Genome-wide profiling of bZIP transcription factors in Camelina sativa: implications for development and stress response.

BACKGROUND: The bZIP transcription factor family, characterized by a bZIP domain, plays vital roles in plant stress responses and development. While this family has been extensively studied in various plant species, its specific functions in Camelina sativa (False Flax) remain underexplored. METHODS AND RESULTS: This study identified 71 bZIP transcription factors in C. sativa, classified into nine distinct groups based on phylogenetic analysis. Subcellular localization predicted a nucleus-specific expression for these bZIPs. Analysis of GRAVY scores revealed a range from 0.469 to -1.256, indicating a spectrum from hydrophobic to hydrophilic properties. Motif analysis uncovered 10 distinct motifs, with one motif being universally present in all CsbZIPs. Conserved domain analysis highlighted several domains beyond the core bZIP domain. Protein-protein interaction predictions suggested a robust network involving CsbZIPs. Moreover, promoter analysis revealed over 60 types of cis-elements, including those responsive to stress. Expression studies through RNA-seq and Real-time RT-qPCR demonstrated high expression of CsbZIPs in roots, leaves, flowers, and stems. Specifically, CsbZIP01, CsbZIP02, CsbZIP44, and CsbZIP60 were consistently up-regulated under cold, salt, and drought stresses, whereas CsbZIP34 and CsbZIP35 were down-regulated. CONCLUSION: This study presents the first comprehensive genome-wide profiling of bZIP transcription factors in Camelina sativa, providing novel insights into their roles in plant development and stress response mechanisms. By identifying and characterizing the bZIP gene family in C. sativa, this research offers new opportunities for improving stress tolerance and crop resilience through targeted genetic approaches, addressing key challenges in agriculture under changing environmental conditions.

Exposure to toxic cadmium concentration induce physiological and molecular mechanisms alleviating herbivory infestation in Wedelia.

Cadmium (Cd) toxicity induces significant disruptions in growth and development, plants have developed strategies to alleviate metal toxicity promoting establishment even during herbivores infestation. The study demonstrates that W. trilobata maintains growth and development under the combined stress of Cd exposure and herbivore invasion by Spodoptera litura, in contrast to W. chinensis. Cd toxicity markedly reduce shoot elongation and total fresh biomass, and a significant decrease in the dry weight of the shoot biomass and leaf count by 19%, 18%, 16%, and 19% in W. trilobata compared to controls. An even more pronounced decrease of 35%, 43%, 45% and 43% was found in W. chinensis. Compared to W. chinensis, W. trilobata showed a higher increase in phytohormone production including abscisic acid (ABA), gibberellic acid (GA3), indole-3-acetic acid (IAA) and methyl jasmonic acid (JA-me) under both Cd and herbivory stress as compared with respective controls. In addition, leaf ultra-structure also showed the highest damage to cell membranous structures by Cd-toxicity in W. chinensis. Furthermore, RNA-seq analysis revealed numerous genes viz., EMSY, MCCA, TIRI, BED-type, ABA, JAZ, CAB-6, CPSI, LHCII, CAX, HNM, ABC-Cd-trans and GBLP being differentially expressed between Cd-stress and herbivory groups in both W. trilobata and W. chinensis, with a particular emphasis on genes associated with metal transport and carbohydrate metabolism. Analyses employing the Gene Ontology (GO) system, the Clusters of Orthologous Groups (COG) categorization, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, highlight the functional and evolutionary relationships among the genes of the Phenylpropanoid and Flavonoid biosynthesis pathways and brassinosterod metabolism, associated with plant growth and development under Cd-toxicity and herbivory. W. trilobata opposite of W. chinensis, significantly improve plant growth and mitigates Cd toxicity through modulation of metabolic processes, and regulation of responsible genes, to sustain its growth under Cd and herbivory stress, which can be used in stress improvement in plants for sustainable ecosystem biodiversity and food security.

Computational analysis and expression profiling of two-component system (TCS) gene family members in mango (Mangifera indica) indicated their roles in stress response.

