Integrative System Biology Analysis of Transcriptomic Responses to Drought Stress in Soybean (Glycine max L.)

Drought is a major abiotic stressor that causes yield losses and limits the growing area for most crops. Soybeans are an important legume crop that is sensitive to water-deficit conditions and suffers heavy yield losses from drought stress. To improve drought-tolerant soybean cultivars through breeding, it is necessary to understand the mechanisms of drought tolerance in soybeans. In this study, we applied several transcriptome datasets obtained from soybean plants under drought stress in comparison to those grown under normal conditions to identify novel drought-responsive genes and their underlying molecular mechanisms. We found 2168 significant up/downregulated differentially expressed genes (DEGs) and 8 core modules using gene co-expression analysis to predict their biological roles in drought tolerance. Gene Ontology and KEGG analyses revealed key biological processes and metabolic pathways involved in drought tolerance, such as photosynthesis, glyceraldehyde-3-phosphate dehydrogenase and cytokinin dehydrogenase activity, and regulation of systemic acquired resistance. Genome-wide analysis of plants’ cis-acting regulatory elements (CREs) and transcription factors (TFs) was performed for all of the identified DEG promoters in soybeans. Furthermore, the PPI network analysis revealed significant hub genes and the main transcription factors regulating the expression of drought-responsive genes in each module. Among the four modules associated with responses to drought stress, the results indicated that GLYMA_04G209700, GLYMA_02G204700, GLYMA_06G030500, GLYMA_01G215400, and GLYMA_09G225400 have high degrees of interconnection and, thus, could be considered as potential candidates for improving drought tolerance in soybeans. Taken together, these findings could lead to a better understanding of the mechanisms underlying drought responses in soybeans, which may useful for engineering drought tolerance in plants

Integrative System Biology Analysis of Transcriptomic Responses to Drought Stress in Soybean (Glycine max L.)

Drought is a major abiotic stressor that causes yield losses and limits the growing area for most crops. Soybeans are an important legume crop that is sensitive to water-deficit conditions and suffers heavy yield losses from drought stress. To improve drought-tolerant soybean cultivars through breeding, it is necessary to understand the mechanisms of drought tolerance in soybeans. In this study, we applied several transcriptome datasets obtained from soybean plants under drought stress in comparison to those grown under normal conditions to identify novel drought-responsive genes and their underlying molecular mechanisms. We found 2168 significant up/downregulated differentially expressed genes (DEGs) and 8 core modules using gene co-expression analysis to predict their biological roles in drought tolerance. Gene Ontology and KEGG analyses revealed key biological processes and metabolic pathways involved in drought tolerance, such as photosynthesis, glyceraldehyde-3-phosphate dehydrogenase and cytokinin dehydrogenase activity, and regulation of systemic acquired resistance. Genome-wide analysis of plants’ cis-acting regulatory elements (CREs) and transcription factors (TFs) was performed for all of the identified DEG promoters in soybeans. Furthermore, the PPI network analysis revealed significant hub genes and the main transcription factors regulating the expression of drought-responsive genes in each module. Among the four modules associated with responses to drought stress, the results indicated that GLYMA_04G209700, GLYMA_02G204700, GLYMA_06G030500, GLYMA_01G215400, and GLYMA_09G225400 have high degrees of interconnection and, thus, could be considered as potential candidates for improving drought tolerance in soybeans. Taken together, these findings could lead to a better understanding of the mechanisms underlying drought responses in soybeans, which may useful for engineering drought tolerance in plants

Potential role of the regulatory miR1119-MYC2 module in wheat (Triticum aestivum L.) drought tolerance

