed

The GARP genes are plant-specific transcription factors (TFs) and play key roles in regulating plant development and abiotic stress resistance. However, few systematic analyses of GARPs have been reported in allotetraploid rapeseed (Brassica napus L.) yet. In the present study, a total of 146 BnaGARP members were identified from the rapeseed genome based on the sequence signature. The BnaGARP TFs were divided into five subfamilies: ARR, GLK, NIGT1/HRS1/HHO, KAN, and PHL subfamilies, and the members within the same subfamilies shared similar exon-intron structures and conserved motif configuration. Analyses of the Ka/Ks ratios indicated that the GARP family principally underwent purifying selection. Several cis-acting regulatory elements, essential for plant growth and diverse biotic and abiotic stresses, were identified in the promoter regions of BnaGARPs. Further, 29 putative miRNAs were identified to be targeting BnaGARPs. Differential expression of BnaGARPs under low nitrate, ammonium toxicity, limited phosphate, deficient boron, salt stress, and cadmium toxicity conditions indicated their potential involvement in diverse nutrient stress responses. Notably, BnaA9.HHO1 and BnaA1.HHO5 were simultaneously transcriptionally responsive to these nutrient stresses in both hoots and roots, which indicated that BnaA9.HHO1 and BnaA1.HHO5 might play a core role in regulating rapeseed resistance to nutrient stresses. Therefore, this study would enrich our understanding of molecular characteristics of the rapeseed GARPs and will provide valuable candidate genes for further in-depth study of the GARP-mediated nutrient stress resistance in rapeseed.

Identification and Expression Profiling of Two Saudi Arabia Catalase Genes from Wheat and Barley in Response to Abiotic and Hormonal Stresses

Catalase is a crucial enzyme in antioxidant defense systems protecting eukaryotes from oxidative stress. These proteins are present in almost all living organisms and play important roles in controlling plant responses to biotic and abiotic stresses by catalyzing the decomposition of H₂O₂. Despite their importance, little is known about their expression in the majority of monocotyledonous species. Here, we isolated and characterized two novel catalase genes from Triticum turgidum and Hordeum vulgare, designated as TtCAT1 and HvCAT1, respectively. Phylogenetic analysis revealed that TtCAT1 and HvCAT1 presented 492 aa and shared an important identity with other catalase proteins belonging to subfamily 1. Using bioinformatic analysis, we predicted the 3D structure models of TtCAT1 and HvCAT1. Interestingly, analysis showed that the novel catalases harbor a peroxisomal targeting signal (PTS1) located at their C-terminus portion, as shown for other catalase proteins. In addition, this motif is responsible for the in silico peroxisomal localization of both proteins. Finally, RT-qPCR analysis showed that TtCAT1 and HvCAT1 are highly expressed in leaves in normal conditions but faintly in roots. Moreover, both genes are upregulated after the application of different stresses such as salt, osmotic, cold, heavy metal, and hormonal stresses. The positive responses of TtCAT1 and HvCAT1 to the various stimuli suggested that these proteins can help to protect both species against environmental stresses.

Overexpression of Pyrus sinkiangensis HAT5 enhances drought and salt tolerance, and low-temperature sensitivity in transgenic tomato

The homeodomain-leucine zipper protein HAT belongs to the homeodomain leucine zipper subfamily (HD-Zip) and is important for regulating plant growth and development and stress tolerance. To investigate the role of HAT5 in tolerance to drought, salt, and low temperature stress, we selected a HAT gene from Pyrus sinkiangensis Yü (Pyrus sinkiangensis T.T. Yu). The sequences were analyzed using ioinformatics, and the overexpressed tomato lines were obtained using molecular biology techniques. The phenotypes, physiological, and biochemical indexes of the wild-type and transgenic tomato lines were observed under different stress conditions. We found that the gene had the highest homology with PbrHAT5. Under drought and NaCl stress, osmotic regulatory substances (especially proline) were significantly accumulated, and antioxidant enzyme activities were enhanced. The malondialdehyde level and relative electrical conductivity of transgenic tomatoes under low temperature (freezing) stress were significantly higher than those of wild-type tomatoes. The reactive oxygen species scavenging system was unbalanced. This study found that PsHAT5 improved the tolerance of tomatoes to drought and salt stress by regulating proline metabolism and oxidative stress ability, reducing the production of reactive oxygen species, and maintaining normal cell metabolism. In conclusion, the PsHAT5 transcription factor has great potential in crop resistance breeding, which lays a theoretical foundation for future excavation of effective resistance genes of the HD-Zip family and experimental field studies.