The two-component system (TCS) gene family is among the most important signal transduction families in plants and is involved in the regulation of various abiotic stresses, cell growth and division. To understand the role of TCS genes in mango (Mangifera indica ), a comprehensive analysis of TCS gene family was carried out in mango leading to identification of 65 MiTCS genes. Phylogenetic analysis divided MiTCSs into three groups (histidine kinases, histidine-containing phosphotransfer proteins, and response regulators) and 11 subgroups. One tandem duplication and 23 pairs of segmental duplicates were found within the MiTCSs . Promoter analysis revealed that MiTCSs contain a large number of cis -elements associated with environmental stresses, hormone response, light signalling, and plant development. Gene ontology analysis showed their involvement in various biological processes and molecular functions, particularly signal transduction. Protein-protein interaction analysis showed that MiTCS proteins interacted with each other. The expression pattern in various tissues and under many stresses (drought, cold, and disease) showed that expression levels varied among various genes in different conditions. MiTCSs 3D structure predictions showed structural conservation among members of the same groups. This information can be further used to develop improved cultivars and will serve as a foundation for gaining more functional insights into the TCS gene family.

Regulatory role of AGC genes in heat stress adaptation in maize (Zea mays).

Heat stress represents a significant environmental challenge that restricts maize (Zea mays ) growth and yield on a global scale. Within the plant kingdom, the AGC gene family, encoding a group of protein kinases, has emerged as crucial players in various stress responses. Nevertheless, a comprehensive understanding of AGC genes in Z. mays under heat-stress conditions remains elusive. A genome-wide analysis was done using bioinformatics techniques to identify 39 AGC genes in Z. mays , categorising them into three subfamilies based on their conserved domains. We investigated their phylogenetic relationships, gene structures (including intron-exon configurations), and expression patterns. These genes are likely involved in diverse signalling pathways, fulfilling distinct roles when exposed to heat stress conditions. Notably, most ZmAGC1.5, ZmAGC1.9, ZmNDR3, ZmNDR5 and ZmIRE3 exhibited significant changes in expression levels under heat stress, featuring a high G-box ratio. Furthermore, we pinpointed a subset of AGC genes displaying highly coordinated expression, implying their potential involvement in the heat stress response pathway. Our study offers valuable insights into the contribution of AGC genes to Z. mays 's heat stress response, thus facilitating the development of heat-tolerant Z. mays varieties.

Rejuvenating potato growth and yield in challenging semiarid and saline sandy Cholistan: harnessing PGPB-coated N and P application strategies.

BACKGROUND: Potato serves as a major non-cereal food crop and income source for small-scale growers in Punjab, Pakistan. Unfortunately, improper fertilization practices have led to low crop yields, worsened by challenging environmental conditions and poor groundwater quality in the Cholistan region. To address this, we conducted an experiment to assess the impact of two fertilizer application approaches on potato cv. Barna using plant growth-promoting bacteria (PGPB) coated biofertilizers. The first approach, termed conventional fertilizer application (CFA), involved four split applications of PGPB-coated fertilizers at a rate of 100:75 kg acre-1 (N and P). The second, modified fertilizer application (MFA), employed nine split applications at a rate of 80:40 kg acre-1. RESULTS: The MFA approach significantly improved various plant attributes compared to the CFA. This included increased plant height (28%), stem number (45%), leaf count (46%), leaf area index (36%), leaf thickness (three-folds), chlorophyll content (53%), quantum yield of photosystem II (45%), photosynthetically active radiations (56%), electrochromic shift (5.6%), proton flux (24.6%), proton conductivity (71%), linear electron flow (72%), photosynthetic rate (35%), water use efficiency (76%), and substomatal CO2 (two-folds), and lowered non-photochemical quenching (56%), non-regulatory energy dissipation (33%), transpiration rate (59%), and stomatal conductance (70%). Additionally, the MFA approach resulted in higher tuber production per plant (21%), average tuber weight (21.9%), tuber diameter (24.5%), total tuber yield (29.1%), marketable yield (22.7%), seed-grade yield (9%), specific gravity (9.6%), and soluble solids (7.1%). It also reduced undesirable factors like goli and downgrade yields by 57.6% and 98.8%, respectively. Furthermore, plants under the MFA approach exhibited enhanced nitrogen (27.8%) and phosphorus uptake (40.6%), with improved N (26.1%) and P uptake efficiency (43.7%) compared to the CFA approach. CONCLUSION: The use of PGPB-coated N and P fertilizers with a higher number of splits at a lower rate significantly boosts potato production in the alkaline sandy soils of Cholistan.

