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

Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L

In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.

Bioinformatics and meta-analysis of expression data to investigate transcriptomic response of wheat root to abiotic stresses

Abiotic stresses are predominant and main causes of the losses in the crop yield. A complexity of systems biology and involvement of numerous genes in the response to abiotic factors have challenged efforts to create tolerant cultivars with sustainable production. The root is the main organ of the plant and determines a plant tolerance under stressful conditions. In this study, we carried out a meta-analysis of expression datasets from wheat root to identify differentially expressed genes, followed by the weighted gene co-expression network analysis (WGCNA) to construct the weighted gene co-expression network. The aim was to identify consensus differentially expressed genes with regulatory functions, gene networks, and biological pathways involved in response of wheat root to a set of abiotic stresses. The meta-analysis using Fisher method (FDR<0.05) identified consensus 526 DEGs from 55,367 probe sets. Although the annotated expression data are limited for wheat, the functional analysis based on the data from model plants could identify the up-regulated seven regulatory genes involved in chromosome organization and response to oxygen-containing compounds. WGCNA identified four gene modules that were mostly associated with the ribosome biogenesis and polypeptide synthesis. This study's findings enhance our understanding of key players and gene networks related to wheat root response to multiple abiotic stresses.

Study of Dandelion (Taraxacum mongolicum Hand.-Mazz.) Salt Response and Caffeic Acid Metabolism under Saline Stress by Transcriptome Analysis

Utilizing salt-tolerant plants is a cost-effective strategy for agricultural production on salinized land. However, little is known about the mechanism of dandelion (Taraxacum mongolicum Hand.-Mazz.) in response to saline stress and caffeic acid biosynthesis. We investigated the morphological and physiological variations of two dandelions, namely, "BINPU2" (dandelion A) and "TANGHAI" (dandelion B) under gradient NaCl concentrations (0, 0.3%, 0.5%, 0.7%, and 0.9%), and analyzed potential mechanisms through a comparison analysis of transcriptomes in the two dandelions. Dandelion A had a high leaf weight; high ρ-coumaric acid, caffeic acid, ferulic acid, and caffeoyl shikimic acid contents; and high activities of POD and Pro. The maximum content of four kinds of phenolic acids mostly occurred in the 0.7% NaCl treatment. In this saline treatment, 2468 and 3238 differentially expressed genes (DEGs) in dandelion A and B were found, of which 1456 and 1369 DEGs in the two dandelions, respectively, showed up-regulation, indicating that more up-regulated DEGs in dandelion A may cause its high salt tolerance. Further, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that dandelion salt response and caffeic acid metabolism were mainly enriched in the phenylpropanoid biosynthesis pathway (ko00940) and response to ethylene (GO: 0009723). The caffeic acid biosynthesis pathway was reconstructed based on DEGs which were annotated to PAL, C4H, 4CL, HCT, C3'H, and CSE. Most of these genes showed a down-regulated mode, except for parts of DEGs of 4CL (TbA05G077650 and TbA07G073600), HCT (TbA03G009110, TbA03G009080, and novel.16880), and COMT (novel.13839). In addition, more up-regulated transcription factors (TFs) of ethylene TFs in dandelion A were found, but the TFs of ERF104, CEJ1, and ERF3 in the two dandelions under saline stress showed an opposite expression pattern. These up-regulated genes could enhance dandelion salt tolerance, and down-regulated DEGs in the caffeic acid biosynthesis pathway, especially CSE (TbA08G014310) and COMT (TbA04G07330), could be important candidate genes in the synthesis of caffeic acid under saline stress. The above findings revealed the potential mechanisms of salt response and caffeic acid metabolism in dandelion under saline stress, and provide references for salt-tolerant plant breeding and cultivation on saline-alkali land in the future.