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops-An Updated Overview

Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study.

The Putative Auto-Inhibitory Domain of Durum Wheat Catalase (TdCAT1) Positively Regulates Bacteria Cells in Response to Different Stress Conditions

Catalase is a crucial enzyme in the antioxidant defense system protecting organisms from oxidative stress. Proteins of this kind play important roles in controlling plant response to biotic and abiotic stresses by catalyzing the decomposition of H2O2. The durum wheat catalase 1, TdCAT1, has been previously isolated and characterized. Here, using bio-informatic analysis, we showed that durum wheat catalase 1 TdCAT1 harbors different novel conserved domains. In addition, TdCAT1 contains various phosphorylation residues and S-Nitrosylation residues located at different positions along the protein sequence. TdCAT1 activity decreased after treatment with λ−phosphatase. On the other hand, we showed that durum wheat catalase 1 (TdCAT1) exhibits a low CAT activity in vitro, whereas a deleted form of TdCAT1 has better activity compared to the full-length protein (TdCAT460), suggesting that TdCAT1 could present a putative autoinhibitory domain in its C-terminal portion. Moreover, we showed that TdCAT1 positively regulates E. coli cells in response to salt, ionic and osmotic stresses as well as heavy metal stress in solid and liquid mediums. Such effects had not been reported and lead us to suggest that the durum wheat catalase 1 TdCAT1 protein could play a positive role in response to a wide array of abiotic stress conditions.

Genome-wide analysis of IQD proteins and ectopic expression of watermelon ClIQD24 in tomato suggests its important role in regulating fruit shape

The plant-specific IQ67 domain (IQD) is the largest class of calmodulin targets found in plants, and plays an important role in many biological processes, especially fruit development processes. However, the functional role of IQD proteins in the development of watermelon (Citrullus lanatus) shape remains unknown, as the IQD protein family in watermelon has not been systematically characterized. Herein, we elucidated the gene structures, chromosomal locations, evolutionary divergence, and functions of 35 IQD genes in the watermelon genome. The transcript profiles and quantitative real-time PCR analysis at different stages of fruit development showed that the ClIQD24 gene was highly expressed on 0 days after pollination. Furthermore, we found that the ectopic overexpression of ClIQD24 promoted tomato fruit elongation, thereby revealing the significance of ClIQD24 in the progression of watermelon shape. Our study will serve as a reference for further investigations on the molecular mechanisms underlying watermelon fruit shape formation.

Genome-wide analysis of the JAZ subfamily of transcription factors and functional verification of BnC08.JAZ1-1 in Brassica napus

BACKGROUND

JAZ subfamily plays crucial roles in growth and development, stress, and hormone responses in various plant species. Despite its importance, the structural and functional analyses of the JAZ subfamily in Brassica napus are still limited.

RESULTS

Comparing to the existence of 12 JAZ genes (AtJAZ1-AtJAZ12) in Arabidopsis, there are 28, 31, and 56 JAZ orthologues in the reference genome of B. rapa, B. oleracea, and B. napus, respectively, in accordance with the proven triplication events during the evolution of Brassicaceae. The phylogenetic analysis showed that 127 JAZ proteins from A. thaliana, B. rapa, B. oleracea, and B. napus could fall into five groups. The structure analysis of all 127 JAZs showed that these proteins have the common motifs of TIFY and Jas, indicating their conservation in Brassicaceae species. In addition, the cis-element analysis showed that the main motif types are related to phytohormones, biotic and abiotic stresses. The qRT-PCR of the representative 11 JAZ genes in B. napus demonstrated that different groups of BnJAZ individuals have distinct patterns of expression under normal conditions or treatments with distinctive abiotic stresses and phytohormones. Especially, the expression of BnJAZ52 (BnC08.JAZ1-1) was significantly repressed by abscisic acid (ABA), gibberellin (GA), indoleacetic acid (IAA), polyethylene glycol (PEG), and NaCl treatments, while induced by methyl jasmonate (MeJA), cold and waterlogging. Expression pattern analysis showed that BnC08.JAZ1-1 was mainly expressed in the vascular bundle and young flower including petal, pistil, stamen, and developing ovule, but not in the stem, leaf, and mature silique and seed. Subcellular localization showed that the protein was localized in the nucleus, in line with its orthologues in Arabidopsis. Overexpression of BnC08.JAZ1-1 in Arabidopsis resulted in enhanced seed weight, likely through regulating the expression of the downstream response genes involved in the ubiquitin-proteasome pathway and phospholipid metabolism pathway.