Exploring the mechanism of transformation in Acacia nilotica (Linn.) triggered by colchicine seed treatment.

BACKGROUND: Acacia nilotica Linn. is a widely distributed tree known for its applications in post-harvest and medicinal horticulture. However, its seed-based growth is relatively slow. Seed is a vital component for the propagation of A. nilotica due to its cost-effectiveness, genetic diversity, and ease of handling. Colchicine, commonly used for polyploidy induction in plants, may act as a pollutant at elevated levels. Its optimal concentration for Acacia nilotica's improved growth and development has not yet been determined, and the precise mechanism underlying this phenomenon has not been established. Therefore, this study investigated the impact of optimized colchicine (0.07%) seed treatment on A. nilotica's morphological, anatomical, physiological, fluorescent, and biochemical attributes under controlled conditions, comparing it with a control. RESULTS: Colchicine seed treatment significantly improved various plant attributes compared to control. This included increased shoot length (84.6%), root length (53.5%), shoot fresh weight (59.1%), root fresh weight (42.8%), shoot dry weight (51.5%), root dry weight (40%), fresh biomass (23.6%), stomatal size (35.9%), stomatal density (41.7%), stomatal index (51.2%), leaf thickness (11 times), leaf angle (2.4 times), photosynthetic rate (40%), water use efficiency (2.2 times), substomatal CO2 (36.6%), quantum yield of photosystem II (13.1%), proton flux (3.1 times), proton conductivity (2.3 times), linear electron flow (46.7%), enzymatic activities of catalase (25%), superoxide dismutase (33%), peroxidase (13.5%), and ascorbate peroxidase (28%), 2,2-diphenyl-1-picrylhydrazyl-radical scavenging activities(23%), total antioxidant capacity (59%), total phenolic (23%), and flavonoid content (37%) with less number of days to 80% germination (57.1%), transpiration rate (53.9%), stomatal conductance (67.1%), non-photochemical quenching (82.8%), non-regulatory energy dissipation (24.3%), and H2O2 (25%) and O-2 levels (30%). CONCLUSION: These findings elucidate the intricate mechanism behind the morphological, anatomical, physiological, fluorescent, and biochemical transformative effects of colchicine seed treatment on Acacia nilotica Linn. and offer valuable insights for quick production of A. nilotica's plants with modification and enhancement from seeds through an eco-friendly approach.

Precision Genome Editing with CRISPR-Cas9.

The CRISPR/Cas9 system is a revolutionary technology for genome editing that allows for precise and efficient modifications of DNA sequences. The system is composed of two main components, the Cas9 enzyme and a guide RNA (gRNA). The gRNA is designed to specifically target a desired DNA sequence, while the Cas9 enzyme acts as molecular scissors to cut the DNA at that specific location. The cell then repairs the digested DNA, either through nonhomologous end joining (NHEJ) or homology-directed repair (HDR), resulting in either indels or precise modifications of DNA sequences with broad implications in biotechnology, agriculture, and medicine. This chapter provides a practical approach for utilizing CRISPR/Cas9 in precise genome editing, including identifying the target gene sequence, designing gRNA and protein (Cas9), and delivering the CRISPR components to target cells.

An integrated network pharmacology approach to discover therapeutic mechanisms of Commiphora wightii for the treatment of Bell's palsy.

Bell's palsy (BP) can result in facial paralysis. Inflammation or injury to the cranial nerves that regulate the facial muscles is primarily responsible for that disease. Commiphora wightii remains recognized as a cure for a few human ailments. This study focused on therapeutic phenomena of C. wightii for the treatment of Bell's palsy, utilizing the network drug discovery and molecular docking techniques. Active biological constituents of C. wightii were retrieved from literature and independent databases. Potential therapeutic targets (431) of 13 bioactive phytochemicals were fetched via SwissTargetPrediction tool. Putative intersecting targets (855) of Bell's palsy were computed through the DisGeNET and GeneCards datasets. Subsequently, by the analysis of potential shared targets (87) of C. wightii and Bell's palsy, a Venn diagram was drawn. DAVID database was used to evaluate gene functional annotations and enriched pathways that are involved in Bell's palsy. STRING database was used for generating the protein-protein relationship complex. Visual presentations of the interactions of potential targets to active chemical constituents were done by the Cytoscape. Whereas, the conformational research sorted out 10 key targets through the protein-protein interactions network. Moreover, the capacity of therapeutic ingredients to interact with a target inhibiting Bell's palsy was confirmed by molecular docking, which might ratify the findings of network pharmacology. In the molecular complex of AKT1-cholesterol, a 100-ns simulation unveiled a graceful stability, with a minimal 0.167 Å ligand shift and resilient hydrogen bonds (ASN54 and SER205). The final 20 ns showcased a P1 motif pirouette, gracefully forming aromatic bonds with H165 and W186, underscoring the complex's dynamic finesse. This study evaluated compound-target interactions and their impact on disease-related genes. It revealed that five genes (AKT1, TNF, MAPK3, EGFR and SRC) of C. wightii might be useful therapeutic targets for the treatment of Bell's palsy, as well as helping in lowering down the blood pressure.Communicated by Ramaswamy H. Sarma.

