A Novel NAC Transcription Factor, PbeNAC1, of Pyrus betulifolia Confers Cold and Drought Tolerance via Interacting with PbeDREBs and Activating the Expression of Stress-Responsive Genes

Functional characterization of VrNAC15 for drought resistance in mung beans

Drought stress has become an important limiting factor in mung bean production, and NAC(NAM/ATAF/CUC) transcription factors are crucial for plant growth under stress conditions, so it is important to study the regulatory role of NAC transcription factors in mung bean under drought stress. In this investigation, VrNAC15, along with its promoter, was cloned, and its structure was meticulously analyzed. Using qPCR, we examined the tissue-specific expression patterns of VrNAC15, particularly under drought stress and ABA exposure. Additionally, We performed ectopic expression of VrNAC15 in Arabidopsis to assess its function.. Gene sequence analysis revealed that VrNAC15 has a total length of 1014 bp, encoding 337 amino acids. It contains a NAM domain, localizes within the nucleus, and exhibits transcriptional activation. Promoter analysis of VrNAC15 identified essential core promoter elements and cis-acting elements related to abscisic acid, methyl jasmonate, gibberellin, adversity stress, light, and metabolism. Expression analysis demonstrated the concentration of VrNAC15 in leaves, with significant alterations following ABA and drought treatments in mung beans. Cluster analysis revealed that VrNAC15 may enhanced drought tolerance in transgenic plants through its expression. Transgenic experiments supported these findings, showing that heterologous expression of VrNAC15 led to enhanced antioxidant and osmotic adjustment capabilities in Arabidopsis plants. This resulted in the maintenance of cell membrane structural integrity during drought stress and normal physiological and biochemical metabolic reactions within cells. This research provides valuable insights into the structural and functional characteristics of the VrNAC15, setting the stage for future endeavors in molecular breeding for improved drought resistance in mung beans.

Discovery of candidate genes involved in ethylene biosynthesis and signal transduction pathways related to peach bud cold resistance

Background: Low temperature pose significant challenges to peach cultivation, causing severe damage to peach buds and restricting production and distribution. Ethylene, an important phytohormone, plays a critical role in enhancing plant cold resistance. Structural genes and transcription factors involved in ethylene biosynthesis and signal transduction pathways are associated with cold resistance. However, no research has specifically addressed their roles in peach cold resistance. Methods: In this study, we aimed for cold-resistance gene discovery in cold-sensitive peach cultivar "21Shiji" (21SJ) and cold-resistance cultivar "Shijizhixing" (SJZX) using RNA-seq and gas chromatography. Results: The findings revealed that under cold stress conditions, ethylene biosynthesis in "SJZX" was significantly induced. Subsequently, a structural gene, PpACO1-1, involved in ethylene biosynthesis in peach buds was significantly upregulated and showed a higher correlation with ethylene release rate. To identify potential transcription factors associated with PpACO1-1 expression and ethylene signal transduction, weighted gene co-expression network analysis was conducted using RNA-seq data. Four transcription factors: PpERF2, PpNAC078, PpWRKY65 and PpbHLH112, were identified. Conclusion: These findings provide valuable theoretical insights for investigating the regulatory mechanisms of peach cold resistance and guiding breeding strategies.

Common Bean (Phaseolus vulgaris L.) NAC Transcriptional Factor PvNAC52 Enhances Transgenic Arabidopsis Resistance to Salt, Alkali, Osmotic, and ABA Stress by Upregulating Stress-Responsive Genes

The NAC family of transcription factors includes no apical meristem (NAM), Arabidopsis thaliana transcription activator 1/2 (ATAF1/2), and cup-shaped cotyledon (CUC2) proteins, which are unique to plants, contributing significantly to their adaptation to environmental challenges. In the present study, we observed that the PvNAC52 protein is predominantly expressed in the cell membrane, cytoplasm, and nucleus. Overexpression of PvNAC52 in Arabidopsis strengthened plant resilience to salt, alkali, osmotic, and ABA stresses. PvNAC52 significantly (p < 0.05) reduced the degree of oxidative damage to cell membranes, proline content, and plant water loss by increasing the expression of MSD1, FSD1, CSD1, POD, PRX69, CAT, and P5CS2. Moreover, the expression of genes associated with abiotic stress responses, such as SOS1, P5S1, RD29A, NCED3, ABIs, LEAs, and DREBs, was enhanced by PvNAC52 overexpression. A yeast one-hybrid assay showed that PvNAC52 specifically binds to the cis-acting elements ABRE (abscisic acid-responsive elements, ACGTG) within the promoter. This further suggests that PvNAC52 is responsible for the transcriptional modulation of abiotic stress response genes by identifying the core sequence, ACGTG. These findings provide a theoretical foundation for the further analysis of the targeted cis-acting elements and genes downstream of PvNAC52 in the common bean.

The WRKY17-WRKY50 complex modulates anthocyanin biosynthesis to improve drought tolerance in apple

Drought stress is increasing worldwide due to global warming, which severely reduces apple (Malus domestica) yield. Clarifying the basis of drought tolerance in apple could accelerate the molecular breeding of drought-tolerant cultivars to maintain apple production. We identified a transcription factor MdWRKY50 by yeast two-hybrid (Y2H) assays as an interactor of the drought-tolerant protein MdWRKY17, and confirmed their interaction by bimolecular fluorescence complementation (BiFC) and pull-down assays. MdWRKY50 was induced by drought and when overexpressed in apple, conferred transgenic apple plants enhanced drought tolerance by directly binding to the promoter of anthocyanin synthetic gene Chalcone synthase (MdCHS) to upregulate its expression for higher anthocyanin. Increased anthocyanin relieves apple plants from oxidative damage under drought stress. MdWRKY50 RNA-interference transgenic apple plants showed opposite phenotypes. The dimerization of MdWRKY50 with mutated MdWRKY17DP mimicking drought-induced phosphorylation by the mitogen-activated protein kinase kinase 2 (MEK2)-MPK6 cascade, compared with MdWRKY17AP and MdWRKY17, further promoted anthocyanin biosynthesis, suggesting dimerization with MdWRKY17 makes MdWRKY50 more powerful in promoting anthocyanin biosynthesis under drought stress. Taken together, we isolated an entire MEK2-MAPK6-MdWRKY17-MdWRKY50-MdCHS pathway for drought tolerance and generated transgenic apple germplasm with enhanced drought tolerance and higher anthocyanin levels.

LiNAC100 contributes to linalool biosynthesis by directly regulating LiLiS in Lilium 'Siberia'

MAIN CONCLUSION

The transcription factor LiNAC100 has a novel function of regulating floral fragrance by directly regulating linalool synthase gene LiLiS. Lilium 'Siberia', an Oriental hybrid, is renowned as both a cut flower and garden plant, prized for its color and fragrance. The fragrance comprises volatile organic compounds (VOCs), primarily monoterpenes found in the plant. While the primary terpene synthases in Lilium 'Siberia' were identified, the transcriptional regulation of these terpene synthase (TPS) genes remains unclear. Thus, understanding the regulatory mechanisms of monoterpene biosynthesis is crucial for breeding flower fragrance, thereby improving ornamental and commercial values. In this study, we isolated a nuclear-localized LiNAC100 transcription factor from Lilium 'Siberia'. The virus-induced gene silencing (VIGS) of LiNAC100 was found to down-regulate the expression of linalool synthase gene (LiLiS) and significantly inhibit linalool synthesis. Conversely, transient overexpression of LiNAC100 produced opposite effects. Additionally, yeast one-hybrid and dual-luciferase assays confirmed that LiNAC100 directly activates LiLiS expression. Our findings reveal that LiNAC100 plays a key role in monoterpene biosynthesis in Lilium 'Siberia', promoting linalool synthesis through the activation of LiLiS expression. These results offer insights into the molecular mechanisms of terpene biosynthesis in Lilium 'Siberia' and open avenues for biotechnological enhancement of floral scent.

