The cold-inducible CBF1 factor-dependent signaling pathway modulates the accumulation of the growth-repressing DELLA proteins via its effect on gibberellin metabolism

Identification of CBF Transcription Factors in Tea Plants and a Survey of Potential CBF Target Genes under Low Temperature

C-repeat binding factors (CBFs) are key signaling genes that can be rapidly induced by cold and bind to the C-repeat/dehydration-responsive motif (CRT/DRE) in the promoter region of the downstream cold-responsive (COR) genes, which play a vital role in the plant response to low temperature. However, the CBF family in tea plants has not yet been elucidated, and the possible target genes regulated by this family under low temperature are still unclear. In this study, we identified five CsCBF family genes in the tea plant genome and analyzed their phylogenetic tree, conserved domains and motifs, and cis-elements. These results indicate that CsCBF3 may be unique in the CsCBF family. This is further supported by our findings from the low-temperature treatment: all the CsCBF genes except CsCBF3 were significantly induced after treatment at 4 °C. The expression profiles of eight tea plant tissues showed that CsCBFs were mainly expressed in winter mature leaves, roots and fruits. Furthermore, 685 potential target genes were identified by transcriptome data and CRT/DRE element information. These target genes play a functional role under the low temperatures of winter through multiple pathways, including carbohydrate metabolism, lipid metabolism, cell wall modification, circadian rhythm, calcium signaling, transcriptional cascade, and hormone signaling pathways. Our findings will further the understanding of the stress regulatory network of CsCBFs in tea plants.

The Methylation Patterns and Transcriptional Responses to Chilling Stress at the Seedling Stage in Rice

Chilling stress is considered the major abiotic stress affecting the growth, development, and yield of rice. To understand the transcriptomic responses and methylation regulation of rice in response to chilling stress, we analyzed a cold-tolerant variety of rice (Oryza sativa L. cv. P427). The physiological properties, transcriptome, and methylation of cold-tolerant P427 seedlings under low-temperature stress (2–3 °C) were investigated. We found that P427 exhibited enhanced tolerance to low temperature, likely via increasing antioxidant enzyme activity and promoting the accumulation of abscisic acid (ABA). The Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) data showed that the number of methylation-altered genes was highest in P427 (5496) and slightly lower in Nipponbare (Nip) and 9311 (4528 and 3341, respectively), and only 2.7% (292) of methylation genes were detected as common differentially methylated genes (DMGs) related to cold tolerance in the three varieties. Transcriptome analyses revealed that 1654 genes had specifically altered expression in P427 under cold stress. These genes mainly belonged to transcription factor families, such as Myeloblastosis (MYB), APETALA2/ethylene-responsive element binding proteins (AP2-EREBP), NAM-ATAF-CUC (NAC) and WRKY. Fifty-one genes showed simultaneous methylation and expression level changes. Quantitative RT-PCR (qRT-PCR) results showed that genes involved in the ICE (inducer of CBF expression)-CBF (C-repeat binding factor)—COR (cold-regulated) pathway were highly expressed under cold stress, including the WRKY genes. The homologous gene Os03g0610900 of the open stomatal 1 (OST1) in rice was obtained by evolutionary tree analysis. Methylation in Os03g0610900 gene promoter region decreased, and the expression level of Os03g0610900 increased, suggesting that cold stress may lead to demethylation and increased gene expression of Os03g0610900. The ICE-CBF-COR pathway plays a vital role in the cold tolerance of the rice cultivar P427. Overall, this study demonstrates the differences in methylation and gene expression levels of P427 in response to low-temperature stress, providing a foundation for further investigations of the relationship between environmental stress, DNA methylation, and gene expression in rice.

The β-amylase PbrBAM3 from pear (Pyrus betulaefolia) regulates soluble sugar accumulation and ROS homeostasis in response to cold stress

β-Amylase (BAM) is involved in sugar metabolism, but the role of BAM genes in cold tolerance remains poorly understood. Here, we report the identification and functional characterization of the chloroplast-localized BAM-encoding gene PbrBAM3 isolated from Pyrus betulaefolia. The transcript levels of PbrBAM3 were up-regulated under cold, dehydration and ABA, but repressed by maltose. Overexpression of PbrBAM3 in tobacco (Nicotiana tabacum) and pear (P. ussuriensis) conferred increased BAM activity, promoted starch degradation after chilling treatments and enhanced tolerance to cold. Under the chilling stress, the transgenic tobacco and P. ussuriensis exhibited lessened reactive oxygen species (ROS) generation, higher levels of antioxidant enzymes activity, and greater accumulation of soluble sugars (specially maltose) than the corresponding wild type plants. Taken together, these results demonstrate that PbrBAM3 plays an important role in cold tolerance, at least in part, by raising the levels of soluble sugars capable of acting as osmolytes or antioxidants.

Transcriptome profiling illustrates expression signatures of dehydration tolerance in developing grasspea seedlings

This study highlights dehydration-mediated temporal changes in physicochemical, transcriptome and metabolome profiles indicating altered gene expression and metabolic shifts, underlying endurance and adaptation to stress tolerance in the marginalized crop, grasspea. Grasspea, often regarded as an orphan legume, is recognized to be fairly tolerant to water-deficit stress. In the present study, 3-week-old grasspea seedlings were subjected to dehydration by withholding water over a period of 144 h. While there were no detectable phenotypic changes in the seedlings till 48 h, the symptoms appeared during 72 h and aggravated upon prolonged dehydration. The physiological responses to water-deficit stress during 72-96 h displayed a decrease in pigments, disruption in membrane integrity and osmotic imbalance. We evaluated the temporal effects of dehydration at the transcriptome and metabolome levels. In total, 5201 genes of various functional classes including transcription factors, cytoplasmic enzymes and structural cell wall proteins, among others, were found to be dehydration-responsive. Further, metabolome profiling revealed 59 dehydration-responsive metabolites including sugar alcohols and amino acids. Despite the lack of genome information of grasspea, the time course of physicochemical and molecular responses suggest a synchronized dehydration response. The cross-species comparison of the transcriptomes and metabolomes with other legumes provides evidence for marked molecular diversity. We propose a hypothetical model that highlights novel biomarkers and explain their relevance in dehydration-response, which would facilitate targeted breeding and aid in commencing crop improvement efforts.

Using Transcriptome to Discover a Novel Melatonin-Induced Sodic Alkaline Stress Resistant Pathway in Solanum lycopersicum L

Melatonin plays important roles in multiple stress responses. However, the downstream signaling pathway and molecular mechanism are unclear until now. Here, we not only revealed the transcriptional control of melatonin-induced sodic alkaline stress tolerance, but also described a screen for key downstream transcriptional factors of melatonin through transcriptome analysis. The melatonin-induced transcriptional network of hormone, transcriptional factors and functional genes has been established under both control and stress conditions. Among these, six candidates of transcriptional factors have been identified via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. Using the virus-induced gene silencing approach, we confirmed that DREB1α and IAA3 were key downstream transcriptional factors of melatonin-induced sodic alkaline stress tolerance at the genetic level. The transcriptions of DREB1α and IAA3 could be activated by melatonin or sodic alkaline treatment. Interestingly, we found that DREB1α could directly upregulate the expression of IAA3 by binding to its promoters. Moreover, several physiological processes of Na+ detoxification, dehydration resistance, high pH buffering and reactive oxygen species scavenging were confirmed to depend or partly depend on DREB1α and IAA3 pathway in melatonin-induced stress tolerance. Taken together, this study suggested that DREB1α and IAA3 are positive resistant modulators, and provided a direct link among melatonin, DREB1α and IAA3 in the sodic alkaline stress tolerance activating in tomato plants.

Comprehensive expression analysis of Arabidopsis GA2-oxidase genes and their functional insights

Bioactive gibberellins (GAs) play multiple roles in plant development and stress responses. GA2-oxidases (GA2oxs) are a class of 2-oxoglutarate-dependent dioxygenases that regulate the deactivation of bioactive GAs. In this study, we investigated the phylogeny and domain structures of the seven GA2ox genes present in the Arabidopsis thaliana genome. Comprehensive expression analysis using translational reporter lines showed that the seven GA2ox genes are differentially expressed during Arabidopsis growth and development: GA2ox1 is specifically expressed in the hypocotyl and lateral root primordium; GA2ox2 is highly expressed in aboveground tissues; GA2ox3 is expressed in the chalazal endosperm of the early embryo sac and inflorescences; GA2ox4 is expressed in the shoot apical meristem and during lateral root initiation; GA2ox6 is expressed in the maturation zone, but not in the meristem or elongating zone of the root; GA2ox7 is constitutively expressed during almost all developmental stages; and GA2ox8 is exclusively expressed in stomatal cells. Overexpression of each of these GA2ox genes inhibited high temperature-induced hypocotyl elongation in both wild-type and elongated hypocotyl 5 plants, which have an elongated hypocotyl phenotype, suggesting that these genes negatively regulate hypocotyl elongation by reducing bioactive GA levels. This study provides a valuable resource for further elucidating the roles of GA2ox genes during different stages of development.