CONCLUSIONS

The systematic identification, phylogenetic, syntenic, and expression analyses of BnJAZs subfamily improve our understanding of their roles in responses to stress and phytohormone in B. napus. In addition, the preliminary functional validation of BnC08.JAZ1-1 in Arabidopsis demonstrated that this subfamily might also play a role in regulating seed weight.

Genome-Wide Characterization of Ascorbate Peroxidase Gene Family in Peanut (Arachis hypogea L.) Revealed Their Crucial Role in Growth and Multiple Stress Tolerance

Ascorbate peroxidase (APX), an important antioxidant enzyme, plays a significant role in ROS scavenging by catalyzing the decrease of hydrogen peroxide under various environmental stresses. Nevertheless, information about the APX gene family and their evolutionary and functional attributes in peanut (Arachis hypogea L.) was not reported. Therefore, a comprehensive genome-wide study was performed to discover the APX genes in cultivated peanut genome. This study identified 166 AhAPX genes in the peanut genome, classified into 11 main groups. The gene duplication analysis showed that AhAPX genes had experienced segmental duplications and purifying selection pressure. Gene structure and motif investigation indicated that most of the AhAPX genes exhibited a comparatively well-preserved exon-intron pattern and motif configuration contained by the identical group. We discovered five phytohormones-, six abiotic stress-, and five growth and development-related cis-elements in the promoter regions of AhAPX. Fourteen putative ah-miRNAs from 12 families were identified, targeting 33 AhAPX genes. Furthermore, we identified 3,257 transcription factors from 38 families (including AP2, ARF, B3, bHLH, bZIP, ERF, MYB, NAC, WRKY, etc.) in 162 AhAPX genes. Gene ontology and KEGG enrichment analysis confirm the role of AhAPX genes in oxidoreductase activity, catalytic activity, cell junction, cellular response to stimulus and detoxification, biosynthesis of metabolites, and phenylpropanoid metabolism. Based on transcriptome datasets, some genes such as AhAPX4/7/17/77/82/86/130/133 and AhAPX160 showed significantly higher expression in diverse tissues/organs, i.e., flower, leaf, stem, roots, peg, testa, and cotyledon. Likewise, only a few genes, including AhAPX4/17/19/55/59/82/101/102/137 and AhAPX140, were significantly upregulated under abiotic (drought and cold), and phytohormones (ethylene, abscisic acid, paclobutrazol, brassinolide, and salicylic acid) treatments. qRT-PCR-based expression profiling presented the parallel expression trends as generated from transcriptome datasets. Our discoveries gave new visions into the evolution of APX genes and provided a base for further functional examinations of the AhAPX genes in peanut breeding programs.

Investigation of proteins' interaction network and the expression pattern of genes involved in the ABA biogenesis and antioxidant system under methanol spray in drought-stressed rapeseed

Drought is one of the most critical abiotic stresses, which significantly impair rapeseed (Brassica napus L.) productivity. Several factors can regulate the stress response, including changes in gene expression in biological pathways, extensive protein interaction networks, and post-translational regulatory factors like microRNAs. External factors can also affect the intensity of the stress response. Therefore, this study investigated protein-protein interactions of some essential genes involved in abscisic acid (ABA) production, antioxidant system, and Krebs cycle. The expression of phyton synthase (PSY), 9-cis-epoxycarotenoid dioxygenase (NCED3), aldehyde oxidase (AAO3), thioredoxin reductase (NTRC), and glutathione reductase (GR) genes in two rapeseed genotypes, i.e., Hyola308 (drought-sensitive) and SLM046 (drought-tolerant) were evaluated using qRT-PCR technique under 72 h of drought stress and methanol foliar application. In the SLM046 (tolerant) genotype, the expression levels of PYS, NCED, AAO3, and GR genes were increased after 8 h of foliar application. The expression level of the NTR gene was increased 8 and 24 h after stress and methanol treatment. In the Hyola308 genotype, PYS, AAO3, NTR, and GR genes' expression level was increased 8 h after methanol foliar application, and the NCED gene was increased 24 h after stress with methanol treatment. In general, methanol foliar application increased the expression levels of several genes. Particularly, the gene expression was considerably higher in the SLM046 genotype than in Hyola308. Bioinformatics prediction of microRNAs targeting PSY, NCED, GR, NTRC, and AAO3 genes was performed, and 38, 38, 13, 11, and 11 microRNAs were predicted for these genes, respectively. The study of effective microRNAs showed that sometimes more than one type of microRNA could affect the desired gene, and in some cases, a conserved family of microRNAs caused the main effect on gene expression. Overall, our results lay the foundation for functional characterization of these genes or gene-miRNA modules in regulating drought stress tolerance in rapeseed.

