Transcriptome Analysis of Poplar Under Salt Stress and Over-Expression of Transcription Factor NAC57 Gene Confers Salt Tolerance in Transgenic Arabidopsis

Physiological and transcriptomic analyses reveal the molecular mechanism of PsAMT1.2 in salt tolerance

Soil salinization has become a global problem and high salt concentration in soil negatively affects plant growth. In our previous study, we found that overexpression of PsAMT1.2 from Populus simonii could improve the salt tolerance of poplar, but the physiological and molecular mechanism was not well understood. To explore the regulation pathway of PsAMT1.2 in salt tolerance, we investigated the morphological, physiological and transcriptome differences between the PsAMT1.2 overexpression transgenic poplar and the wild type under salt stress. The PsAMT1.2 overexpression transgenic poplar showed better growth with increased net photosynthetic rate and higher chlorophyll content compared with wild type under salt stress. The overexpression of PsAMT1.2 increased the catalase, superoxide dismutase, peroxidase and ascorbate peroxidase activities, and therefore probably enhanced the reactive oxygen species clearance ability, which also reduced the degree of membrane lipid peroxidation under salt stress. Meanwhile, the PsAMT1.2 overexpression transgenic poplar maintained a relatively high K+/Na+ ratio under salt stress. RNA-seq analysis indicated that PsAMT1.2 might improve plant salt tolerance by regulating pathways related to the photosynthetic system, chloroplast structure, antioxidant activity and anion transport. Among the 1056 differentially expressed genes, genes related to photosystem I and photosystem II were up-regulated and genes related to chloride channel protein-related were down-regulated. The result of the present study would provide new insight into regulation mechanism of PsAMT1.2 in improving salt tolerance of poplar.

Poplar glutathione S-transferase PtrGSTF8 contributes to reactive oxygen species scavenging and salt tolerance

Glutathione S-transferases (GSTs) constitute a protein superfamily encoded by a large gene family and play a crucial role in plant growth and development. However, their precise functions in wood plant responses to abiotic stress are not fully understood. In this study, we isolated a Phi class glutathione S-transferase-encoding gene, PtrGSTF8, from poplar (Populus alba × P. glandulosa), which is significantly up-regulated under salt stress. Moreover, compared with wild-type (WT) plants, transgenic tobacco plants exhibited significant salt stress tolerance. Under salt stress, PtrGSTF8-overexpressing tobacco plants showed a significant increase in plant height and root length, and less accumulation of reactive oxygen species. In addition, these transgenic tobacco plants exhibited higher superoxide dismutase, peroxidase, and catalase activities and reduced malondialdehyde content compared with WT plants. Quantitative real-time PCR experiments showed that the overexpression of PtrGSTF8 increased the expression of numerous genes related to salt stress. Furthermore, PtrMYB108, a MYB transcription factor involved in salt resistance in poplar, was found to directly activate the promoter of PtrGSTF8, as demonstrated by yeast one-hybrid assays and luciferase complementation assays. Taken together, these findings suggest that poplar PtrGSTF8 contributes to enhanced salt tolerance and confers multiple growth advantages when overexpressed in tobacco.

Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice

Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the 2 serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants.

Comparative Transcriptomics Analysis Reveals the Differences in Transcription between Resistant and Susceptible Pepper (Capsicum annuum L.) Varieties in Response to Anthracnose

Pepper (Capsicum annuum L.) is a herbaceous plant species in the family Solanaceae. Capsicum anthracnose is caused by the genus Colletotrichum. spp., which decreases pepper production by about 50% each year due to anthracnose. In this study, we evaluated the resistance of red ripe fruits from 17 pepper varieties against anthracnose fungus Colletotrichum capsici. We assessed the size of the lesion diameter and conducted significance analysis to identify the resistant variety of B158 and susceptible variety of B161. We selected a resistant cultivar B158 and a susceptible cultivar B161 of pepper and used a transcription to investigate the molecular mechanisms underlying the plant's resistance to C. capsici, of which little is known. The inoculated fruit from these two varieties were used for the comparative transcription analysis, which revealed the anthracnose-induced differential transcription in the resistant and susceptible pepper samples. In the environment of an anthrax infection, we found that there were more differentially expressed genes in resistant varieties compared to susceptible varieties. Moreover, the response to stimulus and stress ability was stronger in the KANG. The transcription analysis revealed the activation of plant hormone signaling pathways, phenylpropanoid synthesis, and metabolic processes in the defense response of peppers against anthracnose. In addition, ARR-B, AP2-EREBP, bHLH, WRKY, and NAC are associated with disease resistance to anthracnose. Notably, WRKY and NAC were found to have a potentially positive regulatory role in the defense response against anthracnose. These findings contribute to a more comprehensive understanding of the resistance mechanisms of red pepper fruit to anthracnose infection, providing valuable molecular insights for further research on the resistance mechanisms and genetic regulations during this developmental stage of pepper.

Wheat WRKY transcription factor TaWRKY24 confers drought and salt tolerance in transgenic plants

Drought and salt stress are major environmental conditions that severely limit plant growth and productivity. WRKY transcription factors play a vital role in the responses against biotic or abiotic stress. In this study, TaWRKY24, a gene of the IIe WRKY family identified in wheat, was cloned and characterized. TaWRKY24 was mainly expressed in wheat leaf and stem and induced by treatment with PEG6000, salt, H2O2, ABA, MeJA, and ethrel. TaWRKY24 transient expression in onion epidermal cells suggested its nuclear localization and its transcriptional activation capability characteristics. Overexpression of TaWRKY24 in tobacco improved the seed germination rate and root growth of seedlings in transgenic lines when subjected to higher mannitol and NaCl concentrations. Further research showed that transgenic lines had higher proline and soluble sugars and lower levels of reactive oxygen species (ROS) and malondialdehyde (MDA). Moreover, compared to normal and negative control plants, TaWRKY24 silenced wheat seedlings had reduced growth under salt and drought stress. This study shows that wheat TaWRKY24 is crucial to plant stress, providing an excellent candidate gene for wheat resistance breeding.

