The ERF transcription factor TaERF3 promotes tolerance to salt and drought stresses in wheat

Apple MdERF4 negatively regulates salt tolerance by inhibiting MdERF3 transcription

Phytohormone ethylene is involved in salt stress response. As a key regulator of ethylene signaling, ethylene response factors (ERFs) have been reported to regulate salt stress tolerance. However, there are few studies on the relationship between ERFs in salt stress response. In this study, we isolated a salt-responsive gene MdERF4. Overexpression of MdERF4 negatively regulated salt stress tolerance and ethylene response, which was contrary to that of MdERF3 transgenic lines. Biochemical assays showed that MdERF4 directly bound to the DRE motif of MdERF3 promoter and suppressed its transcription. In addition, genetic analysis revealed that MdERF4 was involved in ethylene-mediated salt tolerance. Taken together, these findings demonstrated the transcriptional regulation between MdERF4 and MdERF3 in salt stress response and provided new insight into the ethylene-modulated salt stress response.

Plant Hormone Signaling Crosstalks between Biotic and Abiotic Stress Responses

In the natural environment, plants are often bombarded by a combination of abiotic (such as drought, salt, heat or cold) and biotic (necrotrophic and biotrophic pathogens) stresses simultaneously. It is critical to understand how the various response pathways to these stresses interact with one another within the plants, and where the points of crosstalk occur which switch the responses from one pathway to another. Calcium sensors are often regarded as the first line of response to external stimuli to trigger downstream signaling. Abscisic acid (ABA) is a major phytohormone regulating stress responses, and it interacts with the jasmonic acid (JA) and salicylic acid (SA) signaling pathways to channel resources into mitigating the effects of abiotic stresses versus defending against pathogens. The signal transduction in these pathways are often carried out via GTP-binding proteins (G-proteins) which comprise of a large group of proteins that are varied in structures and functions. Deciphering the combined actions of these different signaling pathways in plants would greatly enhance the ability of breeders to develop food crops that can thrive in deteriorating environmental conditions under climate change, and that can maintain or even increase crop yield.

FZP determines grain size and sterile lemma fate in rice

In grass, the spikelet is a unique inflorescence structure that directly determines grain yield. Despite a great deal of research, the molecular mechanisms behind spikelet development are not fully understood. In the study, FZP encodes an ERF domain protein, and functions in grain size and sterile lemma identity. Mutation of FZP causes smaller grains and degenerated sterile lemmas. The small fzp-12 grains were caused by a reduction in cell number and size in the hulls. Interestingly, the sterile lemma underwent a homeotic transformation into a rudimentary glume in the fzp-12 and fzp-13 mutants, whereas the sterile lemma underwent a homeotic transformation into a lemma in FZP over-expressing plants, suggesting that FZP specifically determines the sterile lemma identity. We confirmed the function of FZP by complementation, CRISPR-Cas9 gene editing, and cytological and molecular tests. Additionally, FZP interacts specifically with the GCC-box and DRE motifs, and may be involved in regulation of the downstream genes. Our results revealed that FZP plays a vital role in the regulation of grain size, and first provides clear evidence in support of the hypothesis that the lemma, rudimentary glume, and sterile lemma are homologous organs.

Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.)

The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses. Recent reports have provided novel insights on the role of TFs in osmotic stress tolerance via direct molecular links. However, our knowledge on the regulatory role TFs during osmotic stress tolerance in wheat remains limited. The present review in its first part sheds light on the importance of studying the role of osmotic stress tolerance in wheat plants and second aims to decipher molecular mechanisms of TFs belonging to several classes, including DREB, NAC, MYB, WRKY and bHLH, which have been reported to engage in osmotic stress mediated gene expression in wheat and third part covers the systems biology approaches to understand the transcriptional regulation of osmotic stress and the role of long non-coding RNAs in response to osmotic stress with special emphasis on wheat. The current concept may lead to an understanding in molecular regulation and signalling interaction of TFs under osmotic stress to clarify challenges and problems for devising potential strategies to improve complex regulatory events involved in plant tolerance to osmotic stress adaptive pathways in wheat.

Genome-wide analysis reveals four key transcription factors associated with cadmium stress in creeping bentgrass (Agrostis stolonifera L.)

Cadmium (Cd) toxicity seriously affects the growth and development of plants, so studies on uptake, translocation, and accumulation of Cd in plants are crucial for phytoremediation. However, the molecular mechanism of the plant response to Cd stress remains poorly understood. The main objective of this study was to reveal differentially expressed genes (DEGs) under lower (BT2_5) and higher (BT43) Cd concentration treatments in creeping bentgrass. A total of 463,184 unigenes were obtained from creeping bentgrass leaves using RNA sequencing technology. Observation of leaf tissue morphology showed that the higher Cd concentration damages leaf tissues. Four key transcription factor (TF) families, WRKY, bZIP, ERF, and MYB, are associated with Cd stress in creeping bentgrass. Our findings revealed that these four TFs play crucial roles during the creeping bentgrass response to Cd stress. This study is mainly focused on the molecular characteristics of DEGs under Cd stress using transcriptomic analysis in creeping bentgrass. These results provide novel insight into the regulatory mechanisms of respond to Cd stress and enrich information for phytoremediation.

Abiotic Stress Signaling in Wheat - An Inclusive Overview of Hormonal Interactions During Abiotic Stress Responses in Wheat

Rapid global warming directly impacts agricultural productivity and poses a major challenge to the present-day agriculture. Recent climate change models predict severe losses in crop production worldwide due to the changing environment, and in wheat, this can be as large as 42 Mt/°C rise in temperature. Although wheat occupies the largest total harvested area (38.8%) among the cereals including rice and maize, its total productivity remains the lowest. The major production losses in wheat are caused more by abiotic stresses such as drought, salinity, and high temperature than by biotic insults. Thus, understanding the effects of these stresses becomes indispensable for wheat improvement programs which have depended mainly on the genetic variations present in the wheat genome through conventional breeding. Notably, recent biotechnological breakthroughs in the understanding of gene functions and access to whole genome sequences have opened new avenues for crop improvement. Despite the availability of such resources in wheat, progress is still limited to the understanding of the stress signaling mechanisms using model plants such as Arabidopsis, rice and Brachypodium and not directly using wheat as the model organism. This review presents an inclusive overview of the phenotypic and physiological changes in wheat due to various abiotic stresses followed by the current state of knowledge on the identified mechanisms of perception and signal transduction in wheat. Specifically, this review provides an in-depth analysis of different hormonal interactions and signaling observed during abiotic stress signaling in wheat.

Function of the ERFL1a Transcription Factor in Wheat Responses to Water Deficiency

The APETALA2/ethylene response factor (AP2/ERF) superfamily is involved in the responses of plants to biotic and abiotic stresses; however, the functions and mechanisms of some members of this family in plants are unclear. In our previous study, expression of TaERFL1a, a member of the AP2/ERF family, was remarkably induced in wheat seedlings suffering freezing stress. In this study, we show that its expression was rapidly upregulated in response to salt, cold, and water deficiency, suggesting roles in the responses to abiotic stresses. Further, transient barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) resulted in significantly reduced tolerance to 20% PEG6000-stimulated water deficiency. Subcellular localization and transcriptional activation assays separately showed that TaERFL1a was targeted to the nucleus and possessed transcriptional activation activity. Yeast two-hybrid library screening identified six interacting proteins, and of these, the interactions between TaERFL1a and TaSGT1, and TaERFL1a and TaDAD2 proteins were further confirmed by yeast co-transformation and bimolecular fluorescent complementation (BiFC). Collectively, our results suggest that TaERFL1a is a stress-responsive transcription factor, which could be functionally related to proteins involved in the abiotic stress responses of plants.