Banana MaNAC1 activates secondary cell wall cellulose biosynthesis to enhance chilling resistance in fruit

Chilling injury has a negative impact on the quantity and quality of crops, especially subtropical and tropical plants. The plant cell wall is not only the main source of biomass production, but also the first barrier to various stresses. Therefore, improving the understanding of the alterations in cell wall architecture is of great significance for both biomass production and stress adaptation. Herein, we demonstrated that the cell wall principal component cellulose accumulated during chilling stress, which was caused by the activation of MaCESA proteins. The sequence-multiple comparisons show that a cold-inducible NAC transcriptional factor MaNAC1, a homologue of Secondary Wall NAC transcription factors, has high sequence similarity with Arabidopsis SND3. An increase in cell wall thickness and cellulosic glucan content was observed in MaNAC1-overexpressing Arabidopsis lines, indicating that MaNAC1 participates in cellulose biosynthesis. Over-expression of MaNAC1 in Arabidopsis mutant snd3 restored the defective secondary growth of thinner cell walls and increased cellulosic glucan content. Furthermore, the activation of MaCESA7 and MaCESA6B cellulose biosynthesis genes can be directly induced by MaNAC1 through binding to SNBE motifs within their promoters, leading to enhanced cellulose content during low-temperature stress. Ultimately, tomato fruit showed greater cold resistance in MaNAC1 overexpression lines with thickened cell walls and increased cellulosic glucan content. Our findings revealed that MaNAC1 performs a vital role as a positive modulator in modulating cell wall cellulose metabolism within banana fruit under chilling stress.

NACs, generalist in plant life

Plant-specific NAC proteins constitute a major transcription factor family that is well-known for its roles in plant growth, development, and responses to abiotic and biotic stresses. In recent years, there has been significant progress in understanding the functions of NAC proteins. NAC proteins have a highly conserved DNA-binding domain; however, their functions are diverse. Previous understanding of the structure of NAC transcription factors can be used as the basis for their functional diversity. NAC transcription factors consist of a target-binding domain at the N-terminus and a highly versatile C-terminal domain that interacts with other proteins. A growing body of research on NAC transcription factors helps us comprehend the intricate signalling network and transcriptional reprogramming facilitated by NAC-mediated complexes. However, most studies of NAC proteins have been limited to a single function. Here, we discuss the upstream regulators, regulatory components and targets of NAC in the context of their prospective roles in plant improvement strategies via biotechnology intervention, highlighting the importance of the NAC transcription factor family in plants and the need for further research.

Genome-Wide Identification and Characterization of the NAC Gene Family and Its Involvement in Cold Response in Dendrobium officinale

The NAC (NAM, ATAF1/2 and CUC2) gene family is one of the largest plant-specific transcription factor families, functioning as crucial regulators in diverse biological processes such as plant growth and development as well as biotic and abiotic stress responses. Although it has been widely characterized in many plants, the significance of the NAC family in Dendrobium officinale remained elusive up to now. In this study, a genome-wide search method was conducted to identify NAC genes in Dendrobium officinale (DoNACs) and a total of 110 putative DoNACs were obtained. Phylogenetic analysis classified them into 15 subfamilies according to the nomenclature in Arabidopsis and rice. The members in the subfamilies shared more similar gene structures and conversed protein domain compositions. Furthermore, the expression profiles of these DoNACs were investigated in diverse tissues and under cold stress by RNA-seq data. Then, a total of five up-regulated and five down-regulated, cold-responsive DoNACs were validated through QRT-PCR analysis, demonstrating they were involved in regulating cold stress response. Additionally, the subcellular localization of two down-regulated candidates (DoNAC39 and DoNAC58) was demonstrated to be localized in the nuclei. This study reported the genomic organization, protein domain compositions and expression patterns of the NAC family in Dendrobium officinale, which provided targets for further functional studies of DoNACs and also contributed to the dissection of the role of NAC in regulating cold tolerance in Dendrobium officinale.

The Transcription Factor ZmNAC89 Gene Is Involved in Salt Tolerance in Maize (Zea mays L.)

The NAC gene family has transcription factors specific to plants, which are involved in development and stress response and adaptation. In this study, ZmNAC89, an NAC gene in maize that plays a role in saline-alkaline tolerance, was isolated and characterized. ZmNAC89 was localized in the nucleus and had transcriptional activation activity during in vitro experiments. The expression of ZmNAC89 was strongly upregulated under saline-alkaline, drought and ABA treatments. Overexpression of the ZmNAC89 gene in transgenic Arabidopsis and maize enhanced salt tolerance at the seedling stage. Differentially expressed genes (DEGs) were then confirmed via RNA-sequencing analysis with the transgenic maize line. GO analyses showed that oxidation-reduction process-regulated genes were involved in ZmNAC89-mediated salt-alkaline stress. ZmNAC89 may regulate maize saline-alkali tolerance through the REDOX pathway and ABA signal transduction pathway. From 140 inbred maize lines, 20 haplotypes and 16 SNPs were found in the coding region of the ZmNAC89 gene, including the excellent haplotype HAP20. These results contribute to a better understanding of the response mechanism of maize to salt-alkali stress and marker-assisted selection during maize breeding.

MdNAC104 positively regulates apple cold tolerance via CBF-dependent and CBF-independent pathways

Low temperature is the main environmental factor affecting the yield, quality and geographical distribution of crops, which significantly restricts development of the fruit industry. The NAC (NAM, ATAF1/2 and CUC2) transcription factor (TF) family is involved in regulating plant cold tolerance, but the mechanisms underlying these regulatory processes remain unclear. Here, the NAC TF MdNAC104 played a positive role in modulating apple cold tolerance. Under cold stress, MdNAC104-overexpressing transgenic plants exhibited less ion leakage and lower ROS (reactive oxygen species) accumulation, but higher contents of osmoregulatory substances and activities of antioxidant enzymes. Transcriptional regulation analysis showed that MdNAC104 directly bound to the MdCBF1 and MdCBF3 promoters to promote expression. In addition, based on combined transcriptomic and metabolomic analyses, as well as promoter binding and transcriptional regulation analyses, we found that MdNAC104 stimulated the accumulation of anthocyanin under cold conditions by upregulating the expression of anthocyanin synthesis-related genes, including MdCHS-b, MdCHI-a, MdF3H-a and MdANS-b, and increased the activities of the antioxidant enzymes by promoting the expression of the antioxidant enzyme-encoding genes MdFSD2 and MdPRXR1.1. In conclusion, this study revealed the MdNAC104 regulatory mechanism of cold tolerance in apple via CBF-dependent and CBF-independent pathways.

The NAC transcription factor MdNAC29 negatively regulates drought tolerance in apple

Drought stress is an adverse stimulus that affects agricultural production worldwide. NAC transcription factors are involved in plant development and growth but also play different roles in the abiotic stress response. Here, we isolated the apple MdNAC29 gene and investigated its role in regulating drought tolerance. Subcellular localization experiments showed that MdNAC29 was localized to the nucleus and transcription was induced by the PEG treatment. Over-expression of MdNAC29 reduced drought tolerance in apple plants, calli, and tobacco, and exhibited higher relative conductivity, malondialdehyde (MDA) content, and lower chlorophyll content under drought stress. The transcriptomic analyses revealed that MdNAC29 reduced drought resistance by modulating the expression of photosynthesis and leaf senescence-related genes. The qRT-PCR results showed that overexpression of MdNAC29 repressed the expression of drought-resistance genes. Yeast one-hybrid and dual-luciferase assays demonstrated that MdNAC29 directly repressed MdDREB2A expression. Moreover, the yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that MdNAC29 interacted with the MdPP2-B10 (F-box protein), which responded to drought stress, and MdPP2-B10 enhanced the repressive effect of MdNAC29 on the transcriptional activity of the MdDREB2A. Taken together, our results indicate that MdNAC29 is a negative regulator of drought resistance, and provide a theoretical basis for further molecular mechanism research.

The transcription factor VaNAC72-regulated expression of the VaCP17 gene from Chinese wild Vitis amurensis enhances cold tolerance in transgenic grape (V. vinifera)

Papain-like cysteine proteases (PLCP) play diverse roles in plant biology. In our previous studies, a VaCP17 gene from the cold-tolerant Vitis amurensis accession 'Shuangyou' was isolated and its role in cold tolerance was preliminarily verified in Arabidopsis. Here, we confirmed the function of VaCP17 in cold tolerance by stably overexpressing VaCP17 in the cold-sensitive Vitis vinifera cultivar 'Thompson Seedless' and transiently silencing VaCP17 in 'Shuangyou' leaves. The results showed that overexpression of VaCP17 improved the cold tolerance in 'Thompson Seedless' as manifested by reduced electrolyte leakage and malondialdehyde accumulation, chlorophyll homeostasis, increased antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) activitiy, and rapid up-regulation of stress-related genes (VvKIN2, VvRD29B, and VvNCED1) compared with wild-type line. Conversely, RNA interfere-mediated knockdown of VaCP17 in 'Shuangyou' leaves resulted in opposite physiological and biochemical responses and exacerbated leaves wilting compared with control. Subsequently, by yeast one-hybrid, dual-luciferase assays, and transient overexpression of VaNAC72 in 'Shuangyou' leaves, a VaCP17-interacting protein VaNAC72 was confirmed to promote the expression of VaCP17 under cold stress, which depends on abscisic acid, methyl jasmonate, and salicylic acid signaling. By yeast two-hybrids, bimolecular fluorescence complementation and luciferase complementation assays, it was found that VaNAC72 could form homodimers or heterodimers with VaCBF2. Furthermore, co-expression analysis confirmed that VaNAC72 works synergistically with VaCBF2 or VaCP17 to up-regulate the expression of VaCP17. In conclusion, the study revealed that the VaNAC72-VaCP17 module positively regulated cold tolerance in grapevine, and this knowledge is useful for further revealing the cold-tolerance mechanism of V. amurensis and grape molecular breeding.

Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus

The AP2/ERF transcription factor family is one of the most important gene families in plants and plays a vital role in plant abiotic stress responses. Although Erianthus fulvus is very important in the genetic improvement of sugarcane, there are few studies concerning AP2/ERF genes in E. fulvus. Here, we identified 145 AP2/ERF genes in the E. fulvus genome. Phylogenetic analysis classified them into five subfamilies. Evolutionary analysis showed that tandem and segmental duplication contributed to the expansion of the EfAP2/ERF family. Protein interaction analysis showed that twenty-eight EfAP2/ERF proteins and five other proteins had potential interaction relationships. Multiple cis-acting elements present in the EfAP2/ERF promoter were related to abiotic stress response, suggesting that EfAP2/ERF may contribute to adaptation to environmental changes. Transcriptomic and RT-qPCR analyses revealed that EfDREB10, EfDREB11, EfDREB39, EfDREB42, EfDREB44, EfERF43, and EfAP2-13 responded to cold stress, EfDREB5 and EfDREB42 responded to drought stress, and EfDREB5, EfDREB11, EfDREB39, EfERF43, and EfAP2-13 responded to ABA treatment. These results will be helpful for better understanding the molecular features and biological role of the E. fulvus AP2/ERF genes and lay a foundation for further research on the function of EfAP2/ERF genes and the regulatory mechanism of the abiotic stress response.

Characterization of the NAC Transcription Factor in Passion Fruit (Passiflora edulis) and Functional Identification of PeNAC-19 in Cold Stress

The NAC (NAM, ATAF and CUC) gene family plays an important role in plant development and abiotic stress response. However, up to now, the identification and research of the NAC (PeNAC) family members of passion fruit are still lacking. In this study, 25 PeNACs were identified from the passion fruit genome, and their functions under abiotic stress and at different fruit-ripening stages were analyzed. Furthermore, we analyzed the transcriptome sequencing results of PeNACs under four various abiotic stresses (drought, salt, cold and high temperature) and three different fruit-ripening stages, and verified the expression results of some genes by qRT-PCR. Additionally, tissue-specific analysis showed that most PeNACs were mainly expressed in flowers. In particular, PeNAC-19 was induced by four various abiotic stresses. At present, low temperatures have seriously endangered the development of passion fruit cultivation. Therefore, PeNAC-19 was transformed into tobacco, yeast and Arabidopsis to study their function of resisting low temperature. The results show that PeNAC-19 responded to cold stress significantly in tobacco and Arabidopsis, and could improve the low temperature tolerance of yeast. This study not only improved the understanding of the PeNAC gene family characteristics and evolution, but also provided new insights into the regulation of the PeNAC gene at different stages of fruit maturation and abiotic stresses.

Transcriptomic and metabolomic insights on the molecular mechanisms of flower buds in responses to cold stress in two Camellia oleifera cultivars

INTRODUCTION

The Camellia oleifera (C. oleifera) cultivars 'Huashuo' (HS) and 'Huaxin' (HX) are new high-yielding and economically valuable cultivars that frequently encounter prolonged cold weather during the flowering period, resulting in decreased yields and quality. The flower buds of HS sometimes fail to open or open incompletely under cold stress, whereas the flower buds of HX exhibit delayed opening but the flowers and fruits rarely drop.

METHODS

In this study, flower buds at the same development stage of two C. oleifera cultivars were used as test materials for a combination of physiological, transcriptomic and metabolomic analyses, to unravel the different cold regulatory mechanisms between two cultivars of C. oleifera.

RESULTS AND DISCUSSION

Key differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) involved in sugar metabolism, phenylpropanoid biosynthesis, and hormone signal transduction were significantly higher in HX than in HS, which is consistent with phenotypic observations from a previous study. The results indicate that the flower buds of HX are less affected by long-term cold stress than those of HS, and that cold resistance in C. oleifera cultivars varies among tissues or organs.This study will provide a basis for molecular markers and molecular breeding of C. oleifera.

Comparative analysis of the potential physiological and molecular mechanisms involved in the response to root zone hypoxia in two rootstock seedlings of the Chinese bayberry via transcriptomic analysis

The negative effects of waterlogging can be effectively improved through the use of waterlogging-resistant rootstocks. However, the underlying physiological and molecular mechanisms of Chinese bayberry (Morella rubra) rootstock tolerance to waterlogging have not yet been investigated. This study aims to unravel the molecular regulation mechanisms underlying waterlogging-tolerant rootstocks. Two rootstocks, Morella cerifera (tolerant) and Morella rubra (sensitive), were selected for root zone hypoxia treatments, assessments of hormone levels and antioxidant enzyme activity, and transcriptomic analysis. While the contents of abscisic acid (ABA) and brassinosteroid (BR) in the roots of M. rubra decreased significantly after root zone hypoxia treatment, there were no significant changes in M. cerifera. Both the superoxide dismutase (SOD) activity and malondialdehyde (MDA) content increased in M. cerifera but were decreased in M. rubra. Transcriptome sequencing identified 1,925 (928 up- and 997 downregulated) and 733 (278 up- and 455 downregulated) differentially expressed genes (DEGs) in the two rootstocks. The gene set enrichment analysis showed that 84 gene sets were enriched after root zone hypoxia treatment, including 57 (35 up- and 22 downregulated) and 14 (five up- and nine downregulated) gene sets derived from M. cerifera and M. rubra, respectively, while the remaining 13 gene sets were shared. KEGG pathway analysis showed specific enrichment in six pathways in M. cerifera, including the mitogen-activated protein kinase (MAPK), tyrosine metabolism, glycolysis/gluconeogenesis, ribosome, cyanoamino acid metabolism, and plant-pathogen interaction pathways. Overall, these results provide preliminary insights into the molecular mechanisms of Chinese bayberry tolerance to waterlogging.

Comprehensive analysis of the NAC transcription factor gene family in Kandelia obovata reveals potential members related to chilling tolerance

BACKGROUND

Kandelia obovata is an important mangrove species extensively distributed in Eastern Asia that is susceptible to low-temperature stress. NAC (NAM, ATAF1/2 and CUC2) domain proteins are transcription factors (TFs) that play various roles in plant growth and development and in the plant response to environmental stresses. Nevertheless, genome-wide analyses of K. obovata NAC genes (KoNACs) and their responses to chilling stress have rarely been studied.

METHODS

The KoNAC gene family was identified and characterized using bioinformatic analysis, the subcellular location of some NAC proteins was confirmed using confocal microscopy analysis, and the KoNACs that responded to chilling stress were screened using RNA-seq and qRT-PCR analysis.

RESULTS

A total of 79 KoNACs were identified, and they were unequally distributed across all 18 chromosomes of K. obovata. The KoNAC proteins could be divided into 16 subgroups according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana. The KoNACs exhibited greater synteny with A. thaliana sequences than with Oryza sativa sequences, indicating that KoNACs underwent extensive evolution after the divergence of dicotyledons and monocotyledons. Segmental duplication was the main driving force of the expansions of KoNAC genes. Confocal microscopy analysis verified that the four randomly selected KoNACs localized to the nucleus, indicating the accuracy of the bioinformatic predictions. Tissue expression pattern analysis demonstrated that some KoNAC genes showed tissue-specific expression, suggesting that these KoNACs might be important for plant development and growth. Additionally, the expression levels of 19 KoNACs were significantly (15 positively and 4 negatively) induced by cold treatment, demonstrating that these KoNACs might play important roles during cold stress responses and might be candidate genes for the genetic engineering of K. obovata with enhanced chilling stress tolerance. Coexpression network analysis revealed that 381 coexpressed pairs (between 13 KoNACs and 284 other genes) were significantly correlated.