Genome-Wide Identification and Expression Analysis of SnRK2 Gene Family in Dormant Vegetative Buds of Liriodendron chinense in Response to Abscisic Acid, Chilling, and Photoperiod

Protein kinases play an essential role in plants’ responses to environmental stress signals. SnRK2 (sucrose non-fermenting 1-related protein kinase 2) is a plant-specific protein kinase that plays a crucial role in abscisic acid and abiotic stress responses in some model plant species. In apple, corn, rice, pepper, grapevine, Arabidopsis thaliana, potato, and tomato, a genome-wide study of the SnRK2 protein family was performed earlier. The genome-wide comprehensive investigation was first revealed to categorize the SnRK2 genes in the Liriodendron chinense (L. chinense). The five SnRK2 genes found in the L. chinense genome were highlighted in this study. The structural gene variants, 3D structure, chromosomal distributions, motif analysis, phylogeny, subcellular localization, cis-regulatory elements, expression profiles in dormant buds, and photoperiod and chilling responses were all investigated in this research. The five SnRK2 genes from L. chinense were grouped into groups (I–IV) based on phylogeny analysis, with three being closely related to other species. Five hormones-, six stress-, two growths and biological process-, and two metabolic-related responsive elements were discovered by studying the cis-elements in the promoters. According to the expression analyses, all five genes were up- and down-regulated in response to abscisic acid (ABA), photoperiod, chilling, and chilling, as well as photoperiod treatments. Our findings gave insight into the SnRK2 family genes in L. chinense and opened up new study options.

Genome-Wide Identification and Characterization of CPR5 Genes in Gossypium Reveals Their Potential Role in Trichome Development

Trichomes protect plants against insects, microbes, herbivores, and abiotic damages and assist seed dispersal. The function of CPR5 genes have been found to be involved in the trichome development but the research on the underlying genetic and molecular mechanisms are extremely limited. Herein, genome wide identification and characterization of CPR5 genes was performed. In total, 26 CPR5 family members were identified in Gossypium species. Phylogenetic analysis, structural characteristics, and synteny analysis of CPR5s showed the conserved evolution relationships of CPR5. The promoter analysis of CPR5 genes revealed hormone, stress, and development-related cis-elements. Gene ontology (GO) enrichment analysis showed that the CPR5 genes were largely related to biological regulation, developmental process, multicellular organismal process. Protein-protein interaction analysis predicted several trichome development related proteins (SIM, LGO, and GRL) directly interacting with CPR5 genes. Further, nine putative Gossypium-miRNAs were also identified, targeting Gossypium CPR5 genes. RNA-Seq data of G. arboreum (with trichomes) and G. herbaceum (with no trichomes) was used to perform the co-expression network analysis. GheCPR5.1 was identified as a hub gene in a co-expression network analysis. RT-qPCR of GheCPR5.1 gene in different tissues suggests that this gene has higher expressions in the petiole and might be a key candidate involved in the trichome development. Virus induced gene silencing of GheCPR5.1 (Ghe02G17590) confirms its role in trichome development and elongation. Current results provide proofs of the possible role of CPR5 genes and provide preliminary information for further studies of GheCPR5.1 functions in trichome development.

Alterations of Oxidative Stress Indicators, Antioxidant Enzymes, Soluble Sugars, and Amino Acids in Mustard [Brassica juncea (L.) Czern and Coss.] in Response to Varying Sowing Time, and Field Temperature