Expression of AhDREB1, an AP2/ERF Transcription Factor Gene from Peanut, Is Affected by Histone Acetylation and Increases Abscisic Acid Sensitivity and Tolerance to Osmotic Stress in Arabidopsis

Drought stress negatively affects plant growth and development. An increasing number of reports have revealed the involvement of APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors (TFs) in biotic and abiotic stress regulation in plants. However, research on these TFs in the peanut plant (Arachis hypogaea) has been limited. Here, we isolated a full-length coding sequence (CDS) of the AP2/ERF family gene AhDREB1 from the peanut plant and showed that its expression was induced by Polyethylene Glycol (PEG) 6000 and exogenous abscisic acid (ABA) treatment. When overexpressed in Arabidopsis, AhDREB1 increased both ABA levels and ABA sensitivity, affected the ABA signaling pathway and increased the expression of downstream drought stress-related genes RD29A, P5CS1, P5CS2 and NCED1. These results demonstrate that AhDREB1 can improve tolerance to drought via the ABA-dependent pathway in Arabidopsis. In the peanut plant, the specific histone deacetylases (HDACs) inhibitor trichostatin A (TSA) promotes AhDREB1 transcription and the enrichment level of H3ac was increased in regions of the AhDREB1 gene during TSA and PEG treatment. In summary, histone acetylation can affect the expression of AhDREB1 under osmotic stress conditions, thereby improving plant drought resistance.

OsERF71 confers drought tolerance via modulating ABA signaling and proline biosynthesis

Plants have evolved multiple protective strategies to adapt to adverse environmental conditions. Upland rice (UR) has evolved as a "drought-resistant type". However, little is known about genes or mechanisms in UR that underlying drought tolerance at the molecular level. Here we report isolation and functional characterization of the ERF gene, OsERF71, from the UR variety, IRAT109. The expression of OsERF71 was induced by abscisic acid (ABA) and various abiotic stresses preferentially in IRAT109 under ABA, dehydration, and polyethyleneglycol (PEG) treatments. OsERF71 was verified as a nuclear-localized protein and had transcriptional activity in yeast cells. Overexpression of the OsERF71 in Nipponbare demonstrated a significant increase in tolerance to drought stress and a reduced rate of water loss. In contrast, OsERF71 interference lines were sensitive to drought stress and exhibited a higher rate of water loss. OsERF71-overexpressing lines also showed enhanced tolerance to high salinity. Moreover, OsERF71 regulated the expression of several ABA- responsive and proline biosynthesis genes under drought stress, resulting in enhanced sensitivity to exogenous ABA treatment and proline accumulation. Accordingly, we suggest that OsERF71 plays a positive role in drought stress tolerance by increasing the expression of genes associated with ABA signaling and proline biosynthesis under stress.

Discovery of microRNA-target modules of African rice (Oryza glaberrima) under salinity stress

Oryza glaberrima is the second edible rice in the genus Oryza. It is grown in the African countries. miRNAs are regulatory molecules that are involved in every domains of gene expression including salinity stress response. Although several miRNAs have been reported from various species of Oryza, yet none of them are from this species. Salt treated (200 mM NaCl for 48 h) and control smallRNA libraries of RAM-100, a salt tolerant genotype, each with 2 replications generated 150 conserve and 348 novel miRNAs. We also used smallRNAseq data of NCBI of O. glaberrima to discover additional 246 known miRNAs. Totally, 29 known and 32 novel miRNAs were differentially regulated under salinity stress. Gene ontology and KEGG analysis indicated several targets were involved in vital biological pathways of salinity stress tolerance. Expression of selected miRNAs as indicated by Illumina data were found to be coherent with real time-PCR analysis. However, target gene expression was inversely correlated with their corresponding miRNAs. Finally based upon present results as well as existing knowledge of literature, we proposed the miRNA-target modules that were induced by salinity stress. Therefore, the present findings provide valuable information about miRNA-target networks in salinity adaption of O. glaberrima.

Overexpression of a WRKY Transcription Factor TaWRKY2 Enhances Drought Stress Tolerance in Transgenic Wheat

Drought is a major environmental stress that severely restricts plant growth and crop productivity. A previous study showed that TaWRKY2 from wheat (Triticum aestivum) plays an important role in drought stress tolerance. In the present study, we isolated the promoter of TaWRKY2 and identified multiple regulatory cis-elements in the promoter region. The activity of the TaWRKY2 promoter was induced by drought, salt, heat, and abscisic acid (ABA). We also generated TaWRKY2-overexpressing transgenic wheat, and found that the transgenic seedlings exhibited significantly enhanced tolerance to drought stress, as evidenced by a higher survival rate and lower water loss rate of detached leaves compared with wild type (WT) plants. In addition, the transgenic lines had higher contents of free proline, soluble sugar, and chlorophyll. During a prolonged period of drought stress before the heading stage, the growth of WT plants was inhibited, whereas the TaWRKY2-overexpressing lines progressed to the heading stage. The increased grain yield of the transgenic wheat lines reflected the cumulative effects of longer panicle length, more kernels per spike, and greater aboveground biomass. Our findings show that TaWRKY2 can enhance drought tolerance and increase grain yield in wheat, thus providing a promising candidate target for improving the drought tolerance of wheat cultivars through genetic engineering.

Drought Response in Wheat: Key Genes and Regulatory Mechanisms Controlling Root System Architecture and Transpiration Efficiency

Abiotic stresses such as, drought, heat, salinity, and flooding threaten global food security. Crop genetic improvement with increased resilience to abiotic stresses is a critical component of crop breeding strategies. Wheat is an important cereal crop and a staple food source globally. Enhanced drought tolerance in wheat is critical for sustainable food production and global food security. Recent advances in drought tolerance research have uncovered many key genes and transcription regulators governing morpho-physiological traits. Genes controlling root architecture and stomatal development play an important role in soil moisture extraction and its retention, and therefore have been targets of molecular breeding strategies for improving drought tolerance. In this systematic review, we have summarized evidence of beneficial contributions of root and stomatal traits to plant adaptation to drought stress. Specifically, we discuss a few key genes such as, DRO1 in rice and ERECTA in Arabidopsis and rice that were identified to be the enhancers of drought tolerance via regulation of root traits and transpiration efficiency. Additionally, we highlight several transcription factor families, such as, ERF (ethylene response factors), DREB (dehydration responsive element binding), ZFP (zinc finger proteins), WRKY, and MYB that were identified to be both positive and negative regulators of drought responses in wheat, rice, maize, and/or Arabidopsis. The overall aim of this review is to provide an overview of candidate genes that have been identified as regulators of drought response in plants. The lack of a reference genome sequence for wheat and non-transgenic approaches for manipulation of gene functions in wheat in the past had impeded high-resolution interrogation of functional elements, including genes and QTLs, and their application in cultivar improvement. The recent developments in wheat genomics and reverse genetics, including the availability of a gold-standard reference genome sequence and advent of genome editing technologies, are expected to aid in deciphering of the functional roles of genes and regulatory networks underlying adaptive phenological traits, and utilizing the outcomes of such studies in developing drought tolerant cultivars.

Transcriptome dynamics provide insights into long-term salinity stress tolerance in Triticum aestivum cv. Kharchia Local

Kharchia Local, a wheat (Triticum aestivum) cultivar, is native to the saline-sodic soils of Pali district, Rajasthan, India and well known for its salinity stress tolerance. In the present study, we performed transcriptome sequencing to compare genome wide differential expression pattern between flag leaves of salinity stressed (15 EC) and control plants at anthesis stage. The 63.9 million paired end raw reads were assembled into 74,106 unigenes, of which, 3197 unigenes were found to be differentially expressed. Functional annotation analysis revealed the upregulation of genes associated with various biological processes including signal transduction, phytohormones signaling, osmoregulation, flavonoid biosynthesis, ion transport and ROS homeostasis. Expression pattern of fourteen differentially expressed genes was validated using qRT-PCR and was found to be consistent with the results of the transcriptome sequencing. Present study is the primary report on transcriptome profiling of Kharchia Local flag leaf under long-term salinity stress at anthesis stage. In conclusion, the data generated in this study can improve our knowledge in understanding the molecular mechanism of salinity stress tolerance. It will also serve as a valuable genomic resource in wheat breeding programs.