CONCLUSIONS

Seventy-nine KoNACs were identified in K. obovata, nineteen of which displayed chilling-induced expression patterns. These genes may serve as candidates for functional analyses of KoNACs engaged in chilling stress. Our results lay the foundation for evolutionary analyses of KoNACs and their molecular mechanisms in response to environmental stress.

Bolstered plant tolerance to low temperatures by overexpressing NAC transcription factors: identification of critical variables by meta-analysis

The potential biotechnological application of NAC overexpression has been challenged by meta-analysis, establishing a correlation between the magnitudes of several physiological and biochemical parameters and the enhanced tolerance to cold. Overexpression of various NAC (NAM/ATAF/CUC) transcription factors in different plant systems was shown to confer enhanced tolerance to low temperatures by inducing both common and distinctive stress response pathways. However, lack of consensus on the type of parameters evaluated, their magnitudes, and direction of the responses complicates drawing general conclusions on the effects of NAC expression in plant physiology. We report herein a meta-analysis summarizing the most critical response variables used to study the effect of overexpressing NAC regulators on cold stress tolerance. We found that NAC overexpression affected all of the outcome parameters in stressed plants, and one response in control conditions. Transformed plants displayed an increase of at least 40% in positive responses, while negative outcomes were reduced by at least 30%. The most reported parameters included survival, electrolyte leakage, and malondialdehyde contents, whereas the most sensitive to the treatments were the F_v/F_m parameter, survival, and the activity of catalases. We also explored how different experimental arrangements affected the magnitudes of the responses. NAC-mediated improvements were best observed after severe stress episodes and during brief treatments (ranging from 5 to 24 h), especially in terms of antioxidant activities, accumulation of free proline, and parameters related to membrane integrity. Use of heterologous expression also favored several indicators of plant fitness. Our findings should help both basic and applied research on the influence of NAC expression on enhanced tolerance to cold.

miR164g-MsNAC022 acts as a novel module mediating drought response by transcriptional regulation of reactive oxygen species scavenging systems in apple

Under drought stress, reactive oxygen species (ROS) overaccumulate as a secondary stress that impairs plant performance and thus severely reduces crop yields. The mitigation of ROS levels under drought stress is therefore crucial for drought tolerance. MicroRNAs (miRNAs) are critical regulators of plant development and stress responses. However, the complex molecular regulatory mechanism by which they function during drought stress, especially in drought-triggered ROS scavenging, is not fully understood. Here, we report a newly identified drought-responsive miRNA, miR164g, in the wild apple species Malus sieversii and elucidate its role in apple drought tolerance. Our results showed that expression of miR164g is significantly inhibited under drought stress and it can specifically cleave transcripts of the transcription factor MsNAC022 in M. sieversii. The heterologous accumulation of miR164g in Arabidopsis thaliana results in enhanced sensitivity to drought stress, while overexpression of MsNAC022 in Arabidopsis and the cultivated apple line 'GL-3' (Malus domestica Borkh.) lead to enhanced tolerance to drought stress by raising the ROS scavenging enzymes activity and related genes expression levels, particularly PEROXIDASE (MsPOD). Furthermore, we showed that expression of MsPOD is activated by MsNAC022 in transient assays. Interestingly, Part1 (P1) region is the key region for the positive regulation of MsPOD promoter by MsNAC022, and the different POD expression patterns in M. sieversii and M. domestica is attributed to the specific fragments inserted in P1 region of M. sieversii. Our findings reveal the function of the miR164g-MsNAC022 module in mediating the drought response of M. sieversii and lay a foundation for breeding drought-tolerant apple cultivars.

Characterization of NAC transcription factor NtNAC028 as a regulator of leaf senescence and stress responses

NAC proteins constitute one of the largest transcription factor families and are involved in regulation of plant development and stress responses. Our previous transcriptome analyses of tobacco revealed a significant increase in the expression of NtNAC028 during leaf yellowing. In this study, we found that NtNAC028 was rapidly upregulated in response to high salinity, dehydration, and abscisic acid (ABA) stresses, suggesting a vital role of this gene in abiotic stress response. NtNAC028 loss-of-function tobacco plants generated via CRISPR-Cas9 showed delayed leaf senescence and increased tolerance to drought and salt stresses. Meanwhile NtNAC028 overexpression led to precocious leaf senescence and hypersensitivity to abiotic stresses in Arabidopsis, indicating that NtNAC028 functions as a positive regulator of natural leaf senescence and a negative regulator of stress tolerance. Furthermore, NtNAC028-overexpressing Arabidopsis plants showed lower antioxidant enzyme activities, higher reactive oxygen species (ROS), and H2O2 accumulation under high salinity, resulted in more severe oxidative damage after salt stress treatments. On the other hand, NtNAC028 mutation in tobacco resulted in upregulated expression of ROS-scavenging and abiotic stress-related genes, higher antioxidant enzyme activities, and enhanced tolerance against abiotic stresses, suggesting that NtNAC028 might act as a vital regulator for plant stress response likely by mediating ROS scavenging ability. Collectively, our results indicated that the NtNAC028 plays a key regulatory role in leaf senescence and response to multiple abiotic stresses.

Transcriptomic Analysis Reveals Potential Gene Regulatory Networks Under Cold Stress of Loquat (Eriobotrya japonica Lindl.)

Loquat (Eriobotrya japonica Lindl. ) is one of the most economically important evergreen fruit crops in China, while it often suffered the injury of cold stress in winter and earlier spring, and the annual yield loss of loquat fruits caused by cold or freezing stress was immeasurable. However, knowledge about the physiological response and molecular mechanism under cold stress is still limited. To investigate the potential regulation mechanism pre- and post-cold stress in loquat and the changes in physiological indicators, a comparative transcriptome analysis was performed against a cold-resistant cv. "Huoju" and a cold-sensitive cv. "Ninghaibai". The results of physiological indicators related to cold resistance indicated that rachis was most sensitive to cold stress and was considered as the representative organ to directly evaluate cold resistance of loquat based on subordinate function analysis. Here, we compared the transcriptome profiles of rachis pre- and under cold stress in "Huoju" and "Ninghaibai". A total of 4,347 and 3,513 differentially expressed genes (DEGs) were detected in "Ninghaibai" and "Huoju", among which 223 and 166 were newly identified genes, respectively, most of them were functionally enriched in plant hormone signal transduction (Huoju: 142; Ninghaibai: 200), and there were higher plant hormone content and related DEG expression levels in "Huoju" than that of "Ninghaibai". Moreover, a total of 3,309 differentially expressed transcription factors (DETFs) were identified, and some DEGs and DETFs were screened to be subjected to co-expression network analysis based on the gene expression profile data. Some candidate DEGs, including UDP-glycosyltransferase (UGT), glycosyltransferase (GT), sugar phosphate/phosphate translocator (SPT), sugar transport protein (STP), proline-rich receptor-like protein kinase (PERK), and peroxidise (POD), were significantly affected by cold stress, and the expression level of these genes obtained from real-time quantitative RT-PCR was consistent with the pattern of transcriptome profile, which suggested that these genes might play the vital roles in cold resistance of loquat. Our results provide an invaluable resource for the identification of specific genes and TFs and help to clarify gene transcription during the cold stress response of loquat.

Regulatory network established by transcription factors transmits drought stress signals in plant

Plants are sessile organisms that evolve with a flexible signal transduction system in order to rapidly respond to environmental changes. Drought, a common abiotic stress, affects multiple plant developmental processes especially growth. In response to drought stress, an intricate hierarchical regulatory network is established in plant to survive from the extreme environment. The transcriptional regulation carried out by transcription factors (TFs) is the most important step for the establishment of the network. In this review, we summarized almost all the TFs that have been reported to participate in drought tolerance (DT) in plant. Totally 466 TFs from 86 plant species that mostly belong to 11 families are collected here. This demonstrates that TFs in these 11 families are the main transcriptional regulators of plant DT. The regulatory network is built by direct protein-protein interaction or mutual regulation of TFs. TFs receive upstream signals possibly via post-transcriptional regulation and output signals to downstream targets via direct binding to their promoters to regulate gene expression.