Characterization of the Heat Shock Transcription Factor Family in Lycoris radiata and Its Potential Roles in Response to Abiotic Stresses

Heat shock transcription factors (HSFs) are an essential plant-specific transcription factor family that regulates the developmental and growth stages of plants, their signal transduction, and their response to different abiotic and biotic stresses. The HSF gene family has been characterized and systematically observed in various species; however, research on its association with Lycoris radiata is limited. This study identified 22 HSF genes (LrHSFs) in the transcriptome-sequencing data of L. radiata and categorized them into three classes including HSFA, HSFB, and HSFC, comprising 10, 8, and 4 genes, respectively. This research comprises basic bioinformatics analyses, such as protein sequence length, molecular weight, and the identification of its conserved motifs. According to the subcellular localization assessment, most LrHSFs were present in the nucleus. Furthermore, the LrHSF gene expression in various tissues, flower developmental stages, two hormones stress, and under four different abiotic stresses were characterized. The data indicated that LrHSF genes, especially LrHSF5, were essentially involved in L. radiata development and its response to different abiotic and hormone stresses. The gene-gene interaction network analysis revealed the presence of synergistic effects between various LrHSF genes' responses against abiotic stresses. In conclusion, these results provided crucial data for further functional analyses of LrHSF genes, which could help successful molecular breeding in L. radiata.

Phenotypic and microarray analysis reveals salinity stress-induced oxidative tolerance in transgenic rice expressing a DEAD-box RNA helicase, OsDB10

Helicases are the motor proteins not only involved in the process of mRNA metabolism but also played a significant role in providing abiotic stresses tolerance. In this study, a DEAD-box RNA helicase OsDB10 was cloned and functionally characterized. The transcript levels of OsDB10 were increased both in shoot and root upon salt, heat, cold, and ABA application and was more prominent in shoot compared to root. Genomic integration of OsDB10 in transgenic rice was confirmed by PCR, Southern blot and qRT-PCR analysis. The transgenic plants showed quicker seed germination, reduced necrosis, higher chlorophyll, more survival rate, better seedling growth, and produced more grain yield under salinity stress. Furthermore, transgenic lines also accumulated less Na+ and high K+ ions and salinity tolerance of the transgenic were also assayed by measuring different bio-physiological indices. Moreover, the OsDB10 transgenic plants showed enhanced tolerance to salinity-induced oxidative stress by scavenging ROS and increased activity of antioxidants enzymes. Microarray analysis showed upregulation of transcriptional regulations and metabolic reprogramming as OsDB10 overexpression modulates the expression of many other genes. Altogether, our results confirmed that OsDB10 is a functional DEAD-box RNA helicase and played vital roles in plant defence response against salinity stress.

Genome-Wide Analysis of Stress-Responsive Genes and Alternative Splice Variants in Arabidopsis Roots under Osmotic Stresses

Plant roots show distinct gene-expression profiles from those of shoots under abiotic stress conditions. In this study, we performed mRNA sequencing (mRNA-Seq) to analyze the transcriptional profiling of Arabidopsis roots under osmotic stress conditions-high salinity (NaCl) and drought (mannitol). The roots demonstrated significantly distinct gene-expression changes from those of the aerial parts under both the NaCl and the mannitol treatment. We identified 68 closely connected transcription-factor genes involved in osmotic stress-signal transduction in roots. Well-known abscisic acid (ABA)-dependent and/or ABA-independent osmotic stress-responsive genes were not considerably upregulated in the roots compared to those in the aerial parts, indicating that the osmotic stress response in the roots may be regulated by other uncharacterized stress pathways. Moreover, we identified 26 osmotic-stress-responsive genes with distinct expressions of alternative splice variants in the roots. The quantitative reverse-transcription polymerase chain reaction further confirmed that alternative splice variants, such as those for ANNAT4, MAGL6, TRM19, and CAD9, were differentially expressed in the roots, suggesting that alternative splicing is an important regulatory mechanism in the osmotic stress response in roots. Altogether, our results suggest that tightly connected transcription-factor families, as well as alternative splicing and the resulting splice variants, are involved in the osmotic stress response in roots.

