A novel sweetpotato bZIP transcription factor gene, IbbZIP1, is involved in salt and drought tolerance in transgenic Arabidopsis

A soybean bZIP transcription factor is involved in submergence resistance

Although the functions of basic leucine zipper (bZIP) family transcription factors in the regulation of various abiotic stresses are beginning to be unveiled, the precise roles of bZIP proteins in plants coping with submergence stress remain unclear. Here we identified a bZIP gene GmbZIP71-4 from soybean, which localized in the nucleus. The GmbZIP71-4 over-expressed tabocco line showed reduced submergence resistance due to the decreased abscisic acid (ABA) content. GO and KEGG pathway analysis based on chromatin immunoprecipitation assay sequencing (ChIP-seq) indicated that the differences expressed genes between submergence treatment and control groups were specially enriched in plant hormone signal transduction items, especially those in response to ABA. Electrophoretic mobility shift assays (EMSA) demonstrated that GmbZIP71-4 bound to the promoter of GmABF2 gene, which is consistent with the ChIP-qPCR results. GmbZIP71-4 function as a negative regulator of soybean in responding to submergence stress through manipulating ABA signaling pathway. This findings will set a solid foundation for the understanding of submergence resistance in plants.

Regulatory Dynamics of Plant Hormones and Transcription Factors under Salt Stress

The negative impacts of soil salinization on ion homeostasis provide a significant global barrier to agricultural production and development. Plant physiology and biochemistry are severely affected by primary and secondary NaCl stress impacts, which damage cellular integrity, impair water uptake, and trigger physiological drought. Determining how transcriptional factors (TFs) and hormone networks are regulated in plants in response to salt stress is necessary for developing crops that tolerate salt. This study investigates the complex mechanisms of several significant TF families that influence plant responses to salt stress, involving AP2/ERF, bZIP, NAC, MYB, and WRKY. It demonstrates how these transcription factors (TFs) help plants respond to the detrimental effects of salinity by modulating gene expression through mechanisms including hormone signaling, osmotic stress pathway activation, and ion homeostasis. Additionally, it explores the hormonal imbalances triggered by salt stress, which entail complex interactions among phytohormones like jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) within the hormonal regulatory networks. This review highlights the regulatory role of key transcription factors in salt-stress response, and their interaction with plant hormones is crucial for developing genome-edited crops that can enhance agricultural sustainability and address global food security challenges.

Genome-wide identification, characterization and expression analysis of the bZIP transcription factors in garlic (Allium sativum L.)

Introduction

The bZIP genes (bZIPs) are essential in numerous biological processes, including development and stress responses. Despite extensive research on bZIPs in many plants, a comprehensive genome-wide analysis of bZIPs in garlic has yet to be undertaken.

Methods

In this study, we identified and classified 64 AsbZIP genes (AsbZIPs) into 10 subfamilies. A systematic analysis of the evolutionary characteristics of these AsbZIPs, including chromosome location, gene structure, conserved motifs, and gene duplication, was conducted. Furthermore, we also examined the nucleotide diversity, cis-acting elements, and expression profiles of AsbZIPs in various tissues and under different abiotic stresses and hormone treatments.

Results and Discussion

Our findings revealed that gene replication plays a crucial role in the expansion of AsbZIPs, with a minor genetic bottleneck observed during domestication. Moreover, the identification of cis-acting elements suggested potential associations of AsbZIPs with garlic development, hormone, and stress responses. Several AsbZIPs exhibited tissue-preferential and stress/hormone-responsive expression patterns. Additionally, Asa7G01972 and Asa7G01379 were notably differentially expressed under various stresses and hormone treatments. Subsequent yeast two-hybridization and yeast induction experiments validated their interactions with Asa1G01577, a homologue of ABI5, reinforcing their importance in hormone and abiotic stress responses. This study unveiled the characteristics of the AsbZIP superfamily and lays a solid foundation for further functional analysis of AsbZIP in garlic.

Functional Identification of Malus halliana MhbZIP23 Gene Demonstrates That It Enhances Saline-Alkali Stress Tolerance in Arabidopsis thaliana