The impact of elevated temperature at the reproductive stage of a crop is one of the critical limitations that influence crop growth and productivity globally. This study was aimed to reveal how sowing time and changing field temperature influence on the regulation of oxidative stress indicators, antioxidant enzymes activity, soluble sugars (SS), and amino acids (AA) in Indian Mustard. The current study was carried out during the rabi 2017-2018 and 2018-2019 where, five varieties of mustard viz. Pusa Mustard 25 (PM-25) (V1), PM-26 (V2), BPR-541-4 (V3), RH-406 (V4), and Urvashi (V5) were grown under the field conditions on October 30 (normal sowing; S1), November 18 (late sowing; S2) and November 30 (very late sowing; S3) situations. The S1 and S3 plants, at mid-flowering stage, showed a significant variation in accumulation of SS (8.5 and 17.3%), free AA (235.4 and 224.6%), and proline content (118.1 and 133%), respectively, and played a crucial role in the osmotic adjustment under stress. The results showed that S3 sowing, exhibited a significant induction of the hydrogen peroxide (H₂O₂) (110.2 and 86.6%) and malondialdehyde (23.5 and 47.5%) concentrations, respectively, which indicated the sign of oxidative stress in plants. Interestingly, the polyphenol oxidase, peroxidase, superoxide dismutase, and catalase enzyme activities were also significantly increased in S3 plants compared to S1 plants, indicating their significant roles in ameliorating the oxidative stress. Furthermore, the concentration of fatty acid levels such as palmitic, stearic, oleic, and linoleic acids level also significantly increased in S3 plants, which influenced the seed and oil quality. The study suggests that the late sowing significantly impaired the biochemical mechanisms in Indian mustard. Further, the mustard variety V4 (RH-406) was found to be effective for cultivation as well as environmental stress adoption in Indian soils, and it could be highly useful in breeding for developing heat-tolerant genotypes for ensuring the food security.

Plant Response to Cold Stress: Cold Stress Changes Antioxidant Metabolism in Heading Type Kimchi Cabbage (Brassica rapa L. ssp. Pekinensis)

Cold stress is known as the important yield-limiting factor of heading type Kimchi cabbage (HtKc, Brassica rapa L. ssp. pekinensis), which is an economically important crop worldwide. However, the biochemical and molecular responses to cold stress in HtKc are largely unknown. In this study, we conducted transcriptome analyses on HtKc grown under normal versus cold conditions to investigate the molecular mechanism underlying HtKc responses to cold stress. A total of 2131 genes (936 up-regulated and 1195 down-regulated) were identified as differentially expressed genes and were significantly annotated in the category of “response to stimulus”. In addition, cold stress caused the accumulation of polyphenolic compounds, including p-coumaric, ferulic, and sinapic acids, in HtKc by inducing the phenylpropanoid pathway. The results of the chemical-based antioxidant assay indicated that the cold-induced polyphenolic compounds improved the free-radical scavenging activity and antioxidant capacity, suggesting that the phenylpropanoid pathway induced by cold stress contributes to resistance to cold-induced reactive oxygen species in HtKc. Taken together, our results will serve as an important base to improve the cold tolerance in plants via enhancing the antioxidant machinery.

Genome-Wide Analysis of the Soybean TIFY Family and Identification of GmTIFY10e and GmTIFY10g Response to Salt Stress

TIFY proteins play crucial roles in plant abiotic and biotic stress responses. Our transcriptome data revealed several TIFY family genes with significantly upregulated expression under drought, salt, and ABA treatments. However, the functions of the GmTIFY family genes are still unknown in abiotic stresses. We identified 38 GmTIFY genes and found that TIFY10 homologous genes have the most duplication events, higher selection pressure, and more obvious response to abiotic stresses compared with other homologous genes. Expression pattern analysis showed that GmTIFY10e and GmTIFY10g genes were significantly induced by salt stress. Under salt stress, GmTIFY10e and GmTIFY10g transgenic Arabidopsis plants showed higher root lengths and fresh weights and had significantly better growth than the wild type (WT). In addition, overexpression of GmTIFY10e and GmTIFY10g genes in soybean improved salt tolerance by increasing the PRO, POD, and CAT contents and decreasing the MDA content; on the contrary, RNA interference plants showed sensitivity to salt stress. Overexpression of GmTIFY10e and GmTIFY10g in Arabidopsis and soybean could improve the salt tolerance of plants, while the RNAi of GmTIFY10e and GmTIFY10g significantly increased sensitivity to salt stress in soybean. Further analysis demonstrated that GmTIFY10e and GmTIFY10g genes changed the expression levels of genes related to the ABA signal pathway, including GmSnRK2, GmPP2C, GmMYC2, GmCAT1, and GmPOD. This study provides a basis for comprehensive analysis of the role of soybean TIFY genes in stress response in the future.