Genome-wide analysis of the heat shock transcription factor family reveals saline-alkali stress responses in Xanthoceras sorbifolium

The heat shock transcription factor (HSF) family is involved in regulating growth, development, and abiotic stress. The characteristics and biological functions of HSF family member in X. sorbifolium, an important oil and ornamental plant, have never been reported. In this study, 21 XsHSF genes were identified from the genome of X. sorbifolium and named XsHSF1-XsHSF21 based on their chromosomal positions. Those genes were divided into three groups, A, B, and C, containing 12, one, and eight genes, respectively. Among them, 20 XsHSF genes are located on 11 chromosomes. Protein structure analysis suggested that XsHSF proteins were conserved, displaying typical DNA binding domains (DBD) and oligomerization domains (OD). Moreover, HSF proteins within the same group contain specific motifs, such as motif 5 in the HSFC group. All XsHSF genes have one intron in the CDS region, except XsHSF1 which has two introns. Promoter analysis revealed that in addition to defense and stress responsiveness elements, some promoters also contained a MYB binding site and elements involved in multiple hormones responsiveness and anaerobic induction. Duplication analysis revealed that XsHSF1 and XsHSF4 genes were segmentally duplicated while XsHSF2, XsHSF9, and XsHSF13 genes might have arisen from transposition. Expression pattern analysis of leaves and roots following salt-alkali treatment using qRT-PCR indicated that five XsHSF genes were upregulated and one XsHSF gene was downregulated in leaves upon NaCl treatment suggesting these genes may play important roles in salt response. Additionally, the expression levels of most XsHSFs were decreased in leaves and roots following alkali-induced stress, indicating that those XsHSFs may function as negative regulators in alkali tolerance. MicroRNA target site prediction indicated that 16 of the XsHSF genes may be regulated by multiple microRNAs, for example XsHSF2 might be regulated by miR156, miR394, miR395, miR408, miR7129, and miR854. And miR164 may effect the mRNA levels of XsHSF3 and XsHSF17, XsHSF9 gene may be regulated by miR172. The expression trends of miR172 and miR164 in leaves and roots on salt treatments were opposite to the expression trend of XsHSF9 and XsHSF3 genes, respectively. Promoter analysis showed that XsHSFs might be involved in light and hormone responses, plant development, as well as abiotic stress responses. Our results thus provide an overview of the HSF family in X. sorbifolium and lay a foundation for future functional studies to reveal its roles in saline-alkali response.

New insights on the regulatory network of drought-responsive key genes in Arabidopsis thaliana

Drought stress is complex abiotic stress that seriously affects crop productivity and yield. Many genes with various functions are induced in response to drought stress. The present study aimed to identify drought-responsive hub genes and their related regulation network in Arabidopsis thaliana under drought stress. In this study, RNA-sequencing data of well-watered and drought treatment samples of Arabidopsis were analyzed, and differential expression genes were identified. The gene ontology enrichment and protein-protein interaction network analyses were performed for differential expression genes. Then, the most important hub genes, gene ontology enrichment, co-expression network, and prediction of related miRNAs of hub genes were investigated by in silico approaches. A total of 2462 genes were expressed differentially, of which 1926 transcripts were up-regulated under drought stress, and the rest were down-regulated. WRKY33, WRKY40, AT1G19020, STZ, SYP122, CNI1, CML37, BCS1, AT3G02840, and AT5G54490 were identified as hub genes in drought stress. The gene ontology analysis showed that hub genes significantly enriched in response to hypoxia, chitin, wounding, and salicylic acid-mediated signaling pathway. The hub genes were co-expressed with important drought-responsive genes such as WRKY46, WRKY60, CML38, ERF6, ERF104, and ERF1A. They were regulated by many stress-responsive miRNAs, such as ath-miR5021, miR413, miR5998, and miR162, that could be used as candidate miRNAs for regulating key genes under drought stress. It seems that the regulation network was involved in signaling pathways and protein degradation under drought stress, and it consists of several important genes and miRNAs that are potential candidates for plant improvement and breeding programs.