Saline-alkali stress is a significant abiotic stress that restricts plant growth globally. Basic region leucine zipper (bZIP) transcription factor proteins are widely involved in plants in response to abiotic stress such as saline-alkali stress. Based on transcriptome and quantitative real-time PCR (qRT-PCR), we found that the MhbZIP23 gene could respond to saline-alkali stress. Despite this discovery, the underlying mechanism by which the MhbZIP23 transcription factor responds to saline-alkaline stress remains unexplored. To address this gap in knowledge, we successfully cloned the MhbZIP23 (MD05G1121500) gene from Malus halliana for heterologous expression in Arabidopsis thaliana, facilitating the investigation of its functional role in stress response. Compared to the wild type (WT), Arabidopsis plants demonstrated enhanced growth and a lower degree of wilting when subjected to saline-alkali stress. Furthermore, several physiological indices of the plants altered under such stress conditions. The transgenic Arabidopsis plants (OE-5, 6, and 8), which grew normally, exhibited a higher chlorophyll content and had greater root length in comparison to the control check (CK). MhbZIP23 effectively regulated the levels of the osmoregulatory substance proline (Pro), enhanced the activities of antioxidant enzymes such as peroxidase (POD) and superoxide dismutase (SOD), and reduced the levels of malondialdehyde (MDA) and relative conductivity (REC). These actions improved the ability of plant cells in transgenic Arabidopsis to counteract ROS, as evidenced by the decreased accumulation of O2- and hydrogen peroxide (H2O2). In summary, the MhbZIP23 gene demonstrated effectiveness in alleviating saline-alkali stress in M. halliana, presenting itself as an outstanding resistance gene for apples to combat saline-alkali stress.

Genome-wide analysis of bZIP gene family members in Pleurotus ostreatus, and potential roles of PobZIP3 in development and the heat stress response

The basic leucine zipper (bZIP) transcription factor (TF) is widespread among eukaryotes and serves different roles in fungal processes including nutrient utilization, growth, stress responses and development. The oyster mushroom (Pleurotus ostreatus) is an important and widely cultivated edible mushroom worldwide; nevertheless, reports are lacking on the identification or function of bZIP gene family members in P. ostreatus. Herein, 11 bZIPs on 6 P. ostreatus chromosomes were systematically identified, which were classified into 3 types according to their protein sequences. Phylogenetic analysis of PobZIPs with other fungal bZIPs indicated that PobZIPs may have differentiated late. Cis-regulatory element analysis revealed that at least one type of stress-response-related element was present on each bZIP promoter. RNA-seq and RT-qPCR analyses revealed that bZIP expression patterns were altered under heat stress and different developmental stages. We combined results from GST-Pull-down, EMSA and yeast two-hybrid assays to screen a key heat stress-responsive candidate gene PobZIP3. PobZIP3 overexpression in P. ostreatus enhanced tolerance to high temperature and cultivation assays revealed that PobZIP3 positively regulates the development of P. ostreatus. RNA-seq analysis showed that PobZIP3 plays a role in glucose metabolism pathways, antioxidant enzyme activity and sexual reproduction. These results may support future functional studies of oyster mushroom bZIP TFs.

Transcriptome and Metabolome Analyses Reflect the Molecular Mechanism of Drought Tolerance in Sweet Potato

Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most widely cultivated crops in the world, with outstanding stress tolerance, but drought stress can lead to a significant decrease in its yield. To reveal the response mechanism of sweet potato to drought stress, an integrated physiological, transcriptome and metabolome investigations were conducted in the leaves of two sweet potato varieties, drought-tolerant zhenghong23 (Z23) and a more sensitive variety, jinong432 (J432). The results for the physiological indexes of drought showed that the peroxidase (POD) and superoxide dismutase (SOD) activities of Z23 were 3.68 and 1.21 times higher than those of J432 under severe drought, while Z23 had a higher antioxidant capacity. Transcriptome and metabolome analysis showed the importance of the amino acid metabolism, respiratory metabolism, and antioxidant systems in drought tolerance. In Z23, amino acids such as asparagine participated in energy production during drought by providing substrates for the citrate cycle (TCA cycle) and glycolysis (EMP). A stronger respiratory metabolism ability could better maintain the energy supply level under drought stress. Drought stress also activated the expression of the genes encoding to antioxidant enzymes and the biosynthesis of flavonoids such as rutin, resulting in improved tolerance to drought. This study provides new insights into the molecular mechanisms of drought tolerance in sweet potato.

Meta-Analysis of the Effects of Overexpressed bZIP Transcription Factors in Plants under Drought Stress

The bZIP (basic leucine zipper) transcription factors have been identified as key regulators of plant responses to drought stress, which limits plant growth and yield. Overexpression of bZIP genes has shown potential in enhancing drought tolerance in various plant species. However, the constrained types of individual studies and inconsistencies among experimental approaches has resulted in a lack of statistical significance and limited the extrapolation of bZIP transcription factor overexpression for plant improvement. We conducted a meta-analysis to evaluate ten measured parameters of drought tolerance in bZIP transcription factor-expressing plants as well as moderators affecting the performance of transgenic plants. The results showed that seven parameters, including survival rate as well as the content of regulatory substances (proline accumulation, H2O2 concentration, CAT activity, POD activity, SOD activity and MDA accumulation), were most affected while the impact on physiological status indicators is not significant. In addition, donor/recipient species, treatment medium, duration and methods of simulating drought stress all significantly impacted the degree of drought stress tolerance in plants to some extent among the considered moderators. The findings underscore the potential of bZIP transcription factors as key targets for genetic engineering approaches aimed at improving plant resilience to water scarcity.