Large effect of phosphate-solubilizing bacteria on the growth and gene expression of Salix spp. at low phosphorus levels

Phosphorus is one of the most important nutrients required for plant growth and development. However, owing to its low availability in the soil, phosphorus is also one of the most difficult elements for plants to acquire. Phosphorus released into the soil from bedrock quickly becomes unavailable to plants, forming poorly soluble complexes. Phosphate-solubilizing bacteria (PSB) can solubilize unavailable phosphorus-containing compounds into forms in which phosphorus is readily available, thus promoting plant growth. In this study, two willow species, Salix dasyclados cv. Loden and Salix schwerinii × Salix viminalis cv. Tora, were inoculated with two selected bacterial strains, Pantoea agglomerans and Paenibacillus spp., to evaluate the plant growth parameters and changes in gene expression in the presence of different concentrations of tricalcium phosphate: 0 mM (NP), 1 mM (LP), and 2 mM (HP). Inoculation with PSB increased root, shoot and leaf biomass, and for the HP treatment, significant changes in growth patterns were observed. However, the growth responses to plant treatments tested depended on the willow species. Analysis of the leaf transcriptomes of the phosphate-solubilizing bacterium-inoculated plants showed a large variation in gene expression between the two willow species. For the Tora willow species, upregulation of genes was observed, particularly for those involved in pathways related to photosynthesis, and this effect was strongly influenced by bacterial phosphate solubilization. The Loden willow species was characterized by a general downregulation of genes involved in pathway activity that included ion transport, transcription regulation and chromosomes. The results obtained in this study provide an improved understanding of the dynamics of Salix growth and gene expression under the influence of PSB, contributing to an increase in yield and phosphorus-use efficiency.

Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms

The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na⁺ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.

Over-expression of DREB46 enhances drought tolerance in Populus trichocarpa

The drought responsive element binding (DREB) gene family has a significant role in plant abiotic stress responses. Here, we cloned a drought-inducible DREB gene, DREB46 (Potri.019G075500), and investigated its function in drought tolerance in Populus trichocarpa. Under treatment with exogenous abscisic acid and 6% PEG6000, DREB46 was rapidly and abundantly expressed. We successfully inserted P. trichocarpa DREB46 constructs into P. trichocarpa. After 11 d of drought stress and 3 d of rehydration treatment, the DREB46 over-expression (OE) lines exhibited significantly increased survival rates relative to the wild type (WT). Histochemical staining showed that the accumulation of reactive oxygen species (ROS) in transgenic plants under drought stress was lower than that in WT plants. Furthermore, OE plants displayed higher superoxide dismutase, peroxidase, and catalase activities and proline content, but lower malondialdehyde content than the WT plants under drought stress. In contrast, DREB46-RNA interference (RNAi) lines exhibited the opposite phenotype. Under PEG-6000 stress, OE plants produced significantly more adventitious roots (ARs) than WT plants. In contrast, RNAi-mediated DREB46-inhibited poplar exhibited fewer ARs. Quantitative real-time PCR indicated that WOX11/12a (Potri.013G066900), a gene related to root growth and development regulation, was significantly increased in OE plants. Additionally, yeast two-hybrid (Y2H) assays showed that DREB46 could interact with protein kinase MPK1 (Potri.002G032100) and protein phosphatase PP2C47 (Potri.007G058700), respectively, and this result was also verified by luciferase complementation assay. Transient co-expression results of leaves showed that PP2C47 and DREB46 Agrobacterium-transformed leaves had strong drought tolerance. These results show that DREB46 plays a key role in drought tolerance by inducing the ROS scavenging system and increasing the number of ARs.

Allele-specific expression and chromatin accessibility contribute to heterosis in tea plants (Camellia sinensis)

Heterosis is extensively used to improve crop productivity, yet its allelic and chromatin regulation remains unclear. Based on our resolved genomes of the maternal TGY and paternal HD, we analyzed the contribution of allele-specific expression (ASE) and chromatin accessibility of JGY and HGY, the artificial hybrids of oolong tea with the largest cultivated area in China. The ASE genes (ASEGs) of tea hybrids with maternal-biased were mainly related to the energy and terpenoid metabolism pathways, whereas the ASEGs with paternal-biased tend to be enriched in glutathione metabolism, and these parental bias of hybrids may coordinate and lead to the acquisition of heterosis in more biological pathways. ATAC-seq results showed that hybrids have significantly higher accessible chromatin regions (ACRs) compared with their parents, which may confer broader and stronger transcriptional activity of genes in hybrids. The number of ACRs with significantly increased accessibility in hybrids was much greater than decreased, and the associated alleles were also affected by differential ACRs across different parents, suggesting enhanced positive chromatin regulation and potential genetic effects in hybrids. Core ASEGs of terpene and purine alkaloid metabolism pathways with significant positive heterosis have greater chromatin accessibility in hybrids, and were potentially regulated by several members of the MYB, DOF and TRB families. The binding motif of CsMYB85 in the promoter ACR of the rate-limiting enzyme CsDXS was verified by DAP-seq. These results suggest that higher numbers and more accessible ACRs in hybrids contribute to the regulation of ASEGs, thereby affecting the formation of heterotic metabolites.

