Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice

Identification of responsive genes to multiple abiotic stresses in rice (Oryza sativa): a meta-analysis of transcriptomics data

Abiotic stresses limit the quantity and quality of rice grain production, which is considered a strategic crop in many countries. In this study, a meta-analysis of different microarray data at seedling stage was performed to investigate the effects of multiple abiotic stresses (drought, salinity, cold situation, high temperature, alkali condition, iron, aluminum, and heavy metal toxicity, nitrogen, phosphorus, and potassium deficiency) on rice. Comparative analysis between multiple abiotic stress groups and their control groups indicated 561 differentially expressed genes (DEGs), among which 422 and 139 genes were up-regulated and down-regulated, respectively. Gene Ontology analysis showed that the process of responding to stresses and stimuli was significantly enriched. In addition, pathways such as metabolic process and biosynthesis of secondary metabolites were identified by KEGG pathway analysis. Weighted correlation network analysis (WGCNA) uncovered 17 distinct co-expression modules. Six modules were significantly associated with genes involved in response to abiotic stresses. Finally, to validate the results of the meta-analysis, five genes, including TIFY9 (JAZ5), RAB16B, ADF3, Os01g0124650, and Os05g0142900 selected for qRT-PCR analysis. Expression patterns of selected genes confirmed the results of the meta-analysis. The outcome of this study could help introduce candidate genes that may be beneficial for use in genetic engineering programs to produce more tolerant crops or as markers for selection.

Characterization of the transcriptional responses of Armillaria gallica 012m to GA3

Gastrodia elata needs to establish a symbiotic relationship with Armillaria strains to obtain nutrients and energy. However, the signaling cross talk between G. elata and Armillaria strains is still unclear. During our experiment, we found that the vegetative mycelium of Armillaria gallica 012m grew significantly better in the media containing gibberellic acid (GA3) than the blank control group (BK). To explore the response mechanism, we performed an RNA-sequencing experiment to profile the transcriptome changes of A. gallica 012m cultured in the medium with exogenous GA3. The transcriptome-guided differential expression genes (DEGs) analysis of GA3 and BK showed that a total of 1309 genes were differentially expressed, including 361 upregulated genes and 948 downregulated genes. Some of those DEGs correlated with the biological process, including positive regulation of chromosome segregation, mitotic metaphase/anaphase transition, attachment of mitotic spindle microtubules to kinetochore, mitotic cytokinesis, and nuclear division. These analyses explained that GA3 actively promoted the growth of A. gallica to some extent. Further analysis of protein domain features showed that the deduced polypeptide contained 41 candidate genes of GA receptor, and 27 of them were expressed in our samples. We speculate that GA receptors exist in A. gallica 012m. Comparative studies of proteins showed that the postulated GA receptor domains of A. gallica 012m have a higher homologous correlation with fungi than others based on cluster analysis.

Identification of Key Gene Network Modules and Hub Genes Associated with Wheat Response to Biotic Stress Using Combined Microarray Meta-analysis and WGCN Analysis

Wheat (Triticum aestivum) is one of the major crops worldwide and a primary source of calories for human food. Biotic stresses such as fungi, bacteria, and diseases limit wheat production. Although plant breeding and genetic engineering for biotic stress resistance have been suggested as promising solutions to handle losses caused by biotic stress factors, a comprehensive understanding of molecular mechanisms and identifying key genes is a critical step to obtaining success. Here, a network-based meta-analysis approach based on two main statistical methods was used to identify key genes and molecular mechanisms of the wheat response to biotic stress. A total of 163 samples (21,792 genes) from 10 datasets were analyzed. Fisher Z test based on the p-value and REM method based on effect size resulted in 533 differentially expressed genes (p < 0.001 and FDR < 0.001). WGCNA analysis using a dynamic tree-cutting algorithm was used to construct a co-expression network and three significant modules were detected. The modules were significantly enriched by 16 BP terms and 4 KEGG pathways (Benjamini-Hochberg FDR < 0.001). A total of nine hub genes (a top 1.5% of genes with the highest degree) were identified from the constructed network. The identification of DE genes, gene-gene co-expressing network, and hub genes may contribute to uncovering the molecular mechanisms of the wheat response to biotic stress.

A meta-analysis of microarray data revealed hub genes and transcription factors involved in drought stress response in rice (Oryza sativa L.)