MdbZIP74 negatively regulates osmotic tolerance and adaptability to moderate drought conditions of apple plants

Drought is the most prominent threat to global agricultural production. The basic leucine zipper (bZIP) family is related to the response to a series of abiotic stress. In this case, apple calli and the seedlings of MdbZIP74-RNAi transgenic lines were obtained. Under osmotic stress and moderate drought conditions, the content of malondialdehyde, relative water content and other stress-related assays were measured. MdbZIP74 was found to negatively regulate the osmotic tolerance of apple callus. The growth of MdbZIP74-RNAi calli enhanced resistance without significant production loss. The silencing of MdbZIP74 contributes to redox balance and the adaptability of apple seedlings to moderate drought conditions. Four related differentially expressed genes in the biosynthesis of cytokinin and catabolic pathway were identified through a transcriptome analysis of MdbZIP74-RNAi seedlings under moderate drought conditions. MdLOG8 was further identified as the target of MdbZIP74 involved in the drought adaptability of apple plants using a dual experiment. Further confirmation showed MdLOG8 was maintained in the MdbZIP74-RNAi seedlings presumably acting as the growth regulator to enhance drought adaptability. It was concluded that the correct regulation of cytokinin level under moderate drought conditions maintains the redox balance and avoids the situation of plants surviving with the minimal resources.

The sweet potato B-box transcription factor gene IbBBX28 negatively regulates drought tolerance in transgenic Arabidopsis

B-box (BBX) which are a class of zinc finger transcription factors, play an important role in regulating of photoperiod, photomorphogenesis, and biotic and abiotic stresses in plants. However, there are few studies on the involvement of BBX transcription factors in response to abiotic stresses in sweet potato. In this paper, we cloned the DNA and promoter sequences of IbBBX28. There was one B-box conserved domain in IbBBX28, and the expression of IbBBX28 was induced under drought stress. Under drought stress, compared to wild type Arabidopsis, the protective enzyme activities (SOD, POD, and CAT) were all decreased in IbBBX28-overexpression Arabidopsis but increased in the mutant line bbx28, while the MDA content was increased in the IbBBX28-overexpression Arabidopsis and decreased in the bbx28. Moreover, the expression levels of the resistance-related genes showed the same trend as the protective enzyme activities. These results showed that IbBBX28 negatively regulates drought tolerance in transgenic Arabidopsis. Additionally, the yeast two-hybrid and BiFC assays verified that IbBBX28 interacted with IbHOX11 and IbZMAT2. The above results provide important clues for further studies on the role of IbBBX28 in regulating the stress response in sweet potato.

Transcriptome analysis reveals key drought-stress-responsive genes in soybean

Drought is the most common environmental stress and has had dramatic impacts on soybean (Glycine max L.) growth and yield worldwide. Therefore, to investigate the response mechanism underlying soybean resistance to drought stress, the drought-sensitive cultivar "Liaodou 15" was exposed to 7 (mild drought stress, LD), 17 (moderate drought stress, MD) and 27 (severe drought stress, SD) days of drought stress at the flowering stage followed by rehydration until harvest. A total of 2214, 3684 and 2985 differentially expressed genes (DEGs) in LD/CK1, MD/CK2, and SD/CK3, respectively, were identified by RNA-seq. Weighted gene co-expression network analysis (WGCNA) revealed the drought-response TFs such as WRKY (Glyma.15G021900, Glyma.15G006800), MYB (Glyma.15G190100, Glyma.15G237900), and bZIP (Glyma.15G114800), which may be regulated soybean drought resistance. Second, Glyma.08G176300 (NCED1), Glyma.03G222600 (SDR), Glyma.02G048400 (F3H), Glyma.14G221200 (CAD), Glyma.14G205200 (C4H), Glyma.19G105100 (CHS), Glyma.07G266200 (VTC) and Glyma.15G251500 (GST), which are involved in ABA and flavonoid biosynthesis and ascorbic acid and glutathione metabolism, were identified, suggesting that these metabolic pathways play key roles in the soybean response to drought. Finally, the soybean yield after rehydration was reduced by 50% under severe drought stress. Collectively, our study deepens the understanding of soybean drought resistance mechanisms and provides a theoretical basis for the soybean drought resistance molecular breeding and effectively adjusts water-saving irrigation for soybean under field production.