The transcriptional activity of a temperature-sensitive transcription factor module is associated with pollen shedding time in pine

It has long been known that the pollen shedding time in pine trees is correlated with temperature, but the molecular basis for this has remained largely unknown. To better understand the mechanisms driving temperature response and to identify the hub regulators of pollen shedding time regulation in Pinus tabuliformis Carr., we identified a set of temperature-sensitive genes by carrying out a comparative transcriptome analysis using six early pollen shedding trees (EPs) and six late pollen shedding trees (LPs) during mid-winter and at three consecutive time points in early spring. We carried out a weighted gene co-expression network analysis and constructed a transcription factor (TF) collaborative network, merging the common but differentially expressed TFs of the EPs and LPs into a joint network. We found five hub genes in the core TF module whose expression was rapidly induced by low temperatures. The transcriptional activity of this TF module was strongly associated with pollen shedding time, and likely to produce the fine balance between cold hardiness and growth activity in early spring. We confirmed the key role of temperature in regulating flowering time and identified a transcription factor module associated with pollen shedding time in P. tabuliformis. This suggests that repression of growth activity by repressors is the main mechanism balancing growth and cold hardiness in pine trees in early spring. Our results provide new insights into the molecular mechanisms regulating seasonal flowering time in pines.

Gibberellins Act Downstream of Arabis PERPETUAL FLOWERING1 to Accelerate Floral Induction during Vernalization

Regulation of flowering by endogenous and environmental signals ensures that reproduction occurs under optimal conditions to maximize reproductive success. Involvement of the growth regulator gibberellin (GA) in the control of flowering by environmental cues varies among species. Arabis alpina Pajares, a model perennial member of the Brassicaceae, only undergoes floral induction during vernalization, allowing definition of the role of GA specifically in this process. The transcription factor PERPETUAL FLOWERING1 (PEP1) represses flowering until its mRNA levels are reduced during vernalization. Genome-wide analyses of PEP1 targets identified genes involved in GA metabolism and signaling, and many of the binding sites in these genes were specific to the A. alpina lineage. Here, we show that the pep1 mutant exhibits an elongated-stem phenotype, similar to that caused by treatment with exogenous GA, consistent with PEP1 repressing GA responses. Moreover, in comparison with the wild type, the pep1 mutant contains higher GA4 levels and is more sensitive to GA prior to vernalization. Upon exposure to cold temperatures, GA levels fall to low levels in the pep1 mutant and in wild-type plants, but GA still promotes floral induction and the transcription of floral meristem identity genes during vernalization. Reducing GA levels strongly impairs flowering and inflorescence development in response to short vernalization treatments, but longer treatments overcome the requirement for GA. Thus, GA accelerates the floral transition during vernalization in A. alpina, the down-regulation of PEP1 likely increases GA sensitivity, and GA responses contribute to determining the length of vernalization required for flowering and reproduction.

The BAP Module: A Multisignal Integrator Orchestrating Growth

Coordination of cell proliferation, cell expansion, and differentiation underpins plant growth. To maximise reproductive success, growth needs to be fine-tuned in response to endogenous and environmental cues. This developmental plasticity relies on a cellular machinery that integrates diverse signals and coordinates the downstream responses. In arabidopsis, the BAP regulatory module, which includes the BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) transcription factors (TFs), has been shown to coordinate growth in response to multiple growth-regulating signals. In this Opinion article, we provide an integrative view on the BAP module control of cell expansion and discuss whether its function is conserved or diversified, thus providing new insights into the molecular control of growth.

Identification and characterization of PsDREB2 promoter involved in tissue-specific expression and abiotic stress response from Paeonia suffruticosa

Dehydration-responsive element-binding factor 2 (DREB2) belongs to the C-repeat-binding factor (CBF)/DREB subfamily of proteins. In this study, a 2,245 bp PsDREB2 promoter fragment was isolated from the genome of Paeonia suffruticosa. The fragment was rich in A/T bases and contained TATA box sequences, abscisic acid (ABA)-response elements, and other cis-elements, such as MYB and CAAT box. The promoter was fused with the β-glucuronidase (GUS) reporter gene to generate an expression vector. Arabidopsis thaliana was transformed with a flower dipping method. Gus activity in different tissues and organs of transgenic plants was determined via histochemical staining and quantified via GUS fluorescence. The activity of promoter regulatory elements in transgenic plants under drought, low-temperature, high-salt, and ABA stresses was analyzed. The results showed that the PsDREB2 gene promoter was expressed in the roots, stems, leaves, flowers, and silique pods but not in the seeds of transgenic Arabidopsis. Furthermore, the promoter was induced by drought, low temperature, high salt, and ABA. Hence, the PsDREB2 promoter is tissue- and stress-specific and can be used in the genetic engineering of novel peony cultivars in the future.

Auxin and GA signaling play important roles in the maize response to phosphate deficiency

Phytohormone signaling is involved in the low-phosphate (LP) response and causes root system changes. To understand the roles of auxin and gibberellic acid (GA) in the maize response to LP stress, inbred line Q319 was used to identify the changes in root morphology and the gene expression response to LP stress with or without exogenous auxin, GA or their inhibitors. The root morphology, IAA and GAs concentration and genes related to the LP response, cell elongation and division, auxin transport and signaling, and GA synthesis and signaling were analyzed. The LP-induced maize root morphological adaption was dependent on changes in the expression of related genes, like IPS1, pht1;1 LPR1b, KRPs, and EXPB1-4. The altered local auxin concentration and signaling were involved in promoting axial root elongation and reducing lateral root density and length under LP conditions, which were regulated by PID and PP2A activity and the auxin signaling pathway. The upregulation of the GA synthesis genes AN1, GA20ox1, and GA20ox2 and the downregulation of the GA inactive genes GA2ox1 and GA2ox2 were observed in maize roots subjected to LP stress, and the increased GA biosynthesis and signaling were involved in root growth. Both hormones participate in LP stress response and jointly regulated root modification and LP acclimation in maize.

Cold acclimation by the CBF-COR pathway in a changing climate: Lessons from Arabidopsis thaliana

Cold acclimation is a process used by most temperate plants to cope with freezing stress. In this process, the expression of cold-responsive (COR) genes is activated and the genes undergo physiological changes in response to the exposure to low, non-freezing temperatures and other environmental signals. The C-repeat-binding factors (CBFs) have been demonstrated to regulate the expression of many COR genes. Recent studies have elucidated the molecular mechanisms of how plants transmit cold signals from the plasma membrane to the CBFs and the results have indicated that COR genes are also regulated through CBF-independent pathways. Climate change is expected to have a major impact on cold acclimation and freezing tolerance of plants. However, how climate change affects plant cold acclimation at the molecular level remains unclear. This mini-review focuses on recent advances in cold acclimation in Arabidopsis thaliana and discusses how signaling can be potentially impacted by climate change. Understanding how plants acquire cold acclimation is valuable for the improvement of the freezing tolerance in plants and for predicting the effects of climate change on plant distribution and agricultural yield.

Seed enhancing treatments: comparative analysis of germination characteristics of 23 key herbaceous species used in European restoration programmes

The response of seeds from 23 wild plant species to a range of seed enhancing treatments was studied. We tested the hypothesis that sensitivity of the 23 species to these compounds is related to their ecological niche. The three ecological niches considered were open land, open-pioneer and woodland. Hence, the germination of a species is likely adapted to different light conditions and other environmental signals related to the niche. As representatives of environmental signals, the effects of smoke-related compounds (karrikinolide, KAR₁ ), nitrate and plant growth regulator (gibberellic acid, GA₃ ) on germination were studied. Seeds were exposed to these additives in the imbibition medium; all described as germination cues. We also investigated the effect of light regimes and additives on germination parameters, which included final germination, germination rate and uniformity of germination. Seeds were placed to germinate under three light conditions: constant red light, constant darkness and 12 h white light photoperiod. We observed inhibition by KAR under light in some species, which may have ecological implications. The results showed that no single treatment increased the germination of all the tested species, rather a wide variation of responsiveness of the different species to the three compounds was found. Additionally, no interaction was found between responsiveness to compounds and ecological niche. However, species in the same ecological niche and dormancy class showed a similar responsiveness to light. Species that share a similar environment have similar light requirements for germination, while differences exist among species in their responsiveness to other germination cues.