Combined transcriptomic and physiological metabolomic analyses elucidate key biological pathways in the response of two sorghum genotypes to salinity stress

Sorghum is an important food crop with high salt tolerance. Therefore, studying the salt tolerance mechanism of sorghum has great significance for understanding the salt tolerance mechanism of C4 plants. In this study, two sorghum species, LRNK1 (salt-tolerant (ST)) and LR2381 (salt-sensitive (SS)), were treated with 180 mM NaCl salt solution, and their physiological indicators were measured. Transcriptomic and metabolomic analyses were performed by Illumina sequencing and liquid chromatography-mass spectrometry (LC-MS) technology, respectively. The results demonstrated that the plant height, leaf area, and chlorophyll contents in LRNK1 were significantly higher than in LR2381. Functional analysis of differently expressed genes (DEGs) demonstrated that plant hormone signal transduction (GO:0015473), carbohydrate catabolic processes (GO:0016052), and photosynthesis (GO:0015979) were the main pathways to respond to salt stress in sorghum. The genes of the two varieties showed different expression patterns under salt stress conditions. The metabolomic data revealed different profiles of salicylic acid and betaine between LRNK1 and LR2381, which mediated the salt tolerance of sorghum. In conclusion, LRNK1 sorghum responds to salt stress via a variety of biological processes, including energy reserve, the accumulation of salicylic acid and betaine, and improving the activity of salt stress-related pathways. These discoveries provide new insights into the salt tolerance mechanism of sorghum and will contribute to sorghum breeding.

Overexpression of PagERF072 from Poplar Improves Salt Tolerance

Extreme environments, especially drought and high salt conditions, seriously affect plant growth and development. Ethylene-responsive factor (ERF) transcription factors play an important role in salt stress response. In this study, a significantly upregulated ERF gene was identified in 84K (Populus alba × P. glandulosa), which was named PagERF072. PagERF072 was confirmed to be a nuclear-localized protein. The results of yeast two-hybrid (Y2H) assay showed that PagERF072 protein exhibited no self-activating activity, and yeast one-hybrid (Y1H) demonstrated that PagERF072 could specifically bind to GCC-box element. Under salt stress, the transgenic poplar lines overexpressing PagERF072 showed improved salt tolerance. The activities of peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) in transgenic poplars were significantly increased relative to those of wild-type (WT) plants, whereas malondialdehyde (MDA) content showed an opposite trend. In addition, reactive oxygen species (ROS) was significantly reduced, and the expression levels of POD- and SOD-related genes were significantly increased in transgenic poplars under salt stress compared with WT. All results indicate that overexpression of the PagERF072 gene can improve the salt tolerance of transgenic poplars.

Overexpression of PeNAC122 gene promotes wood formation and tolerance to osmotic stress in poplars

Finding the adequate balance between wood formation and abiotic stress resistance is still an important challenge for industrial woody crops. In this study, PeNAC122, a member of the NAC transcription factor (TF) family highly expressed in xylem, was cloned from Populus euphratica. Tissue expression and β-glucuronidase (GUS) staining showed that PeNAC122 was exclusively expressed in phloem fiber and secondary xylem of stems. Subcellular and yeast transactivation assays confirmed that PeNAC122 protein existed in the nucleus and did not have transcriptional activation and inhibitory activity. Overexpression of PeNAC122 poplar lines exhibited reduced plant height, thickened xylem, and accumulated lignin content in stems, and also upregulates the expression of secondary cell wall biosynthetic genes. Moreover, overexpression of PeNAC122 lines displayed more tolerance to PEG6000-induced osmotic stress, with stronger photosynthetic performance, higher antioxidant enzyme activity, and less accumulation of reactive oxygen species in leaves, and higher expression levels of stress response genes DREB2A, RD29, and NCED3. These results indicate that PeNAC122 plays a crucial role in wood formation and abiotic stress tolerance, which, in addition to potential use in improving wood quality, provides further insight into the role of NAC family TFs in balancing wood development and abiotic stress resistance.

Functional analysis of PagNAC045 transcription factor that improves salt and ABA tolerance in transgenic tobacco

BACKGROUND

Salt stress causes inhibition of plant growth and development, and always leads to an increasing threat to plant agriculture. Transcription factors regulate the expression of various genes for stress response and adaptation. It's crucial to reveal the regulatory mechanisms of transcription factors in the response to salt stress.

RESULTS

A salt-inducible NAC transcription factor gene PagNAC045 was isolated from Populus alba×P. glandulosa. The PagNAC045 had a high sequence similarity with NAC045 (Potri.007G099400.1) in P. trichocarpa, and they both contained the same conserved motifs 1 and 2, which constitute the highly conserved NAM domain at the N-terminus. Protein-protein interaction (PPI) prediction showed that PagNAC045 potentially interacts with many proteins involved in plant hormone signaling, DNA-binding and transcriptional regulation. The results of subcellular localization and transient expression in tobacco leaves confirmed the nuclear localization of PagNAC045. Yeast two-hybrid revealed that PagNAC045 protein exhibits transcriptional activation property and the activation domain located in its C-terminus. In addition, the 1063 bp promoter of PagNAC045 was able to drive GUS gene expression in the leaves and roots. In poplar leaves and roots, PagNAC045 expression increased significantly by salt and ABA treatments. Tobacco seedlings overexpressing PagNAC045 exhibited enhanced tolerance to NaCl and ABA compared to the wild-type (WT). Yeast one-hybrid assay demonstrated that a bHLH104-like transcription factor can bind to the promoter sequence of PagNAC045.

CONCLUSION

The PagNAC045 functions as positive regulator in plant responses to NaCl and ABA-mediated stresses.