Transcriptome-wide analysis reveals core transcriptional regulators associated with culm development and variation in Dendrocalamus sinicus, the strongest woody bamboo in the world

Transcription factors (TFs) play indispensable roles in plant development and stress responses. As the largest woody bamboo species in the world, Dendrocalamus sinicus is endemic to Yunnan Province, China, and possesses two natural variants characterized by culm shape, namely straight or bent culms. Understanding the transcriptional regulation network of D. sinicus provides a unique opportunity to clarify the growth and development characteristics of woody bamboos. In this study, 10,236 TF transcripts belonging to 57 families were identified from transcriptome data of two variants at different developmental stages, from which we constructed a transcriptional regulatory network and unigene-coding protein-TFs interactive network of culm development for this attractive species. Gene function enrichment analysis revealed that hormone signaling and MAPK signaling pathways were two most enriched pathways in TF-regulated network. Based on PPI analysis, 50 genes interacting with nine TFs were screened as the core regulation components related to culm development. Of them, 18 synergistic genes of seven TFs, including nuclear cap-binding protein subunit 1, transcription factor GTE9-like, and ATP-dependent DNA helicase DDX11 isoform X1, involved in culm-shape variation. Most of these genes would interact with MYB, C3H, and ARF transcription factors. Six members with two each from ARF, C3H, and MYB transcription factor families and six key interacting genes (IAA3, IAA19, leucine-tRNA ligase, nuclear cap-binding protein subunit 1, elongation factor 2, and coiled-coil domain-containing protein 94) cooperate with these transcription factors were differentially expressed at development stage of young culms, and were validated by quantitative PCR. Our results represent a crucial step towards understanding the regulatory mechanisms of TFs involved in culm development and variation of D. sinicus.

Identification of a DEAD-box RNA Helicase BnRH6 Reveals Its Involvement in Salt Stress Response in Rapeseed (Brassica napus)

Rapeseed (Brassica napus) is one of the most important vegetable oil crops worldwide. Abiotic stresses such as salinity are great challenges for its growth and productivity. DEAD-box RNA helicase 6 (RH6) is a subfamily member of superfamily 2 (SF2), which plays crucial roles in plant growth and development. However, no report is available on RH6 in regulating plant abiotic stress response. This study investigated the function and regulatory mechanism for BnRH6. BnRH6 was targeted to the nucleus and cytoplasmic processing body (P-body), constitutively expressed throughout the lifespan, and induced by salt stress. Transgenic overexpressing BnRH6 in Brassica and Arabidopsis displayed salt hypersensitivity, manifested by lagging seed germination (decreased to 55−85% of wild-type), growth stunt, leaf chlorosis, oxidative stress, and over-accumulation of Na ions with the K+/Na+ ratio being decreased by 18.3−28.6%. Given the undesirable quality of knockout Brassica plants, we utilized an Arabidopsis T-DNA insertion mutant rh6-1 to investigate downstream genes by transcriptomics. We constructed four libraries with three biological replicates to investigate global downstream genes by RNA sequencing. Genome-wide analysis of differentially expressed genes (DEGs) (2-fold, p < 0.05) showed that 41 genes were upregulated and 66 genes were downregulated in rh6-1 relative to wild-type under salt stress. Most of them are well-identified and involved in transcription factors, ABA-responsive genes, and detoxified components or antioxidants. Our research suggests that BnRH6 can regulate a group of salt-tolerance genes to negatively promote Brassica adaptation to salt stress.

Effects of exogenous calcium on the drought response of the tea plant (Camellia sinensis (L.) Kuntze)

Background

Drought is one of the major factors reducing the yield of many crops worldwide, including the tea crop (Camellia sinensis (L.) Kuntze). Calcium participates in most of cellular signaling processes, and its important role in stress detection and triggering a response has been shown in many crops. The aim of this study was to evaluate possible effects of calcium on the tea plant response to drought.

Methods

Experiments were conducted using 3-year-old potted tea plants of the best local cultivar Kolkhida. Application of ammonium nitrate (control treatment) or calcium nitrate (Ca treatment) to the soil was performed before drought induction. Next, a 7-day drought was induced in both groups of plants. The following physiological parameters were measured: relative electrical conductivity, pH of cell sap, and concentrations of cations, sugars, and amino acids. In addition, relative expression levels of 40 stress-related and crop quality-related genes were analyzed.