Overexpression of ERF1-V from Haynaldia villosa Can Enhance the Resistance of Wheat to Powdery Mildew and Increase the Tolerance to Salt and Drought Stresses

The APETALA 2/Ethylene-responsive element binding factor (AP2/ERF) transcription factor gene family is widely involved in the biotic and abiotic stress regulation. Haynaldia villosa (VV, 2n = 14), a wild species of wheat, is a potential gene pool for wheat improvement. H. villosa confers high resistance to several wheat diseases and high tolerance to some abiotic stress. In this study, ERF1-V, an ethylene-responsive element-binding factor gene of the AP2/ERF transcription factor gene family from wild H. villosa, was cloned and characterized. Sequence and phylogenetic analysis showed that ERF1-V is a deduced B2 type ERF gene. ERF1-V was first identified as a Blumeria graminis f. sp. tritici (Bgt) up-regulated gene, and later found to be induced by drought, salt and cold stresses. In responses to hormones, ERF1-V was up-regulated by ethylene and abscisic acid, but down-regulated by salicylic acid and jasmonic acid. Over expression of ERF1-V in wheat could improve resistance to powdery mildew, salt and drought stress. Chlorophyll content, malondialdehyde content, superoxide dismutase and peroxidase activity were significantly differences between the recipient Yangmai158 and the transgenic plants following salt treatment. Furthermore, the expression levels of some stress responsive genes were differences after drought or salt treatments. Although ERF1-V was activated by the constitutive promoter, the agronomic traits, including flowering time, plant height, effective tiller number, spikelet number per spike and grain size, did not changed significantly. ERF1-V is a valuable gene for wheat improvement by genetic engineering.

Genome-Wide Identification and Analysis of MAPK and MAPKK Gene Families in Bread Wheat (Triticum aestivum L.)

The mitogen-activated protein kinase (MAPK) cascade is a universal signal transduction module that plays a vital role in regulating growth and development, as well as environmental stress responses in plants. Wheat is one of the most important crops worldwide. Although the MAPK kinase kinase (MAP3K) family in wheat has been investigated, the MAPK and MAPK kinase (MAP2K) gene families remain unknown at present. Here, 54 MAPK and 18 MAPKK genes were identified in wheat using recent genomic information. Phylogenetic analysis of Triticum aestivum L. MAPKs and MAPKKs (TaMAPKs and TaMAPKKs) together with homologous genes from other species classified them into four groups, and the clustering was consistent with the genomic exon/intron structures. Conserved motif analysis found that MAPK proteins contained a typical TXY phosphorylation site and MAPKK proteins contained an S/T-X5-S/T motif. RNA-seq data mapping analysis showed that MAPK and MAPKK genes in group IV had tissue-specific expression profiles, whereas each group I member showed relatively high expression in all organs. Expression patterns of TaMAPK and TaMAPKK genes under stress conditions were also investigated and stress-responsive candidates were identified. Co-expression network analysis identified 11 TaMAPK genes and 6 TaMAPKK genes involved in the interaction network pathway. Overall, this study provided useful information for evolutionary and functional surveys of MAPK and MAPKK gene families in wheat and beyond.

Cloning of a functional mannose-6-phosphate reductase (M6PR) gene homolog from Egyptian celery plants (Apium graveolens): overexpression in non-mannitol producing plants resulted in mannitol accumulation in transgenic individuals

Salinity is a major limiting factor affecting crops production, survival and distribution worldwide. Engineering dehydration stress tolerance in commercial crops is a trait of economic importance, especially in saline-affected areas. In this work, we are reporting the cloning of the M6PR gene homolog (encoding a key enzyme, mannose-6-phosphate reductase, for mannitol biosynthesis in celery) from Egyptian celery plants. Using RACE technique, the full-length Egyptian-M6PR gene (1333 bp) was cloned into pRI-201AN plant expression vector. Analysis of the cloned gene revealed that both American and Egyptian clones had both start and stop codons in frame and was found to be 930 base long. The newly cloned EM6PR gene was found to be 126 base longer than its American counterpart at the non-coding region. Six differences at nucleotide level between the Egyptian and American sequences were observed, three of which in the coding region resulting in three polymorphic amino acids differences (tryptophan vs. leucine, glutamine vs. histidine and isoleucine vs. leucine). The newly cloned gene was introduced to tobacco via Agrobacterium and PCR analysis of T0 plants indicated the presence of the EM6PR gene into 10 out of 38 tobacco individuals. Moreover, RT-PCR analysis confirmed the presence of EM6PR transcripts in 9 out of the 10 PCR positive plants. GC/MS analysis of some RT positive individuals indicated the accumulation of mannitol in transgenics tobacco, while mannitol was absent in non-transgenic controls.

Genetic Engineering: A Possible Strategy for Protein-Energy Malnutrition Regulation

Protein-energy malnutrition (PEM) has adversely affected the generations of developing countries. It is a syndrome that in severity causes death. PEM generally affects infants of 1-5 age group. This manifestation is maintained till adulthood in the form of poor brain and body development. The developing nations are continuously making an effort to curb PEM. However, it is still a prime concern as it was in its early years of occurrence. Transgenic crops with high protein and enhanced nutrient content have been successfully developed. Present article reviews the studies documenting genetic engineering-mediated improvement in the pulses, cereals, legumes, fruits and other crop plants in terms of nutritional value, stress tolerance, longevity and productivity. Such genetically engineered crops can be used as a possible remedial tool to eradicate PEM.

Cotton GhERF38 gene is involved in plant response to salt/drought and ABA

ERF (ethylene-responsive factor) transcription factors play important roles in plant stress signaling transduction pathways. However, their specific roles during diverse abiotic stresses tolerance in Gossypium hirsutum are largely unknown. Here, a novel ERF transcription factor, designated GhERF38, homologous to AtERF38 in Arabidopsis, was isolated from cotton (Gossypium hirsutum L). GhERF38 expression was up-regulated by salt, drought and ABA treatments. Subcellular localization results indicated that GhERF38 was localized in the cell nucleus. Over-expression of GhERF38 in Arabidopsis reduced plant tolerance to salt and drought stress as indicated by a decline of seed germination, plant greenness frequency, primary roots length and the survival rate in transgenic plants compared to those of wild type plants under salt or drought treatment. Besides, stress tolerance related physiological parameters such as proline content, relative water content, soluble sugar and chlorophyll content were all significantly lower in transgenic plants than those of wild type plants under salt or drought treatment. Furthermore, over-expression of GhERF38 in Arabidopsis resulted in ABA sensitivity in transgenic plants during both seed germination and seedling growth. Interestingly, the stomatal aperture of guard cells in the transgenic plants was larger than that in transgenic plant after ABA treatment, suggesting that GhERF38-overexpressing plants were insensitive to ABA in terms of stomatal closure. Furthermore, expressions of the stress-related genes were altered in the GhERF38 transgenic plants under high salinity, drought or ABA treatment. Together, our results revealed that GhERF38 functions as a novel regulator that is involved in response to salt/drought stress and ABA signaling during plant development.

A novel AP2/ERF family transcription factor from Glycine soja, GsERF71, is a DNA binding protein that positively regulates alkaline stress tolerance in Arabidopsis

KEY MESSAGE

Here we first found that GsERF71, an ERF factor from wild soybean could increase plant alkaline stress tolerance by up-regulating H+-ATPase and by modifing the accumulation of Auxin. Alkaline soils are widely distributed all over the world and greatly limit plant growth and development. In our previous transcriptome analyses, we have identified several ERF (ethylene-responsive factor) genes that responded strongly to bicarbonate stress in the roots of wild soybean G07256 (Glycine soja). In this study, we cloned and functionally characterized one of the genes, GsERF71. When expressed in epidermal cells of onion, GsERF71 localized to the nucleus. It can activate the reporters in yeast cells, and the C-terminus of 170 amino acids is essential for its transactivation activity. Yeast one-hybrid and EMSA assays indicated that GsERF71 specifically binds to the cis-acting elements of the GCC-box, suggesting that GsERF71 may participate in the regulation of transcription of the relevant biotic and abiotic stress-related genes. Furthermore, transgenic Arabidopsis plants overexpressing GsERF71 showed significantly higher tolerance to bicarbonate stress generated by NaHCO3 or KHCO3 than the wild type (WT) plants, i.e., the transgenic plants had greener leaves, longer roots, higher total chlorophyll contents and lower MDA contents. qRT-PCR and rhizosphere acidification assays indicated that the expression level and activity of H+-ATPase (AHA2) were enhanced in the transgenic plants under alkaline stress. Further analysis indicated that the expression of auxin biosynthetic genes and IAA contents were altered to a lower extent in the roots of transgenic plants than WT plants under alkaline stress in a short-term. Together, our data suggest that GsERF71 enhances the tolerance to alkaline stress by up-regulating the expression levels of H+-ATPase and by modifying auxin accumulation in transgenic plants.