Overexpression of a Zea mays Brassinosteroid-Signaling Kinase Gene ZmBSK1 Confers Salt Stress Tolerance in Maize

Salinity has become a crucial environmental factor seriously restricting maize (Zea mays L.) growth, development and productivity. However, how plants respond to salt stress is still poorly understood. In this study, we report that a maize brassinosteroid-signaling kinase gene ZmBSK1 plays a significant role in salt stress response. Expression pattern analysis revealed that the transcript level of ZmBSK1 was upregulated by NaCl treatment both in maize leaves, roots, and stems. Phenotypic and physiological analysis showed that overexpression of ZmBSK1 in maize improved salt tolerance by reducing the malondialdehyde (MDA) content, the percentage of electrolyte leakage, O₂ ^- and H₂O₂ accumulation under salt stress, relying on the increases of antioxidant defense enzyme activities and proline content. qRT-PCR analysis showed that overexpression of ZmBSK1 also positively modulated the expression levels of reactive oxygen species (ROS)-scavenging and proline biosynthesis-related genes under salt stress. Moreover, immunoprecipitation-mass spectrometry (IP-MS) assay and firefly luciferase complementation imaging (LCI) assay showed that ZmBSK1 could associate with heat shock protein ZmHSP8 and 14-3-3-like protein ZmGF14-6, and their gene expression levels could be significantly induced by NaCl treatment in different maize tissues. Our findings unravel the new function of ZmBSK1 in salt stress response, which provides the theoretical bases for the improvement of maize salt resistance.

Identification of genes involved in drought tolerance in seedlings of the desert grass, Psammochloa villosa (Poaceae), based on full-length isoform sequencing and de novo assembly from short reads

Psammochloa villosa is a perennial herbaceous plant that is dominant within arid regions of the Inner Mongolian Plateau and the Qinghai-Tibet Plateau in China, where it is an endemic species and exhibits strong drought tolerance and wind resistance. To study drought tolerance in P. villosa and determine its molecular basis, we simulated high and moderate drought stress in a controlled environment and then analyzed transcriptome sequences by combining long-read sequences from a representative, wild-grown individual with short reads from the treatment groups. We obtained 184,076 high-quality isoforms as a reference and 168,650 genes (91.6%), which we were able to annotate according to public databases. Ultimately, we obtained 119,005 unigenes representing the transcriptome of P. villosa under drought stress and, among these, we identified 3089 differentially expressed genes and 1484 transcription factors. Physiologically, P. villosa that was exposed to high and moderate drought stress had reduced germination rates and shorter buds but generated more chlorophyll, which is atypical under drought stress and possibly reflects an adaptation of these plants to their arid environment. We inferred that significantly upregulated genes were annotated as 'Chlorophyll a-b binding protein' and 'Light-harvesting chlorophyll-protein' among drought and control groups. Broadly, our analyses revealed that drought stress triggered many genome-level responses, especially related to mitigation of radical oxygen species (ROS), which increase in concentration under drought stress. In particular, in the high drought stress group compared with the control, GO enrichment analysis revealed a significant enrichment of upregulated genes (n = 10) involved in mitigation of oxidative stress. Similarly, using KEGG we found significant enrichment of genes in the phenylpropanoid biosynthesis pathway (11 genes), which yields phenols that scavenge ROS. We also inferred that many genes involved in metabolism of arginine and proline, which may serve as both scavengers of ROS and osmoprotectants that interact with stress response genes based on our protein-protein interaction network analysis. We verified the relative expression levels of eight genes associated with mitigation of ROS, DNA repair, and transmembrane transporter activity using qRT-PCR, and the results were consistent with our inferences from transcriptomes. This study provides insights into the genomic and physiological basis of drought tolerance in P. villosa and represents a resource for development of the species as a forage crop via molecular breeding within arid lands.

Comprehensive Transcriptome Analysis Uncovers Distinct Expression Patterns Associated with Early Salinity Stress in Annual Ryegrass (Lolium Multiflorum L.)

Soil salination is likely to reduce crop production worldwide. Annual ryegrass (Lolium multiflorum L.) is one of the most important forages cultivated in temperate and subtropical regions. We performed a time-course comparative transcriptome for salinity-sensitive (SS) and salinity-insensitive (SI) genotypes of the annual ryegrass at six intervals post-stress to describe the transcriptional changes and identify the core genes involved in the early responses to salt stress. Our study generated 215.18 Gb of clean data and identified 7642 DEGs in six pairwise comparisons between the SS and SI genotypes of annual ryegrass. Function enrichment of the DEGs indicated that the differences in lipid, vitamins, and carbohydrate metabolism are responsible for variation in salt tolerance of the SS and SI genotypes. Stage-specific profiles revealed novel regulation mechanisms in salinity stress sensing, phytohormones signaling transduction, and transcriptional regulation of the early salinity responses. High-affinity K+ (HAKs) and high-affinity K1 transporter (HKT1) play different roles in the ionic homeostasis of the two genotypes. Moreover, our results also revealed that transcription factors (TFs), such as WRKYs, ERFs, and MYBs, may have different functions during the early signaling sensing of salt stress, such as WRKYs, ERFs, and MYBs. Generally, our study provides insights into the mechanisms of the early salinity response in the annual ryegrass and accelerates the breeding of salt-tolerant forage.

Overexpression of the Tectona grandis TgNAC01 regulates growth, leaf senescence and confer salt stress tolerance in transgenic tobacco plants

NAC transcription factors play critical roles in xylem secondary development and in regulation of stress response in plants. NAC proteins related to secondary cell wall development were recently identified and characterized in Tectona grandis (teak), one of the hardwood trees of highest economic importance in the world. In this work, we characterized the novel TgNAC01 gene, which is involved in signaling pathways that mediate teak response to stress. Abscisic acid (ABA) increases TgNAC01 expression in teak plants. Therefore, this gene may have a role in signaling events that mediate ABA-dependent osmotic stress responsive in this plant species. Stable expression in tobacco plants showed that the TgNAC01 protein is localized in the cell nucleus. Overexpression of TgNAC01 in two out three independent transgenic tobacco lines resulted in increased growth, leaf senescence and salt tolerance compared to wild type (WT) plants. Moreover, the stress tolerance of transgenic plants was affected by levels of TgNAC01 gene expression. Water potential, gas exchange and chlorophyll fluorescence were used to determine salt stress tolerance. The 35S:TgNAC01-6 line under 300 mM NaCl stress responded with a significant increase in photosynthesis rate, stomatal conductance, transpiration and carboxylation efficiency, but lower water potential compared to WT plants. The data indicate that the TgNAC01 transcription factor acts as a transcriptional activator of the ABA-mediated regulation and induces leaf senescence.