Although there are various studies attempted to clarify the genetic mechanism of plant response to drought stress that reduces crop yield, a meta-analysis can integrate the results of them to provide a better picture of the issue. Therefore, in this study, several microarray datasets of rice were meta-analysed under drought stress and normal condition using the R packages. Accordingly, differentially expressed genes (meta-DEGs) were identified. The results showed 643 and 677 upregulated and downregulated genes, respectively. The significant common Gene Ontology (GO) terms between the up- and downregulated genes were responses to abiotic stimulus , water deprivation , oxygen-containing compound and abscisic acid . The transcription factors (TF) survey showed that bHLH under drought stress activates up genes 42% more than down genes while bzip Homeodomain activates down genes 54% more than up genes. The hub downregulated genes obtained from this study were mainly related to photosynthesis and the hub upregulated genes were mainly related to stress tolerance which include heat shock proteins (HSPs), late embryogenesis abundant (LEAs), calmodulin-like protein (CML), phosphatase 2C (PP2Cs) and IAA genes. Moreover, this meta-analysis data were compared with other experimental data and the results confirmed the up and down expression of them. Our findings can provide novel insights into the molecular mechanism of rice (Oryza sativa L.) response to drought stress.

A systems biology study unveils the association between a melatonin biosynthesis gene, O-methyl transferase 1 (OMT1) and wheat (Triticum aestivum L.) combined drought and salinity stress tolerance

Enhanced levels of endogenous melatonin in the root of wheat, mainly through the OMT1 gene, augment the antioxidant system, reestablish redox homeostasis and are associated with combined stress tolerance. A systems biology approach, including a collection of computational analyses and experimental assays, led us to uncover some aspects of a poorly understood phenomenon, namely wheat (Triticum aestivum L.) combined drought and salinity stress tolerance. Accordingly, a cross-study comparison of stress experiments was performed via a meta-analysis of Expressed Sequence Tags (ESTs) data from wheat roots to uncover the overlapping gene network of drought and salinity stresses. Identified differentially expressed genes were functionally annotated by gene ontology enrichment analysis and gene network analysis. Among those genes, O-methyl transferase 1 (OMT1) was highlighted as a more important (hub) gene in the dual-stress response gene network. Afterwards, the potential roles of OMT1 in mediating physiochemical indicators of stress tolerance were investigated in two wheat genotypes differing in abiotic stress tolerance. Regression analysis and correspondence analysis (CA) confirmed that the expression profiles of the OMT1 gene and variations in melatonin content, antioxidant enzyme activities, proline accumulation, H₂O₂ and malondialdehyde (MDA) contents are significantly associated with combined stress tolerance. These results reveal that the OMT1 gene may contribute to wheat combined drought and salinity stress tolerance through augmenting the antioxidant system and re-establishing redox homeostasis, probably via the regulation of melatonin biosynthesis as a master regulator molecule. Our findings provide new insights into the roles of melatonin in wheat combined drought and salinity stress tolerance and suggest a novel plausible regulatory node through the OMT1 gene to improve multiple-stress tolerant crops.

Rubisco activase A (RcaA) is a central node in overlapping gene network of drought and salinity in Barley (Hordeum vulgare L.) and may contribute to combined stress tolerance

Co-occurrence of abiotic stresses, especially drought and salinity, is a natural phenomenon in field conditions and is worse for crop production than any single stress. Nowadays, rigorous methods of meta-analysis and systems biology have made it possible to perform cross-study comparisons of single stress experiments, which can uncover main overlapping mechanisms underlying tolerance to combined stress. In this study, a meta-analysis of RNA-Seq data was conducted to obtain the overlapping gene network of drought and salinity stresses in barley (Hordeum vulgare L.), which identified Rubisco activase A (RcaA) as a hub gene in the dual-stress response. Thereafter, a greenhouse experiment was carried out using two barley genotypes with different abiotic stress tolerance and evaluated several physiochemical properties as well as the expression profile and protein activity of RcaA. Finally, machine learning analysis was applied to uncover relationships among combined stress tolerance and evaluated properties. We identified 441 genes which were differentially expressed under both drought and salinity stress. Results revealed that the photosynthesis pathway and, in particular, the RcaA gene are major components of the dual-stress responsive transcriptome. Comparative physiochemical and molecular evaluations further confirmed that enhanced photosynthesis capability, mainly through regulation of RcaA expression and activity as well as accumulation of proline content, have a significant association with combined drought and salinity stress tolerance in barley. Overall, our results clarify the importance of RcaA in combined stress tolerance and may provide new insights for future investigations.