Transcriptome analysis of creeping bentgrass exposed to drought stress and polyamine treatment

Creeping bentgrass is an important cool-season turfgrass species sensitive to drought. Treatment with polyamines (PAs) has been shown to improve drought tolerance; however, the mechanism is not yet fully understood. Therefore, this study aimed to evaluate transcriptome changes of creeping bentgrass in response to drought and exogenous spermidine (Spd) application using RNA sequencing (RNA-Seq). The high-quality sequences were assembled and 18,682 out of 49,190 (38%) were detected as coding sequences. A total of 22% and 19% of genes were found to be either up- or down-regulated due to drought while 20% and 34% genes were either up- or down- regulated in response to Spd application under drought conditions, respectively. Gene ontology (GO) and enrichment analysis were used to interpret the biological processes of transcripts and relative transcript abundance. Enriched or differentially expressed transcripts due to drought stress and/or Spd application were primarily associated with energy metabolism, transport, antioxidants, photosynthesis, signaling, stress defense, and cellular response to water deprivation. This research is the first to provide transcriptome data for creeping bentgrass under an abiotic stress using RNA-Seq analysis. Differentially expressed transcripts identified here could be further investigated for use as molecular markers or for functional analysis in responses to drought and Spd.

Improved drought tolerance in wheat plants overexpressing a synthetic bacterial cold shock protein gene SeCspA

Cold shock proteins (CSPs) enhance acclimatization of bacteria to adverse environmental circumstances. The Escherichia coli CSP genes CspA and CspB were modified to plant-preferred codon sequences and named as SeCspA and SeCspB. Overexpression of exogenous SeCspA and SeCspB in transgenic Arabidopsis lines increased germination rates, survival rates, and increased primary root length compared to control plants under drought and salt stress. Investigation of several stress-related parameters in SeCspA and SeCspB transgenic wheat lines indicated that these lines possessed stress tolerance characteristics, including lower malondialdehyde (MDA) content, lower water loss rates, lower relative Na⁺ content, and higher chlorophyll content and proline content than the control wheat plants under drought and salt stresses. RNA-seq and qRT-PCR expression analysis showed that overexpression of SeCsp could enhance the expression of stress-responsive genes. The field experiments showed that the SeCspA transgenic wheat lines had great increases in the 1000-grain weight and grain yield compared to the control genotype under drought stress conditions. Significant differences in the stress indices revealed that the SeCspA transgenic wheat lines possessed significant and stable improvements in drought tolerance over the control plants. No such improvement was observed for the SeCspB transgenic lines under field conditions. Our results indicated that SeCspA conferred drought tolerance and improved physiological traits in wheat plants.

Ectopic Expression of OsSta2 Enhances Salt Stress Tolerance in Rice

Salt stress can severely reduce crop yields. To understand how rice (Oryza sativa) plants respond to this environmental challenge, we investigated the genes involved in conferring salt tolerance by screening T-DNA tagging lines and identified OsSta2-D (Oryza sativa Salt tolerance activation 2-Dominant). In that line, expression of OsSta2 was enhanced by approximately eightfold when compared with the non-transformed wild type (WT). This gene was highly expressed in the callus, roots, and panicles. To confirm its role in stress tolerance, we generated transgenic rice that over-expresses OsSta2 under a maize ubiquitin promoter. The OsSta2-Ox plants were salt-tolerant at the vegetative stage, based on our calculations of chlorophyll fluorescence (Fv/Fm), fresh and dry weights, chlorophyll concentrations, and survival rates. Under normal paddy field conditions, the Ox plants were somewhat shorter than the WT control but had improved agronomic traits such as higher total grain yield. They were also more tolerant to osmotic stress and hypersensitive to abscisic acid. Based on all of these results, we suggest that OsSta2 has important roles in determining yields as well as in conferring tolerance to salt stresses.

A novel ethylene responsive factor CitERF13 plays a role in photosynthesis regulation

Ethylene responsive factors (ERFs) act as critical downstream components of the ethylene signalling pathway in regulating plant development and stress responses. However little is known about its role in regulation of photosynthesis. Here, we identified an ethylene-inducible ERF gene in citrus, CitERF13. Transient over-expression of CitERF13 in N. tabacum leaves, resulted in a significant decrease in net photosynthetic rate. Closer examination of photosynthetic activity of PSII and PSI indicated that CitERF13 overexpression led to declines of Fv/Fm, Y(II) and Y(I). However, change in NPQ was less pronounced. CitERF13 overexpression also significantly reduced Vc,max, Jmax and AQY, indicating inhibition of the Calvin cycle. The expression of photosynthesis-related genes was suppressed to a variable extent in leaf blades transiently over-expressing CitERF13. CitERF13 transient overexpression in tobacco or citrus both resulted in a decline of Chlorophyll content and CitERF13 overexpressing tobacco leaf disc was more susceptible to chlorosis in response to MV-mediated oxidative stress. The results suggest that CitERF13 is potentially involved in suppressing photosynthesis through multiple pathways, for instance, inhibiting photochemical activity of photosynthesis, CO2 carboxylation capacity and chlorophyll metabolism.

The ethylene response factor OsERF109 negatively affects ethylene biosynthesis and drought tolerance in rice

Drought is an important factor limiting plant development and crop production. Dissecting the factors involved in this process is the key for enhancement of plant tolerance to drought stress by genetic approach. Here, we evaluated the regulatory function of a novel rice ethylene response factor (ERF) OsERF109 in drought stress. Expression of OsERF109 was rapidly induced by stress and phytohormones. Subcellular localization and transactivation assay demonstrated that OsERF109 was localized in nucleus and possessed transactivation activity. Transgenic plants overexpressing (OE) and knockdown with RNA interfering (RI) OsERF109 exhibited significantly reduced and improved drought resistance, respectively, indicating that OsERF109 negatively regulates drought resistance in rice. Furthermore, measurement by gas chromatography showed that ethylene contents were less in OE while more in RI lines than these in wild types, supporting the data of drought tolerance and water loss in transgenic lines. Quantitative real-time PCR analysis also proved the regulation of OsERF109 in the expression of OSACS6, OSACO2, and OsERF3, which have been identified to play important roles in ethylene biosynthesis. Based on these results, our data evidence that OsERF109 regulates drought resistance by affecting the ethylene biosynthesis in rice. Overall, our study reveals the negative role of OsERF109 in ethylene biosynthesis and drought tolerance in rice.

Toward Unveiling the Mechanisms for Transcriptional Regulation of Proline Biosynthesis in the Plant Cell Response to Biotic and Abiotic Stress Conditions

Proline accumulation occurs in plants following the exposure to a wide array of stress conditions, as well as during numerous physiological and adaptive processes. Increasing evidence also supports the involvement of proline metabolism in the plant response to pathogen attack. This requires that the biosynthetic pathway is triggered by components of numerous and different signal transduction chains. Indeed, several reports recently described activation of genes coding for enzymes of the glutamate pathway by transcription factors (TFs) belonging to various families. Here, we summarize some of these findings with special emphasis on rice, and show the occurrence of a plethora of putative TF binding sites in the promoter of such genes.

Regulation of Apetala2/Ethylene Response Factors in Plants

Multiple environmental stresses affect growth and development of plants. Plants try to adapt under these unfavorable condition through various evolutionary mechanisms like physiological and biochemical alterations connecting various network of regulatory processes. Transcription factors (TFs) like APETALA2/ETHYLENE RESPONSE FACTORS (AP2/ERFs) are an integral component of these signaling cascades because they regulate expression of a wide variety of down stream target genes related to stress response and development through different mechanism. This downstream regulation of transcript does not always positively or beneficially affect the plant but also they display some developmental defects like senescence and reduced growth under normal condition or sensitivity to stress condition. Therefore, tight auto/cross regulation of these TFs at transcriptional, translational and domain level is crucial to understand. The present manuscript discuss the multiple regulation and advantage of plasticity and specificity of these family of TFs to a wide or single downstream target(s) respectively. We have also discussed the concern which comes with the unwanted associated traits, which could only be averted by further study and exploration of these AP2/ERFs.