Drought-Responsive NAC Transcription Factor RcNAC72 Is Recognized by RcABF4, Interacts with RcDREB2A to Enhance Drought Tolerance in Arabidopsis

RcNAC72, a key transcription factor that may respond to drought stress in Rosa chinensis 'Old Blush', was selected in our previous study. In the present study, we found that RcNAC72 is localized in the nucleus and is a transcriptional activator. RcNAC72 expression could be significantly induced by drought, low temperature, salt as well as abscisic acid (ABA) treatment. Analysis of the promoter revealed that multiple abiotic stress and hormone response elements were located in the promoter region. The promoter could respond to drought, low temperature, salt and ABA treatments to activate GUS gene expression. Overexpressing RcNAC72 in Arabidopsis thaliana enhanced sensitivity to ABA and tolerance to drought stress. Silencing of RcNAC72 by virus-induced gene silencing (VIGS) in rose leaves significantly reduced leaf water loss tolerance and leaf extension capacity. Physical interaction of RcNAC72 with RcDREB2A was shown by means of the yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. RcABF4 was demonstrated to be able to bind to the promoter of RcNAC72 by means of the yeast one-hybrid (Y1H) assay. These results provide new insights into the regulatory network of RcNAC72 response to drought stress in roses.

Pear genetics: Recent advances, new prospects, and a roadmap for the future

Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for "pear-omics".

AvNAC030, a NAC Domain Transcription Factor, Enhances Salt Stress Tolerance in Kiwifruit

Kiwifruit (Actinidia chinensis Planch) is suitable for neutral acid soil. However, soil salinization is increasing in kiwifruit production areas, which has adverse effects on the growth and development of plants, leading to declining yields and quality. Therefore, analyzing the salt tolerance regulation mechanism can provide a theoretical basis for the industrial application and germplasm improvement of kiwifruit. We identified 120 NAC members and divided them into 13 subfamilies according to phylogenetic analysis. Subsequently, we conducted a comprehensive and systematic analysis based on the conserved motifs, key amino acid residues in the NAC domain, expression patterns, and protein interaction network predictions and screened the candidate gene AvNAC030. In order to study its function, we adopted the method of heterologous expression in Arabidopsis. Compared with the control, the overexpression plants had higher osmotic adjustment ability and improved antioxidant defense mechanism. These results suggest that AvNAC030 plays a positive role in the salt tolerance regulation mechanism in kiwifruit.

Label-Free Quantitative Proteome Analysis Reveals the Underlying Mechanisms of Grain Nuclear Proteins Involved in Wheat Water-Deficit Response

In this study, we performed the first nuclear proteome analysis of wheat developing grains under water deficit by using a label-free based quantitative proteomic approach. In total, we identified 625 unique proteins as differentially accumulated proteins (DAPs), of which 398 DAPs were predicted to be localized in nucleus. Under water deficit, 146 DAPs were up-regulated and mainly involved in the stress response and oxidation-reduction process, while 252 were down-regulated and mainly participated in translation, the cellular amino metabolic process, and the oxidation-reduction process. The cis-acting elements analysis of the key nuclear DAPs encoding genes demonstrated that most of these genes contained the same cis-acting elements in the promoter region, mainly including ABRE involved in abscisic acid response, antioxidant response element, MYB responsive to drought regulation and MYC responsive to early drought. The cis-acting elements related to environmental stress and hormones response were relatively abundant. The transcription expression profiling of the nuclear up-regulated DAPs encoding genes under different organs, developmental stages and abiotic stresses was further detected by RNA-seq and Real-time quantitative polymerase chain reaction, and more than 50% of these genes showed consistency between transcription and translation expression. Finally, we proposed a putative synergistic responsive network of wheat nuclear proteome to water deficit, revealing the underlying mechanisms of wheat grain nuclear proteome in response to water deficit.

Regulon: An overview of plant abiotic stress transcriptional regulatory system and role in transgenic plants

Population growth is increasing rapidly around the world, in these consequences we need to produce more foods to full fill the demand of increased population. The world is facing global warming due to urbanizations and industrialization and in this concerns plants exposed continuously to abiotic stresses which is a major cause of crop hammering every year. Abiotic stresses consist of Drought, Salt, Heat, Cold, Oxidative and Metal toxicity which damage the crop yield continuously. Drought and salinity stress severally affected in similar manner to plant and the leading cause of reduction in crop yield. Plants respond to various stimuli under abiotic or biotic stress condition and express certain genes either structural or regulatory genes which maintain the plant integrity. The regulatory genes primarily the transcription factors that exert their activity by binding to certain cis DNA elements and consequently either up regulated or down regulate to target expression. These transcription factors are known as masters regulators because its single transcript regulate more than one gene, in this context the regulon word is fascinating more in compass of transcription factors. Progress has been made to better understand about effect of regulons (AREB/ABF, DREB, MYB, and NAC) under abiotic stresses and a number of regulons reported for stress responsive and used as a better transgenic tool of Arabidopsis and Rice.

AP2/ERF, an important cold stress-related transcription factor family in plants: A review

Increasing the vulnerability of plants especially crops to a wide range of cold stress reduces plant growth, development, yield production, and plant distribution. Cold stress induces physiological, morphological, biochemical, phenotypic, and molecular changes in plants. Transcription factor (TF) is one of the most important regulators that mediate gene expression. TF is activated by the signal transduction pathway, together with cis-acting element modulate the transcription of cold-responsive genes which contribute to increasing cold tolerance in plants. Here, AP2/ERF TF family is one of the most important cold stress-related TF families that along with other TF families, such as WRKY, bHLH, bZIP, MYB, NAC, and C2H2 interrelate to enhance cold stress tolerance. Over the past decade, significant progress has been found to solve the role of transcription factors (TFs) in improving cold tolerance in plants, such as omics analysis. Furthermore, numerous studies have identified and characterized the complexity of cold stress mechanisms among TFs or between TFs and other factors (endogenous and exogenous) including phytohormones, eugenol, and light. The role, function, and relationship among these TFs or between TFs and other factors to enhance cold tolerance still need to be clarified. Here, the current study analysed the role of AP2/ERF TF and the linkages among AP2/ERF with MYB, WRKY, bZIP, bHLH, C2H2, or NAC against cold stress tolerance.

Identification and functional characterization of Gh_D01G0514 (GhNAC072) transcription factor in response to drought stress tolerance in cotton

Cotton encounters long-term drought stress problems resulting in major yield losses. Transcription factors (TFs) plays an important role in response to biotic and abiotic stresses. The coexpression patterns of gene networks associated with drought stress tolerance were investigated using transcriptome profiles. Applying a weighted gene coexpression network analysis, we discovered a salmon module with 144 genes strongly linked to drought stress tolerance. Based on coexpression and RT-qPCR analysis GH_D01G0514 was selected as the candidate gene, as it was also identified as a hub gene in both roots and leaves with a consistent expression in response to drought stress in both tissues. For validation of GH_D01G0514, Virus Induced Gene Silencing was performed and VIGS plants showed significantly higher excised leaf water loss and ion leakage, while lower relative water and chlorophyll contents as compared to WT (Wild type) and positive control plants. Furthermore, the WT and positive control seedlings showed higher CAT and SOD activities, and lower activities of hydrogen peroxide and MDA enzymes as compared to the VIGS plants. Gh_D01G0514 (GhNAC072) was localized in the nucleus and cytoplasm. Y2H assay demonstrates that Gh_D01G0514 has a potential of auto activation. It was observed that the Gh_D01G0514 was highly upregulated in both tissues based on RNA Seq and RT-qPCR analysis. Thus, we inferred that, this candidate gene might be responsible for drought stress tolerance in cotton. This finding adds significantly to the existing knowledge of drought stress tolerance in cotton and deep molecular analysis are required to understand the molecular mechanisms underlying drought stress tolerance in cotton.

Plant Responses to Abiotic Stresses and Rhizobacterial Biostimulants: Metabolomics and Epigenetics Perspectives

In response to abiotic stresses, plants mount comprehensive stress-specific responses which mediate signal transduction cascades, transcription of relevant responsive genes and the accumulation of numerous different stress-specific transcripts and metabolites, as well as coordinated stress-specific biochemical and physiological readjustments. These natural mechanisms employed by plants are however not always sufficient to ensure plant survival under abiotic stress conditions. Biostimulants such as plant growth-promoting rhizobacteria (PGPR) formulation are emerging as novel strategies for improving crop quality, yield and resilience against adverse environmental conditions. However, to successfully formulate these microbial-based biostimulants and design efficient application programs, the understanding of molecular and physiological mechanisms that govern biostimulant-plant interactions is imperatively required. Systems biology approaches, such as metabolomics, can unravel insights on the complex network of plant-PGPR interactions allowing for the identification of molecular targets responsible for improved growth and crop quality. Thus, this review highlights the current models on plant defence responses to abiotic stresses, from perception to the activation of cellular and molecular events. It further highlights the current knowledge on the application of microbial biostimulants and the use of epigenetics and metabolomics approaches to elucidate mechanisms of action of microbial biostimulants.