Characteristics and Expression Analysis of FmTCP15 under Abiotic Stresses and Hormones and Interact with DELLA Protein in Fraxinus mandshurica Rupr

The TEOSINTE BRANCHED1, CYCLOIDEA, and PROLIFERATION CELL FACTOR (TCP) transcription factor is a plant-specific gene family and acts on multiple functional genes in controlling growth, development, stress response, and the circadian clock. In this study, a class I member of the TCP family from Fraxinus mandshurica Rupr. was isolated and named FmTCP15, which encoded a protein of 362 amino acids. Protein structures were analyzed and five ligand binding sites were predicted. The phylogenetic relationship showed that FmTCP15 was most closely related to Solanaceae and Plantaginaceae. FmTCP15 was localized in the nuclei of F. mandshurica protoplast cells and highly expressed in cotyledons. The expression pattern revealed the FmTCP15 response to multiple abiotic stresses and hormone signals. Downstream genes for transient overexpression of FmTCP15 in seedlings were also investigated. A yeast two-hybrid assay confirmed that FmTCP15 could interact with DELLA proteins. FmTCP15 participated in the GA-signaling pathway, responded to abiotic stresses and hormone signals, and regulated multiple genes in these biological processes. Our study revealed the potential value of FmTCP15 for understanding the molecular mechanisms of stress and hormone signal responses.

Eyes on the future - evidence for trade-offs between growth, storage and defense in Norway spruce

Carbon (C) allocation plays a central role in tree responses to environmental changes. Yet, fundamental questions remain about how trees allocate C to different sinks, for example, growth vs storage and defense. In order to elucidate allocation priorities, we manipulated the whole-tree C balance by modifying atmospheric CO₂ concentrations [CO₂ ] to create two distinct gradients of declining C availability, and compared how C was allocated among fluxes (respiration and volatile monoterpenes) and biomass C pools (total biomass, nonstructural carbohydrates (NSC) and secondary metabolites (SM)) in well-watered Norway spruce (Picea abies) saplings. Continuous isotope labelling was used to trace the fate of newly-assimilated C. Reducing [CO₂ ] to 120 ppm caused an aboveground C compensation point (i.e. net C balance was zero) and resulted in decreases in growth and respiration. By contrast, soluble sugars and SM remained relatively constant in aboveground young organs and were partially maintained with a constant allocation of newly-assimilated C, even at expense of root death from C exhaustion. We conclude that spruce trees have a conservative allocation strategy under source limitation: growth and respiration can be downregulated to maintain 'operational' concentrations of NSC while investing newly-assimilated C into future survival by producing SM.

Comparative transcriptome analysis reveals significant differences in the regulation of gene expression between hydrogen cyanide- and ethylene-treated Arabidopsis thaliana

BACKGROUND

Hydrogen cyanide (HCN) is a small gaseous molecule that is predominantly produced as an equimolar co-product of ethylene (ET) biosynthesis in plants. The function of ET is of great concern and is well studied; however, the function of HCN is largely unknown. Similar to ET, HCN is a simple and diffusible molecule that has been shown to play a regulatory role in the control of some metabolic processes in plants. Nevertheless, it is still controversial whether HCN should be regarded as a signalling molecule, and the cross-talk between HCN and ET in gene expression regulation remains unclear. In this study, RNA sequencing (RNA-seq) was performed to compare the differentially expressed genes (DEGs) between HCN and ET in Arabidopsis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were subsequently performed to investigate the function and pathway enrichment of DEGs. Parts of key genes were confirmed by quantitative real-time PCR.

RESULTS

The results showed that at least 1305 genes and 918 genes were significantly induced by HCN and ET, respectively. Interestingly, a total of 474 genes (|log₂ FC| ≥1) were co-regulated by HCN and ET. GO and KEGG analyses indicated that the co-regulated genes by HCN and ET were enriched in plant responses to stress and plant hormone signal transduction pathways, indicating that HCN may cooperate with ET and participate in plant growth and development and stress responses. However, a total of 831 genes were significantly induced by HCN but not by ET, indicating that in addition to ET, HCN is in essence a key signalling molecule in plants. Importantly, our data showed that the possible regulatory role of a relatively low concentration of HCN does not depend on ET feedback induction, although there are some common downstream components were observed.

CONCLUSION

Our findings provide a valuable resource for further exploration and understanding of the molecular regulatory mechanisms of HCN in plants and provide novel insight into HCN cross-talk with ET and other hormones in the regulation of plant growth and plant responses to environmental stresses.

Cold stress signalling in female reproductive tissues

Cold stress is a significant threat for plant productivity and impacts on plant distribution and crop production, particularly so when it occurs during the growth phase. A developmental stage at risk is that of flowering, since a single stress event during sensitive stages, such as the full-bloom stage of fruit trees can be fatal for reproductive success. Although pollen development and fertilization are widely viewed as the most critical reproductive phases, the development and function of female reproductive tissues, which in Angiosperms are embedded in the gynoecium, are also affected by cold stress. Today however, we have essentially no understanding of the cold stress response pathways that act during floral organogenesis. In this review, we briefly summarize our current knowledge of cold stress signalling modules active in vegetative tissues that may provide a framework of general principles also transferable to female reproductive tissues. We then align these signalling cascades with those that govern gynoecium development to identify factors that may act in both processes and could thereby contribute to cold stress responses in female reproductive tissues.

SlHY5 Integrates Temperature, Light, and Hormone Signaling to Balance Plant Growth and Cold Tolerance

During the transition from warm to cool seasons, plants experience decreased temperatures, shortened days, and decreased red/far-red (R/FR) ratios of light. The mechanism by which plants integrate these environmental cues to maintain plant growth and adaptation remains poorly understood. Here, we report that low temperature induced the transcription of PHYTOCHROME A and accumulation of LONG HYPOCOTYL5 (SlHY5, a basic Leu zipper transcription factor) in tomato (Solanum lycopersicum) plants, especially under short day conditions with low R/FR light ratios. Reverse genetic approaches and physiological analyses revealed that silencing of SlHY5 increased cold susceptibility in tomato plants, whereas overexpression of SlHY5 enhanced cold tolerance. SlHY5 directly bound to and activated the transcription of genes encoding a gibberellin-inactivation enzyme, namely GIBBERELLIN2-OXIDASE4, and an abscisic acid biosynthetic enzyme, namely 9-CIS-EPOXYCAROTENOID DIOXYGENASE6 (SlNCED6). Thus, phytochrome A-dependent SlHY5 accumulation resulted in an increased abscisic acid/gibberellin ratio, which was accompanied by growth cessation and induction of cold response. Furthermore, silencing of SlNCED6 compromises short day- and low R/FR-induced tomato resistance to cold stress. These findings provide insight into the molecular genetic mechanisms by which plants integrate environmental stimuli with hormones to coordinate their growth with impending cold temperatures. Moreover, this work reveals a molecular mechanism that plants have evolved for growth and survival in response to seasonal changes.

Growth rate regulation is associated with developmental modification of source efficiency

Plants modulate their growth rate according to seasonal and environmental cues using a suite of growth repressors known to interact directly with cellular machinery controlling cell division and growth. Mutants lacking growth repressors show increased growth rates^1,2, but the mechanism by which these plants ensure source availability for faster growth is unclear. Here, we undertake a comprehensive analysis of the fast-growth phenotype of a quintuple growth-repressor mutant, using a combination of theoretical and experimental approaches to understand the physiological basis of source-sink coordination. Our results show that, in addition to the control of tissue growth rates, growth repressors also affect tissue composition and leaf thickness, modulating the efficiency of production of new photosynthetic capacity. Modelling suggests that increases in growth efficiency underlie growth-rate differences between the wild type and spatula della growth-repressor mutant, with spatula della requiring less carbon to synthesize a comparable photosynthetic capability to the wild type, and fixing more carbon per unit mass. We conclude that through control of leaf development, growth repressors regulate both source availability and sink strength to achieve growth-rate variation without risking a carbon deficit.