In Silico Comparison of WRKY Transcription Factors in Wild and Cultivated Soybean and Their Co-expression Network Arbitrating Disease Resistance.

WRKY Transcription factors (TFs) play critical roles in plant defence mechanisms that are activated in response to biotic and abiotic stresses. However, information on the Glycine soja WRKYs (GsoWRKYs) is scarce. Owing to its importance in soybean breeding, here we identified putative WRKY TFs in wild soybean, and compared the results with Glycine max WRKYs (GmaWRKYs) by phylogenetic, conserved motif, and duplication analyses. Moreover, we explored the expression trends of WRKYs in G. max (oomycete, fungi, virus, bacteria, and soybean cyst nematode) and G. soja (soybean cyst nematode), and identified commonly expressed WRKYs and their co-expressed genes. We identified, 181 and 180 putative WRKYs in G. max and G. soja, respectively. Though the number of WRKYs in both studied species is almost the same, they differ in many ways, i.e., the number of WRKYs on corresponding chromosomes, conserved domain structures, WRKYGQK motif variants, and zinc-finger motifs. WRKYs in both species grouped in three major clads, i.e., I-III, where group-II had sub-clads IIa-IIe. We found that GsoWRKYs expanded mostly through segmental duplication. A large number of WRKYs were expressed in response to biotic stresses, i.e., Phakospora pachyrhizi, Phytoplasma, Heterodera glycines, Macrophomina phaseolina, and Soybean mosaic virus; 56 GmaWRKYs were commonly expressed in soybean plants infected with these diseases. Finally, 30 and 63 GmaWRKYs and GsoWRKYs co-expressed with 205 and 123 non-WRKY genes, respectively, indicating that WRKYs play essential roles in biotic stress tolerance in Glycine species.

Identification and expression analysis of SBP-Box-like (SPL) gene family disclose their contribution to abiotic stress and flower budding in pigeon pea (Cajanus cajan).

The SPL gene family (for Squamosa Promoter-binding like Proteins) represents specific transcription factors that have significant roles in abiotic stress tolerance, development and the growth processes of different plants, including initiation of the leaf, branching and development of shoot and fruits. The SPL gene family has been studied in different plant species; however, its role is not yet fully explored in pigeon pea (Cajanus cajan ). In the present study, 11 members of the CcSPL gene family were identified in C. cajan . The identified SPLs were classified into nine groups based on a phylogenetic analysis involving SPL protein sequences from C. cajan , Arabidopsis thaliana , Cicer arietinum , Glycine max , Phaseolus vulgaris , Vigna unguiculata and Arachis hypogaea . Further, the identification of gene structure, motif analysis, domain analysis and presence of cis -regulatory elements in the SPL family members were studied. Based on RNA-sequencing data, gene expression analysis was performed, revealing that CcSPL2.1, 3 and 13A were significantly upregulated for salt-tolerance and CcSPL14 and 15 were upregulated in a salt-susceptible cultivar. Real-time qPCR validation indicated that CcSPL3, 4, 6 and 13A were upregulated under salt stress conditions. Therefore, molecular docking was performed against the proteins of two highly expressed genes (CcSPL3 and CcSPL14 ) with three ligands: abscisic acid, gibberellic acid and indole-3-acetic acid. Afterward, their binding affinity was obtained and three-dimensional structures were predicted. In the future, our study may open avenues for harnessing CcSPL genes in pigeon pea for enhanced abiotic stress resistance and developmental traits.