The NAC-type transcription factor GmNAC20 improves cold, salinity tolerance, and lateral root formation in transgenic rice plants

NAC-type transcription factors are crucial players in the abiotic stress responses of plants. Soybean NAC-type transcription factor GmNAC20 was transformed into rice genome via Agrobacterium method of transformation to improve abiotic stress tolerance. Integration and expression of GmNAC20 were verified by the DNA blot hybridization, immunoblotting, RT-PCR, and quantitative RT-PCR in T3 generation of transgenic rice plants. Significant expression of GmNAC20 was found in transgenic plants under salinity, cold, and IAA treatments. The transgenic rice plants expressing GmNAC20 displayed enhanced salinity and cold stress tolerance via upregulating the abiotic stress-responsive genes. Furthermore, T3 transgenic plants retained relative water content, chlorophyll content with enhanced accumulation of proline content than wild-type plants under salinity, and cold stress environments. The decrease in MDA content and electrolyte leakage with a significant increase in antioxidant enzyme activities were noticed in transgenic rice plants under either salinity or cold stress conditions, compared to wild-type plants. Overexpression of GmNAC20 in rice plants also induced the lateral root formation, associated with upregulation of auxin signaling-related genes. Taken together, our results indicated that GmNAC20 acts as a positive regulator for conferring salinity and cold tolerance in rice plants and appropriate candidate for improving salinity and cold stress in other important food crops.

Overexpression of Cerasus humilis ChAOX2 improves the tolerance of Arabidopsis to salt stress

Alternative oxidase (AOX) has a well-established involvement in plant growth and stress tolerance in many studies. In this study, we isolated and characterized the AOX2 from Cerasus humilis. The ChAOX2 Open Reading Frame (ORF) contains 1029 nucleotides and encodes 342 amino acid residues. The inferred amino acid sequence of ChAOX2 shared the highest sequence similarity with a homolog from Prunus yedoensis. The ChAOX2 transcripts were relatively abundant in the old leaves and significantly up-regulated by salt stress. Subcellular localization analysis showed that ChAOX2 was located in the mitochondria. We transformed ChAOX2 into wild-type Arabidopsis thaliana and found that compared with wild-type and aox mutant lines, heterotopic expression of ChAOX2 increased proline content, and peroxidase and superoxide dismutase activities, while decreasing relative conductivity and the reactive oxygen species level. Further, the ratio of alternate respiration to the total respiration in plants that overexpressed ChAOX2 was significantly higher than that in wild-type and mutant plants under salt stress. These results indicate that ChAOX2 plays a key role in salt tolerance.

Intraspecific plasticity in hydraulic and stomatal regulation under drought is linked to aridity at the seed source in a wild pear species

Adaptations of fruit trees to future climate are a current research priority due to the rapid increase in air temperature and changes in precipitation patterns. This is aimed at securing sustainable food production for our growing populations. Key physiological traits in trees conferring drought tolerance are resistance to embolism and stomatal control over water loss. Recently, we have shown in the field that a native wild pear species performs better under drought than two cultivated pear species. A comparative greenhouse study was conducted to investigate traits associated with drought tolerance in four ecotypes of a wild pear species (Pyrus syriaca Boiss), compared with a wild pear species (Pyrus betulifolia Bunge) commonly used as a pear rootstock. Seed sources were collected from semi-arid, sub-humid and humid sites across northern Israel. Measurements of water relations, leaf physiology, hydraulic conductivity and percent loss of hydraulic conductivity (PLC) were conducted under standard irrigation, drought and recovery from drought. The four P. syriaca ecotypes maintained significantly higher leaf gas exchange values and water-use efficiency and had lower PLC than the rootstock species under prolonged drought as well as during recovery. Across the four ecotypes, stomatal closure occurred at stem water potential (Ψ) around -3.5 MPa; however, Ψ at 50% PLC ranged from -4.1 MPa in the humid ecotype to -5.2 MPa in one of the semi-arid ecotypes, rendering the latter with a higher hydraulic safety margin (the Ψ difference between stomatal closure and 50% PLC). Divergence of the ecotypes in xylem vulnerability to embolism closely matched the mean annual precipitation at their seed sources. Thus, selection of pear ecotypes from populations in semi-arid sites may be better than the currently used plant material for preparing our cultivated species for hotter and drier future climate.

The interplay between ABA/ethylene and NAC TFs in tomato fruit ripening: a review

This review contains functional roles of NAC transcription factors in the transcriptional regulation of ripening in tomato fruit, describes the interplay between ABA/ethylene and NAC TFs in tomato fruit ripening. Fruit ripening is regulated by a complex network of transcription factors (TFs) and genetic regulators in response to endogenous hormones and external signals. Studying the regulation of fruit ripening has important significance for controlling fruit quality, enhancing nutritional value, improving storage conditions and extending shelf-life. Plant-specific NAC (named after no apical meristem (NAM), Arabidopsis transcription activator factor 1/2 (ATAF1/2) and Cup-shaped cotyledon (CUC2)) TFs play essential roles in plant development, ripening and stress responses. In this review, we summarize the recent progress on the regulation of NAC TFs in fruit ripening, discuss the interactions between NAC and other factors in controlling fruit development and ripening, and emphasize how NAC TFs are involved in tomato fruit ripening through the ethylene and abscisic acid (ABA) pathways. The signaling network regulating ripening is complex, and both hormones and individual TFs can affect the status or activity of other network participants, which can alter the overall ripening network regulation, including response signals and fruit ripening. Our review helps in the systematic understanding of the regulation of NAC TFs involved in fruit ripening and provides a basis for the development or establishment of complex ripening regulatory network models.

Ectopic expression of GmHP08 enhances resistance of transgenic Arabidopsis toward drought stress

Ectopic expression of Glycine max two-component system member GmHP08 in Arabidopsis enhanced drought tolerance of transgenic plants, possibly via ABA-dependent pathways. Phosphorelay by two-component system (TCS) is a signal transduction mechanism which has been evolutionarily conserved in both prokaryotic and eukaryotic organisms. Previous studies have provided lines of evidence on the involvement of TCS genes in plant perception and responses to environmental stimuli. In this research, drought-associated functions of GmHP08, a TCS member from soybean (Glycine max L.), were investigated via its ectopic expression in Arabidopsis system. Results from the drought survival assay showed that GmHP08-transgenic plants exhibited higher survival rates compared with their wild-type (WT) counterparts, indicating better drought resistance of the former group. Analyses revealed that the transgenic plants outperformed the WT in various regards, i.e. capability of water retention, prevention of hydrogen peroxide accumulation and enhancement of antioxidant enzymatic activities under water-deficit conditions. Additionally, the expression of stress-marker genes, especially antioxidant enzyme-encoding genes, in the transgenic plants were found greater than that of the WT plants. In contrary, the expression of SAG13 gene, one of the senescence-associated genes, and of several abscisic acid (ABA)-related genes was repressed. Data from this study also revealed that the ectopic expression lines at germination and early seedling development stages were hypersensitive to exogenous ABA treatment. Taken together, our results demonstrated that GmHP08 could play an important role in mediating plant response to drought, possibly via an ABA-dependent manner.

Functional Characterization of PsnNAC036 under Salinity and High Temperature Stresses

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

GmNAC06, a NAC domain transcription factor enhances salt stress tolerance in soybean

KEY MESSAGE

We found GmNAC06 plays an important role in salt stress responses through the phenotypic, physiological and molecular analyses of OE, VC, and Mutant composite soybean. Salinization affects 20% of all cultivated land worldwide because of the high salinity of irrigation water and the excessive use of water, and this amount is increasing daily. NAC (NAM, ATAF, and CUC) have been found to be involved in salt stress. In this study, a soybean NAC gene, GmNAC06 (Glyma06g21020.1), was cloned and functionally characterized. The results of expression analysis suggested that salt stress could influence the expression level of GmNAC06. The subcellular localization analysis results suggested that GmNAC06 may function as a transcription factor. Under salt stress, the overexpression technology combined with CRISPR-Cas9 system found that GmNAC06 could cause the accumulation of proline and glycine betaine to alleviate or avoid the negative effects of ROS; similarly, it could control the Na+/K+ ratios in hairy roots to maintain ionic homeostasis. The fresh weight of the transgenic hairy roots and the histochemical ROS staining of wild leaves suggested that transgenic hairy roots influence the function of wild leaves under salt stress conditions. Moreover, the expression levels of GmUBC2 and GmHKT1 were higher in the GmNAC06 hairy roots than in the control. Thus, the overexpression of GmNAC06 in hairy roots notably causes an entire composite plant to exhibit salt tolerance. The phenotype of composite soybean plants and transgenic Arabidopsis plants suggest that GmNAC06 plays a role in response to salt stress and could be useful in generating salt tolerant transgenic crops.