Mechanistic Insights Into Trehalose-Mediated Cold Stress Tolerance in Rapeseed (Brassica napus L.) Seedlings

Cold stress (CS) severely affects several physiological, biochemical, and molecular mechanisms and limits the growth and production of rapeseed (Brassica napus L.). Trehalose (Tre) acts as a growth modulator, which is extensively used to improve the tolerance to multiple plant stresses. Further, Tre also serves as an external force in inducing plant signaling molecules, regulating the expression of stress-responsive genes, and enhancing the CS tolerance in plants. Nevertheless, the importance of exogenous Tre in improving the CS tolerance in rapeseed is still unclear. Therefore, the current study was designed to get mechanistic insights into Tre-mediated CS tolerance in rapeseed seedlings. To explore the Tre role, we designed four treatments [control (CK), CK + 20 mM L^-1 Tre, Cold, and Cold + 20 mM L^-1 Tre] and three CS conditions (4, 0, and -4°C). The results showed that Tre treatments significantly mitigated the adverse effects of CS on the seedlings and increased the survival rate of Tre-treated seedlings under CS conditions. The exogenous Tre dramatically increased the contents of osmoprotectants, including the soluble sugar (SS), soluble protein (SP), and proline (Pro), and the activities of antioxidant enzymes, such as catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and ascorbate peroxidase (APX) were also increased under CS conditions. Additionally, Tre decreased the malondialdehyde (MDA) contents to protect the rapeseed seedlings. Moreover, Tre also remarkably augmented the expression levels of antioxidant genes (CAT12, POD34, and FSD7), CS-responsive marker genes (CBF1, CBF2, CBF4, COR6.6, COR15, COR25, COL1, and KIN1), and Tre-biosynthesis genes (TPS4, TPS8, and TPS9). Briefly, exogenous Tre not only regulates the antioxidant and osmotic balance, but it also significantly participates in Tre metabolism and signaling network to improve the CS tolerance in rapeseed. Thus, Tre-induced supervisory connections between physiological or/and biochemical attributes provide information to dissect the mechanisms of Tre-mediated CS tolerance.

Drought tolerance induction and growth promotion by indole acetic acid producing Pseudomonas aeruginosa in Vigna radiata

Drought accompanied with reduced precipitation is one of the key manacles to global agricultural throughput and is expected to escalate further hence posing major challenges to future food safety. For a sustainable agricultural environment, drought resistant plant growth promoting rhizobacteria (PGPR) are new encouraging prospect, which are inexpensive and have no side effects, as those of synthetic fertilizers. In the present study, five strains of Pseudomonas aeruginosa, the strain MK513745, strain MK513746, strain MK513747, strain MK513748, and strain MK513749 were used as drought tolerant PGPR with multiple traits of IAA production, N fixation, P solubilization, siderophore producing capabilities. The strain MK513745 and strain MK513749 produced higher quantities of indole acetic acid (116±0.13 and 108±0.26 μg ml^-1). MK513749 yielded 12 different indole compounds in GCMS analysis. The strain MK513748 yielded maximum S.I. (3.33mm) for phosphate solubilizing test. Maximum nitrogen concentration was produced (0.18 μg ml^-1) by strain MK513746. Percent siderophore units ranged from 2.65% to 2.83% as all five pseudomonas strains were siderophore positive. In all growth experiments of plant microbe interaction two varieties of Vigna radiata (AZRI-06, NM-11) plants inoculated with P. aeruginosa strains under drought stress responded significantly (P<0.05) better than control stressed plants. Maximum shoot length was enhanced up-to 125%, pod/plant 172%, number of grains 65%, 100 seed weight 95%, 100 seed straw weight 124% and total yield 293% were recorded in plants inoculated with drought stress tolerant PGPR in both varieties as compared to respective stressed control plants. Photosynthetic activity, membrane stability (45%), water content (68%) and antioxidant efficacy (19%) were improved with PGPR inoculations. The variety NM-11 (V2) was more tolerant to drought stress with inoculations of Pseudomonas strains than AZRI-06 (V1). Inoculations with these indole acetic acid producing strains would be suitable for plant growth promotion in areas facing water deficiency.