MicroRNA (miRNA)-target gene modules are essential components of plants' abiotic stress signalling pathways Little is known about the drought-responsive miRNA-target modules in wheat, but systems biology approaches have enabled the prediction of these regulatory modules and systematic study of their roles in responses to abiotic stresses. Using such an approach, we sought miRNA-target module(s) that may be differentially expressed under drought and non-stressed conditions by mining Expressed Sequence Tag (EST) libraries of wheat roots and identified a strong candidate (miR1119-MYC2). We then assessed molecular and physiochemical differences between two wheat genotypes with contrasting drought tolerance in a controlled drought experiment and assessed possible relationships between their tolerance and evaluated traits. We found that the miR1119-MYC2 module significantly responds to drought stress in wheat roots. It is differentially expressed between the contrasting wheat genotypes and under drought versus non-stressed conditions. We also found significant associations between the module's expression profiles and ABA hormone content, water relations, photosynthetic activities, H2O2 levels, plasma membrane damage, and antioxidant enzyme activities in wheat. Collectively, our results suggest that a regulatory module consisting of miR1119 and MYC2 may play an important role in wheat's drought tolerance

Potential role of the regulatory miR1119-MYC2 module in wheat (Triticum aestivum L.) drought tolerance

MicroRNA (miRNA)-target gene modules are essential components of plants’ abiotic stress signalling pathways Little is known about the drought-responsive miRNA-target modules in wheat, but systems biology approaches have enabled the prediction of these regulatory modules and systematic study of their roles in responses to abiotic stresses. Using such an approach, we sought miRNA-target module(s) that may be differentially expressed under drought and non-stressed conditions by mining Expressed Sequence Tag (EST) libraries of wheat roots and identified a strong candidate (miR1119-MYC2). We then assessed molecular and physiochemical differences between two wheat genotypes with contrasting drought tolerance in a controlled drought experiment and assessed possible relationships between their tolerance and evaluated traits. We found that the miR1119-MYC2 module significantly responds to drought stress in wheat roots. It is differentially expressed between the contrasting wheat genotypes and under drought versus non-stressed conditions. We also found significant associations between the module’s expression profiles and ABA hormone content, water relations, photosynthetic activities, H2O2 levels, plasma membrane damage, and antioxidant enzyme activities in wheat. Collectively, our results suggest that a regulatory module consisting of miR1119 and MYC2 may play an important role in wheat’s drought tolerance

Expression of Hemagglutinin\u2013Neuraminidase and fusion epitopes of Newcastle Disease Virus in transgenic tobacco

Background: Newcastle disease is an important avian infectious disease that brings about vast economic damage for poultry industry. Transgenic plants represent a cost-effective system for the production of therapeutic proteins and are widely used for the production of poultry vaccines. In an attempt to develop a recombinant vaccine, a plant expression binary vector pBI121, containing the genes encoding Hemagglutinin\u2013Neuraminidase (HN) and Fusion (F) epitopes of Newcastle Disease Virus (NDV) under the control of CaMV35S promoter and NOS terminator was constructed and introduced into the tobacco ( Nicotiana tabacum ) plant by Agrobacterium -mediated transformation. Results: Putative transgenic plantswere screened in a selection medium containing 50 mg/L kanamycin and 30mg/L meropenem. Integration of the foreign gene in plant genome was confirmed by PCR. Expression of foreign gene was analyzed at transcription level by RT-PCR and at translation level by means of dot blotting and ELISA. All analyses confirmed the expression of recombinant protein. Conclusion: Developments in genetic engineering have led to plant-based systems for recombinant vaccine production. In this research, tobacco plant was used to express F and HN epitopes of NDV. Our results indicate that for the production of recombinant vaccine, it is a novel strategy to use concatenated epitopes without their genetic fusion onto larger scaffold structure such as viral coat protein

EFFECT OF GRADED LEVELS OF NPK ON HERB, OIL YIELD AND OIL COMPOSITION OF BASIL (OCIMUM BASILICUM L.)

ABSTRACT A field experiment was carried out using a randomized complete block design (RCBD) to evaluate the effect of four levels of N, P and K fertilizer (Kg