PeSNAC-1 a NAC transcription factor from moso bamboo (Phyllostachys edulis) confers tolerance to salinity and drought stress in transgenic rice

NAC (NAM, AFAT and CUC) proteins play necessary roles in plant response to environmental stresses. However, the functional roles of NAC genes in moso bamboo (Phyllostachys edulis), an essential economic perennial woody bamboo species, are not well documented. In this study, we retrieved 152 PeNAC genes from the moso bamboo V2 genome, and PeSNAC-1 was isolated and functionally characterized. PeSNAC-1 was localized in the nucleus and had no transactivation activity in yeast. PeSNAC-1 extremely expressed in rhizome and young roots (0.1 and 0.5 cm) and was significantly induced by drought and salt treatments but repressed by abscisic acid (ABA), methyl jasmonate and high temperature (42 °C) in moso bamboo. Under water shortage and salinity conditions, survival ratios, Fv/Fm values, physiological indexes such as activities of superoxide dismutase, peroxidase and catalase and contents of malondialdehyde, H2O2 and proline were significantly higher in transgenic rice than the wild type, which suggests enhanced tolerance to drought and salt stress in PeSANC-1 overexpressed plants. Transcript levels of Na+/H+ antiporter and Na+ transporter genes (OsSOS1, OsNHX1 and OsHKT1;5), ABA signaling and biosynthesis genes (OsABI2, OsRAB16, OsPP2C68, OsLEA3-1, OsLEA3, OsNCED3, OsNCED4 and OsNCED5) and ABA-independent genes (OsDREB1A, OsDREB1B and OsDREB2A) were substantially higher in transgenic as compared with the wild type. Moreover, protein interaction analysis revealed that PeSNAC-1 could interact with stress responsive PeSNAC-2/4 and PeNAP-1/4/5 in both yeast and plant cells, which indicates a synergistic effect of those proteins in regulating the moso bamboo stress response. Our data demonstrate that PeSNAC-1 likely improved salt and drought stress tolerance via modulating gene regulation in both ABA-dependent and independent signaling pathways in transgenic rice. In addition, PeSNAC-1 functions as an important positive stress regulator in moso bamboo, participating in PeSNAC-1 and PeSNAC-2/4 or PeSNAC-1 and PeNAP-1/4/5 interaction networks.

Identification of nitric oxide (NO)-responsive genes under hypoxia in tomato (Solanum lycopersicum L.) root

Flooding periods, as one probable consequence of climate change, will lead more frequently to plant hypoxic stress. Hypoxia sensing and signaling in the root, as the first organ encountering low oxygen, is therefore crucial for plant survival under flooding. Nitric oxide has been shown to be one of the main players involved in hypoxia signaling through the regulation of ERFVII transcription factors stability. Using SNP as NO donor, we investigated the NO-responsive genes, which showed a significant response to hypoxia. We identified 395 genes being differentially regulated under both hypoxia and SNP-treatment. Among them, 251 genes showed up- or down-regulation under both conditions which were used for further biological analysis. Functional classification of these genes showed that they belong to different biological categories such as primary carbon and nitrogen metabolism (e.g. glycolysis, fermentation, protein and amino acid metabolism), nutrient and metabolites transport, redox homeostasis, hormone metabolism, regulation of transcription as well as response to biotic and abiotic stresses. Our data shed light on the NO-mediated gene expression modulation under hypoxia and provides potential targets playing a role in hypoxia tolerance. These genes are interesting candidates for further investigating their role in hypoxia signaling and survival.

Characterization of PcLEA14, a Group 5 Late Embryogenesis Abundant Protein Gene from Pear (Pyrus communis)

Fruit trees need to overcome harsh winter climates to ensure perennially; therefore, they are strongly influenced by environmental stress. In the present study, we focused on the pear homolog PcLEA14 belonging to the unique 5C late embryogenesis abundant (LEA) protein group for which information is limited on fruit trees. PcLEA14 was confirmed to belong to this protein group using phylogenetic tree analysis, and its expression was induced by low-temperature stress. The seasonal fluctuation in its expression was considered to be related to its role in enduring overwinter temperatures, which is particularly important in perennially. Moreover, the function of PcLEA14 in low-temperature stress tolerance was revealed in transgenic Arabidopsis. Subsequently, the pear homolog of dehydration-responsive element-binding protein/C-repeat binding factor1 (DREB1), which is an important transcription factor in low-temperature stress tolerance and is uncharacterized in pear, was analyzed after bioinformatics analysis revealed the presence of DREB cis-regulatory elements in PcLEA14 and the dormancy-related gene, both of which are also expressed during low temperatures. Among the five PcDREBs, PcDREB1A and PcDREB1C exhibited similar expression patterns to PcLEA14 whereas the other PcDREBs were not expressed in winter, suggesting their different physiological roles. Our findings suggest that the low-temperature tolerance mechanism in overwintering trees is associated with group 5C LEA proteins and DREB1.

The role of NAC transcription factor in plant cold response

The NAC transcription factor (TF) is one of the largest families of TFs in plants and plays an important role in plant growth, development, and response to environmental stress. The structural and functional characteristics of NAC TFs have been uncovered in the past years, including sequence binding features of the DNA-binding domain located in the N-terminus and dynamic interplay between the domain located at the C-terminus and other proteins. Studies on NAC TF are increasing in number; these studies distinctly contribute to our understanding of the regulatory networks of NAC-mediated complex signaling and transcriptional reprogramming. Previous studies have indicated that NAC TFs are key regulators of the plant stress response. However, these studies have been for six years so far and mainly focused on drought and salt stress. There are relatively few reports about NAC TFs in plant cold signal pathway and no related reviews have been published. In this review article, we summarize the structural features of NAC TFs, the target genes, upstream regulators and interaction proteins of stress-responsive NAC TFs, and the roles NAC TFs play in plant cold stress signal pathway.

PbMC1a/1b regulates lignification during stone cell development in pear (Pyrus bretschneideri) fruit

Programmed cell death (PCD) and secondary cell wall (SCW) thickening in pear fruit are accompanied by the deposition of cellulose and lignin to form stone cells. Metacaspase is an important protease for development, tissue renewal and PCD. The understanding of the molecular mechanism whereby pear (Pyrus) metacaspase promotes PCD and cell wall lignification is still limited. In this study, the Metacaspases gene family (PbMCs) from P. bretschneideri was identified. PbMC1a/1b was associated with lignin deposition and stone cell formation by physiological data, semiquantitative real-time polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR). Relative to wild-type (WT) Arabidopsis, the overexpression of PbMC1a/1b increased lignin deposition and delayed growth, thickened the cell walls of vessels, xylary fibers and interfascicular fibers, and increased the expression of lignin biosynthetic genes. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and GST pull-down assays indicated that the PbMC1a/1b protein physically interacted with PbRD21. Simultaneously, the transient expression of PbMC1a/1b and PbRD21 led to significant changes in the expression of genes and lignin contents in pear fruits and flesh calli. These results indicate that PbMC1a/1b plays an important role in cell wall lignification, possibly by interacting with PbRD21 to increase the mRNA levels of some lignin synthesis-associated genes and promote the formation of stone cells in pear fruit.

Transcription Factors in Plant Stress Responses: Challenges and Potential for Sugarcane Improvement

Increasing vulnerability of crops to a wide range of abiotic and biotic stresses can have a marked influence on the growth and yield of major crops, especially sugarcane (Saccharum spp.). In response to various stresses, plants have evolved a variety of complex defense systems of signal perception and transduction networks. Transcription factors (TFs) that are activated by different pathways of signal transduction and can directly or indirectly combine with cis-acting elements to modulate the transcription efficiency of target genes, which play key regulators for crop genetic improvement. Over the past decade, significant progresses have been made in deciphering the role of plant TFs as key regulators of environmental responses in particular important cereal crops; however, a limited amount of studies have focused on sugarcane. This review summarizes the potential functions of major TF families, such as WRKY, NAC, MYB and AP2/ERF, in regulating gene expression in the response of plants to abiotic and biotic stresses, which provides important clues for the engineering of stress-tolerant cultivars in sugarcane.