Cross-Talk Signaling in Rice During Combined Drought and Bacterial Blight Stress

Due to climatic changes, rice crop is affected by moisture deficit stress and pathogens. Tissue water limitation besides reducing growth rates, also renders the crop susceptible to the infection by Xanthomonas oryzae pv. oryzae (Xoo) that causes bacterial leaf blight. Independently, both drought adaptation and Xoo resistance have been extensively studied. Though the cross-talk between drought and Xoo stress responses have been explored from individual stress studies, examining the combinatorial stress response is limited in rice. Recently published combined stress studies showed that under the combined stress, maintenance of carbon assimilation is hindered and such response is regulated by overlapping cellular mechanisms that are different from either of the individual stresses. Several receptors, MAP kinases, transcription factors, and ribosomal proteins, are predicted for playing a role in cellular homeostasis and protects cells from combined stress effects. Here we provide a critical analysis of these aspects using information from the recently published combined stress literature. This review is useful for researchers to comprehend combinatorial stress response of rice plants to drought and Xoo.

AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in Arabidopsis

Dynamic environmental changes such as extreme temperature, water scarcity and high salinity affect plant growth, survival, and reproduction. Plants have evolved sophisticated regulatory mechanisms to adapt to these unfavorable conditions, many of which interface with plant hormone signaling pathways. Abiotic stresses alter the production and distribution of phytohormones that in turn mediate stress responses at least in part through hormone- and stress-responsive transcription factors. Among these, the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) family transcription factors (AP2/ERFs) have emerged as key regulators of various stress responses, in which they also respond to hormones with improved plant survival during stress conditions. Apart from participation in specific stresses, AP2/ERFs are involved in a wide range of stress tolerance, enabling them to form an interconnected stress regulatory network. Additionally, many AP2/ERFs respond to the plant hormones abscisic acid (ABA) and ethylene (ET) to help activate ABA and ET dependent and independent stress-responsive genes. While some AP2/ERFs are implicated in growth and developmental processes mediated by gibberellins (GAs), cytokinins (CTK), and brassinosteroids (BRs). The involvement of AP2/ERFs in hormone signaling adds the complexity of stress regulatory network. In this review, we summarize recent studies on AP2/ERF transcription factors in hormonal and abiotic stress responses with an emphasis on selected family members in Arabidopsis. In addition, we leverage publically available Arabidopsis gene networks and transcriptome data to investigate AP2/ERF regulatory networks, providing context and important clues about the roles of diverse AP2/ERFs in controlling hormone and stress responses.

A gene-stacking approach to overcome the trade-off between drought stress tolerance and growth in Arabidopsis

The molecular breeding of drought stress-tolerant crops is imperative for stable food and biomass production. However, a trade-off exists between plant growth and drought stress tolerance. Many drought stress-tolerant plants overexpressing stress-inducible genes, such as DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 1A (DREB1A), show severe growth retardation. Here, we demonstrate that the growth of DREB1A-overexpressing Arabidopsis plants could be improved by co-expressing growth-enhancing genes whose expression is repressed under drought stress conditions. We used Arabidopsis GA REQUIRING 5 (GA5), which encodes a rate-limiting gibberellin biosynthetic enzyme, and PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), which encodes a transcription factor regulating cell growth in response to light and temperature, for growth improvement. We observed an enhanced biomass and floral induction in the GA5 DREB1A and PIF4 DREB1A double overexpressors compared with those in the DREB1A overexpressors. Although the GA5 DREB1A double overexpressors continued to show high levels of drought stress tolerance, the PIF4 DREB1A double overexpressors showed lower levels of stress tolerance than the DREB1A overexpressors due to repressed expression of DREB1A. A multiomics analysis of the GA5 DREB1A double overexpressors showed that the co-expression of GA5 and DREB1A additively affected primary metabolism, gene expression and plant hormone profiles in the plants. These multidirectional analyses indicate that the inherent trade-off between growth and drought stress tolerance in plants can be overcome by appropriate gene-stacking approaches. Our study provides a basis for using genetic modification to improve the growth of drought stress-tolerant plants for the stable production of food and biomass.

Cold Influences Male Reproductive Development in Plants: A Hazard to Fertility, but a Window for Evolution

Being sessile organisms, plants suffer from various abiotic stresses including low temperature. In particular, male reproductive development of plants is extremely sensitive to cold which may dramatically reduce viable pollen shed and plant fertility. Cold stress disrupts stamen development and prominently interferes with the tapetum, with the stress-responsive hormones ABA and gibberellic acid being greatly involved. In particular, low temperature stress delays and/or inhibits programmed cell death of the tapetal cells which consequently damages pollen development and causes male sterility. On the other hand, studies in Arabidopsis and crops have revealed that ectopically decreased temperature has an impact on recombination and cytokinesis during meiotic cell division, implying a putative role for temperature in manipulating plant genomic diversity and architecture during the evolution of plants. Here, we review the current understanding of the physiological impact of cold stress on the main male reproductive development processes including tapetum development, male meiosis and gametogenesis. Moreover, we provide insights into the genetic factors and signaling pathways that are involved, with putative mechanisms being discussed.

BYPASS1-LIKE, A DUF793 Family Protein, Participates in Freezing Tolerance via the CBF Pathway in Arabidopsis

The C-REPEAT BINDING FACTOR signaling pathway is strictly modulated by numerous factors and is essential in the cold response of plants. Here, we show that the DUF793 family gene BYPASS1-LIKE modulates freezing tolerance through the CBFs in Arabidopsis. The expression of B1L was rapidly induced under cold treatment. Comparing to wild type, B1L knockout mutants were more sensitive to freezing treatment, whereas B1L-overexpressing lines were more tolerant. The expression of CBFs and CBF target genes was significantly decreased in b1l mutant. Using yeast two-hybrid screening system, 14-3-3λ was identified as one of proteins interacting with B1L. The interaction was confirmed with bimolecular fluorescence complementation assay and co-immunoprecipitation assay. Biochemical assays revealed that b1l mutation promoted the degradation of CBF3 compared to wild type, whereas 14-3-3κλ mutant and b1l 14-3-3κλ mutant suppressed the degradation of CBF3. Consistently, 14-3-3κλ and b1l 14-3-3κλ mutants showed enhanced freezing tolerance compared to wild type. These results indicate that B1L enhances the freezing tolerance of plants, at least partly through stabilizing CBF. Our findings improve our understanding of the regulation of CBF in response to cold stress.

Changes in apoplastic peroxidase activity and cell wall composition are associated with cold-induced morpho-anatomical plasticity of wheat leaves

Temperate grasses, such as wheat, become compact plants with small thick leaves after exposure to low temperature. These responses are associated with cold hardiness, but their underlying mechanisms remain largely unknown. Here we analyse the effects of low temperature on leaf morpho-anatomical structure, cell wall composition and activity of extracellular peroxidases, which play key roles in cell elongation and cell wall thickening, in two wheat cultivars with contrasting cold-hardening ability. A combined microscopy and biochemical approach was applied to study actively growing leaves of winter (ProINTA-Pincén) and spring (Buck-Patacón) wheat developed under constant warm (25 °C) or cool (5 °C) temperature. Cold-grown plants had shorter leaves but longer inter-stomatal epidermal cells than warm-grown plants. They had thicker walls in metaxylem vessels and mestome sheath cells, paralleled with accumulation of wall components, predominantly hemicellulose. These effects were more pronounced in the winter cultivar (Pincén). Cold also induced a sharp decrease in apoplastic peroxidase activity within the leaf elongating zone of Pincén, and a three-fold increase in the distal mature zone of the leaf. This was consistent with the enhanced cell length and thicker cell walls in this cultivar at 5 °C. The different response to low temperature of apoplastic peroxidase activity and hemicellulose between leaf zones and cultivar types suggests they might play a central role in the development of cold-induced compact morphology and cold hardening. New insights are presented on the potential temperature-driven role of peroxidases and hemicellulose in cell wall dynamics of grasses.