Overview of the Wheat Genetic Transformation and Breeding Status in China

In the past two decades, Chinese scientists have achieved significant progress on three aspects of wheat genetic transformation. First, the wheat transformation platform has been established and optimized to improve the transformation efficiency, shorten the time required from starting of transformation procedure to the fertile transgenic wheat plants obtained as well as to overcome the problem of genotype-dependent for wheat genetic transformation in wide range of wheat elite varieties. Second, with the help of many emerging techniques such as CRISPR/cas9 function of over 100 wheat genes has been investigated. Finally, modern technology has been combined with the traditional breeding technique such as crossing to accelerate the application of wheat transformation. Overall, the wheat end-use quality and the characteristics of wheat stress tolerance have been improved by wheat genetic engineering technique. So far, wheat transgenic lines integrated with quality-improved genes and stress tolerant genes have been on the way of Production Test stage in the field. The debates and the future studies on wheat transformation have been discussed, and the brief summary of Chinese wheat breeding research history has also been provided in this review.

LcMKK, a MAPK kinase from Lycium chinense, confers cadmium tolerance in transgenic tobacco by transcriptional upregulation of ethylene responsive transcription factor gene

Cadmium (Cd) is a highly toxic element to plants. Ethylene is an important phytohormone in the regulation of plant growth, development and stress response. Mitogen-activated protein kinase (MAPK) activation has been observed in plants exposed to Cd stress and was suggested to be involved in ethylene biosynthesis. We hypothesized that there may be a link between MAPK cascades and ethylene signalling in Cd-stressed plants. To test this hypothesis, the expression of LcMKK, LchERF and LcGSH1 genes, endogenous ethylene accumulation, GSH content and Cd concentration in Lycium chinense with or without Cd stress treatment were studied. Our results showed that LcMKK gene expression can be induced by the treatment of Cd in L. chinense. The transgenic tobacco expressing 35S::LcMKK showed greater tolerance to Cd stress and enhanced expression of NtERF and NtGSH1 genes, indicating that LcMKK is associated with the enhanced expression level of ERF and GSH synthesis-related genes in tobacco. We also found that endogenous ethylene and GSH content can be induced by Cd stress in L. chinense, and inhibited by cotreatment with PD98059, an inhibitor of MAPK kinase. Evidences presented here suggest that under Cd stress, GSH accumulation occurred at least partially by enhanced LcMKK gene expression and the ethylene signal transduction pathways might be involved in this accumulation.

Temporal and spatial expression and function of TaDlea3 in Triticum aestivum during developmental stages under drought stress

Drought stress is a major factor limiting wheat growth and productivity. Late embryogenesis abundant (LEA) proteins are tolerant to water-related stress. To reveal the regulatory mechanisms of LEA proteins under drought stress, we cloned a novel group 3 LEA gene, namely, TaDlea3, from wheat (Triticum aestivum L.) Shaanhe 6. Subcellular localization assay showed that TaDlea3 protein accumulated in the cytoplasm. Quantitative real-time polymerase chain reaction results revealed that TaDlea3 expression was induced by drought stress. Western blot results indicated that TaDlea3 protein expression gradually increased with drought stress during four different developmental stages. Under normal conditions, no obvious phenotype difference was observed between the transgenic and wild-type seedlings. Meanwhile, the overexpression of TaDlea3 in Arabidopsis resulted in enhanced tolerance to drought stress, as determined by the assessment of antioxidant enzyme activities. Our results provide a basis for highly detailed functional analyses of LEA proteins and offer a promising approach for improving the tolerances of wheat cultivars to drought stress through genetic engineering.

Transcription factors involved in drought tolerance and their possible role in developing drought tolerant cultivars with emphasis on wheat (Triticum aestivum L.)

TFs involved in drought tolerance in plants may be utilized in future for developing drought tolerant cultivars of wheat and some other crops. Plants have developed a fairly complex stress response system to deal with drought and other abiotic stresses. These response systems often make use of transcription factors (TFs); a gene encoding a specific TF together with -its target genes constitute a regulon, and take part in signal transduction to activate/silence genes involved in response to drought. Since, five specific families of TFs (out of >80 known families of TFs) have gained widespread attention on account of their significant role in drought tolerance in plants, TFs and regulons belonging to these five multi-gene families (AP2/EREBP, bZIP, MYB/MYC, NAC and WRKY) have been described and their role in improving drought tolerance discussed in this brief review. These TFs often undergo reversible phosphorylation to perform their function, and are also involved in complex networks. Therefore, some details about reversible phosphorylation of TFs by different protein kinases/phosphatases and the co-regulatory networks, which involve either only TFs or TFs with miRNAs, have also been discussed. Literature on transgenics involving genes encoding TFs and that on QTLs and markers associated with TF genes involved in drought tolerance has also been reviewed. Throughout the review, there is a major emphasis on wheat as an important crop, although examples from the model cereal rice (sometimes maize also), and the model plant Arabidopsis have also been used. This knowledge base may eventually allow the use of TF genes for development of drought tolerant cultivars, particularly in wheat.

A novel Ap2/ERF transcription factor from Stipa purpurea leads to enhanced drought tolerance in Arabidopsis thaliana

SpERF1 acts as a positive regulator, contributing to drought stress tolerance in A. thaliana through activating DRE/CRT elements in the promoters of abiotic stress-responsive genes. Stipa purpurea is an endemic perennial grass species in alpine arid and semi-arid meadows on the Qinghai-Xizang Plateau, which is highly tolerant against drought and cold. ERF transcription factors are known to regulate gene expression under abiotic and biotic treatments. Herein, we isolated a full-length ERF gene CDS from S. purpurea named SpERF1, which was induced by drought, cold, and jasmonic acid stresses. Subcellular localization revealed that SpERF1 is a nuclear protein, consistent with its roles as a transcription factor. Overexpression of SpERF1 enhanced drought tolerance of transgenic Arabidopsis thaliana via the activation of DRE/CRT elements in the promoters of abiotic stress-responsive genes. Furthermore, increased accumulation of proline indicated that SpERF1 might be involved in proline synthesis in the transgenic lines, allowing them to have a better buffering capacity and membrane protection under drought stress. This study indicated that SpERF1 might be an attractive target in the genetic engineering for improving stress tolerance in other crops. Moreover, SpERF1 protein function analysis increased our understanding of S. purpurea's ability to adapt to the adverse conditions of the Qinghai-Xizang Plateau.

Arg156 in the AP2-Domain Exhibits the Highest Binding Activity among the 20 Individuals to the GCC Box in BnaERF-B3-hy15, a Mutant ERF Transcription Factor from Brassica napus

To develop mutants of the ERF factor with more binding activities to the GCC box, we performed in vitro directed evolution by using DNA shuffling and screened mutants through yeast one-hybrid assay. Here, a series of mutants were obtained and used to reveal key amino acids that induce changes in the DNA binding activity of the BnaERF-B3 protein. With the BnaERF-B3-hy15 as the template, we produced 12 mutants which host individual mutation of potential key residues. We found that amino acid 156 is the key site, and the other 18 mutants host the 18 corresponding individual amino acid residues at site 156. Among the 20 individuals comprising WT (Gly156), Mu3 (Arg156), and 18 mutants with other 18 amino acid residues, Arg156 in the AP2-domain is the amino acid residue with the highest binding activity to the GCC box. The structure of the α-helix in the AP2-domain affects the binding activity. Other residues within AP2-domain modulated binding activity of ERF protein, suggesting that these positions are important for binding activity. Comparison of the mutant and wild-type transcription factors revealed the relationship of protein function and sequence modification. Our result provides a potential useful resource for understanding the trans-activation of ERF proteins.