Identification of novel inhibitors against VP40 protein of Marburg virus by integrating molecular modeling and dynamics approaches.

Marburg virus (MV) is a highly etiological agent of haemorrhagic fever in humans and has spread across the world. Its outbreaks caused a 23-90% human death rate. However, there are currently no authorized preventive or curative measures yet. VP40 is the MV matrix protein, which builds protein shell underneath the viral envelope and confers hallmark filamentous. VP40 alone is able to induce assembly and budding of filamentous virus-like particles (VLPs), which resemble authentic virions. As a result, this research is credited with clarifying the function of VP40 and leading to the discovery of new therapeutic targets effective in combating MV disease (MVD). Virtual screening, molecular docking and molecular dynamics (MD) simulation were used to find the putative active chemicals based on a 3D pharmacophore model of the protein's active site cavity. Initially, andrographidine-C, a potent inhibitor was selected for the development of the pharmacophore model. Later, a library of 30,000 compounds along with the andrographidine-C was docked against VP40 protein. Three best hits including avanafil, diuvaretin and macrourone were subjected to further MD simulation analysis, as these compounds had better binding affinities as compared to andrographidine-C. Furthermore, throughout the 100 ns simulations, the back bone of VP40 protein in presence of avanafil, diuvaretin and macrourone remained stable which was further validated by MM-PBSA analysis. Additionally, all of these compounds depict maximum drug-like properties. The predicted drugs based on the ligand, avanafil, diuvaretin and macrourone could be exploited and developed as an alternative or complementary therapy for the treatment of MVD.Communicated by Ramaswamy H. Sarma.

Molecular characterization of genes involved in tolerance of cadmium in Triticum aestivum (L.) under Cd stress.

The NRAMPs (natural resistance-associated macrophage proteins) are major transporters for the absorption and transport of metals like Pb, Zn, Mn, Fe, and Cd in plants. While NRAMP gene family members have been extensively studied as metal transporters in model and other plants, little information has been reported on their role in Triticum aestivum, particularly in response to Cd stress. Current study reported 13 NRAMP candidates in the genome of T. aestivum. Phylogenetic analysis divided these into three clades. Motif and gene structure study showed that members in the same clades shared the same location and pattern, which further supported the phylogenetic analysis. The analysis of cis-acting elements in promoter sequences of NRAMP genes in wheat identified stress-responsive transcription factor binding sites. Multiple sequence alignment identified the conservation of important residues. Based on RNA-seq and qRT-PCR analysis, Cd stress-responsive variations of TaNRAMP gene expression were reported. This study provides comprehensive data to understand the TaNRAMP gene family, its features, and its expression, which will be a helpful framework for functional research.

Combined application of hot water treatment and eucalyptus leaf extract postpones senescence in harvested green chilies by conserving their antioxidants: a sustainable approach.

BACKGROUND: Green chili is the predominant vegetable in tropical and subtropical regions with high economic value. However, after harvest, it exhibits vigorous metabolic activities due to the high moisture level, leading to a reduction in bioactive compounds and hence reduced shelf life and nutritional quality. Low temperature storage results in the onset of chilling injury symptoms. Therefore, developing techniques to increase the shelf life of green chilies and safeguard their nutritional value has become a serious concern for researchers. In this regard, an experiment was conducted to evaluate the impact of the alone or combined application of hot water treatment (HWT) (45 °C for 15 min) and eucalyptus leaf extract (ELE) (30%) on 'Golden Hot' chilies in comparison to the control. After treatment, chilies were stored at 20 ± 1.5 °C for 20 days. RESULTS: HWT + ELE-treated chilies had a significant reduction in fruit weight loss (14.6%), fungal decay index (35%), red chili percentage (41.2%), soluble solid content (42.9%), ripening index (48.9%), and reactive oxygen species production like H2O2 (55.1%) and O-2 (46.5%) during shelf in comparison to control, followed by the alone application of HWT and ELE. Furthermore, the combined use of HWT and ELE effectively improved the antioxidative properties of stored chilies including DPPH radical scavenging activities (54.6%), ascorbic acid content (28.4%), phenolic content (31.8%), as well as the enzyme activities of POD (103%), CAT (128%), SOD (26.5%), and APX (43.8%) in comparison to the control. Additionally, the green chilies underwent HWT + ELE treatment also exhibited higher chlorophyll levels (100%) and general appearance (79.6%) with reduced anthocyanin content (40.8%) and wrinkling (43%), leading to a higher marketable fruit (41.3%) than the control. CONCLUSION: The pre-storage application of HWT and ELE could be used as an antimicrobial, non-chemical, non-toxic, and eco-friendly treatment for preserving the postharvest quality of green chilies at ambient temperature (20 ± 1.5 °C).

