Abiotic environmental stresses are important factors that limit the growth, fiber yield, and quality of cotton. In this study, an integrative meta-analysis and a system-biology analysis were performed to explore the underlying transcriptomic mechanisms that are critical for response to stresses. From the meta-analysis, it was observed that a total of 1465 differentially expressed genes (DEGs) between normal and stress conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were significantly enriched in the ubiquitin-dependent process, biosynthesis of secondary metabolites, plant hormone, and signaled transduction. The results also indicated that some of DEGs were assigned to transcription factors (TFs). A total of 148 TFs belonged to 25 conserved families were identified that among them S1Fa-like, ERF, NAC, bZIP families, were the most abundant groups. Moreover, we searched in upstream regions of DEGs for over-represented DNA motifs and were able to identify 11 conserved sequence motifs. The functional analysis of these motifs revealed that they were involved in regulation of transcription, DNA replication, cytoskeleton organization, and translation. Weighted gene co-expression network analysis (WGCNA) uncovered 12 distinct co-expression modules. Four modules were significantly associated with genes involved in response to stress and cell wall organization. The network analysis also identified hub genes such as RTNLB5 and PRA1, which may be involved in regulating stress response. The findings could help to understand the mechanisms of response to abiotic stress and introduce candidate genes that may be beneficial to cotton plant breeding programs.

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.

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.

Cadmium and drought stress are the most destructive of the abiotic stresses with negative effects on both metabolism and photosynthesis. The present experiment aimed to analyze the impact of inoculation with Bacillus paralicheniformis and Trichoderma asperellum on the growth and antioxidant response modulation of maize (Zea mays L.), under drought and Cadmium (Cd) stresses. Regarding plant biomass analysis, fungi inoculation increased leaf dry biomass significantly (11.92%) towards uninoculated ones. The leaf area was affected significantly by bacterial application, 12.15% more than the control. A significant trend (drought+ Cd stress) was observed between fungi-inoculated maize leaves (15.07 µmol/g FW) and bacterial-inoculated leaves (18.71 µmol/g FW) regarding the malondialdehyde quantity. Furthermore, the activities of superoxide dismutase were notably higher (9.63–40.88%) in microorganism-inoculated roots. Similarly, under drought + Cd stress, peroxidase demonstrated a higher activity under bacterial inoculation than fungal ones (92.11% more). The maximum translocation factor was observed in the uninoculated group (under Cd stress), while the bioconcentration factor under drought stress showed a significant increase by microorganisms. The maximum relative water content under bacterial inoculation (82.66%) was achieved. The fungi and bacterial inoculation minimized Cd accumulation in the leaf significantly under drought and drought + Cd stress. Generally, the microorganism inoculation positively and partially maintained the plant’s performance, despite the presence of drought and Cd stress.

Plant viruses participate as biotrophic parasites in complex interactions with their hosts, resulting in the regulation of a diverse range of chloroplast/mitochondria-related genes that are essential for mediating immune responses. In this study, integrative systems biology approaches were applied to identify chloroplast/mitochondrial genes during viral infections caused by a wide number of viruses in Arabidopsis thaliana, tobacco (Nicotiana tabacum L.), and rice (Oryza sativa L.). These findings indicated that 1.5% of the DEGs were common between Arabidopsis/tobacco and Arabidopsis/rice, whereas 0.1% of the DEGs were shared among all species. Approximately 90% of common DEGs are uniquely associated with chloroplasts and mitochondria in the host defense against viral infection and replication. The functions of WRKY, NAC, and MYB transcription factors in imparting resistance to viral infections can be established. Promoter analysis revealed that AP2/EREBP, DOF, and C2H2 zinc finger factors included the most frequent binding sites and played a more important role in plant-viral interactions. Comparative analysis revealed several miRNAs with defensive functions including miRNA156, miRNA160, and miRNA169. The PPI network revealed several key hub genes mostly related to chloroplasts/mitochondria, including ZAT6, CML37, CHLI, DREB, F27B13.20, and ASP2 with upregulation, also PLGG1, PSBY, APO2, POR, ERF, and CSP with downregulation. Moreover, novel hub genes with unknown functions, such as AT2G41640 and AT3G57380 have been identified. This study represents the first preliminary systems biology approach to elucidate the roles of chloroplast/mitochondria-related genes in Arabidopsis, tobacco, and rice against viral challenges by introducing valuable candidate genes for enhanced genetic engineering programs to develop virus-resistant crop varieties.

Soil salinity is an emerging phenomenon threatening arid and semiarid areas due to changing climatic events. Salinity, in combination with other elemental contaminants, can often harm crop performance and productivity. This experiment was conducted to evaluate the mitigating effect of Claroideoglomus etunicatum, an arbuscular mycorrhizal fungus (AMF), on combined boron (B) toxicity and salt stress symptoms in maize plants. After the stress and AMF treatments, plants were subjected to a wide range of analyses, such as AMF colonization rates, ion leakage, plant biomass, and concentration of B, phosphorus, sodium, potassium, iron, zinc, copper, and manganese in root and shoot tissues. The results showed that the combined stress did not affect the AMF colonization rate. AMF inoculation significantly increased plant biomass, the K⁺/Na⁺ ratio, and shoot B, sodium, and copper concentrations, but reduced root B concentrations and ion leakage. AMF inoculation slightly increased root dry weight and the sodium, potassium, zinc, copper and Mn contents in shoots under combined B and salinity stress, while AMF reduced the electrolyte leakage in leaves. It is inferred that AMF can ameliorate B toxicity in maize by improving biomass and reducing B concentration in plant tissues. Our research implies that C. etunicatum could be a valuable candidate for assisting in the remediation of boron-contaminated and saline soils.