Microbial-based biological treatments improved the nutritional, nutraceutical and functional properties of greenhouse sweet pepper (Capsicum annuum L.)

Sweet pepper (Capsicum annum) is an important vegetable with high economic and nutritional value. The present study was conducted to evaluate the effectiveness of biological treatments on the nutritional, nutraceutical and functional status of greenhouse sweet peppers cv. Nirvin. Plants were divided into two categories: Peppers that were biologically treated included five microbial-based fertilizers and insecticide and those that were chemically treated contained a large number of chemical fertilizers and pesticides. The results showed that the total phenolic content, antioxidant activity, and leaf chlorophyll content were significantly higher (1.16, 1.14, and 1.09-fold) in the biologically treated plants compared to those that received the chemical treatment. The concentration of Fe, K, Mg, P, Ca, Cu, Si, and Mn also increased in the fruits of biologically treated sweet pepper plants. Fe, Mg, and P content of the leaves was higher in the chemically treated plants, while, the concentration of Zn and Cu showed the higher values in the leaves of the biologically treated plants. There was no significant difference between biological and chemical treatments in plant height as well as the number of flowers and fruits per plant. In conclusion, biological treatment could significantly improve the nutritional, nutraceutical and functional values of sweet peppers. Considering the risk of environmental pollution, the high cost of chemical fertilizers and pesticides, as well as their adverse impact on human health and the ecosystem, biological treatment can be a suitable alternative for sweet pepper management programs

Meta-Analysis of Common and Differential Transcriptomic Responses to Biotic and Abiotic Stresses in Arabidopsis thaliana

Environmental stresses adversely affect crop growth and yield, resulting in major losses to plants. These stresses occur simultaneously in nature, and we therefore conducted a meta-analysis in this study to identify differential and shared genes, pathways, and transcriptomic mechanisms involved in Arabidopsis response to biotic and abiotic stresses. The results showed a total of 436/21 significant up-/downregulated differentially expressed genes (DEGs) in response to biotic stresses, while 476 and 71 significant DEGs were respectively up- and downregulated in response to abiotic stresses in Arabidopsis thaliana. In addition, 21 DEGs (2.09%) were commonly regulated in response to biotic and abiotic stresses. Except for WRKY45 and ATXTH22, which were respectively up-/down- and down-/upregulated in response to biotic and abiotic stresses, other common DEGs were upregulated in response to all biotic and abiotic treatments. Moreover, the transcription factors (TFs) bHLH, MYB, and WRKY were the common TFs in response to biotic and abiotic stresses. In addition, ath-miR414 and ath-miR5658 were identified to be commonly expressed in response to both biotic and abiotic stresses. The identified common genes and pathways during biotic and abiotic stresses may provide potential candidate targets for the development of stress resistance breeding programs and for the genetic manipulation of crop plants

Meta-Analysis of Common and Differential Transcriptomic Responses to Biotic and Abiotic Stresses in Arabidopsis thaliana

Environmental stresses adversely affect crop growth and yield, resulting in major losses to plants. These stresses occur simultaneously in nature, and we therefore conducted a meta-analysis in this study to identify differential and shared genes, pathways, and transcriptomic mechanisms involved in Arabidopsis response to biotic and abiotic stresses. The results showed a total of 436/21 significant up-/downregulated differentially expressed genes (DEGs) in response to biotic stresses, while 476 and 71 significant DEGs were respectively up- and downregulated in response to abiotic stresses in Arabidopsis thaliana. In addition, 21 DEGs (2.09%) were commonly regulated in response to biotic and abiotic stresses. Except for WRKY45 and ATXTH22, which were respectively up-/down- and down-/upregulated in response to biotic and abiotic stresses, other common DEGs were upregulated in response to all biotic and abiotic treatments. Moreover, the transcription factors (TFs) bHLH, MYB, and WRKY were the common TFs in response to biotic and abiotic stresses. In addition, ath-miR414 and ath-miR5658 were identified to be commonly expressed in response to both biotic and abiotic stresses. The identified common genes and pathways during biotic and abiotic stresses may provide potential candidate targets for the development of stress resistance breeding programs and for the genetic manipulation of crop plants