Effect of foliar applied zinc sulphate on phenotypic variability, association and heritability of yield and zinc biofortification related traits of wheat genotypes.

Wheat is an important food crop worldwide, providing substantial calories and nourishment. Genetic variability in wheat germplasm is crucial for the development of cultivars with desirable features. This two years study (2020-21 and 2021-22) was conducted to evaluate 13 diverse wheat genotypes factorially combined with foliar-applied zinc sulphate (0, 0.4, 0.6%) arranged in a triplicate randomized complete block design. Boxplot analysis revealed the significant (P < 0.01) phenotypic variation of wheat germplasm for all the studied traits, but maximum variation was observed for yield and Zn biofortification-related traits. Correlation and path analysis revealed a significant (P < 0.01) association among yield and biofortification-related traits. Zinc uptake showed maximum strength of association (r = 0.96, p < 0.01) with grain Zn concentration. The Biplot analysis showed the graphical representation of wheat accessions based on similar characteristics and then assort into distinct groups. Broadsense heritability (Hbs) was calculated to determine the proportion of variation transmitted to future generations. The high value of Hbs for yield and Zn biofortification-related traits indicates that these traits are governed by the additive type of gene action and can be fixed in early segregating generations. In crux, this study validated the genetic variability in existing wheat genotypes for yield and Zn biofortification-related traits and may be helpful to devise an efficient breeding program for wheat Zn biofortification.

Integrated omics and machine learning-assisted profiling of cysteine-rich-receptor-like kinases from three peanut spp. revealed their role in multiple stresses.

Arachis hypogaea (peanut) is a leading oil and protein-providing crop with a major food source in many countries. It is mostly grown in tropical regions and is largely affected by abiotic and biotic stresses. Cysteine-rich receptor-like kinases (CRKs) is a family of transmembrane proteins that play important roles in regulating stress-signaling and defense mechanisms, enabling plants to tolerate stress conditions. However, almost no information is available regarding this gene family in Arachis hypogaea and its progenitors. This study conducts a pangenome-wide investigation of A. hypogaea and its two progenitors, A. duranensis and A. ipaensis CRK genes (AhCRKs, AdCRKs, and AiCRKs). The gene structure, conserved motif patterns, phylogenetic history, chromosomal distribution, and duplication were studied in detail, showing the intraspecies structural conservation and evolutionary patterns. Promoter cis-elements, protein-protein interactions, GO enrichment, and miRNA targets were also predicted, showing their potential functional conservation. Their expression in salt and drought stresses was also comprehensively studied. The CRKs identified were divided into three groups, phylogenetically. The expansion of this gene family in peanuts was caused by both types of duplication: tandem and segmental. Furthermore, positive as well as negative selection pressure directed the duplication process. The peanut CRK genes were also enriched in hormones, light, development, and stress-related elements. MicroRNA (miRNA) also targeted the AhCRK genes, which suggests the regulatory association of miRNAs in the expression of these genes. Transcriptome datasets showed that AhCRKs have varying expression levels under different abiotic stress conditions. Furthermore, the multi-stress responsiveness of the AhCRK genes was evaluated using a machine learning-based method, Random Forest (RF) classifier. The 3D structures of AhCRKs were also predicted. Our study can be utilized in developing a detailed understanding of the stress regulatory mechanisms of the CRK gene family in peanuts and its further studies to improve the genetic makeup of peanuts to thrive better under stress conditions.

Postharvest starch and sugars adjustment in potato tubers of wide-ranging dormancy genotypes subjected to various sprout forcing techniques.