Evolutionary and functional characterisation of glutathione peroxidases showed splicing mediated stress responses in Maize

Maize (Zea mays L) is an important cereal with extensive adaptability and multifaceted usages. However, various abiotic and biotic stresses limit the productivity of maize across the globe. Exposure of plant to stresses disturb the balance between reactive oxygen species (ROS) production and scavenging, which subsequently increases cellular damage and death of plants. Tolerant genotypes have evolved higher output of scavenging antioxidative defence compounds (ADCs) during stresses as one of the protective mechanisms. The glutathione peroxidases (GPXs) are the broad class of ADCs family. The plant GPXs catalyse the reduction of hydrogen peroxide (H₂O₂), lipid hydroperoxides and organic hydroperoxides to the corresponding alcohol, and facilitate the regulation of stress tolerance mechanisms. The present investigation was framed to study the maize GPXs using evolutionary and functional analyses. Seven GPX genes with thirteen splice-variants and sixty-three types of cis-acting elements were identified through whole-genome scanning in maize. Evolutionary analysis of GPXs in monocots and dicots revealed mixed and lineage-specific grouping patterns in phylogeny. The expression of ZmGPX splice variants was studied in drought and waterlogging tolerant (L1621701) and sensitive (PML10) genotypes in root and shoot tissues. Further, the differential expression of splice variants of ZmGPX1, ZmGPX3, ZmGPX6 and ZmGPX7 and regulatory network analysis suggested the splicing and regulatory elements mediated stress responses. The present investigation suggests targeting the splicing machinery of GPXs as an approach to enhance the stress tolerance in maize.

Novel small molecules targeting bZIP23 TF improve stomatal conductance and photosynthesis under mild drought stress by regulating ABA

Drought-induced abscisic acid (ABA) accumulation plays a key role in plant water relations by regulating stomatal movements. Although ABA helps in the survival of the plants, reduced carbon gain affects plant productivity. To improve crop productivity under mild drought stress conditions, it is necessary to manipulate ABA responses. Other research groups have used forward chemical genomics for the identification of ABA agonists and antagonists aiming to manipulate ABA biosynthesis and signalling. In the present study, we identified indolyl-ethyl amine and serotonin small molecules using a reverse chemical genomics approach, with these acting as potent inhibitors of ABA biosynthesis through transient regulation of bZIP23 transcription factor activity. In rice, wheat and soybean, each of the small molecules enhanced the germination of seeds, even in the presence of ABA. These molecules nullified the effect of ABA on intact and detached leaves, resulting in higher photosynthesis. Furthermore, these small molecules effectively reduced the transcription levels of bZIP23 targeting NCED4, PP2C49 and CO3 genes. Rice plants treated with the small molecules were found to have improved stomatal conductance, spikelet fertility and yield compared to untreated plants under mild drought stress conditions. Our results suggest that indolyl-ethyl amine and serotonin small molecules could be utilized to improve yield under mild drought conditions.

Blocking IbmiR319a Impacts Plant Architecture and Reduces Drought Tolerance in Sweet Potato

MicroRNA319 (miR319) plays a key role in plant growth, development, and multiple resistance by repressing the expression of targeted TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) genes. Two members, IbmiR319a and IbmiR319c, were discovered in the miR319 gene family in sweet potato (Ipomoea batatas [L.] Lam). Here, we focused on the biological function and potential molecular mechanism of the response of IbmiR319a to drought stress in sweet potato. Blocking IbmiR319a in transgenic sweet potato (MIM319) resulted in a slim and tender phenotype and greater sensitivity to drought stress. Microscopic observations revealed that blocking IbmiR319a decreased the cell width and increased the stomatal distribution in the adaxial leaf epidermis, and also increased the intercellular space in the leaf and petiole. We also found that the lignin content was reduced, which led to increased brittleness in MIM319. Quantitative real-time PCR showed that the expression levels of key genes in the lignin biosynthesis pathway were much lower in the MIM319 lines than in the wild type. Ectopic expression of IbmiR319a-targeted genes IbTCP11 and IbTCP17 in Arabidopsis resulted in similar phenotypes to MIM319. We also showed that the expression of IbTCP11 and IbTCP17 was largely induced by drought stress. Transcriptome analysis indicated that cell growth-related pathways, such as plant hormonal signaling, were significantly downregulated with the blocking of IbmiR319a. Taken together, our findings suggest that IbmiR319a affects plant architecture by targeting IbTCP11/17 to control the response to drought stress in sweet potato.