Impact of Nanomaterials on the Regulation of Gene Expression and Metabolomics of Plants under Salt Stress

Plant salinity resistance results from a combination of responses at the physiological, molecular, cellular, and metabolic levels. This article focuses on plant stress tolerance mechanisms for controlling ion homeostasis, stress signaling, hormone metabolism, anti-oxidative enzymes, and osmotic balance after nanoparticle applications. Nanoparticles are used as an emerging tool to stimulate specific biochemical reactions related to plant ecophysiological output because of their small size, increased surface area and absorption rate, efficient catalysis of reactions, and adequate reactive sites. Regulated ecophysiological control in saline environments could play a crucial role in plant growth promotion and survival of plants under suboptimal conditions. Plant biologists are seeking to develop a broad profile of genes and proteins that contribute to plant salt resistance. These plant metabolic profiles can be developed due to advancements in genomic, proteomic, metabolomic, and transcriptomic techniques. In order to quantify plant stress responses, transmembrane ion transport, sensors and receptors in signaling transduction, and metabolites involved in the energy supply require thorough study. In addition, more research is needed on the plant salinity stress response based on molecular interactions in response to nanoparticle treatment. The application of nanoparticles as an aspect of genetic engineering for the generation of salt-tolerant plants is a promising area of research. This review article addresses the use of nanoparticles in plant breeding and genetic engineering techniques to develop salt-tolerant crops.

Pretreating poplar cuttings with low nitrogen ameliorates salt stress responses by increasing stored carbohydrates and priming stress signaling pathways

Soil salinity is a widespread stress in semi-arid forests worldwide, but how to manage nitrogen (N) nutrition to improve plant saline tolerance remains unclear. Here, the cuttings of a widely distributed poplar from central Asia, Populus russikki Jabl., were exposed to either normal or low nitrogen (LN) concentrations for two weeks in semi-controlled greenhouse, and then they were added with moderate salt solution or not for another two weeks to evaluate their physiological, biochemical, metabolites and transcriptomic profile changes. LN-pretreating alleviated the toxicity caused by the subsequent salt stress in the poplar plants, demonstrated by a significant reduction in the influx of Na⁺ and Cl^- and improvement of the K⁺/Na⁺ ratio. The other salt-stressed traits were also ameliarated, indicated by the variations of chlorophyll content, PSII photochemical activity and lipid peroxidation. Stress alleviation resulted from two different processes. First, LN pretreatment caused a significant increase of non-structural carbohydrates (NSC), allowed for an increased production of osmolytes and a higher potential fueling ion transport under subsequent salt condition, along with increased transcript levels of the cation/H⁺ ATPase. Second, LN pretreatment enhanced the transcript levels of stress signaling components and phytohormones pathway as well as antioxidant enzyme activities. The results indicate that early restrictions of N supply could enhance posterior survival under saline stress in poplar plants, which is important for plantation programs and restoration activities in semi-arid areas.

Transcriptome of Cenostigma pyramidale roots, a woody legume, under different salt stress times

Salinity stress has a significant impact on the gain of plant biomass. Our study provides the first root transcriptome of Cenostigma pyramidale, a tolerant woody legume from a tropical dry forest, under three different salt stress times (30 min, 2 h, and 11 days). The transcriptome was assembled using the RNA sequencing (RNA-Seq) de novo pipeline from GenPipes. We observed 932, 804, and 3157 upregulated differentially expressed genes (DEGs) and 164, 273, and 1332 downregulated DEGs for salt over 30 min, 2 h, and 11 days, respectively. For DEGs annotated with the Viridiplantae clade in the early stress periods, the response to salt stress was mainly achieved by stabilizing homeostasis of such ions like Na⁺ and K⁺ , signaling by Ca²⁺ , transcription factor modulation, water transport, and oxidative stress. For salt stress at 11 days, we observed a higher modulation of transcription factors including the WRKY, MYB, bHLH, NAC, HSF, and AP2-EREBP families, as well as DEGs involved in hormonal responses, water transport, sugar metabolism, proline, and reactive oxygen scavenging mechanisms. Five selected DEGs (K⁺ transporter, aquaporin, glutathione S-transferase, cyclic nucleotide-gated channel, and superoxide dismutase) were validated by qPCR. Our results indicated that C. pyramidale had an early perception of salt stress modulating ionic channels and transporters, and as the stress progressed, the focus turned to the antioxidant system, aquaporins, and complex hormone responses. The results of this first root transcriptome provide clues on how this native species modulate gene expression to achieve salt stress tolerance.

Advances and Perspectives of Transgenic Technology and Biotechnological Application in Forest Trees

Transgenic technology is increasingly used in forest-tree breeding to overcome the disadvantages of traditional breeding methods, such as a long breeding cycle, complex cultivation environment, and complicated procedures. By introducing exogenous DNA, genes tightly related or contributed to ideal traits-including insect, disease, and herbicide resistance-were transferred into diverse forest trees, and genetically modified (GM) trees including poplars were cultivated. It is beneficial to develop new varieties of GM trees of high quality and promote the genetic improvement of forests. However, the low transformation efficiency has hampered the cultivation of GM trees and the identification of the molecular genetic mechanism in forest trees compared to annual herbaceous plants such as Oryza sativa. In this study, we reviewed advances in transgenic technology of forest trees, including the principles, advantages and disadvantages of diverse genetic transformation methods, and their application for trait improvement. The review provides insight into the establishment and improvement of genetic transformation systems for forest tree species. Challenges and perspectives pertaining to the genetic transformation of forest trees are also discussed.