Gene expression analysis reveals important pathways for drought response in leaves and roots of a wheat cultivar adapted to rainfed cropping in the Cerrado biome

Drought limits wheat production in the Brazilian Cerrado biome. In order to search for candidate genes associated to the response to water deficit, we analyzed the gene expression profiles, under severe drought stress, in roots and leaves of the cultivar MGS1 Aliança, a well-adapted cultivar to the Cerrado. A set of 4,422 candidate genes was found in roots and leaves. The number of down-regulated transcripts in roots was higher than the up-regulated transcripts, while the opposite occurred in leaves. The number of common transcripts between the two tissues was 1,249, while 2,124 were specific to roots and 1,049 specific to leaves. Quantitative RT-PCR analysis revealed a 0.78 correlation with the expression data. The candidate genes were distributed across all chromosomes and component genomes, but a greater number was mapped on the B genome, particularly on chromosomes 3B, 5B and 2B. When considering both tissues, 116 different pathways were induced. One common pathway, among the top three activated pathways in both tissues, was starch and sucrose metabolism. These results pave the way for future marker development and selection of important genes and are useful for understanding the metabolic pathways involved in wheat drought response.

Virus-Induced Gene Silencing Identifies an Important Role of the TaRSR1 Transcription Factor in Starch Synthesis in Bread Wheat

The function of a wheat starch regulator 1 (TaRSR1) in regulating the synthesis of grain storage starch was determined using the barley stripe mosaic virus-virus induced gene-silencing (BSMV-VIGS) method in field experiments. Chlorotic stripes appeared on the wheat spikes infected with barley stripe mosaic virus-virus induced gene-silencing- wheat starch regulator 1 (BSMV-VIGS-TaRSR1) at 15 days after anthesis, at which time the transcription levels of the TaRSR1 gene significantly decreased. Quantitative real-time PCR was also used to measure the transcription levels of 26 starch synthesis-related enzyme genes in the grains of BSMV-VIGS-TaRSR1-silenced wheat plants at 20, 27, and 31 days after anthesis. The results showed that the transcription levels of some starch synthesis-related enzyme genes were markedly induced at different sampling time points: TaSSI, TaSSIV, TaBEIII, TaISA1, TaISA3, TaPHOL, and TaDPE1 genes were induced at each of the three sampling time points and TaAGPS1-b, TaAGPL1, TaAGPL2, TaSSIIb, TaSSIIc, TaSSIIIb, TaBEI, TaBEIIa, TaBEIIb, TaISA2, TaPHOH, and TaDPE2 genes were induced at one sampling time point. Moreover, both the grain starch contents, one thousand kernel weights, grain length and width of BSMV-VIGS-TaRSR1-infected wheat plants significantly increased. These results suggest that TaRSR1 acts as a negative regulator and plays an important role in starch synthesis in wheat grains by temporally regulating the expression of specific starch synthesis-related enzyme genes.

Ectopic Expression of DREB Transcription Factor, AtDREB1A, Confers Tolerance to Drought in Transgenic Salvia miltiorrhiza

Drought decreases crop productivity more than any other type of environmental stress. Transcription factors (TFs) play crucial roles in regulating plant abiotic stress responses. The Arabidopsis thaliana gene DREB1A/CBF3, encoding a stress-inducible TF, was introduced into Salvia miltiorrhiza Ectopic expression of AtDREB1A resulted in increased drought tolerance, and transgenic lines had higher relative water content and Chl content, and exhibited an increased photosynthetic rate when subjected to drought stress. AtDREB1A transgenic plants generally displayed lower malondialdehyde (MDA), but higher superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) activities under drought stress. In particular, plants with ectopic AtDREB1A expression under the control of the stress-induced RD29A promoter exhibited more tolerance to drought compared with p35S::AtDREB1A transgenic plants, without growth inhibition or phenotypic aberrations. Differential gene expression profiling of wild-type and pRD29A::AtDREB1A transgenic plants following drought stress revealed that the expression levels of various genes associated with the stress response, photosynthesis, signaling, carbohydrate metabolism and protein protection were substantially higher in transgenic plants. In addition, the amount of salvianolic acids and tanshinones was significantly elevated in AtDREB1A transgenic S. miltiorrhiza roots, and most of the genes in the related biosynthetic pathways were up-regulated. Together, these results demonstrated that inducing the expression of a TF can effectively regulate multiple genes in the stress response pathways and significantly improve the resistance of plants to abiotic stresses. Our results also suggest that genetic manipulation of a TF can improve production of valuable secondary metabolites by regulating genes in associated pathways.

Transgenic poplar overexpressing the endogenous transcription factor ERF76 gene improves salinity tolerance

The ethylene response factor (ERF) family is one of the largest plant-specific transcription factor families, playing an important role in plant development and response to stresses. The ERF76 gene is a member of the poplar ERF transcription factor gene family. First, we validated that the ERF76 gene expressed in leaf and root tissues is responsive to salinity stress. We then successfully cloned the ERF76 cDNA fragment containing an open reading frame from di-haploid Populus simonii × Populus nigra and proved that ERF76 protein is targeted to the nucleus. Finally, we transferred the gene into the same poplar clone by the Agrobacterium-mediated leaf disc method. Using both RNA-Seq and reverse transcription-quantitative polymerase chain reaction, we validated that expression level of ERF76 is significantly higher in transgenic plants than that in the nontransgenic control. Using RNA-Seq data, we have identified 375 genes that are differentially expressed between the transgenic plants and the control under salt treatment. Among the differentially expressed genes, 16 are transcription factor genes and 45 are stress-related genes, both of which are upregulated significantly in transgenic plants, compared with the control. Under salt stress, the transgenic plants showed significant increases in plant height, root length, fresh weight, and abscisic acid (ABA) and gibberellin (GA) concentration compared with the control, suggesting that overexpression of ERF76 in transgenic poplar upregulated the expression of stress-related genes and increased the ability of ABA and GA biosynthesis, which resulted in stronger tolerance to salt stress.

Arabidopsis DREB1B in transgenic Salvia miltiorrhiza increased tolerance to drought stress without stunting growth

Multiple stress response genes are controlled by transcription factors in a coordinated manner; therefore, these factors can be used for molecular plant breeding. CBF1/DREB1B, a known stress-inducible gene, was isolated from Arabidopsis thaliana and introduced into Salvia miltiorrhiza under the control of the CaMV35S or RD29A promoter. Under drought stress, relative water content, chlorophyll content, and the net photosynthetic rate were observed to be higher in the transgenic lines than in the wild type (WT). Moreover, O2(-) and H2O2 accumulation was observed to be lower in the transgenic lines. Additional analyses revealed that the AtDREB1B transgenic plants generally displayed lesser malondialdehyde (MDA) but higher superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities than the WT under drought stress. Quantitative real-time polymerase chain reaction of a subset of genes involved in photosynthesis, stress response, carbohydrate metabolism, and cell protection further verified that AtDREB1B could enhance tolerance to drought by activating different downstream DREB/CBF genes in the transgenic plants. Furthermore, no growth inhibition was detected in transgenic S. miltiorrhiza plants that expressed AtDREB1B driven by either the constitutive CaMV35S promoter or the stress-inducible RD29A promoter. Together, these results suggest that AtDREB1B is a good candidate gene for increasing drought tolerance in transgenic S. miltiorrhiza.