Differential gene expression in non-transgenic and transgenic "M.26" apple overexpressing a peach CBF gene during the transition from eco-dormancy to bud break

The CBF signal pathway is responsible for a significant portion of plant responses to low temperature and freezing. Overexpression of CBF genes in model organisms such as Arabidopsis thaliana enhances abiotic stress tolerance but also reduces growth. In addition to these effects, overexpression of the peach (Prunus persica [L.] Batsch) CBF1 gene in transgenic apple (Malus x domestica Borkh.) line T166 also results in early entry into and late exit from dormancy. Although the regulation of dormancy-induction and dormancy-release occur while the CBF regulon is operative in perennial, woody plants, how overexpression of CBF1 affects these dormancy-related changes in gene expression is incompletely understood. The objective of the present study was to characterize global changes in gene expression in peach CBF1-overexpressing and non-transformed apple bark tissues at different states of dormancy via RNA-seq. RNA-seq bioinformatics data was confirmed by RT-qPCR on a number of genes. Results indicate that the greatest number of significantly differentially expressed genes (DEGs) occurred in April when dormancy release and bud break normally occur but are delayed in Line T166. Genes involved in storage and inactivation of auxin, GA, and cytokinin were generally upregulated in T166 in April, while those for biosynthesis, uptake or signal transduction were generally downregulated in T166. Genes for cell division and cambial growth were also downregulated in T166 relative to the non-transformed line. These data suggest that overexpression of the peach CBF1 gene impacts growth hormone homeostasis and as a result the activation of growth in the spring, and most likely growth cessation in the fall as well.

CBF-dependent and CBF-independent regulatory pathways contribute to the differences in freezing tolerance and cold-regulated gene expression of two Arabidopsis ecotypes locally adapted to sites in Sweden and Italy

Arabidopsis thaliana (Arabidopsis) increases in freezing tolerance in response to low nonfreezing temperatures, a phenomenon known as cold acclimation. The CBF regulatory pathway, which contributes to cold acclimation, includes three genes—CBF1, CBF2 and CBF3—encoding closely-related transcription factors that regulate the expression of more than 100 genes—the CBF regulon—that impart freezing tolerance. Here we compare the CBF pathways of two Arabidopsis ecotypes collected from sites in Sweden (SW) and Italy (IT). Previous studies showed that the SW ecotype was more freezing tolerant than the IT ecotype and that the IT ecotype had a nonfunctional CBF2 gene. Here we present results establishing that the difference in CBF2 alleles contributes to the difference in freezing tolerance between the two ecotypes. However, other differences in the CBF pathway as well as CBF-independent pathways contribute the large majority of the difference in freezing tolerance between the two ecotypes. The results also provided evidence that most cold-induced CBF regulon genes in both the SW and IT ecotypes are coregulated by CBF-independent pathways. Additional analysis comparing our results with those published by others examining the Col-0 accession resulted in the identification of 44 CBF regulon genes that were conserved among the three accessions suggesting that they likely have important functions in life at low temperature. The comparison further supported the conclusion that the CBF pathway can account for a large portion of the increase in freezing tolerance that occurs with cold acclimation in a given accession, but that CBF-independent pathways can also make a major contribution.

Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction

The thickening of plant organs is supported by secondary growth, a process by which new vascular tissues (xylem and phloem) are produced. Xylem is composed of several cell types, including xylary fibers, parenchyma and vessel elements. In Arabidopsis, it has been shown that fibers are promoted by the class-I KNOX gene KNAT1 and the plant hormones gibberellins, and are repressed by a small set of receptor-like kinases; however, we lack a mechanistic framework to integrate their relative contributions. Here, we show that DELLAs, negative elements of the gibberellin signaling pathway, physically interact with KNAT1 and impair its binding to KNAT1-binding sites. Our analysis also indicates that at least 37% of the transcriptome mobilized by KNAT1 is potentially dependent on this interaction, and includes genes involved in secondary cell wall modifications and phenylpropanoid biosynthesis. Moreover, the promotion by constitutive overexpression of KNAT1 of fiber formation and the expression of genes required for fiber differentiation were still reverted by DELLA accumulation, in agreement with post-translational regulation of KNAT1 by DELLA proteins. These results suggest that gibberellins enhance fiber development by promoting KNAT1 activity.

Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice

Weedy rice is an important germplasm resource for rice improvement because it has useful genes for many abiotic stresses including cold tolerance. We identified the cold tolerance and cold sensitivity of two weedy rice lines (WR 03-35 and WR 03-26) and two cultivated rice lines (Kongyu 131 and 9311). During the seedling stage of these lines, we used RNA-seq to measure changes in weedy rice and cultivated rice whole-genome transcriptome before and after cold treatment. We identified 14,213 and 14,730 differentially expressed genes (DEGs) in cold-tolerant genotypes (WR 03-35, Kongyu 131), and 9219 and 720 DEGs were observed in two cold-sensitive genotypes (WR 03-26, 9311). Many common and special DEGs were analyzed in cold-tolerant and cold-sensitive genotypes, respectively. Some typical genes related to cold stress such as the basic helix-loop-helix (bHLH) gene and leucine-rich repeat (LRR) domain gene etc. The number of these DEGs in cold-tolerant genotypes is more than those found in cold-sensitive genotypes. The gene ontology (GO) enrichment analyses showed significantly enriched terms for biological processes, cellular components and molecular functions. In addition, some genes related to several plant hormones such as abscisic acid (ABA), gibberellic acid (GA), auxin and ethylene were identified. To confirm the RNA-seq data, semi-quantitative RT-PCR and qRT-PCR were performed on 12 randomly selected DEGs. The expression patterns of RNA-seq on these genes corresponded with the semi-quantitative RT-PCR and qRT-PCR method. This study suggests the gene resources related to cold stress from weedy rice could be valuable for understanding the mechanisms involved in cold stress and rice breeding for improving cold tolerance.

SUMO Suppresses the Activity of the Jasmonic Acid Receptor CORONATINE INSENSITIVE1

Plants respond rapidly to sudden environmental cues, often responding prior to changes in the hormone levels that coordinate these responses. How this is achieved is not fully understood. The integrative role of the phytohormone jasmonic acid (JA) relies upon the plant's ability to control the levels of JASMONATE ZIM (JAZ) domain-containing repressor proteins. Here, we demonstrate that regardless of intrinsic JA levels, Small Ubiquitin-like Modifier (SUMO)-conjugated JAZ proteins inhibit the JA receptor CORONATINE INSENSITIVE1 (COI1) from mediating non-SUMOylated JAZ degradation. The SUMO-deconjugating proteases OVERLY TOLERANT TO SALT1 (OTS1) and OTS2 regulate JAZ protein SUMOylation and stability. The ots1 ots2 double mutants accumulate SUMOylated and non-SUMOylated JAZ repressor proteins but show no change in endogenous JA levels compared with wild-type plants. SUMO1-conjugated JAZ proteins bind to COI1 independently of the JA mimic coronatine. SUMO inhibits JAZ binding to COI1. We identify the SUMO interacting motif in COI1 and demonstrate that this is vital to SUMO-dependent inhibition of COI1. Necrotroph infection of Arabidopsis thaliana promotes SUMO protease degradation, and this increases JAZ SUMOylation and abundance, which in turn inhibits JA signaling. This study reveals a mechanism for rapidly regulating JA responses, allowing plants to adapt to environmental changes.

Exogenously applied spermidine alleviates photosynthetic inhibition under drought stress in maize (Zea mays L.) seedlings associated with changes in endogenous polyamines and phytohormones

Drought stress (DS) is a major environmental factor limiting plant growth and crop productivity worldwide. It has been established that exogenous spermidine (Spd) stimulates plant tolerance to DS. The effects of exogenous Spd on plant growth, photosynthetic performance, and chloroplast ultrastructure as well as changes in endogenous polyamines (PAs) and phytohormones were investigate in DS-resistant (Xianyu 335) and DS-sensitive (Fenghe 1) maize seedlings under well-watered and DS treatments. Exogenous Spd alleviated the stress-induced reduction in growth, photosynthetic pigment content, photosynthesis rate (P_n) and photochemical quenching (q_P) parameters, including the maximum photochemistry efficiency of photosystem II (PSII) (F_v/F_m), PSII operating efficiency (ФPSII), and qP coefficient. Exogenous Spd further enhanced stress-induced elevation in non-photochemical quenching (NPQ) and the de-epoxidation state of the xanthophyll cycle (DEPS). Microscopic analysis revealed that seedlings displayed a more ordered arrangement of chloroplast ultrastructure upon Spd application during DS. Exogenous Spd increased the endogenous PA concentrations in the stressed plants. Additionally, exogenous Spd increased indoleacetic acid (IAA), zeatin riboside (ZR) and gibberellin A₃ (GA₃) and decreased salicylic acid (SA) and jasmonate (JA) concentrations under DS. These results indicate that exogenous Spd can alleviate the growth inhibition and damage to the structure and function of the photosynthetic apparatus caused by DS and that this alleviation may be associated with changes in endogenous PAs and phytohormones. This study contributes to advances in the knowledge of Spd-induced drought tolerance.