Efficient Regeneration of �Caralis� Alstroemeria Cultivar from Rhizome Explants

In this paper, the effects of a number of growth regulators as well as supplements to the Murashige and Skoog (MS) basal medium were evaluated on the regeneration of Alstroemeria rhizome explants. In the first experiment the effects of three cytokinins (BA, TDZ and 2IP each at 0.5, 1 and 2 mg/l) in combination with NAA (0.2 mg/l), followed by another PGR combination of 2IP (at 0.5, 1 and 2 mg/l) with NAA (0 and 0.2 mg/l), on regeneration of rhizome-derived explants, was investigated. Through the second experiment, the effects of a number of supplements, including glucose (30 g/l as the alternative for sucrose), casein hydrolysate (1 g/l), asparagine and glutamine, (each at 30 mg/l) added to MS medium, containing 1 mg/l BA and 0.2 mg/l NAA, was examined on rhizome explants� regeneration. Among the tested cytokinins, BA induced better regeneration of rhizome explants, resulting in a higher number of shoots compared to the other cytokinins. A medium supplemented with 1 mg/l BA and 0.2 mg/l NAA proved to be the most effective, with an average of 4.16 regenerated shoots per explant. In the second PGR combination, addition of NAA at 0.2 mg/l improved regeneration, compared to NAA-free treatments. In the second experiment, glucose substitution for sucrose improved regeneration with an average of 5.10 regenerated shoots per explant, compared to 4.16 shoots in sucrose-containing medium; whereas glutamine and asparagine (with 2.66 shoots) and casein hydrolysate (with 3.80 shoots) showed a negative influence on rhizome explants� regeneration

Ultrasound application for the decontamination of roselle (Hibiscus sabdariffa L.) seeds: Influence on fungal inhibition and seed quality

Seed decay is a major problem caused by pathogens that adversely affect seed yield and quality in agricultural production. Herein, the effect of 28 KHz ultrasound treatment for 20, 40 and 60 min and 1.5% sodium hypochlorite solution for 20 min was assessed for the decontamination of roselle (Hibiscus sabdariffa L.) seeds. In addition, seed germination indices, seedling growth traits, total phenolic content and the activity of defense-related enzymes, viz. peroxidase, superoxide dismutase, catalase and malondialdehyde were measured in the treated seeds. An isolate of Fusarium solani was obtained from roselle seeds and identified as the causal agent of roselle seed rot based on morphological and molecular characteristics. After six days of seed storage, the microbial infection caused the highest seed rot in the control seeds on the average of 56.67%, whereas ultrasound treatment for 60 min could remarkably reduce the seed decay by 3.33%. At the end of seed storage, the fungal load showed the highest (7.72 Log CFU ml−1) and lowest (6.99 Log CFU ml−1) rates in the control and ultrasound treatment for 60 min, respectively. Total phenolic content was significantly increased in ultrasound treatment for 60 min compared to control and sodium hypochlorite treatments. Moreover, the activity of peroxidase, superoxide dismutase and catalase was noticeably improved in ultrasound treatment for 60 min. Furthermore, ultrasound treatment did not show any adverse effects on seed germination indices and seedling growth traits of the roselle plants. Overall, ultrasound treatment for 60 min could effectively decrease roselle seed decay and the fungal load without changing seed and seedling quality

Expression of Hemagglutinin–Neuraminidase and fusion epitopes of Newcastle Disease Virus in transgenic tobacco

Background: Newcastle disease is an important avian infectious disease that brings about vast economic damage for poultry industry. Transgenic plants represent a cost-effective system for the production of therapeutic proteins and are widely used for the production of poultry vaccines. In an attempt to develop a recombinant vaccine, a plant expression binary vector pBI121, containing the genes encoding Hemagglutinin–Neuraminidase (HN) and Fusion (F) epitopes of Newcastle Disease Virus (NDV) under the control of CaMV35S promoter and NOS terminator was constructed and introduced into the tobacco (Nicotiana tabacum) plant by Agrobacterium-mediated transformation. Results: Putative transgenic plants were screened in a selection medium containing 50 mg/L kanamycin and 30 mg/L meropenem. Integration of the foreign gene in plant genome was confirmed by PCR. Expression of foreign gene was analyzed at transcription level by RT-PCR and at translation level by means of dot blotting and ELISA. All analyses confirmed the expression of recombinant protein. Conclusion: Developments in genetic engineering have led to plant-based systems for recombinant vaccine production. In this research, tobacco plant was used to express F and HN epitopes of NDV. Our results indicate that for the production of recombinant vaccine, it is a novel strategy to use concatenated epitopes without their genetic fusion onto larger scaffold structure such as viral coat protein