Overexpression of a novel cold-responsive transcript factor LcFIN1 from sheepgrass enhances tolerance to low temperature stress in transgenic plants

As a perennial forage crop broadly distributed in eastern Eurasia, sheepgrass (Leymus chinensis (Trin.) Tzvel) is highly tolerant to low-temperature stress. Previous report indicates that sheepgrass is able to endure as low as -47.5 °C,allowing it to survive through the cold winter season. However, due to the lack of sufficient studies, the underlying mechanism towards the extraordinary low-temperature tolerance is unclear. Although the transcription profiling has provided insight into the transcriptome response to cold stress, more detailed studies are required to dissect the molecular mechanism regarding the excellent abiotic stress tolerance. In this work, we report a novel transcript factor LcFIN1 (L. chinensis freezing-induced 1) from sheepgrass. LcFIN1 showed no homology with other known genes and was rapidly and highly induced by cold stress, suggesting that LcFIN1 participates in the early response to cold stress. Consistently, ectopic expression of LcFIN1 significantly increased cold stress tolerance in the transgenic plants, as indicated by the higher survival rate, fresh weight and other stress-related indexes after a freezing treatment. Transcriptome analysis showed that numerous stress-related genes were differentially expressed in LcFIN1-overexpressing plants, suggesting that LcFIN1 may enhance plant abiotic stress tolerance by transcriptional regulation. Electrophoretic mobility shift assays and CHIP-qPCR showed that LcCBF1 can bind to the CRT/DRE cis-element located in the promoter region of LcFIN1, suggesting that LcFIN1 is directly regulated by LcCBF1. Taken together, our results suggest that LcFIN1 positively regulates plant adaptation response to cold stress and is a promising candidate gene to improve crop cold tolerance.

Identification of Differentially Expressed Genes Related to Dehydration Resistance in a Highly Drought-Tolerant Pear, Pyrus betulaefolia, as through RNA-Seq

Drought is a major abiotic stress that affects plant growth, development and productivity. Pear is one of the most important deciduous fruit trees in the world, but the mechanisms of drought tolerance in this plant are still unclear. To better understand the molecular basis regarding drought stress response, RNA-seq was performed on samples collected before and after dehydration in Pyrus betulaefolia. In total, 19,532 differentially expressed genes (DEGs) were identified. These genes were annotated into 144 Gene Ontology (GO) terms and 18 clusters of orthologous groups (COG) involved in 129 Kyoto Encyclopedia of Genes and Genomes (KEGG) defined pathways. These DEGs comprised 49 (26 up-regulated, 23 down-regulated), 248 (166 up-regulated, 82 down-regulated), 3483 (1295 up-regulated, 2188 down-regulated), 1455 (1065 up-regulated, 390 down-regulated) genes from the 1 h, 3 h and 6 h dehydration-treated samples and a 24 h recovery samples, respectively. RNA-seq was validated by analyzing the expresson patterns of randomly selected 16 DEGs by quantitative real-time PCR. Photosynthesis, signal transduction, innate immune response, protein phosphorylation, response to water, response to biotic stimulus, and plant hormone signal transduction were the most significantly enriched GO categories amongst the DEGs. A total of 637 transcription factors were shown to be dehydration responsive. In addition, a number of genes involved in the metabolism and signaling of hormones were significantly affected by the dehydration stress. This dataset provides valuable information regarding the Pyrus betulaefolia transcriptome changes in response to dehydration and may promote identification and functional analysis of potential genes that could be used for improving drought tolerance via genetic engineering of non-model, but economically-important, perennial species.

Recent Advances in Utilizing Transcription Factors to Improve Plant Abiotic Stress Tolerance by Transgenic Technology

Agricultural production and quality are adversely affected by various abiotic stresses worldwide and this will be exacerbated by the deterioration of global climate. To feed a growing world population, it is very urgent to breed stress-tolerant crops with higher yields and improved qualities against multiple environmental stresses. Since conventional breeding approaches had marginal success due to the complexity of stress tolerance traits, the transgenic approach is now being popularly used to breed stress-tolerant crops. So identifying and characterizing the critical genes involved in plant stress responses is an essential prerequisite for engineering stress-tolerant crops. Far beyond the manipulation of single functional gene, engineering certain regulatory genes has emerged as an effective strategy now for controlling the expression of many stress-responsive genes. Transcription factors (TFs) are good candidates for genetic engineering to breed stress-tolerant crop because of their role as master regulators of many stress-responsive genes. Many TFs belonging to families AP2/EREBP, MYB, WRKY, NAC, bZIP have been found to be involved in various abiotic stresses and some TF genes have also been engineered to improve stress tolerance in model and crop plants. In this review, we take five large families of TFs as examples and review the recent progress of TFs involved in plant abiotic stress responses and their potential utilization to improve multiple stress tolerance of crops in the field conditions.

MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants

The microRNAs (miRNAs) are small (20-24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed.

Identification of a regulatory element responsible for salt induction of rice OsRAV2 through ex situ and in situ promoter analysis

Salt is a major environmental stress factor that can affect rice growth and yields. Recent studies suggested that members of the AP2/ERF domain-containing RAV (related to ABI3/VP1) TF family are involved in abiotic stress adaptation. However, the transcriptional response of rice RAV genes (OsRAVs) to salt has not yet been fully characterized. In this study, the expression patterns of all five OsRAVs were examined under salt stress. Only one gene, OsRAV2, was stably induced by high-salinity treatment. Further expression profile analyses indicated that OsRAV2 is transcriptionally regulated by salt, but not KCl, osmotic stress, cold or ABA (abscisic acid) treatment. To elucidate the regulatory mechanism of the stress response at the transcriptional level, we isolated and characterized the promoter region of OsRAV2 (P OsRAV2 ). Transgenic analysis indicated that P OsRAV2 is induced by salt stress but not osmotic stress or ABA treatment. Serial 5' deletions and site-specific mutations in P OsRAV2 revealed that a GT-1 element located at position -664 relative to the putative translation start site is essential for the salt induction of P OsRAV2 . The regulatory function of the GT-1 element in the salt induction of OsRAV2 was verified in situ in plants with targeted mutations generated using the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system. Taken together, our results indicate that the GT-1 element directly controls the salt response of OsRAV2. This study provides a better understanding of the putative functions of OsRAVs and the molecular regulatory mechanisms of plant genes under salt stress.

Arabidopsis EDT1/HDG11 improves drought and salt tolerance in cotton and poplar and increases cotton yield in the field

Drought and salinity are two major environmental factors limiting crop production worldwide. Improvement of drought and salt tolerance of crops with transgenic approach is an effective strategy to meet the demand of the ever-growing world population. Arabidopsis ENHANCED DROUGHT TOLERANCE1/HOMEODOMAIN GLABROUS11 (AtEDT1/HDG11), a homeodomain-START transcription factor, has been demonstrated to significantly improve drought tolerance in Arabidopsis, tobacco, tall fescue and rice. Here we report that AtHDG11 also confers drought and salt tolerance in upland cotton (Gossypium hirsutum) and woody plant poplar (Populus tomentosa Carr.). Our results showed that both the transgenic cotton and poplar exhibited significantly enhanced tolerance to drought and salt stress with well-developed root system. In the leaves of the transgenic cotton plants, proline content, soluble sugar content and activities of reactive oxygen species-scavenging enzymes were significantly increased after drought and salt stress compared with wild type. Leaf stomatal density was significantly reduced, whereas stomatal and leaf epidermal cell size were significantly increased in both the transgenic cotton and poplar plants. More importantly, the transgenic cotton showed significantly improved drought tolerance and better agronomic performance with higher cotton yield in the field both under normal and drought conditions. These results demonstrate that AtHDG11 is not only a promising candidate for crops improvement but also for woody plants.

Genome-wide association mapping of time-dependent growth responses to moderate drought stress in Arabidopsis

Large areas of arable land are often confronted with irregular rainfall resulting in limited water availability for part(s) of the growing seasons, which demands research for drought tolerance of plants. Natural variation was observed for biomass accumulation upon controlled moderate drought stress in 324 natural accessions of Arabidopsis. Improved performance under drought stress was correlated with early flowering and lack of vernalization requirement, indicating overlap in the regulatory networks of flowering time and drought response or correlated responses of these traits to natural selection. In addition, plant size was negatively correlated with relative water content (RWC) independent of the absolute water content (WC), indicating a prominent role for soluble compounds. Growth in control and drought conditions was determined over time and was modelled by an exponential function. Genome-wide association (GWA) mapping of temporal plant size data and of model parameters resulted in the detection of six time-dependent quantitative trait loci (QTLs) strongly associated with drought. Most QTLs would not have been identified if plant size was determined at a single time point. Analysis of earlier reported gene expression changes upon drought enabled us to identify for each QTL the most likely candidates.