Populus trichocarpa PtNF-YA9, A Multifunctional Transcription Factor, Regulates Seed Germination, Abiotic Stress, Plant Growth and Development in Arabidopsis

NF-YAs play important roles in abiotic stress. However, their characteristics and functions in abiotic stress of poplar, a model woody plant, have not been fully investigated. Here, the biological functions of PtNF-YA9 (Potri.011G101000), an NF-YA gene from Populus trichocarpa, were first fully investigated. PtNF-YA9 is located in the nucleus. The expression of PtNF-YA9 was reduced by mannitol, NaCl, and abscisic acid (ABA). The GUS staining of ProNF-YA9::GUS transgenic lines was also reduced by mannitol treatments. In the PtNF-YA9-overexpressed Arabidopsis (OxPtNA9), OxPtNA9 lines exhibited sensitivity to simulated drought, ABA, and salinity stress during germination stage, and growth arrest emerged at post-germination stage. These phenomena might involve the ABA signaling pathway via the regulation of ABI3, ABI4, and ABI5. At vegetative stages, OxPtNA9 lines decreased in water loss via promoting stomatal closure and displayed high instantaneous water-use efficiency (WUE) of the leaf to exhibit enhanced drought tolerance. Furthermore, OxPtNA9 lines exhibited long primary root in the half-strength Murashige-Skoog agar medium supplemented with NaCl and conferred strong tolerance in the soil under salt stress. Additionally, PtNF-YA9 exhibited dwarf phenotype, short hypocotyl, small leaf area and biomass, delayed flowering, and increased chlorophyll content. Above all, our research proposes a model in which PtNF-YA9 not only plays a key role in reducing plant growth but also can play a primary role in the mechanism of an acclimatization strategy in response to adverse environmental conditions.

Molecular Regulation of CBF Signaling in Cold Acclimation

Cold stress restricts plant growth, development, and distribution. Understanding how plants transduce and respond to cold signals has long been a topic of interest. Traditional genetic and molecular analyses have identified C-repeat/DREB binding factors (CBFs) as key transcription factors that function in cold acclimation. Recent studies revealed the involvement of pivotal protein kinases and transcription factors in CBF-dependent signaling, expanding our knowledge of cold signal transduction from perception to downstream gene expression events. In this review, we summarize recent advances in our understanding of the molecular regulation of these core components of the CBF cold signaling pathway. Knowledge of the mechanism underlying the ability of plants to survive freezing temperatures will facilitate the development of crop plants with increased freezing tolerance.

Global insights of protein responses to cold stress in plants: Signaling, defence, and degradation

Cold stress (CS) as one of the unfavorable abiotic tensions proceeds different aspects of plant responses. These responses are generated through CS effects on crucial processes such as photosynthesis, energy metabolism, ROS homeostasis, membrane fluidity and cell wall architecture. As a tolerance response, plants apply proteins in various strategies such as transferring the message of cold entrance named as signaling, producing defensive and protective molecules against the stress and degrading some unfavorable or unnecessary proteins to produce other required ones. A change in one part of these networks can irritate alternations in others. These strategies as acclimation mechanisms are conducted through gene expression reprogramming to provide a new adjusted metabolic homeostasis dependent on the stress severity and duration and plant species. Investigating protein alterations in metabolic pathways and their role in adjusting cellular components from upstream to downstream levels can provide a profound knowledge of plants tolerance mechanism against the damaging effects of CS. In this review, we summarized the activity of some cold-responsive proteins from the perception phase to tolerance response against CS.

Differential physiological and metabolic response to low temperature in two zoysiagrass genotypes native to high and low latitude

Low temperature is one of the important limiting factors for growing season and geographical distribution of plants. Zoysiagrass (Zoysia Willd) is one of the widely used warm-season turfgrass that is distribute in many parts of the world. Zoysaigrass native to high latitude may have evolved higher cold tolerance than the ones native to low latitude. The objective of this study was to investigate the cold stress response in zoysiagrass native to diverse latitude at phenotypic, physiological and metabolic levels. Two zoysiagrass (Z. japonica) genotypes, Latitude-40 (higher latitude) and Latitude-22 (lower latitude) were subjected to four temperature treatments (optimum, 30/25°C, day/night; suboptimum, 18/12°C; chilling, 8/2°C; freezing, 2/-4°C) progressively in growth chambers. Low temperature (chilling and freezing) increased leaf electrolyte leakage (EL) and reduced plant growth, turf quality, chlorophyll (Chl) content, photochemical efficiency (Fv/Fm) and photosynthesis (P_n, net photosynthetic rate; g_s, stomatal conductance; intercellular CO₂; T_r, transpiration rate) in two genotypes, with more rapid changes in Latitude-22. Leaf carbohydrates content (glucose, fructose, sucrose, trehalose, fructan, starch) increased with the decreasing of temperature, to a great extend in Latitude-40. Leaf abscisic acid (ABA), salicylic acid (SA) and jasmonic acid (JA) content increased, while indole-3-acetic acid (IAA), gibberellic acid (GA₃) and trans-zeatin ribside (t-ZR) content decreased with the reduction of temperature, with higher content in Latitude-40 than in Latitude-22. Chilling and freezing induced the up-regulation of C-repeat binding factor (ZjCBF), late embryogenesis abundant (ZjLEA3) and dehydration-responsive element binding (ZjDREB1) transcription factors in two genotypes, whereas those genes exhibited higher expression levels in Latitude-40, particularly under freezing temperature. These results suggested that zoysiagrass native to higher latitude exhibited higher freezing tolerance may attribute to the higher carbohydrates serving as energy reserves and stress protectants that stabilize cellular membranes. The phytohormones may serve signals in regulating plant growth, development and adaptation to low temperature as well as inducing the up-regulated ZjCBF, ZjLEA3 and ZjDREB1 expressions thus result in a higher cold tolerance.

To defend or to grow: lessons from Arabidopsis C24

The emergence of Arabidopsis as a model species and the availability of genetic and genomic resources have resulted in the identification and detailed characterization of abiotic stress signalling pathways. However, this has led only to limited success in engineering abiotic stress tolerance in crops. This is because there needs to be a deeper understanding of how to combine resistances to a range of stresses with growth and productivity. The natural variation and genomic resources of Arabidopsis thaliana (Arabidopsis) are a great asset to understand the mechanisms of multiple stress tolerances. One natural variant in Arabidopsis is the accession C24, and here we provide an overview of the increasing research interest in this accession. C24 is highlighted as a source of tolerance for multiple abiotic and biotic stresses, and a key accession to understand the basis of basal immunity to infection, high water use efficiency, and water productivity. Multiple biochemical, physiological, and phenological mechanisms have been attributed to these traits in C24, and none of them constrains productivity. Based on the uniqueness of C24, we postulate that the use of variation derived from natural selection in undomesticated species provides opportunities to better understand how complex environmental stress tolerances and resource use efficiency are co-ordinated.

Ectopic expression of StCBF1and ScCBF1 have different functions in response to freezing and drought stresses in Arabidopsis

Solanum tuberosum potato species constitute the bulk of economically and agronomically important potato production. However, S. tuberosum is a drought- and frost-sensitive species that is incapable of acclimating to the cold. Solanum commersonii is a tuber-bearing wild potato species that exhibits greater frost and drought resistance than S. tuberosum. CBF/DREB (C-REPET BINDING FACTOR/DROUGHT RESPONSE ELEMENT BINGING FACTOR) transcription factors play important roles in response to a variety of abiotic stresses, such as cold, drought and salt stresses. To explore different functions between S. tuberosum CBF1 (StCBF1) and S. commersonii CBF1 (ScCBF1), Arabidopsis was transformed with the ScCBF1 and StCBF1 genes driven by a constitutive CaMV35S promoter. Our results reveal that the ScCBF1 transgenic lines are much more tolerant to freezing and drought than the StCBF1 transgenic lines. The development of transgenic plants was altered, resulting in dwarf phenotype with delayed flowering and thicker and additional rosette leaves. The expression levels of several COR (COLD-RESPONSIVE) genes and development-related genes, including genes that inhibited plant growth (GA2ox7, RGL3) and delayed flowering (FLC) were higher in transgenic plants. These results suggest that these two potato CBF1 play important roles in the plant response to abiotic stress and can influence plant growth and development, and ScCBF1 plays a more pronounced function than StCBF1.