S1-bZIP Transcription Factors Play Important Roles in the Regulation of Fruit Quality and Stress Response

Sugar metabolism not only determines fruit sweetness and quality but also acts as signaling molecules to substantially connect with other primary metabolic processes and, therefore, modulates plant growth and development, fruit ripening, and stress response. The basic region/leucine zipper motif (bZIP) transcription factor family is ubiquitous in eukaryotes and plays a diverse array of biological functions in plants. Among the bZIP family members, the smallest bZIP subgroup, S1-bZIP, is a unique one, due to the conserved upstream open reading frames (uORFs) in the 5' leader region of their mRNA. The translated small peptides from these uORFs are suggested to mediate Sucrose-Induced Repression of Translation (SIRT), an important mechanism to maintain sucrose homeostasis in plants. Here, we review recent research on the evolution, sequence features, and biological functions of this bZIP subgroup. S1-bZIPs play important roles in fruit quality, abiotic and biotic stress responses, plant growth and development, and other metabolite biosynthesis by acting as signaling hubs through dimerization with the subgroup C-bZIPs and other cofactors like SnRK1 to coordinate the expression of downstream genes. Direction for further research and genetic engineering of S1-bZIPs in plants is suggested for the improvement of quality and safety traits of fruit.

Genome-Wide Characterization and Expression Analysis of bZIP Gene Family Under Abiotic Stress in Glycyrrhiza uralensis

bZIP gene family is one of the largest transcription factor families. It plays an important role in plant growth, metabolic, and environmental response. However, complete genome-wide investigation of bZIP gene family in Glycyrrhiza uralensis remains unexplained. In this study, 66 putative bZIP genes in the genome of G. uralensis were identified. And their evolutionary classification, physicochemical properties, conserved domain, functional differentiation, and the expression level under different stress conditions were further analyzed. All the members were clustered into 13 subfamilies (A–K, M, and S). A total of 10 conserved motifs were found in GubZIP proteins. Members from the same subfamily shared highly similar gene structures and conserved domains. Tandem duplication events acted as a major driving force for the evolution of bZIP gene family in G. uralensis. Cis-acting elements and protein–protein interaction networks showed that GubZIPs in one subfamily are involved in multiple functions, while some GubZIPs from different subfamilies may share the same functional category. The miRNA network targeting GubZIPs showed that the regulation at the transcriptional level may affect protein–protein interaction networks. We suspected that domain-mediated interactions may categorize a protein family into subfamilies in G. uralensis. Furthermore, the tissue-specific gene expression patterns of GubZIPs were analyzed using the public RNA-seq data. Moreover, gene expression level of 66 bZIP family members under abiotic stress treatments was quantified by using qRT-PCR. The results of this study may serve as potential candidates for functional characterization in the future.

Group-C/S1 bZIP heterodimers regulate MdIPT5b to negatively modulate drought tolerance in apple species

Cytokinins play a central role in delaying senescence, reducing oxidative damage and maintaining plant growth during drought. This study showed that the ectopic expression of ProRE-deleted MdIPT5b, a key enzyme involved in cytokinin metabolism, increased the drought tolerance of transgenic Malus domestica (apple) callus and Solanum lycopersicum (tomato) seedlings by maintaining cytokinin homeostasis, and thus maintaining redox balance. Under restricted watering regimes, the yields of transgenic tomato plants were enhanced. Heterodimers of C/S1 bZIP are involved in the cytokinin-mediated drought response. The heterodimers bind the ProRE of MdIPT5b promoter, thus directly suppressing gene transcription. Single C/S1 bZIP members could not independently function as suppressors. However, specific paired members (heterodimers of MdbZIP80 with MdbZIP2 or with MdbZIP39) effectively suppressed transcription. The α-helical structure is essential for the heterodimerization of C/S1 bZIP members and for synergistic transcriptional suppression. As negative regulators of drought tolerance, suppressing either MdbZIP2 or MdbZIP39 alone does not improve the expression of MdIPT5b and did not increase the drought tolerance of transgenic apple callus. However, this could be achieved when they were co-suppressed. The suppression of MdbZIP80 alone could improve MdIPT5b expression and increase the drought tolerance of transgenic apple callus. However, these effects were reversed in response to the cosuppression of MdbZIP80 and MdIPT5b. Similar results were also observed during delayed dark-induced senescence in apple leaves. In conclusion, the apple C/S1 bZIP network (involving MdbZIP2, MdbZIP39 and MdbZIP80) directly suppressed the expression of MdIPT5b, thus negatively modulating drought tolerance and dark-induced senescence in a functionally redundant manner.