Transcriptome-based approaches for clarification of nutritional responses and improvement of crop production

Genome-wide transcriptome profiling is a powerful tool for identifying key genes and pathways involved in plant development and physiological processes. This review summarizes studies that have used transcriptome profiling mainly in rice to focus on responses to macronutrients such as nitrogen, phosphorus and potassium, and spatio-temporal root profiling in relation to the regulation of root system architecture as well as nutrient uptake and transport. We also discuss strategies based on meta- and co-expression analyses with different attributed transcriptome data, which can be used for investigating the regulatory mechanisms and dynamics of nutritional responses and adaptation, and speculate on further advances in transcriptome profiling that could have potential application to crop breeding and cultivation.

Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice

Nitrogen-use efficiency (NUE) is a function of N-response and yield that is controlled by many genes and phenotypic parameters that are poorly characterized. This study compiled all known yield-related genes in rice and mined them from the N-responsive microarray data to find 1,064 NUE-related genes. Many of them are novel genes hitherto unreported as related to NUE, including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases. They were further shortlisted to 62 NUE-candidate genes following hierarchical methods, including quantitative trait locus (QTL) co-localization, functional evaluation in the literature, and protein-protein interactions (PPIs). They were localized to chromosomes 1, 3, 5, and 9, of which chromosome 1 with 26 genes emerged as a hotspot for NUE spanning 81% of the chromosomes. Further, co-localization of the NUE genes on NUE-QTLs resolved differences in the earlier studies that relied mainly on N-responsive genes regardless of their role in yield. Functional annotations and PPIs for all the 1,064 NUE-related genes and also the shortlisted 62 candidates revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes. In silico expression analysis confirmed differential expression of the 62 NUE-candidate genes in a tissue/stage-specific manner. Experimental validation in two contrasting genotypes revealed that high NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency in comparison to low NUE rice. Feature Selection Analysis independently identified one-third of the common genes at every stage of hierarchical shortlisting, offering 6 priority targets to validate for improving the crop NUE.

Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study

We studied the correlation of synonymous codon usage (SCU) on gene expression levels under drought stress in rice. Sixty genes related to drought stress (with high, intermediate and low expression) were selected from rice meta-analysis data and various codon usage indices such as the effective number of codon usage (ENC), codon adaptation index (CAI) and relative synonymous codon usage (RSCU) were calculated. We found that in genes highly expressing under drought 1) GC content was higher, 2) ENC value was lower, 3) the preferred codons of some amino acids changed and 4) the RSCU ratio of GC-end codons relative to AT-end codons for 18 amino acids increased significantly compared with those in other genes. We introduce ARSCU as the Average ratio of RSCUs of GC-end codons to AT-end codons in each gene that could significantly separate high-expression genes under drought from low-expression genes. ARSCU is calculated using the program ARSCU-Calculator developed by our group to help predicting expression level of rice genes under drought. An index above ARSCU threshold is expected to indicate that the gene under study may belong to the "high expression group under drought". This information may be applied for codon optimization of genes for rice genetic engineering. To validate these findings, we further used 60 other genes (randomly selected subset of 43233 genes studied for their response to drought stress). ARSCU value was able to predict the level of expression at 88.33% of the cases. Using third set of 60 genes selected amongst high expressing genes not related to drought, only 31.65% of the genes showed ARSCU value of higher than the set threshold. This indicates that the phenomenon we described in this report may be unique for drought related genes. To justify the observed correlation between CUB and high expressing genes under drought, possible role of tRNA post transcriptional modification and tRFs was hypothesized as possible underlying biological mechanism.