Rice tocopherol deficiency 1 encodes a homogentisate phytyltransferase essential for tocopherol biosynthesis and plant development in rice

RTD1 encodes a homogentisate phytyltransferase catalyzing a key step in rice tocopherol biosynthesis, confers cold tolerance and regulates rice development by affecting the accumulation of DELLA protein SLENDER RICE1. Tocopherols are one of the most important lipid-soluble antioxidants having indispensable roles in living organisms. The physiological functions of tocopherols have been comprehensively characterized in animals and artificial membranes. However, genetic and molecular functions of tocopherols in plants are less understood. This study aimed to isolate a tocopherol-deficient mutant rtd1 in rice. The rtd1 mutant showed overall growth retardation throughout the growth period. Most of the agronomic traits were impaired in rtd1. Map-based cloning revealed that the RTD1 gene encoded a homogentisate phytyltransferase, a key enzyme catalyzing the committed step in tocopherol biosynthesis. RTD1 was preferentially expressed in green leafy tissues, and the protein was located in chloroplasts. Cold tolerance was found to be reduced in rtd1. The cold-related C-repeat-binding factor (CBF)/dehydration-responsive element-binding protein 1 (DREB1) genes were significantly upregulated in rtd1 under natural growth conditions. Moreover, rtd1 exhibited a reduced response to gibberellin (GA).The transcript and protein levels of DELLA protein-coding gene SLENDER RICE 1 (SLR1) in rice was increased in rtd1. However, the GA content was not changed, suggesting a transcriptional, not posttranslational, regulation of SLR1. These findings implied that tocopherols play important roles in regulating rice growth and development.

An Overview of the Genetics of Plant Response to Salt Stress: Present Status and the Way Forward

Salinity is one of the major threats faced by the modern agriculture today. It causes multidimensional effects on plants. These effects depend upon the plant growth stage, intensity, and duration of the stress. All these lead to stunted growth and reduced yield, ultimately inducing economic loss to the farming community in particular and to the country in general. The soil conditions of agricultural land are deteriorating at an alarming rate. Plants assess the stress conditions, transmit the specific stress signals, and then initiate the response against that stress. A more complete understanding of plant response mechanisms and their practical incorporation in crop improvement is an essential step towards achieving the goal of sustainable agricultural development. Literature survey shows that investigations of plant stresses response mechanism are the focus area of research for plant scientists. Although these efforts lead to reveal different plant response mechanisms against salt stress, yet many questions still need to be answered to get a clear picture of plant strategy to cope with salt stress. Moreover, these studies have indicated the presence of a complicated network of different integrated pathways. In order to work in a progressive way, a review of current knowledge is critical. Therefore, this review aims to provide an overview of our understanding of plant response to salt stress and to indicate some important yet unexplored dynamics to improve our knowledge that could ultimately lead towards crop improvement.

Transcriptome Profiles Reveal the Crucial Roles of Hormone and Sugar in the Bud Dormancy of Prunus mume

Bud dormancy transition is a vital developmental process for perennial plant survival. The process is precisely regulated by diverse endogenous genetic factors and environmental cues, but the mechanisms are not yet fully understood. Prunus mume is an ideal crop for bud dormancy analysis because of its early spring-flowering characteristics and small sequenced genome. Here, we analyzed the transcriptome profiles at the three endodormancy stages and natural flush stage using RNA sequencing combined with phytohormone and sugar content measurements. Significant alterations in hormone contents and carbohydrate metabolism have been observed, and α-amylases, Glucan Hydrolase Family 17 and diphosphate-glycosyltransferase family might play crucial roles in the interactions between hormones and sugars. The following hypothetical model for understanding the molecular mechanism of bud dormancy in Prunus mume is proposed: low temperatures exposure induces the significant up-regulation of eight C-repeat binding factor genes, which directly promotes all six dormancy-associated MADS-box genes, resulting in dormancy establishment. The prolonged cold and/or subsequently increasing temperature then decreases the expression levels of these two gene families, which alleviates the inhibition of FLOWERING LOCUS T and reopens the growth-promoting pathway, resulting in dormancy release and the initiation of the bud break process.

Deep sequencing-based characterization of transcriptome of Pyrus ussuriensis in response to cold stress

Pyrus ussuriensis is extremely cold hardy when fully acclimated, but knowledge relevant to the molecular mechanisms underlying this economically valuable trait is still limited so far. In this study, global transcriptome profiles of Pyrus ussuriensis under cold conditions (4 °C) over a time course were generated by high-throughput sequencing. In total, >57,121,199 high quality clean reads were obtained with approximately 11.0 M raw data for each library. Among them, the values of 66.84%-72.03% of clean reads in the digital transcript abundance measurement could be well mapped to the pear genome database, resulting in the identification of 8544 differentially expressed genes (DEGs) having 43 Gene Ontology (GO) terms and 17 clusters of orthologous groups (COG) involved in 385 Kyoto Encyclopedia of Genes and Genomes (KEGG) defined pathways. These comprised 3124 (1033 up-regulated, 2091 down-regulated), 1243 (729 up-regulated, 514 down-regulated), and 750 (458 up-regulated, 292 down-regulated) genes from the cold-treated samples at 5, 12 and 24 h, respectively. The accuracy of the RNA-Seq derived transcript expression data was validated by analyzing the expression patterns of 16 DGEs by quantitative real-time PCR. Plant-pathogen interaction, plant hormone signal transduction, Photosynthesis, signal transduction, innate immune response and response to biotic stimulus were the most significantly enriched GO categories among in the DEGs. A total of 335 transcription factors were shown to be cold responsive. In addition, a number of genes involved in the catabolism and signaling of hormones were significantly affected by the cold stress. The RNA-Seq and digital expression profiling provides valuable insights into the understanding the molecular events related to cold responses in Pyrus ussuriensis and dataset may help guide future identification and functional analysis of potential genes that are important for enhancing cold hardiness.

Genome-wide identification and expression analysis of GRAS family transcription factors in tea plant (Camellia sinensis)

GRAS proteins are important transcription factors that play multifarious roles in regulating the growth and development as well as stress responses of plants. Tea plant is an economically important leaf -type beverage crop. Information concerning GRAS family transcription factors in tea plant is insufficient. In this study, 52 CsGRAS genes encoding GRAS proteins were identified from tea plant genome database. Phylogenetic analysis of the identified GRAS proteins from tea plant, Arabidopsis, and rice divided these proteins into at least 13 subgroups. Conserved motif analysis revealed that the gene structure and motif compositions of the proteins were considerably conserved among the same subgroup. Functional divergence analysis indicated that the shifted evolutionary rate might act as a major evolutionary force driving subfamily-specific functional diversification. Transcriptome analysis showed that the transcriptional levels of CsGRAS genes under non-stress conditions varied among different tea plant cultivars. qRT-PCR analysis revealed tissue and development stage-specific expression patterns of CsGRAS genes in tea plant. The expression patterns of CsGRAS genes in response to abiotic stresses and gibberellin treatment suggested the possible multiple functions of these genes. This study provides insights into the potential functions of GRAS genes.

Identification and functional analysis of cassava DELLA proteins in plant disease resistance against cassava bacterial blight

Gibberellin (GA) is an essential plant hormone in plant growth and development as well as various stress responses. DELLA proteins are important repressors of GA signal pathway. GA and DELLA have been extensively investigated in several model plants. However, the in vivo roles of GA and DELLA in cassava, one of the most important crops and energy crops in the tropical area, are unknown. In this study, systematic genome-wide analysis identified 4 MeDELLAs in cassava, as evidenced by the evolutionary tree, gene structures and motifs analyses. Gene expression analysis found that 4 MeDELLAs were commonly regulated by flg22 and Xanthomonas axonopodis pv manihotis (Xam). Through overexpression in Nicotiana benthamiana, we found that 4 MeDELLAs conferred improved disease resistance against cassava bacterial blight. Through virus-induced gene silencing (VIGS) in cassava, we found that MeDELLA-silenced plants exhibited decreased disease resistance, with less callose deposition and lower transcript levels of defense-related genes. This is the first study identifying MeDELLAs as positive regulators of disease resistance against cassava bacterial blight.