Transcription factors as key molecular target to strengthen the drought stress tolerance in plants

Amid apprehension of global climate change, crop plants are inevitably confronted with a myriad of abiotic stress factors during their growth that inflicts a serious threat to their development and overall productivity. These abiotic stresses comprise extreme temperature, pH, high saline soil, and drought stress. Among different abiotic stresses, drought is considered the most calamitous stressor with its serious impact on the crops' yield stability. The development of climate-resilient crops that withstands reduced water availability is a major focus of the scientific fraternity to ensure the food security of the sharply increasing population. Numerous studies aim to recognize the key regulators of molecular and biochemical processes associated with drought stress tolerance response. A few potential candidates are now considered as promising targets for crop improvement. Transcription factors act as a key regulatory switch controlling the gene expression of diverse biological processes and, eventually, the metabolic processes. Understanding the role and regulation of the transcription factors will facilitate the crop improvement strategies intending to develop and deliver agronomically-superior crops. Therefore, in this review, we have emphasized the molecular avenues of the transcription factors that can be exploited to engineer drought tolerance potential in crop plants. We have discussed the molecular role of several transcription factors, such as basic leucine zipper (bZIP), dehydration responsive element binding (DREB), DNA binding with one finger (DOF), heat shock factor (HSF), MYB, NAC, TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP), and WRKY. We have also highlighted candidate transcription factors that can be used for the development of drought-tolerant crops.

Functional annotations of ESTs of Stevia rebaudiana involved in abiotic stress signaling through computational approach

Stevia rebaudiana (Bertoni) is known as a natural sweetener plant to produced steviol glycosides. The steviol glycosides biosynthesis is limited in S. rebaudiana plants due to the alteration in the environmental circumstances such as drought, cold, salt and light. These environmental circumstances are a common side-effect in plants affecting the plant growth, metabolism and yield of secondary metabolites. Due to absence of complete genome annotations, the plant metabolites signaling is difficult in order to get the exact enzymatic flow to the product. In this article, we have analyzed the ESTs of S. rebaudiana and predicted their role in plant signaling in term of cis-regulatory elements, their biological function respect to abiotic stress. Further, the predicted abiotic stress responsive factors were also analyzed in order to predict the relevant genes or proteins function in comparison with the genome of Arabidopsis thaliana. Total 5,548 ESTs of stevia were retrieved from NCBI database. EST-contigs assembled from 5393 were 619 contigs and 2,894 singletons elements were identified by assembler program. Due to short expressed sequences related to singletons, it is excluded for further study. Further, retrieved ESTs were resulted in to 619 EST-contigs by using the clustering method. Out of 619, 15 contigs belongs to transcription factor families while 292 contigs, belongs to five enzyme classes. Out of 619 contigs, the 529 contigs showing the correct gene ontology in term of biological process (BP), molecular Functions (MF) and cellular component (CC). Further, these contigs were also screened for metabolic pathways analyses using KEG database. In this, 390 metabolic pathways and 67 involved for signal transduction were identified from 619 contigs. The co-expression analysis was revealed by gene investigators and STRING 10.0 with 0.40 correlations and 0.9 mutual connection. In projected PPI network, the recognized factors (WD40-like protein, MYB-HB like, AP2-EREBP, C2H2, Hap3/NF-YB, bHLH, C2C2-CO-like, CW-Zn, FHA-SMAD, Nin like, SBP3, TIFY, Tc-PD, Znf-B and bIP) belong to plant signaling and MAPK signaling pathways. These TFs introduce as a candidate genes responsive factors may lead to enhanced plant growth and metabolism by overexpression.

Gene expression for secondary metabolite biosynthesis in hop (Humulus lupulus L.) leaf lupulin glands exposed to heat and low-water stress

Hops are valued for their secondary metabolites, including bitter acids, flavonoids, oils, and polyphenols, that impart flavor in beer. Previous studies have shown that hop yield and bitter acid content decline with increased temperatures and low-water stress. We looked at physiological traits and differential gene expression in leaf, stem, and root tissue from hop (Humulus lupulus) cv. USDA Cascade in plants exposed to high temperature stress, low-water stress, and a compound treatment of both high temperature and low-water stress for six weeks. The stress conditions imposed in these experiments caused substantial changes to the transcriptome, with significant reductions in the expression of numerous genes involved in secondary metabolite biosynthesis. Of the genes involved in bitter acid production, the critical gene valerophenone synthase (VPS) experienced significant reductions in expression levels across stress treatments, suggesting stress-induced lability in this gene and/or its regulatory elements may be at least partially responsible for previously reported declines in bitter acid content. We also identified a number of transcripts with homology to genes shown to affect abiotic stress tolerance in other plants that may be useful as markers for breeding improved abiotic stress tolerance in hop. Lastly, we provide the first transcriptome from hop root tissue.