The development of an efficient, safe, and environment-friendly technique to terminate tuber dormancy in potatoes (Solanum tuberosum L.) is of great concern due to the immense scope of multiple cropping all over the globe. The breakage of tuber dormancy has been associated with numerous physiological changes, including a decline in the level of starch and an increase in the levels of sugars during storage of freshly harvested seed potatoes, although their consistency across genotypes and various dormancy-breaking techniques have not yet been fully elucidated. The purpose of the present research is to assess the efficacy of four different dormancy-breaking techniques, such as soaking in 90, 60, or 30 mg L-1 solutions of benzyl amino purine (BAP) and 30, 20, or 10 mg L-1 gibberellic acid (GA3) alone and in the combination of optimized concentrations; cold pre-treatment at 6, 4, or 2 °C; electric shock at 80, 60, 40, or 20 Vs; and irradiation at 3.5, 3, 2.5, 2, 1.5, or 1 kGy on the tuber dormancy period and sprout length of six genotypes. Furthermore, the changes that occurred in tuber weight and endogenous starch, sucrose, fructose, and glucose contents in experimental genotypes following the application of these techniques were also examined. Overall, the most effective technique to terminate tuber dormancy and hasten spout growth was the combined application of BAP and GA3, which reduced the length of dormancy by 9.6 days compared to the untreated control, following 6.7 days of electric current, 4.4 days of cold pre-treatment, and finally irradiation (3.3 days). The 60 mg L-1 solution of BAP greatly reduced the dormancy period in all genotypes but did not affect the sprout length at all. The genotypes showed a weak negative correlation (r = - 0.4) (P < 0.05) of endogenous starch contents with dormancy breakage and weight loss or a moderate (r = - 0.5) correlation with sprout length, but a strong positive correlation (r = 0.8) of tuber glucose, fructose, and sucrose contents with dormancy breakage and weight loss. During 3 weeks of storage, sprouting commencement and significant weight loss occurred as tuber dormancy advanced towards breakage due to a reduction in starch and an increase in the sucrose, fructose, and glucose contents of the tubers. These findings could be advantageous for postponing or accelerating seed potato storage as well as investigating related physiological research in the future.

Genome-wide identification and expression profiling of two-component system (TCS) genes in Brassica oleracea in response to shade stress.

The Two-component system (TCS) consists of Histidine kinases (HKs), Phosphotransfers (HPs), and response regulator (RR) proteins. It has an important role in signal transduction to respond to a wide variety of abiotic stresses and hence in plant development. Brassica oleracea (cabbage) is a leafy vegetable, which is used for food and medicinal purposes. Although this system was identified in several plants, it had not been identified in Brassica oleracea yet. This genome-wide study identified 80 BoTCS genes consisting of 21 HKs, 8 HPs, 39 RRs, and 12 PRRs. This classification was done based on conserved domains and motif structure. Phylogenetic relationships of BoTCS genes with Arabidopsis thaliana, Oryza sativa, Glycine max, and Cicer arietinum showed conservation in TCS genes. Gene structure analysis revealed that each subfamily had conserved introns and exons. Both tandem and segmental duplication led to the expansion of this gene family. Almost all of the HPs and RRs were expanded through segmental duplication. Chromosomal analysis showed that BoTCS genes were dispersed across all nine chromosomes. The promoter regions of these genes were found to contain a variety of cis-regulatory elements. The 3D structure prediction of proteins also confirmed the conservation of structure within subfamilies. MicroRNAs (miRNAs) involved in the regulation of BoTCSs were also predicted and their regulatory roles were also evaluated. Moreover, BoTCSs were docked with abscisic acid to evaluate their binding. RNA-seq-based expression analysis and validation by qRT-PCR showed significant variation of expression for BoPHYs, BoERS1.1, BoERS2.1, BoERS2.2, BoRR10.2, and BoRR7.1 suggesting their importance in stress response. These genes showing unique expression can be further used in manipulating the plant's genome to make the plant more resistant the environmental stresses which will ultimately help in the increase of plant's yield. More specifically, these genes have altered expression in shade stress which clearly indicates their importance in biological functions. These findings are important for future functional characterization of TCS genes in generating stress-responsive cultivars.

Rice straw based silicon nanoparticles improve morphological and nutrient profile of rice plants under salinity stress by triggering physiological and genetic repair mechanisms.