Results

Under drought stress, leaf electrolyte leakage differed significantly, indicating greater damage to cell membranes in control plants than in Ca-treated plants. Calcium application resulted in greater pH of cell sap; higher accumulation of tyrosine, methionine, and valine; and a greater Mg²⁺ content as compared to control plants. Drought stress downregulated most of the quality-related genes in both groups of tea plants. By contrast, significant upregulation of some genes was observed, namely CRK45, NAC26, TPS11, LOX1, LOX6, Hydrolase22, DREB26, SWEET2, GS, ADC, DHN2, GOLS1, GOLS3, and RHL41. Among them, three genes (LOX1, RHL41, and GOLS1) showed 2-3 times greater expression in Ca-treated plants than in control plants. Based on these results, it can be speculated that calcium affects galactinol biosynthesis and participates in the regulation of stomatal aperture not only through activation of abscisic-acid signaling but also through jasmonic-acid pathway activation. These findings clarify calcium-mediated mechanisms of drought defense in tree crops. Thus, calcium improves the drought response in the tea tree.

BETA-AMYLASE9 is a plastidial nonenzymatic regulator of leaf starch degradation

β-Amylases (BAMs) are key enzymes of transitory starch degradation in chloroplasts, a process that buffers the availability of photosynthetically fixed carbon over the diel cycle to maintain energy levels and plant growth at night. However, during vascular plant evolution, the BAM gene family diversified, giving rise to isoforms with different compartmentation and biological activities. Here, we characterized BETA-AMYLASE 9 (BAM9) of Arabidopsis (Arabidopsis thaliana). Among the BAMs, BAM9 is most closely related to BAM4 but is more widely conserved in plants. BAM9 and BAM4 share features including their plastidial localization and lack of measurable α-1,4-glucan hydrolyzing capacity. BAM4 is a regulator of starch degradation, and bam4 mutants display a starch-excess phenotype. Although bam9 single mutants resemble the wild-type (WT), genetic experiments reveal that the loss of BAM9 markedly enhances the starch-excess phenotypes of mutants already impaired in starch degradation. Thus, BAM9 also regulates starch breakdown, but in a different way. Interestingly, BAM9 gene expression is responsive to several environmental changes, while that of BAM4 is not. Furthermore, overexpression of BAM9 in the WT reduced leaf starch content, but overexpression in bam4 failed to complement fully that mutant's starch-excess phenotype, suggesting that BAM9 and BAM4 are not redundant. We propose that BAM9 activates starch degradation, helping to manage carbohydrate availability in response to fluctuations in environmental conditions. As such, BAM9 represents an interesting gene target to explore in crop species.

A Dual Strategy of Breeding for Drought Tolerance and Introducing Drought-Tolerant, Underutilized Crops into Production Systems to Enhance Their Resilience to Water Deficiency

Water scarcity is the primary constraint on crop productivity in arid and semiarid tropical areas suffering from climate alterations; in accordance, agricultural systems have to be optimized. Several concepts and strategies should be considered to improve crop yield and quality, particularly in vulnerable regions where such environmental changes cause a risk of food insecurity. In this work, we review two strategies aiming to increase drought stress tolerance: (i) the use of natural genes that have evolved over time and are preserved in crop wild relatives and landraces for drought tolerance breeding using conventional and molecular methods and (ii) exploiting the reservoir of neglected and underutilized species to identify those that are known to be more drought-tolerant than conventional staple crops while possessing other desired agronomic and nutritive characteristics, as well as introducing them into existing cropping systems to make them more resilient to water deficiency conditions. In the past, the existence of drought tolerance genes in crop wild relatives and landraces was either unknown or difficult to exploit using traditional breeding techniques to secure potential long-term solutions. Today, with the advances in genomics and phenomics, there are a number of new tools available that facilitate the discovery of drought resistance genes in crop wild relatives and landraces and their relatively easy transfer into advanced breeding lines, thus accelerating breeding progress and creating resilient varieties that can withstand prolonged drought periods. Among those tools are marker-assisted selection (MAS), genomic selection (GS), and targeted gene editing (clustered regularly interspaced short palindromic repeat (CRISPR) technology). The integration of these two major strategies, the advances in conventional and molecular breeding for the drought tolerance of conventional staple crops, and the introduction of drought-tolerant neglected and underutilized species into existing production systems has the potential to enhance the resilience of agricultural production under conditions of water scarcity.