Unlocking the inherent potential of plant genetic resources: food security and climate adaptation strategy in Fiji and the Pacific

Pacific Island Countries (PICs) are the center of origin and diversity for several root, fruit and nut crops, which are indispensable for food security, rural livelihoods, and cultural identity of local communities. However, declining genetic diversity of traditional food crops and high vulnerability to climate change are major impediments for maintaining agricultural productivity. Limited initiatives to achieve food self-sufficiency and utilization of Plant Genetic Resources (PGR) for enhancing resilience of agro-ecosystems are other serious constraints. This review focuses on the visible and anticipated impacts of climate ge, on major food and tree crops in agriculture and agroforestry systems in the PICs. We argue that crop improvement through plant breeding is a viable strategy to enhance food security and climatic resilience in the region. The exploitation of adaptive traits: abiotic and biotic stress tolerance, yield and nutritional efficiency, is imperative in a world threatened by climatic extremes. However, the insular constraints of Fiji and other small PICs are major limitations for the utilization of PGR through high throughput techniques which are also cost prohibitive. Crop Improvement programs should instead focus on the identification, conservation, documentation and dissemination of information on unique landraces, community seed banks, introduction of new resistant genotypes, and sustaining and enhancing allelic diversity.

Physiological Characteristic Changes and Full-Length Transcriptome of Rose (Rosa chinensis) Roots and Leaves in Response to Drought Stress

Rose (Rosa chinensis) is the most important ornamental crops worldwide. However, the physiological and molecular mechanism of rose under drought stress remains elusive. In this study, we analyzed the changes of photosynthetic and phytohormone levels in the leaves and roots of rose seedlings grown under control (no drought), mild drought (MD) and severe drought stress. The total chlorophyll content and water use efficiency were significantly enhanced under MD in rose leaves. In addition, the concentration of ABA was higher in the leaves compared to the roots, whereas the roots accumulated more IAA, methylindole-3-acetic acid and indole-3-propionic acid. We also constructed the first full-length transcriptome for rose, and identified 96,201,862 full-length reads of average length 1,149 bp that included 65,789 novel transcripts. A total of 3,657 and 4,341 differentially expressed genes (DEGs) were identified in rose leaves and roots respectively. KEGG pathway analysis showed enrichment of plant hormone, signal transduction and photosynthesis are among the DEGs. 42,544 alternatively spliced isoforms were also identified, and alternative 3' splice site was the major alternative splicing (AS) event among the DEGs. Variations in the AS patterns of three genes between leaves and roots indicated the possibility of tissue-specific posttranscriptional regulation in response to drought stress. Furthermore, 2,410 novel long non-coding RNAs were detected that may participate in regulating the drought-induced DEGs. Our findings identified previously unknown splice sites and new genes in the rose transcriptome, and elucidated the drought stress-responsive genes as well as their intricate regulatory networks.

Ectopic expression of MYB repressor GmMYB3a improves drought tolerance and productivity of transgenic peanuts (Arachis hypogaea L.) under conditions of water deficit

Peanut is widely grown and provides protein and edible oil for millions of people. Peanut growth and productivity are frequently negatively affected by abiotic and biotic environmental factors. However, the research on improving peanut germplasm resources by genetic transformation is very limited. Here, the novel R2R3-MYB repressor GmMYB3a was introduced into peanut plants by Agrobacterium-mediated transformation for the first time for thorough evaluation of the function of GmMYB3a in drought stress plant responses. We generated GmMYB3a-transgenic peanut plants. The GmMYB3a-overexpressing lines showed significantly improved physiological responses and no yield loss non-transgenic plants, in terms of survival rates. Thus, the GmMYB3a-overexpressing plants showed better photosynthetic performance, higher relative water content, and greater water use efficiency, demonstrating their adaptive capacity to water deficit. We conclude that overexpression of GmMYB3a can improve drought tolerance and productivity in peanut.

Is Silicon a Panacea for Alleviating Drought and Salt Stress in Crops?