Understanding the Integrated Pathways and Mechanisms of Transporters, Protein Kinases, and Transcription Factors in Plants under Salt Stress

Abiotic stress is the major threat confronted by modern-day agriculture. Salinity is one of the major abiotic stresses that influence geographical distribution, survival, and productivity of various crops across the globe. Plants perceive salt stress cues and communicate specific signals, which lead to the initiation of defence response against it. Stress signalling involves the transporters, which are critical for water transport and ion homeostasis. Various cytoplasmic components like calcium and kinases are critical for any type of signalling within the cell which elicits molecular responses. Stress signalling instils regulatory proteins and transcription factors (TFs), which induce stress-responsive genes. In this review, we discuss the role of ion transporters, protein kinases, and TFs in plants to overcome the salt stress. Understanding stress responses by components collectively will enhance our ability in understanding the underlying mechanism, which could be utilized for crop improvement strategies for achieving food security.

Functional Characterization of PsnNAC036 under Salinity and High Temperature Stresses

Plant growth and development are challenged by biotic and abiotic stresses including salinity and heat stresses. For Populus simonii × P. nigra as an important greening and economic tree species in China, increasing soil salinization and global warming have become major environmental challenges. We aim to unravel the molecular mechanisms underlying tree tolerance to salt stress and high temprerature (HT) stress conditions. Transcriptomics revealed that a PsnNAC036 transcription factor (TF) was significantly induced by salt stress in P. simonii × P. nigra. This study focuses on addressing the biological functions of PsnNAC036. The gene was cloned, and its temporal and spatial expression was analyzed under different stresses. PsnNAC036 was significantly upregulated under 150 mM NaCl and 37 °C for 12 h. The result is consistent with the presence of stress responsive cis-elements in the PsnNAC036 promoter. Subcellular localization analysis showed that PsnNAC036 was targeted to the nucleus. Additionally, PsnNAC036 was highly expressed in the leaves and roots. To investigate the core activation region of PsnNAC036 protein and its potential regulatory factors and targets, we conducted trans-activation analysis and the result indicates that the C-terminal region of 191-343 amino acids of the PsnNAC036 was a potent activation domain. Furthermore, overexpression of PsnNAC036 stimulated plant growth and enhanced salinity and HT tolerance. Moreover, 14 stress-related genes upregulated in the transgenic plants under high salt and HT conditions may be potential targets of the PsnNAC036. All the results demonstrate that PsnNAC036 plays an important role in salt and HT stress tolerance.

Transcriptome analysis of salt-responsive and wood-associated NACs in Populus simonii × Populus nigra

BACKGROUND

NAC (NAM, ATAF1-2, and CUC2) family is one of the largest plant-specific transcription factor families known to play significant roles in plant development processes and stress responses.

RESULTS

In the study, a total of 112 NACs were identified to be differentially expressed in the comparisons of leaves and stems, leaves and roots, roots and stems of Populus simonii×P. nigra among 289 members by RNA-Seq. And 148, 144 and 134 NACs were detected to be salt-responsive in the roots, stems and leaves under 150 mM NaCl stress, respectively. Among them, a total of 53 salt-responsive NACs were shared across the three tissues. Under salt stress, 41/37 NACs were identified to be up/down-regulated in the leaves of Populus simonii × P.nigra among 170 non-redundant NACs by RT-qPCR, which was similar with RNA-Seq results. The expression pattern analysis of 6 NACs including four randomly up-regulated genes (NAC86, NAC105, NAC139 and NAC163) and two down-regulated genes (NAC15 and NAC149) indicated a few NACs showed specific temporal and spatial expression patterns in the three tissues of Populus simonii×P.nigra. Based on transcriptome screening and phylogenic analysis of differentially expressed NACs in different tissues under salt stress, 18 potential NACs associated with wood formation and 20 involved in stress responses were identified in Populus simonii×P.nigra.

CONCLUSIONS

The study further gains an understanding of the connection of tissue specificity and gene function in poplar, and lays the foundation of functional analysis of poplar NACs in stress responses.

Insights of Molecular Mechanism of Xylem Development in Five Black Poplar Cultivars

Black poplar (Populus deltoides, P. nigra, and their hybrids) is the main poplar cultivars in China. It offers interesting options of large-scale biomass production for bioenergy due to its rapid growth and high yield. Poplar wood properties were associated with chemical components and physical structures during wood formation. In this study, five poplar cultivars, P. euramericana 'Zhonglin46' (Pe1), P. euramericana 'Guariento' (Pe2), P. nigra 'N179' (Pn1), P. deltoides 'Danhong' (Pd1), and P. deltoides 'Nanyang' (Pd2), were used to explore the molecular mechanism of xylem development. We analyzed the structural differences of developing xylem in the five cultivars and profiled the transcriptome-wide gene expression patterns through RNA sequencing. The cross sections of the developing xylem showed that the cell wall thickness of developed fiber in Pd1 was thickest and the number of xylem vessels of Pn1 was the least. A total of 10,331 differentially expressed genes were identified among 10 pairwise comparisons of the five cultivars, most of them were related to programmed cell death and secondary cell wall thickening. K-means cluster analysis and Gene Ontology enrichment analysis showed that the genes highly expressed in Pd1 were related to nucleotide decomposition, metabolic process, transferase, and microtubule cytoskeleton; whereas the genes highly expressed in Pn1 were involved in cell wall macromolecule decomposition and polysaccharide binding processes. Based on a weighted gene co-expression network analysis, a large number of candidate regulators for xylem development were identified. And their potential regulatory roles to cell wall biosynthesis genes were validated by a transient overexpression system. This study provides a set of promising candidate regulators for genetic engineering to improve feedstock and enhance biofuel conversion in the bioenergy crop Populus.