The agricultural sector is facing numerous challenges worldwide, owing to global climate change and limited resources. Crop production is limited by numerous abiotic constraints. Among them, salinity stress as a combination of osmotic and ionic stress adversely influences the physiological and biochemical processes of the plant. Nanotechnology facilitates the production of crops either directly by eradicating the losses due to challenging environmental conditions or indirectly by improving tolerance against salinity stress. In this study, the protective role of silicon nanoparticles (SiNPs) was determined in two rice genotypes, N-22 and Super-Bas, differing in salinity tolerance. The SiNPs were confirmed through standard material characterization techniques, which showed the production of spherical-shaped crystalline SiNPs with a size in the range of 14.98-23.74 nm, respectively. Salinity stress adversely affected the morphological and physiological parameters of both varieties, with Super-Bas being more affected. Salt stress disturbed the ionic balance by minimizing the uptake of K+ and Ca2+ contents and increased the uptake of Na+ in plants. Exogenous SiNPs alleviated the toxic effects of salt stress and promoted the growth of both N-22 and Super-Bas, chlorophyll contents (16% and 13%), carotenoids (15% and 11%), total soluble protein contents (21% and 18%), and the activities of antioxidant enzymes. Expression analysis from quantitative real-time PCR showed that SiNPs relieved plants from oxidative bursts by triggering the expression of HKT genes. Overall, these findings demonstrate that SiNPs significantly alleviated salinity stress by triggering physiological and genetic repair mechanisms, offering a potential solution for food security.

Omics-assisted characterization of two-component system genes from Gossypium Raimondii in response to salinity and molecular interaction with abscisic acid.

The two-component system (TCS) genes are involved in a wide range of physiological processes in prokaryotes and eukaryotes. In plants, the TCS elements help in a variety of functions, including cell proliferation, response to abiotic and biotic stresses, leaf senescence, nutritional signaling, and division of chloroplasts. Three different kinds of proteins make up the TCS system in plants. These are known as HKs (histidine kinases), HPs (histidine phosphotransfer), and RRs (response regulators). We investigated the genome of Gossypium raimondii and discovered a total of 59 GrTCS candidates, which include 23 members of the HK family, 8 members of the HP family, and 28 members of the RR family. RR candidates are further classified as type-A (6 members), type-B (11 members), type-C (2 members), and pseudo-RRs (9 members). The GrTCS genes were analyzed in comparison with the TCS components of other plant species such as Arabidopsis thaliana, Cicer arietinum, Sorghum bicolor, Glycine max, and Oryza sativa. This analysis revealed both conservation and changes in their structures. We identified 5 pairs of GrTCS syntenic homologs in the G. raimondii genome. All 59 TCS genes in G. raimondii are located on all thirteen chromosomes. The GrTCS promoter regions have several cis-regulatory elements, which function as switches and respond to a wide variety of abiotic stresses. RNA-seq and real-time qPCR analysis showed that the majority of GrTCS genes are differentially regulated in response to salt and cold stress. 3D structures of GrTCS proteins were predicted to reveal the specific function. GrTCSs were docked with abscisic acid to assess their binding interactions. This research establishes the groundwork for future functional studies of TCS elements in G. raimondii, which will further focus on stress resistance and overall development.

Bioplastics from waste biomass of marine and poultry industries.

Plastics are indispensable and typically derived from non-renewable sources. The extensive production and indiscriminate use of synthetic plastics pose a serious threat to the environment and lead to problems due to their non-biodegradability. Various forms of plastics that are used in daily life should be limited and replaced by biodegradable materials. To deal with the challenges of sustainability or environmental issues that occur due to the production and disposal of synthetic plastics, biodegradable and environment-friendly plastics are crucial. Utilizing renewable sources such as keratin derived from chicken feathers and chitosan from shrimp cell wastes as an alternative to obtain safe bio-based polymers has gained much attention because of rising environmental issues. Approximately, 2-5 billion tons of waste are produced by the poultry and marine industries each year, adversely impacting the environment. These polymers are more acceptable and ecofriendly compared with conventional plastics due to their biostability, biodegradability, and excellent mechanical properties. The replacement of synthetic plastic packaging with biodegradable polymers from animal by-products significantly reduces the volume of waste generated. This review highlights important aspects such as the classification of bioplastics, properties and use of waste biomass for bioplastics production, their structure, mechanical properties, and demand in industrial sectors such as agriculture, biomedicine, and food packaging.