Combined QTL mapping and RNA-Seq profiling reveals candidate genes associated with cadmium tolerance in barley

The high toxicity of cadmium (Cd) and its ready uptake by plants has become a major agricultural problem. To investigate the genetic architecture and genetic regulation of Cd tolerance in barley, we conducted quantitative trait loci (QTL) analysis in the phenotypically polymorphic Oregon Wolfe Barley (OWB) mapping population, derived from a cross between Rec and Dom parental genotypes. Through evaluating the Cd tolerance of 87 available doubled haploid lines of the OWB mapping population at the seedling stage, one minor and one major QTL were detected on chromosomes 2H and 6H, respectively. For chlorosis and necrosis traits, the major QTL explained 47.24% and 38.59% of the phenotypic variance, respectively. RNA-Seq analysis of the parental seedlings under Cd treatment revealed 542 differentially expressed genes between Cd-tolerant Rec and Cd-susceptible Dom genotypes. By analyzing sequence variations in transcribed sequences of the parental genotypes, 155,654 SNPs and 1,525 InDels were identified between the two contrasting genotypes and may contribute to Cd tolerance. Finally, by integrating the data from the identified QTLs and RNA-Seq analysis, 16 Cd tolerance-related candidate genes were detected, nine of which were metal ion transporters. These results provide promising candidate genes for further gene cloning and improving Cd tolerance in barley.

Microarray analysis of transcriptional responses to salt and drought stress in Arabidopsis thaliana

Microarray expression profile analysis is a useful approach to increase our knowledge about genes involved in regulatory networks and signal transduction pathways related to abiotic stress tolerance. Salt and drought, as two important abiotic stresses, adversely affect plant productivity in the world every year. To understand stress response mechanisms and identify genes and proteins which play critical roles in these mechanisms, the study of individual genes and proteins cannot be considered as an effective approach. On the other hand, the availability of new global data provides us an effective way to shed some light on the central role of molecules involved in stress response mechanisms in the plant. A meta-analysis of salt and drought stress responses was carried out using 38 samples of different experiments from leaves and roots of Arabidopsis plants exposed to drought and salt stresses. We figured out the number of differentially expressed genes (DEGs) was higher in roots under both stresses. Also, we found that the number of common DEGs under both stresses was more in roots and also the number of common DEGs in both tissues under salt stress was more than drought stress. The highest percent of DEGs was related to cell and cell part (about 87%). Around 9% and 7% of DEGs in roots and leaves encoded transcription factors, respectively. Network analysis revealed that three transcription factor families HSF, AP2/ERF and C2H2, may have critical roles in salt and drought stress response mechanisms in Arabidopsis ​and some proteins like STZ may be introduced as a new candidate gene for enhancing salt and drought tolerance in crop plants.

Analysis of chickpea gene co-expression networks and pathways during heavy metal stress

Crop productivity and yield are adversely affected by abiotic and biotic stresses. Therefore, finding out the genes responsible for stress tolerance is a significant stride towards crop improvement. A gene co-expression network is a powerful tool to detect the most connected genes during heavy metal (HM) stress in plants. The most connected genes may be responsible for HM tolerance by altering the different metabolic pathways during the biotic and abiotic stress. In the same line we have performed the GSE86807 microarray analysis of chickpea during exposure to chromium, cadmium and arsenic and analyzed the data. Common differentially expressed genes (DEGs) during exposure to chromium, cadmium and arsenic were identified and a co-expression network study was carried out. Hub and bottleneck genes were explored on the basis of degree and betweenness centrality, respectively. A gene set enrichment analysis study revealed that genes like haloacid dehydrogenase, cinnamoyl CoA reductase, F-box protein, GDSL esterase lipase, cellulose synthase, beta-glucosidase 13 and isoflavone hydroxylase are significantly enriched and regulate the different pathways like riboflavin metabolism, phenyl propanoid biosynthesis, amino acid biosynthesis, isoflavonoid biosynthesis and indole alkaloid biosynthesis.

Comparative analysis of Cd-responsive maize and rice transcriptomes highlights Cd co-modulated orthologs

Background

Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, comparative RNAseq-based transcriptome analysis was conducted to dissect differentially expressed genes (DEGs) in maize roots exposed to cadmium (Cd) stress.

Results

To unveil conserved Cd-responsive genes in cereal plants, the obtained 5166 maize DEGs were compared with 2567 Cd-regulated orthologs in rice roots, and this comparison generated 880 universal Cd-responsive orthologs groups composed of 1074 maize DEGs and 981 rice counterparts. More importantly, most of the orthologous DEGs showed coordinated expression pattern between Cd-treated maize and rice, and these include one large orthologs group of pleiotropic drug resistance (PDR)-type ABC transporters, two clusters of amino acid transporters, and 3 blocks of multidrug and toxic compound extrusion (MATE) efflux family transporters, and 3 clusters of heavy metal-associated domain (HMAD) isoprenylated plant proteins (HIPPs), as well as all 4 groups of zinc/iron regulated transporter protein (ZIPs). Additionally, several blocks of tandem maize paralogs, such as germin-like proteins (GLPs), phenylalanine ammonia-lyases (PALs) and several enzymes involved in JA biosynthesis, displayed consistent co-expression pattern under Cd stress.