Over-expression of transcription factor ARK1 gene leads to down-regulation of lignin synthesis related genes in hybrid poplar '717'

Improving wood growth rate and wood quality are worthy goals in forest genetics and breeding research. The ARK1 gene is one member of the ARBORKNOX family in all plants, which play an essential role in the process of plant growth and development, but the mechanism associated with its gene network regulation is poorly investigated. In order to generate over-expression transgenic hybrid poplar, the agrobacterium-mediated transformation was used to obtain transgenic hybrid poplar ‘717’ plants to provide insight into the function of the ARK1 gene in poplar. Moreover, the morphology of transgenic plants was observed, and transcriptome analysis was performed to explore the ARK1 gene function. The results showed that there were significant differences in pitch, stem diameter, petiole length, leaf width, leaf length and seedling height between ARK1 transgenic seedlings and non-transgenic seedlings. The transgenic seedlings usually had multiple branches and slender leaves, with some leaves not being fully developed. The results of transcriptome analysis showed that the differentially expressed genes were involved in the growth of poplars, including proteins, transcription factors and protein kinases. Genes related to the positive regulation in plant hormone signal transduction pathways were up-regulated, and the genes related to lignin synthesis were down-regulated. The RT-qPCR analysis confirmed the expression levels of the genes involved in the plant hormone signal transduction pathways and phenylpropanoid pathway. In conclusion, the ARK1 gene had a positive regulatory effect on plant growth, and the gene’s coding enzymes related to lignin synthesis were down-regulated.

Light-Dependent Activation of the GCN2 Kinase Under Cold and Salt Stress Is Mediated by the Photosynthetic Status of the Chloroplast

Regulation of cytosolic mRNA translation is a key node for rapid adaptation to environmental stress conditions. In yeast and animals, phosphorylation of the α-subunit of eukaryotic translation initiation factor eIF2 is the most thoroughly characterized event for regulating global translation under stress. In plants, the GCN2 kinase (General Control Nonderepressible-2) is the only known kinase for eIF2α. GCN2 is activated under a variety of stresses including reactive oxygen species (ROS). Here, we provide new evidence that the GCN2 kinase in Arabidopsis is also activated rapidly and in a light-dependent manner by cold and salt treatments. These treatments alone did not repress global mRNA ribosome loading in a major way. The activation of GCN2 was accompanied by a more oxidative environment and was attenuated by inhibitors of photosynthetic electron transport, suggesting that it is gated by the redox poise or the reactive oxygen status of the chloroplast. In keeping with these results, gcn2 mutant seedlings were more sensitive than wild type to both cold and salt in a root elongation assay. These data suggest that cold and salt stress may both affect the status of the cytosolic translation apparatus via the conserved GCN2-eIF2α module. The potential role of the GCN2 kinase pathway in the global repression of translation under abiotic stress is discussed.

Over-expression of poplar NAC15 gene enhances wood formation in transgenic tobacco

BACKGROUND

NAC (NAM/ATAF/CUC) is one of the largest plant-specific transcription factor (TF) families known to play significant roles in wood formation. Acting as master gene regulators, a few NAC genes can activate secondary wall biosynthesis during wood formation in woody plants.

RESULTS

In the present study, firstly, we screened 110 differentially expressed NAC genes in the leaves, stems, and roots of di-haploid Populus simonii×P. nigra by RNA-Seq. Then we identified a nucleus-targeted gene, NAC15 gene, which was one of the highly expressed genes in the stem among 110 NAC family members. Thirdly, we conducted expression pattern analysis of NAC15 gene, and observed NAC15 gene was most highly expressed in the xylem by RT-qPCR. Moreover, we transferred NAC15 gene into tobacco and obtained 12 transgenic lines overexpressing NAC15 gene (TLs). And the relative higher content of hemicellulose, cellulose and lignin was observed in the TLs compared to the control lines containing empty vector (CLs). It also showed darker staining in the culms of the TLs with phloroglucinol staining, compared to the CLs. Furthermore, the relative expression level of a few lignin- and cellulose-related genes was significantly higher in the TLs than that in the CLs.

CONCLUSIONS

The overall results indicated that NAC15 gene is highly expressed in the xylem of poplar and may be a potential candidate gene playing an important role in wood formation in transgenic tobacco.

Comparative Transcriptome and Proteome Analysis of Salt-Tolerant and Salt-Sensitive Sweet Potato and Overexpression of IbNAC7 Confers Salt Tolerance in Arabidopsis

Salt stress is one of the major devastating factors affecting the growth and yield of almost all crops, including the crucial staple food crop sweet potato. To understand their molecular responses to salt stress, comparative transcriptome and proteome analysis of salt-tolerant cultivar Xushu 22 and salt-sensitive cultivar Xushu 32 were investigated. The results showed the two genotypes had distinct differences at the transcription level and translation level even without salt stress, while inconsistent expression between the transcriptome and proteome data was observed. A total of 16,396 differentially expressed genes (DEGs) and 727 differentially expressed proteins (DEPs) were identified. Wherein, 1,764 DEGs and 93 DEPs were specifically expressed in the tolerant genotype. Furthermore, the results revealed that the significantly upregulated genes were mainly related to the regulation of ion accumulation, stress signaling, transcriptional regulation, redox reactions, plant hormone signal transduction, and secondary metabolite accumulation, which may be involved in the response of sweet potato to salt stress and/or may determine the salt tolerance difference between the two genotypes. In addition, 1,618 differentially expressed regulatory genes were identified, including bZIP, bHLH, ERF, MYB, NAC, and WRKY. Strikingly, transgenic Arabidopsis overexpressing IbNAC7 displayed enhanced salt tolerance compared to WT plants, and higher catalase (CAT) activity, chlorophyll and proline contents, and lower malondialdehyde (MDA) content and reactive oxygen species (ROS) accumulation were detected in transgenic plants compared with that of WT under salt stress. Furthermore, RNA-seq and qRT-PCR analysis displayed that the expression of many stress-related genes was upregulated in transgenic plants. Collectively, these findings provide revealing insights into sweet potato molecular response to salt stress and underlie the complex salt tolerance mechanisms between genotypes, and IbNAC7 was shown as a promising candidate gene to enhance salt tolerance of sweet potato.

Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement

In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.

Transcriptome analysis of harvested bell peppers (Capsicum annuum L.) in response to cold stress

Bell peppers are valued for their plentiful vitamin C and nutritional content. Pepper fruits are susceptible to cold storage, which leads to chilling injury (CI); however, the crucial metabolic product and molecular basis response to cold stress have not been elucidated definitely yet. To comprehensively understand the gene regulation network and CI mechanisms in response to cold stress on a molecular level, we performed high-throughput RNA-Seq analysis to investigate genome-wide expression profiles in bell peppers at different storage temperatures (4 °C and 10 °C). A total of 61.55 Gb of clean data were produced; 3863 differentially expressed genes (DEGs) including 1669 up-regulated and 2194 down-regulated were annotated and classified between the CI group and control. Together, a total of 41 cold-induced transcription factor families comprising 250 transcription factors (TFs) were identified. Notably, numerous DEGs involved in biomembrane stability, dehydration and osmoregulation, and plant hormone signal transduction processes were discovered. The transcriptional level of 20 DEGs was verified by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Our results present transcriptome profiles of bell peppers in response to cold stress; the data obtained may be useful for the identification of key candidate genes and elucidation of the mechanisms underlying membrane damage during chilling injury.

Transcriptome analysis of transcription factor genes under multiple abiotic stresses in Populus simonii × P.nigra

Transcription factor (TF) genes play essential roles in abiotic stress responses as master switches in complex regulatory networks. In the present study, the transcript abundance of 4287 TF genes in Populus simonii × P.nigra were profiled under NaCl, KCl, CdCl₂ and PEG stresses, respectively. A total of 118 up-regulated and 226 down-regulated TFs were identified to be shared in the four stress conditions. Among the top seven TF families (ERF, NAC, WRKY, MYB, bHLH, C2H2, bZIP), there were 76 up-regulated TFs found common in the four stresses, and 67% of them were likely to be involved in stress responses. We identified three TFs, which can enhance stress tolerance of transgenic plants, were members of the most significantly up-regulated genes in the respective TF family. Among them, a highly salt-inducible ERF gene, ERF76, was proved to activate the expression of other TFs in the transgenic poplar lines overexpressing ERF76. Transcriptome analysis indicated there was a synergistic effect of TFs on improving salinity tolerance of the transgenic plants. Of significant interest in the study is the discovery of the role and interactions of various TF genes under multiple stress conditions.

Functional characterization of poplar NAC13 gene in salt tolerance

Transcription factor (TF) genes play a critical role in plant abiotic and biotic stress responses. In this study, we cloned a poplar TF NAC13 gene (Potri.001G404100.1), which is significantly up-regulated to salt stress. Then we developed gene overexpression and antisense suppression constructions driven by CaMV35S, and successfully transferred them to a poplar variety 84 K (Populus alba × P. glandulosa), respectively. Evidence from molecular assay indicated that NAC13 overexpression and antisense suppression fragments have been integrated into the poplar genome. The morphological and physiological characterization and salt treatment results indicated the NAC13-overexpressing transgenic plants enhance salt tolerance significantly, compared to wide type. In contrast, the NAC13-suppressing transgenic plants are significantly sensitive to salt stress, compared to wide type. Evidence from transgenic Arabidopsis expressing GUS gene indicated that the gene driven by NAC13 promoter is mainly expressed in the roots and leaves of young plants. These studies indicate that the NAC13 gene plays a vital role in salt stress response.

Over-Expression of ERF38 Gene Enhances Salt and Osmotic Tolerance in Transgenic Poplar

Ethylene response factor (ERF) gene family plays an important role in abiotic stress responses. In this study, we isolated a salt-inducible ERF gene, ERF38 (Potri.006G138900.1), from the 84K poplar (Populus alba × Populus glandulosa) and investigated its functions in salt and osmotic tolerance. We identified that ERF38 protein was targeted to nucleus and had no self-activation. Results from yeast-one-hybrid indicated that the ERF38 protein can specifically bind to the dehydration responsive element (DRE). We then successfully transferred the ERF38 gene into the 84K poplar. Under respective salt and polyethylene glycol (PEG)-6000 stresses, four of the physiological traits, including peroxidase (POD) and superoxide dismutase (SOD) activities, soluble protein content, and proline content, increased significantly in the transgenic plants, compared to the wild type. Regarding the other two parameters, hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) content, their increments in the transgenic lines under the stresses, which were compared to the water control, were significantly low than that of the wild type. In addition, reactive oxygen species (ROS) are scavenged in the transgenic lines under the stresses, but not in the wild type (WT). Interestingly, when challenged with the stresses, expression levels of a few genes associated with POD and SOD metabolism were significantly increased in the transgenic poplars. In all, evidence from morphological, physiological, and biochemical analyses indicated that over-expression of ERF38 gene can improve salt and osmotic tolerance in the transgenic poplar.