Transcriptomic Insights into Phenological Development and Cold Tolerance of Wheat Grown in the Field

Cold acclimation and winter survival in cereal species is determined by complicated environmentally regulated gene expression. However, studies investigating these complex cold responses are mostly conducted in controlled environments that only consider the responses to single environmental variables. In this study, we have comprehensively profiled global transcriptional responses in crowns of field-grown spring and winter wheat (Triticum aestivum) genotypes and their near-isogenic lines with the VRN-A1 alleles swapped. This in-depth analysis revealed multiple signaling, interactive pathways that influence cold tolerance and phenological development to optimize plant growth and development in preparation for a wide range of over-winter stresses. Investigation of genetic differences at the VRN-A1 locus revealed that a vernalization requirement maintained a higher level of cold response pathways while VRN-A1 genetically promoted floral development. Our results also demonstrated the influence of genetic background on the expression of cold and flowering pathways. The link between delayed shoot apex development and the induction of cold tolerance was reflected by the gradual up-regulation of abscisic acid-dependent and C-REPEAT-BINDING FACTOR pathways. This was accompanied by the down-regulation of key genes involved in meristem development as the autumn progressed. The chromosome location of differentially expressed genes between the winter and spring wheat genetic backgrounds showed a striking pattern of biased gene expression on chromosomes 6A and 6D, indicating a transcriptional regulation at the genome level. This finding adds to the complexity of the genetic cascades and gene interactions that determine the evolutionary patterns of both phenological development and cold tolerance traits in wheat.

Transcriptomic changes in Cucurbita pepo fruit after cold storage: differential response between two cultivars contrasting in chilling sensitivity

Background

Zucchini fruit is susceptible to chilling injury (CI), but the response to low storage temperature is cultivar dependent. Previous reports about the response of zucchini fruit to chilling storage have been focused on the physiology and biochemistry of this process, with little information about the molecular mechanisms underlying it. In this work, we present a comprehensive analysis of transcriptomic changes that take place after cold storage in zucchini fruit of two commercial cultivars with contrasting response to chilling stress.

Results

RNA-Seq analysis was conducted in exocarp of fruit at harvest and after 14 days of storage at 4 and 20 °C. Differential expressed genes (DEGs) were obtained comparing fruit stored at 4 °C with their control at 20 °C, and then specific and common up and down-regulated DEGs of each cultivar were identified. Functional analysis of these DEGs identified similarities between the response of zucchini fruit to low temperature and other stresses, with an important number of GO terms related to biotic and abiotic stresses overrepresented in both cultivars. This study also revealed several molecular mechanisms that could be related to chilling tolerance, since they were up-regulated in cv. Natura (CI tolerant) or down-regulated in cv. Sinatra (CI sensitive). These mechanisms were mainly those related to carbohydrate and energy metabolism, transcription, signal transduction, and protein transport and degradation. Among DEGs belonging to these pathways, we selected candidate genes that could regulate or promote chilling tolerance in zucchini fruit including the transcription factors MYB76-like, ZAT10-like, DELLA protein GAIP, and AP2/ERF domain-containing protein.

Conclusions

This study provides a broader understanding of the important mechanisms and processes related to coping with low temperature stress in zucchini fruit and allowed the identification of some candidate genes that may be involved in the acquisition of chilling tolerance in this crop. These genes will be the basis of future studies aimed to identify markers involved in cold tolerance and aid in zucchini breeding programs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4500-9) contains supplementary material, which is available to authorized users.

NAC transcription factor JUNGBRUNNEN1 enhances drought tolerance in tomato

Water deficit (drought stress) massively restricts plant growth and the yield of crops; reducing the deleterious effects of drought is therefore of high agricultural relevance. Drought triggers diverse cellular processes including the inhibition of photosynthesis, the accumulation of cell-damaging reactive oxygen species and gene expression reprogramming, besides others. Transcription factors (TF) are central regulators of transcriptional reprogramming and expression of many TF genes is affected by drought, including members of the NAC family. Here, we identify the NAC factor JUNGBRUNNEN1 (JUB1) as a regulator of drought tolerance in tomato (Solanum lycopersicum). Expression of tomato JUB1 (SlJUB1) is enhanced by various abiotic stresses, including drought. Inhibiting SlJUB1 by virus-induced gene silencing drastically lowers drought tolerance concomitant with an increase in ion leakage, an elevation of hydrogen peroxide (H₂ O₂ ) levels and a decrease in the expression of various drought-responsive genes. In contrast, overexpression of AtJUB1 from Arabidopsis thaliana increases drought tolerance in tomato, alongside with a higher relative leaf water content during drought and reduced H₂ O₂ levels. AtJUB1 was previously shown to stimulate expression of DREB2A, a TF involved in drought responses, and of the DELLA genes GAI and RGL1. We show here that SlJUB1 similarly controls the expression of the tomato orthologs SlDREB1, SlDREB2 and SlDELLA. Furthermore, AtJUB1 directly binds to the promoters of SlDREB1, SlDREB2 and SlDELLA in tomato. Our study highlights JUB1 as a transcriptional regulator of drought tolerance and suggests considerable conservation of the abiotic stress-related gene regulatory networks controlled by this NAC factor between Arabidopsis and tomato.

Constitutive gibberellin response in grafted tomato modulates root-to-shoot signaling under drought stress

Plants are sessile organisms that must perceive and respond to various environmental constraints throughout their life cycle. Among these constraints, drought stress has become the main limiting factor to crop production around the world. Water deprivation is perceived primarily by the roots, which efficiently signal the shoot to trigger drought responses in order to maximize a plant's ability to survive. In this study, the tomato (Solanum lycopersicum L.) mutant procera (pro), with a constitutive response to gibberellin (GA), and its near isogenic line cv. Micro-Tom (MT), were used in reciprocal grafting under well-watered and water stress conditions to evaluate the role of GA signaling in root-to-shoot communication during drought stress. Growth, oxidative stress, gene expression, water relations and hormonal content were measured in order to provide insights into GA-mediated adjustments to water stress. All graft combinations with pro (i.e. pro/pro, MT/pro and pro/MT) prevented the reduction of growth under stress conditions without a reduction in oxidative stress. The increase of oxidative stress was followed by upregulation of SlDREB2, a drought-tolerance related gene, in all drought-stressed plants. Scions harboring the pro mutation tended to increase the abscisic acid (ABA) content, independent of the rootstock. Moreover, the GA sensitivity of the rootstock modulated stomatal conductance and water use efficiency under drought stress, indicating GA and ABA crosstalk in the adjustment of growth and water economy.

Crosstalk of PmCBFs and PmDAMs Based on the Changes of Phytohormones under Seasonal Cold Stress in the Stem of Prunus mume

Plants facing the seasonal variations always need a growth restraining mechanism when temperatures turn down. C-repeat binding factor (CBF) genes work essentially in the cold perception. Despite lots of researches on CBFs, the multiple crosstalk is still interesting on their interaction with hormones and dormancy-associated MADS (DAM) genes in the growth and dormancy control. Therefore, this study highlights roles of PmCBFs in cold-induced dormancy from different orgens. And a sense-response relationship between PmCBFs and PmDAMs is exhibited in this process, jointly regulated by six PmCBFs and PmDAM4-6. Meantime, GA3 and ABA showed negative and positive correlation with PmCBFs expression levels, respectively. We also find a high correlation between IAA and PmDAM1-3. Finally, we display the interaction mode of PmCBFs and PmDAMs, especially PmCBF1-PmDAM1. These results can disclose another view of molecular mechanism in plant growth between cold-response pathway and dormancy regulation together with genes and hormones.

MLK1 and MLK2 Coordinate RGA and CCA1 Activity to Regulate Hypocotyl Elongation in Arabidopsis thaliana

Gibberellins (GAs) modulate diverse developmental processes throughout the plant life cycle. However, the interaction between GAs and the circadian rhythm remains unclear. Here, we report that MUT9p-LIKE KINASE1 (MLK1) and MLK2 mediate the interaction between GAs and the circadian clock to regulate hypocotyl elongation in Arabidopsis thaliana DELLA proteins function as master growth repressors that integrate phytohormone signaling and environmental pathways in plant development. MLK1 and MLK2 interact with the DELLA protein REPRESSOR OF ga1-3 (RGA). Loss of MLK1 and MLK2 function results in plants with short hypocotyls and hyposensitivity to GAs. MLK1/2 and RGA directly interact with CIRCADIAN CLOCK ASSOCIATED1 (CCA1), which targets the promoter of DWARF4 (DWF4) to regulate its roles in cell expansion. MLK1/2 antagonize the ability of RGA to bind CCA1, and these factors coordinately regulate the expression of DWF4 RGA suppressed the ability of CCA1 to activate expression from the DWF4 promoter, but MLK1/2 reversed this suppression. Genetically, MLK1/2 act in the same pathway as RGA and CCA1 in hypocotyl elongation. Together, our results provide insight into the mechanism by which MLK1 and MLK2 antagonize the function of RGA in hypocotyl elongation and suggest that MLK1/2 coordinately mediate the regulation of plant development by GAs and the circadian rhythm in Arabidopsis.