Out of the 1074 maize DEGs, approximately 30 maize Cd-responsive genes such as ZmHIPP27, stress-responsive NAC transcription factor (ZmSNAC1) and 9-cis-epoxycarotenoid dioxygenase (NCED, vp14) were also common stress-responsive genes reported to be uniformly regulated by multiple abiotic stresses. Moreover, the aforementioned three promising Cd-upregulated genes with rice counterparts were identified to be novel Cd-responsive genes in maize.

Meanwhile, one maize glutamate decarboxylase (ZmGAD1) with Cd co-modulated rice ortholog was selected for further analysis of Cd tolerance via heterologous expression, and the results suggest that ZmGAD1 can confer Cd tolerance in yeast and tobacco leaves.

Conclusions

These novel findings revealed the conserved function of Cd-responsive orthologs and paralogs, which would be valuable for elucidating the genetic basis of the plant response to Cd stress and unraveling Cd tolerance genes.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5109-8) contains supplementary material, which is available to authorized users.

Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress

Multiple environmental stresses adversely affect plant growth and development. Plants under multiple stress condition trigger cascade of signals and show response unique to specific stress as well as shared responses, common to individual stresses. Here, we aim to identify common and unique genetic components during stress response mechanisms liable for cross-talk between stresses. Although drought and cold stress have been widely studied, insignificant information is available about how their combination affects plants. To that end, we performed meta-analysis and co-expression network comparison of drought and cold stress response in Arabidopsis thaliana by analyzing 390 microarray samples belonging to 29 microarray studies. We observed 6120 and 7079 DEGs (differentially expressed genes) under drought and cold stress respectively, using Rank Product methodology. Statistically, 28% (2890) DEGs were found to be common in both the stresses (i.e.; drought and cold stress) with most of them having similar expression pattern. Further, gene ontology-based enrichment analysis have identified shared biological processes and molecular mechanisms such as—‘photosynthesis’, ‘respiratory burst’, ‘response to hormone’, ‘signal transduction’, ‘metabolic process’, ‘response to water deprivation’, which were affected under cold and drought stress. Forty three transcription factor families were found to be expressed under both the stress conditions. Primarily, WRKY, NAC, MYB, AP2/ERF and bZIP transcription factor family genes were highly enriched in all genes sets and were found to regulate 56% of common genes expressed in drought and cold stress. Gene co-expression network analysis by WGCNA (weighted gene co-expression network analysis) revealed 21 and 16 highly inter-correlated gene modules with specific expression profiles under drought and cold stress respectively. Detection and analysis of gene modules shared between two stresses revealed the presence of four consensus gene modules.

Genetic factors underlying boron toxicity tolerance in rice: genome-wide association study and transcriptomic analysis

Boron (B) toxicity is a nutritional disorder affecting crop production in many parts of the world. This study explored genetic factors associated with B tolerance in rice (Oryza sativa L.) through an integrated genome mapping and transcriptomic approach. Variation in B tolerance was first evaluated by screening a panel of 137 indica genotypes in B toxic conditions (+2 mM B), followed by genome-wide association study (GWAS). Leaf bronzing and greenness were significantly correlated with shoot and root dry weight, but B uptake was not correlated with any stress phenotype. Single nucleotide polymorphism (SNP) markers exceeding a significance value of –log10P>4.0 were obtained for four traits, namely leaf bronzing, shoot dry weight, root dry weight, and root length. Linkage disequilibrium block analysis of the corresponding chromosomal regions revealed candidate loci containing 75 gene models. Two contrasting genotypes from the panel were selected for transcriptomic analysis, which included gene ontology enrichment analysis of differentially regulated genes and investigating transcriptional responses of GWAS candidate genes. Characteristic expression patterns associated with tolerance or sensitivity were seen in genes related to biochemical binding, transport, transcriptional regulation, and redox homeostasis. These results advance the understanding of genetic and physiological factors associated with B tolerance in rice.