Genome-Wide Identification and Characterization of SET Domain Family Genes in Brassica napus L

SET domain group encoding proteins function as histone lysine methyltransferases. These proteins are involved in various biological processes, including plant development and adaption to the environment by modifying the chromatin structures. So far, the SET domain genes (SDGs) have not been systematically investigated in Brassica napus (B. napus). In the current study, through genome-wide analysis, a total of 122 SDGs were identified in the B. napus genome. These BnSDGs were subdivided into seven (I-VII) classes based on phylogeny analysis, domain configurations, and motif distribution. Segmental duplication was involved in the evolution of this family, and the duplicated genes were under strong purifying selection. The promoter sequence of BnSDGs consisted of various growth, hormones, and stress-related cis-acting elements along with transcription factor binding sites (TFBSs) for 20 TF families in 59 of the 122 BnSDGs. The gene ontology (GO) analysis revealed that BnSDGs were closely associated with histone and non-histone methylation and metal binding capacity localized mostly in the nucleus. The in silico expression analysis at four developmental stages in leaf, stem root, floral organ, silique, and seed tissues showed a broad range of tissue and stage-specific expression pattern. The expression analysis under four abiotic stresses (dehydration, cold, ABA, and salinity) also provided evidence for the importance of BnSDGs in stress environments. Based on expression analysis, we performed reverse transcription-quantitative PCR for 15 target BnSDGs in eight tissues (young leaf, mature leaf, root, stem, carpel, stamen, sepal, and petals). Our results were in accordance with the in silico expression data, suggesting the importance of these genes in plant development. In conclusion, this study lays a foundation for future functional studies on SDGs in B. napus.

Genome-Wide Identification and Expression Profiling of DUF221 Gene Family Provides New Insights Into Abiotic Stress Responses in Potato

The domain of the unknown function 221 proteins regulate several processes in plants, including development, growth, hormone transduction mechanism, and abiotic stress response. Therefore, a comprehensive analysis of the potato genome was conducted to identify the deafness-dystonia peptide (DDP) proteins' role in potatoes. In the present study, we performed a genome-wide analysis of the potato domain of the unknown function 221 (DUF221) genes, including phylogenetic inferences, chromosomal locations, gene duplications, gene structures, and expression analysis. In our results, we identified 10 DDP genes in the potato genome. The phylogenetic analysis results indicated that StDDPs genes were distributed in all four clades, and clade IV was the largest clade. The gene duplication under selection pressure analysis indicated various positive and purifying selections in StDDP genes. The putative stu-miRNAs from different families targeting StDDPs were also predicted in the present study. Promoter regions of StDDP genes contain different cis-acting components involved in multiple stress responses, such as phytohormones and abiotic stress-responsive factors. The analysis of the tissue-specific expression profiling indicated the StDDPs gene expression in stem, root, and leaf tissues. We subsequently observed that StDDP4, StDDP5, and StDDP8 showed higher expressions in roots, stems, and leaves. StDDP5 exhibited high expression against heat stress response, and StDDP7 showed high transcript abundance against salt stress in potatoes. Under abscisic acid (ABA) and indole acetic acid (IAA) treatments, seven StDDP genes' expressions indicated that ABA and IAA performed important roles in immunity response. The expression profiling and real-time qPCR of stems, roots, and leaves revealed StDDPs' significant role in growth and development. These expression results of DDPs are primary functional analysis and present basic information for other economically important crops.

Reactive Oxygen Species, Antioxidant Responses and Implications from a Microbial Modulation Perspective

Simple Summary

Environmental conditions are subject to unprecedented changes due to recent progressive anthropogenic activities on our planet. Plants, as the frontline of food security, are susceptible to these changes, resulting in the generation of unavoidable byproducts of metabolism (ROS), which eventually affect their productivity. The response of plants to these unfavorable conditions is highly intricate and depends on several factors, among them are the species/genotype tolerance level, intensity, and duration of stress factors. Defensive mechanisms in plant systems, by nature, are concerned primarily with generating enzymatic and non-enzymatic antioxidants. In addition to this, plant-microbe interactions have been found to improve immune systems in plants suffering from drought and salinity stress.