NAC Family Transcription Factors in Carrot: Genomic and Transcriptomic Analysis and Responses to Abiotic Stresses

Carrot is an annual or biennial herbaceous plant of the Apiaceae family. Carrot is an important vegetable, and its fresh taproot, which contains rich nutrients, is the main edible part. In the life cycle of carrot, NAC family transcription factors (TFs) are involved in almost all physiological processes. The function of NAC TFs in carrot remains unclear. In this study, 73 NAC family TF members in carrot were identified and characterized using transcriptome and genome databases. These members were divided into 14 subfamilies. Multiple sequence alignment was performed, and the conserved domains, common motifs, phylogenetic tree, and interaction network of DcNAC proteins were predicted and analyzed. Results showed that the same group of NAC proteins of carrot had high similarity. Eight DcNAC genes were selected to detect their expression profiles under abiotic stress treatments. The expression levels of the selected DcNAC genes significantly increased under treatments with low temperature, high temperature, drought, and salt stress. Results provide potentially useful information for further analysis of the roles of DcNAC transcription factors in carrot.

Physiological, biochemical and gene-expressional responses to water deficit in apple subjected to partial root-zone drying (PRD)

Water scarcity is one of the major factors limiting apple production. Partial root-zone drying (PRD) is a water-saving irrigation technique necessary to improve the efficiency of irrigation techniques to optimize the amount of fruit produced with the volume of water used. The apple trees cv. Red Delicious were exposed to four treatments, including (1) control with 100% of the crop evapotranspiration (ETc) needs; (2) alternate partial root-zone drying with 75% of the ETc needs (APRD75); (3) fixed partial root-zone drying with 75% of the ETc needs (FPRD75); (4) fixed partial root-zone irrigation with 50% of the ETc needs (FPRD50) in a semiarid region of Iran. Results showed that leaf water potential (Ψ _leaf), and chlorophyll were significantly decreased in FPRD50 compared to control and other PRD treatments. APRD75 and FPRD75 treatments significantly enhanced (+) -catechin (+C), epicatechin (EC), chlorogenic acid (CGA), caffeic acid (CA) as well as increased water use efficiency (WUE) (by 30-40% compared to control) without significant reduction of yield. PRD reduced gibberellic acid (GA3) and kinetin, while, increased the abscisic acid (ABA) and salicylic acid (SA) levels. The abiotic stress-responsive transcription factors (TFs) MdoMYB121, MdoMYB155, MdbZIP2, and MdbZIP48 were highly expressed in all PRD treatments. Our results demonstrated that APRD75 and FPRD75 have the potential to stimulate antioxidant defense mechanisms, hormonal signaling pathways, and expression of drought-tolerance TFs to improve WUE while maintaining crop yield. Therefore, APRD75andFPRD75 with water savings as compared to full irrigation might be a suitable strategy for irrigation apple trees under water scarcity.

Transcriptomic analyses of Pinus koraiensis under different cold stresses

Background

Pinus koraiensis is an evergreen tree species with strong cold resistance. However, the transcriptomic patterns in response to cold stress are poorly understood for P. koraiensis. In this study, global transcriptome profiles were generated for P. koraiensis under cold stress (− 20 °C) over time by high-throughput sequencing.

Results

More than 763 million clean reads were produced, which assembled into a nonredundant data set of 123,445 unigenes. Among them, 38,905 unigenes had homology with known genes, 18,239 were assigned to 54 gene ontology (GO) categories and 18,909 were assigned to 25 clusters of orthologous groups (COG) categories. Comparison of transcriptomes of P. koraiensis seedlings grown at room temperature (20 °C) and low temperature (− 20 °C) revealed 9842 differential expressed genes (DEGs) in the 6 h sample, 9250 in the 24 h sample, and 9697 in the 48 h sample. The number of DEGs in the pairwise comparisons of 6 h, 24 h and 48 h was relatively small. The accuracy of the RNA-seq was validated by analyzing the expression patterns of 12 DEGs by quantitative real-time PCR (qRT-PCR). In this study, 34 DEGs (22 upregulated and 12 downregulated) were involved in the perception and transmission of cold signals, 96 DEGs (41 upregulated and 55 downregulated) encoding 8 transcription factors that regulated cold-related genes expression, and 27 DEGs (17 upregulated and 10 downregulated) were involved in antioxidant mechanisms in response to cold stress. Among them, the expression levels of c63631_g1 (annexin D1), c65620_g1 (alpha-amylase isozyme 3C), c61970_g1 (calcium-binding protein KIC), c51736_g1 (ABA), c58408_g1 (DREB3), c66599_g1 (DREB3), c67548_g2 (SOD), c55044_g1 (CAT), c71938_g2 (CAT) and c11358_g1 (GPX) first increased significantly and then decreased significantly with the extension of stress time.

Conclusions

A large number of DEGs were identified in P. koraiensis under cold stress, especially the DEGs involved in the perception and transmission of cold signals, the DEGs encoding TFs related to cold regulation and the DEGs removing ROS in antioxidation mechanisms. The transcriptome and digital expression profiling of P. koraiensis could facilitate the understanding of the molecular control mechanism related to cold responses and provide the basis for the molecular breeding of conifers.

The Soybean GmNAC019 Transcription Factor Mediates Drought Tolerance in Arabidopsis in an Abscisic Acid-Dependent Manner

Being master regulators of gene expression, transcription factors (TFs) play important roles in determining plant growth, development and reproduction. To date, many TFs have been shown to positively mediate plant responses to environmental stresses. In the current study, the biological functions of a stress-responsive NAC [NAM (No Apical Meristem), ATAF1/2 (Arabidopsis Transcription Activation Factor1/2), CUC2 (Cup-shaped Cotyledon2)]-TF encoding gene isolated from soybean (GmNAC019) in relation to plant drought tolerance and abscisic acid (ABA) responses were investigated. By using a heterologous transgenic system, we revealed that transgenic Arabidopsis plants constitutively expressing the GmNAC019 gene exhibited higher survival rates in a soil-drying assay, which was associated with lower water loss rate in detached leaves, lower cellular hydrogen peroxide content and stronger antioxidant defense under water-stressed conditions. Additionally, the exogenous treatment of transgenic plants with ABA showed their hypersensitivity to this phytohormone, exhibiting lower rates of seed germination and green cotyledons. Taken together, these findings demonstrated that GmNAC019 functions as a positive regulator of ABA-mediated plant response to drought, and thus, it has potential utility for improving plant tolerance through molecular biotechnology.

Ectopic Expression of Glycine maxGmNAC109 Enhances Drought Tolerance and ABA Sensitivity in Arabidopsis

The NAC (NAM, ATAF1/2, CUC2) transcription factors are widely known for their various functions in plant development and stress tolerance. Previous studies have demonstrated that genetic engineering can be applied to enhance drought tolerance via overexpression/ectopic expression of NAC genes. In the present study, the dehydration- and drought-inducible GmNAC109 from Glycine max was ectopically expressed in Arabidopsis (GmNAC109-EX) plants to study its biological functions in mediating plant adaptation to water deficit conditions. Results revealed an improved drought tolerance in the transgenic plants, which displayed greater recovery rates by 20% to 54% than did the wild-type plants. In support of this finding, GmNAC109-EX plants exhibited lower water loss rates and decreased endogenous hydrogen peroxide production in leaf tissues under drought, as well as higher sensitivity to exogenous abscisic acid (ABA) treatment at germination and early seedling development stages. In addition, analyses of antioxidant enzymes indicated that GmNAC109-EX plants possessed stronger activities of superoxide dismutase and catalase under drought stress. These results together demonstrated that GmNAC109 acts as a positive transcriptional regulator in the ABA-signaling pathway, enabling plants to cope with adverse water deficit conditions.

Identification and Expression Analysis of the NAC Gene Family in Coffea canephora

The NAC gene family is one of the largest families of transcriptional regulators in plants, and it plays important roles in the regulation of growth and development as well as in stress responses. Genome-wide analyses have been performed in diverse plant species, but there is still no systematic analysis of the NAC genes of Coffea canephora Pierre ex A. Froehner. In this study, we identified 63 NAC genes from the genome of C. canephora. The basic features and comparison analysis indicated that the NAC gene members increased via duplication events during the evolution of the plant. Phylogenetic analysis divided the NAC proteins from C. canephora, Arabidopsis and rice into 16 subgroups. Analysis of the expression patterns of CocNACs under cold stress and coffee bean development indicated that 38 CocNACs were differentially expressed under cold stress; six genes may play important roles in the process of cold acclimation, and four genes among 54 CocNACs showing a variety of expression patterns during different developmental stages of coffee beans may be positively related to the bean development. This study can expand our understanding of the functions of the CocNAC gene family in cold responses and bean development, thereby potentially intensifying the molecular breeding programs of Coffea spp. plants.

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.