Engineering food crops to grow in harsh environments

Achieving sustainable agriculture and producing enough food for the increasing global population will require effective strategies to cope with harsh environments such as water and nutrient stress, high temperatures and compacted soils with high impedance that drastically reduce crop yield. Recent advances in the understanding of the molecular, cellular and epigenetic mechanisms that orchestrate plant responses to abiotic stress will serve as the platform to engineer improved crop plants with better designed root system architecture and optimized metabolism to enhance water and nutrients uptake and use efficiency and/or soil penetration. In this review we discuss such advances and how the generated knowledge could be used to integrate effective strategies to engineer crops by gene transfer or genome editing technologies.

Generation of Wheat Transcription Factor FOX Rice Lines and Systematic Screening for Salt and Osmotic Stress Tolerance

Transcription factors (TFs) play important roles in plant growth, development, and responses to environmental stress. In this study, we collected 1,455 full-length (FL) cDNAs of TFs, representing 45 families, from wheat and its relatives Triticum urartu, Aegilops speltoides, Aegilops tauschii, Triticum carthlicum, and Triticum aestivum. More than 15,000 T0 TF FOX (Full-length cDNA Over-eXpressing) rice lines were generated; of these, 10,496 lines set seeds. About 14.88% of the T0 plants showed obvious phenotypic changes. T1 lines (5,232 lines) were screened for salt and osmotic stress tolerance using 150 mM NaCl and 20% (v/v) PEG-4000, respectively. Among them, five lines (591, 746, 1647, 1812, and J4065) showed enhanced salt stress tolerance, five lines (591, 746, 898, 1078, and 1647) showed enhanced osmotic stress tolerance, and three lines (591, 746, and 1647) showed both salt and osmotic stress tolerance. Further analysis of the T-DNA flanking sequences showed that line 746 over-expressed TaEREB1, line 898 over-expressed TabZIPD, and lines 1812 and J4065 over-expressed TaOBF1a and TaOBF1b, respectively. The enhanced salt and osmotic stress tolerance of lines 898 and 1812 was confirmed by retransformation of the respective genes. Our results demonstrate that a heterologous FOX system may be used as an alternative genetic resource for the systematic functional analysis of the wheat genome.

Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)

BACKGROUND

Hexaploid wheat (Triticum aestivum) is a globally important crop. Heat, drought and their combination dramatically reduce wheat yield and quality, but the molecular mechanisms underlying wheat tolerance to extreme environments, especially stress combination, are largely unknown. As an allohexaploid, wheat consists of three closely related subgenomes (A, B, and D), and was reported to show improved tolerance to stress conditions compared to tetraploid. But so far very little is known about how wheat coordinates the expression of homeologous genes to cope with various environmental constraints on the whole-genome level.

RESULTS

To explore the transcriptional response of wheat to the individual and combined stress, we performed high-throughput transcriptome sequencing of seedlings under normal condition and subjected to drought stress (DS), heat stress (HS) and their combination (HD) for 1 h and 6 h, and presented global gene expression reprograms in response to these three stresses. Gene Ontology (GO) enrichment analysis of DS, HS and HD responsive genes revealed an overlap and complexity of functional pathways between each other. Moreover, 4,375 wheat transcription factors were identified on a whole-genome scale based on the released scaffold information by IWGSC, and 1,328 were responsive to stress treatments. Then, the regulatory network analysis of HSFs and DREBs implicated they were both involved in the regulation of DS, HS and HD response and indicated a cross-talk between heat and drought stress. Finally, approximately 68.4 % of homeologous genes were found to exhibit expression partitioning in response to DS, HS or HD, which was further confirmed by using quantitative RT-PCR and Nullisomic-Tetrasomic lines.

CONCLUSIONS

A large proportion of wheat homeologs exhibited expression partitioning under normal and abiotic stresses, which possibly contributes to the wide adaptability and distribution of hexaploid wheat in response to various environmental constraints.

Overexpression of GmERF5, a new member of the soybean EAR motif-containing ERF transcription factor, enhances resistance to Phytophthora sojae in soybean

Phytophthora root and stem rot of soybean [Glycine max (L.) Merr.], caused by Phytophthora sojae Kaufmann and Gerdemann, is a destructive disease throughout the soybean planting regions in the world. Here, we report insights into the function and underlying mechanisms of a novel ethylene response factor (ERF) in soybean, namely GmERF5, in host responses to P. sojae. GmERF5-overexpressing transgenic soybean exhibited significantly enhanced resistance to P. sojae and positively regulated the expression of the PR10, PR1-1, and PR10-1 genes. Sequence analysis suggested that GmERF5 contains an AP2/ERF domain of 58 aa and a conserved ERF-associated amphiphilic repression (EAR) motif in its C-terminal region. Following stress treatments, GmERF5 was significantly induced by P. sojae, ethylene (ET), abscisic acid (ABA), and salicylic acid (SA). The activity of the GmERF5 promoter (GmERF5P) was upregulated in tobacco leaves with ET, ABA, Phytophthora nicotianae, salt, and drought treatments, suggesting that GmERF5 could be involved not only in the induced defence response but also in the ABA-mediated pathway of salt and drought tolerance. GmERF5 could bind to the GCC-box element and act as a repressor of gene transcription. It was targeted to the nucleus when transiently expressed in Arabidopsis protoplasts. GmERF5 interacted with a basic helix-loop-helix transcription factor (GmbHLH) and eukaryotic translation initiation factor (GmEIF) both in yeast cells and in planta. To the best of our knowledge, GmERF5 is the first soybean EAR motif-containing ERF transcription factor demonstrated to be involved in the response to pathogen infection.

MicroRNA: a new target for improving plant tolerance to abiotic stress

MicroRNAs (miRNAs) are an extensive class of endogenous, small RNA molecules that sit at the heart of regulating gene expression in multiple developmental and signalling pathways. Recent studies have shown that abiotic stresses induce aberrant expression of many miRNAs, thus suggesting that miRNAs may be a new target for genetically improving plant tolerance to certain stresses. These studies have also shown that miRNAs respond to environmental stresses in a miRNA-, stress-, tissue-, and genotype-dependent manner. During abiotic stress, miRNAs function by regulating target genes within the miRNA-target gene network and by controlling signalling pathways and root development. Generally speaking, stress-induced miRNAs lead to down-regulation of negative regulators of stress tolerance whereas stress-inhibited miRNAs allow the accumulation and function of positive regulators. Currently, the majority of miRNA-based studies have focused on the identification of miRNAs that are responsive to different stress conditions and analysing their expression profile changes during these treatments. This has predominately been accomplished using deep sequencing technologies and other expression analyses, such as quantitative real-time PCR. In the future, more function and expression studies will be necessary in order to elucidate the common miRNA-mediated regulatory mechanisms that underlie tolerance to different abiotic stresses. The use of artificial miRNAs, as well as overexpression and knockout/down of both miRNAs and their targets, will be the best techniques for determining the specific roles of individual miRNAs in response to environmental stresses.

From Genetics to Functional Genomics: Improvement in Drought Signaling and Tolerance in Wheat

Drought being a yield limiting factor has become a major threat to international food security. It is a complex trait and drought tolerance response is carried out by various genes, transcription factors (TFs), microRNAs (miRNAs), hormones, proteins, co-factors, ions, and metabolites. This complexity has limited the development of wheat cultivars for drought tolerance by classical breeding. However, attempts have been made to fill the lost genetic diversity by crossing wheat with wild wheat relatives. In recent years, several molecular markers including single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs) associated with genes for drought signaling pathways have been reported. Screening of large wheat collections by marker assisted selection (MAS) and transformation of wheat with different genes/TFs has improved drought signaling pathways and tolerance. Several miRNAs also provide drought tolerance to wheat by regulating various TFs/genes. Emergence of OMICS techniques including transcriptomics, proteomics, metabolomics, and ionomics has helped to identify and characterize the genes, proteins, metabolites, and ions involved in drought signaling pathways. Together, all these efforts helped in understanding the complex drought tolerance mechanism. Here, we have reviewed the advances in wide hybridization, MAS, QTL mapping, miRNAs, transgenic technique, genome editing system, and above mentioned functional genomics tools for identification and utility of signaling molecules for improvement in wheat drought tolerance.