Evaluation of Different RNA Extraction Methods from Agropatch Suppressor Assay for Small Quantities of Plant Tissue and Their Application for Analysis of Gene Expression

The agroinfiltration assay provides fast and efficient way to transiently express genes into plant cells by Agrobacterium tumefaciens. Extraction of RNA of high quality and sufficient amounts is prerequisite for gene expression studies such as quantitative Real Time PCR (q-PCR) from infiltrated areas in agropatch suppressor assay with small quantities of plant tissue. To attain prime RNA extraction from small tissues of infiltrated N. benthamiana plants with Potato virus A helper component proteinase viral suppressor protein, the efficiency of three RNA extraction methods (LiCl, TRIzol reagent and commercial kit) was evaluated. The total RNA yield with LiCl method was 2.83 and 33.2-fold greater than that of TRIzol reagent and commercial kit, respectively. Also, total RNA yield using TRIzol reagent was 11.7-fold higher than that with commercial kit. The A260/A280 ratio mean for TRI reagent (1.95) and kit (1.9) extractions were within the optimum range.q-PCR revealed that the cycle threshold values of housekeeping gene, EIF-1α and target genes AGO1 and ATG6 for RNA extracted using LiCl and kit were 1.07 to 1.3 and 1.02 to 1.12 times higher than those evaluated with the TRIzol method. Overall, TRIzol method showed the most effective approach for obtaining RNA from N. benthamiana patches in gene expression studies

Transcriptome Meta-Analysis Identifies Candidate Hub Genes and Pathways of Pathogen Stress Responses in Arabidopsis thaliana

Following a pathogen attack, plants defend themselves using multiple defense mechanisms to prevent infections. We used a meta-analysis and systems-biology analysis to search for general molecular plant defense responses from transcriptomic data reported from different pathogen attacks in Arabidopsis thaliana. Data from seven studies were subjected to meta-analysis, which revealed a total of 3694 differentially expressed genes (DEGs), where both healthy and infected plants were considered. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis further suggested that the DEGs were involved in several biosynthetic metabolic pathways, including those responsible for the biosynthesis of secondary metabolites and pathways central to photosynthesis and plant–pathogen interactions. Using network analysis, we highlight the importance of WRKY40, WRKY46 and STZ, and suggest that they serve as major points in protein–protein interactions. This is especially true regarding networks of composite-metabolic responses by pathogens. In summary, this research provides a new approach that illuminates how different mechanisms of transcriptome responses can be activated in plants under pathogen infection and indicates that common genes vary in their ability to regulate plant responses to the pathogens studied herein

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

Transcriptome Meta-Analysis Identifies Candidate Hub Genes and Pathways of Pathogen Stress Responses in Arabidopsis thaliana

Following a pathogen attack, plants defend themselves using multiple defense mechanisms to prevent infections. We used a meta-analysis and systems-biology analysis to search for general molecular plant defense responses from transcriptomic data reported from different pathogen attacks in Arabidopsis thaliana. Data from seven studies were subjected to meta-analysis, which revealed a total of 3694 differentially expressed genes (DEGs), where both healthy and infected plants were considered. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis further suggested that the DEGs were involved in several biosynthetic metabolic pathways, including those responsible for the biosynthesis of secondary metabolites and pathways central to photosynthesis and plant–pathogen interactions. Using network analysis, we highlight the importance of WRKY40, WRKY46 and STZ, and suggest that they serve as major points in protein–protein interactions. This is especially true regarding networks of composite-metabolic responses by pathogens. In summary, this research provides a new approach that illuminates how different mechanisms of transcriptome responses can be activated in plants under pathogen infection and indicates that common genes vary in their ability to regulate plant responses to the pathogens studied herein

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