Abstract

Plants are exposed to various environmental stresses in their lifespan that threaten their survival. Reactive oxygen species (ROS), the byproducts of aerobic metabolism, are essential signalling molecules in regulating multiple plant developmental processes as well as in reinforcing plant tolerance to biotic and abiotic stimuli. However, intensified environmental challenges such as salinity, drought, UV irradiation, and heavy metals usually interfere with natural ROS metabolism and homeostasis, thus aggravating ROS generation excessively and ultimately resulting in oxidative stress. Cellular damage is confined to the degradation of biomolecular structures, including carbohydrates, proteins, lipids, pigments, and DNA. The nature of the double-edged function of ROS as a secondary messenger or harmful oxidant has been attributed to the degree of existing balance between cellular ROS production and ROS removal machinery. The activities of enzyme-based antioxidants, catalase (CAT, EC 1.11.1.6), monodehydroascorbate reductase (MDHAR, E.C.1.6.5.4), dehydroascorbate reductase (DHAR, EC 1.8.5.1), superoxide dismutase (SOD, EC 1.15.1.1), ascorbate peroxidase (APX, EC 1.11.1.11), glutathione reductase (GR, EC 1.6.4.2), and guaiacol peroxidase (GPX, EC 1.11.1.7); and non-enzyme based antioxidant molecules, ascorbate (AA), glutathione (GSH), carotenoids, α-tocopherol, prolines, flavonoids, and phenolics, are indeed parts of the defensive strategies developed by plants to scavenge excess ROS and to maintain cellular redox homeostasis during oxidative stress. This review briefly summarises current knowledge on enzymatic and non-enzymatic antioxidant machinery in plants. Moreover, additional information about the beneficial impact of the microbiome on countering abiotic/biotic stresses in association with roots and plant tissues has also been provided.

Catalase (CAT) Gene Family in Wheat (Triticum aestivum L.): Evolution, Expression Pattern and Function Analysis

Catalases (CATs) are present in almost all living organisms and play important roles in plant development and response to various stresses. However, there is relatively little information on CAT genes in wheat and related Triticeae species. A few studies on CAT family genes in wheat have been reported. In this study, ten CAT proteins (TaCATs) were identified in wheat and classified into three groups based on their phylogenetic features and sequence analysis. The analysis of the structure and motif composition of the TaCAT proteins suggested that a segmental duplication event occurred in the TaCAT gene family. Collinearity relationship analysis among different species showed that there were three orthologous CAT genes in rice and in maize. By analyzing the cis-elements in the promoter regions, we speculated that TaCAT genes expression might be regulated by light, oxygen deficit, methyl jasmonate and abscisic acid, and by transcription factors such as MYB. A Gene Ontology (GO)-based analysis showed that TaCAT proteins may be related to the response to various stresses, are cytoplasm localized, and may function as antioxidant enzymes. RT-qPCR and transcriptome data analyses exhibited distinct expression patterns of TaCAT genes in different tissues and in response to various treatments. In this study, a comprehensive analysis of wheat CAT genes was performed, enriching our knowledge of CAT genes and providing a foundation for further functional analyses of this gene family in wheat.

Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed

TCP proteins are plant-specific transcription factors that have multipurpose roles in plant developmental procedures and stress responses. Therefore, a genome-wide analysis was performed to categorize the TCP genes in the rapeseed genome. In this study, a total of 80 BnTCP genes were identified in the rapeseed genome and grouped into two main classes (PCF and CYC/TB1) according to phylogenetic analysis. The universal evolutionary analysis uncovered that BnTCP genes had experienced segmental duplications and positive selection pressure. Gene structure and conserved motif examination presented that Class I and Class II have diverse intron-exon patterns and motifs numbers. Overall, nine conserved motifs were identified and varied from 2 to 7 in all TCP genes; and some of them were gene-specific. Mainly, Class II (PCF and CYC/TB1) possessed diverse structures compared to Class I. We identified four hormone- and four stress-related responsive cis-elements in the promoter regions. Moreover, 32 bna-miRNAs from 14 families were found to be targeting 21 BnTCPs genes. Gene ontology enrichment analysis presented that the BnTCP genes were primarily related to RNA/DNA binding, metabolic processes, transcriptional regulatory activities, etc. Transcriptome-based tissue-specific expression analysis showed that only a few genes (mainly BnTCP9, BnTCP22, BnTCP25, BnTCP48, BnTCP52, BnTCP60, BnTCP66, and BnTCP74) presented higher expression in root, stem, leaf, flower, seeds, and silique among all tested tissues. Likewise, qRT-PCR-based expression analysis exhibited that BnTCP36, BnTCP39, BnTCP53, BnTCP59, and BnTCP60 showed higher expression at certain time points under various hormones and abiotic stress conditions but not by drought and MeJA. Our results opened the new groundwork for future understanding of the intricate mechanisms of BnTCP in various developmental processes and abiotic stress signaling pathways in rapeseed.