Salinity affects around 20% of all arable land while an even larger area suffers from recurrent drought. Together these stresses suppress global crop production by as much as 50% and their impacts are predicted to be exacerbated by climate change. Infrastructure and management practices can mitigate these detrimental impacts, but are costly. Crop breeding for improved tolerance has had some success but is progressing slowly and is not keeping pace with climate change. In contrast, Silicon (Si) is known to improve plant tolerance to a range of stresses and could provide a sustainable, rapid and cost-effective mitigation method. The exact mechanisms are still under debate but it appears Si can relieve salt stress via accumulation in the root apoplast where it reduces "bypass flow of ions to the shoot. Si-dependent drought relief has been linked to lowered root hydraulic conductance and reduction of water loss through transpiration. However, many alternative mechanisms may play a role such as altered gene expression and increased accumulation of compatible solutes. Oxidative damage that occurs under stress conditions can be reduced by Si through increased antioxidative enzymes while Si-improved photosynthesis has also been reported. Si fertilizer can be produced relatively cheaply and to assess its economic viability to improve crop stress tolerance we present a cost-benefit analysis. It suggests that Si fertilization may be beneficial in many agronomic settings but may be beyond the means of smallholder farmers in developing countries. Si application may also have disadvantages, such as increased soil pH, less efficient conversion of crops into biofuel and reduced digestibility of animal fodder. These issues may hamper uptake of Si fertilization as a routine agronomic practice. Here, we critically evaluate recent literature, quantifying the most significant physiological changes associated with Si in plants under drought and salinity stress. Analyses show that metrics associated with photosynthesis, water balance and oxidative stress all improve when Si is present during plant exposure to salinity and drought. We further conclude that most of these changes can be explained by apoplastic roles of Si while there is as yet little evidence to support biochemical roles of this element.

The Sweetpotato BTB-TAZ Protein Gene, IbBT4, Enhances Drought Tolerance in Transgenic Arabidopsis

BTB-TAZ (BT)-domain proteins regulate plant development and pathogen defense. However, their roles in resistance to abiotic stresses remain largely unknown. In this study, we found that the sweetpotato BT protein-encoding gene IbBT4 significantly enhanced the drought tolerance of Arabidopsis. IbBT4 expression was induced by PEG6000, H₂O₂ and brassinosteroids (BRs). The IbBT4-overexpressing Arabidopsis seeds presented higher germination rates and longer roots in comparison with those of WT under 200 mM mannitol stress. Under drought stress the transgenic Arabidopsis plants exhibited significantly increased survival rates and BR and proline contents and decreased water loss rates, MDA content and reactive oxygen species (ROS) levels. IbBT4 overexpression upregulated the BR signaling pathway and proline biosynthesis genes and activated the ROS-scavenging system under drought stress. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that the IbBT4 protein interacts with BR-ENHANCED EXPRESSION 2 (BEE2). Taken together, these results indicate that the IbBT4 gene provides drought tolerance by enhancing both the BR signaling pathway and proline biosynthesis and further activating the ROS-scavenging system in transgenic Arabidopsis.

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering

BACKGROUND

Drought stress is a major abiotic factor that affects rapeseed (Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs' response to drought stress is still lacking, especially in the case of B. napus. In order to further understand the molecular mechanism of the response of B. napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) responding drought stress and rehydration treatment at the seedling stage.

RESULTS

A total of 5546 down-regulated and 6997 up-regulated mRNAs were detected in Q2 compared with 7824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up- regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. LncRNA-mRNA interaction network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. We further identified 34 transcription factors (TFs) corresponding to 126 differentially expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differentially expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes. Notably, some lncRNAs were co-expressed with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs co-located with XLOC_052298, XLOC_094954 and XLOC_012868 were mainly categorized as signal transport and defense/stress response.

CONCLUSIONS

The results of this study increased our understanding of expression characterization of rapeseed lncRNAs in response to drought stress and re-watering, which would be useful to provide a reference for the further study of the function and action mechanisms of lncRNAs under drought stress and re-watering.

The Soybean bZIP Transcription Factor Gene GmbZIP2 Confers Drought and Salt Resistances in Transgenic Plants

Abiotic stresses, such as drought and salt, are major environmental stresses, affecting plant growth and crop productivity. Plant bZIP transcription factors (bZIPs) confer stress resistances in harsh environments and play important roles in each phase of plant growth processes. In this research, 15 soybean bZIP family members were identified from drought-induced de novo transcriptomic sequences of soybean, which were unevenly distributed across 12 soybean chromosomes. Promoter analysis showed that these 15 genes were rich in ABRE, MYB and MYC cis-acting elements which were reported to be involved in abiotic stress responses. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis indicated that 15 GmbZIP genes could be induced by drought and salt stress. GmbZIP2 was significantly upregulated under stress conditions and thus was selected for further study. Subcellular localization analysis revealed that the GmbZIP2 protein was located in the cell nucleus. qRT-PCR results show that GmbZIP2 can be induced by multiple stresses. The overexpression of GmbZIP2 in Arabidopsis and soybean hairy roots could improve plant resistance to drought and salt stresses. The result of differential expression gene analysis shows that the overexpression of GmbZIP2 in soybean hairy roots could enhance the expression of the stress responsive genes GmMYB48, GmWD40, GmDHN15, GmGST1 and GmLEA. These results indicate that soybean bZIPs played pivotal roles in plant resistance to abiotic stresses.