Genome-wide transcriptome analysis of the salt stress tolerance mechanism in Rosa chinensis

The MYC Gene RrbHLH105 Contributes to Salt Stress-Induced Geraniol in Rose by Regulating Trehalose-6-Phosphate Signalling

Rose (Rosa rugosa) is an important perfume plant, but its cultivation is significantly constrained by salt stress. Terpenes represent the most abundant volatile aromatic compounds in roses, yet little is known about how terpene metabolism responds to salt stress. In this study, salt-treated rose petals presented significant accumulation of monoterpenes, including geraniol, due to the disruption of jasmonic acid (JA) biosynthesis and signalling. Overexpression and silencing analyses revealed a MYC transcription factor involved in JA signalling (RrbHLH105) as a repressor of geraniol biosynthesis. RrbHLH105 was shown to activate the trehalose-6-phosphate synthase genes RrTPS5 and RrTPS8 by binding to the E-box (5'-CANNTG-3'). The increased trehalose-6-phosphate content and decreased geraniol content in rose petals overexpressing TPS5 or RrTPS8, along with the high accumulation of geraniol in petals where both RrbHLH105 and TPSs were cosilenced, indicate that trehalose signalling plays a role in the negative regulation of geraniol accumulation via the RrbHLH105-TPS module. In summary, the suppression of RrbHLH105 by salt stress leads to excessive geraniol accumulation through the inhibition of both RrbHLH105-mediated JA signalling and RrTPS-mediated trehalose signalling in rose petals. Additionally, this study highlights the emerging role of RrbHLH105 as a critical integrator of JA and trehalose signalling crosstalk.

Genome-wide identification of HSP90 gene family in Rosa chinensis and its response to salt and drought stresses

Heat shock protein 90 (HSP90) is important for many organisms, including plants. Based on the whole genome information, the gene number, gene structure, evolutionary relationship, protein structure, and active site of the HSP90 gene family in Rosa chinensis and Rubus idaeus were determined, and the expression of the HSP90 gene under salt, and drought stresses in two rose varieties Wangxifeng and Sweet Avalanche were analyzed. Six and eight HSP90 genes were identified from R. chinensis and Ru. idaeus, respectively. Phylogenetic analysis revealed that the analyzed genes were divided into two Groups and four subgroups (Classes 1a, 1b, 2a, and 2b). Although members within the same classes displayed highly similar gene structures, while the gene structures and conserved domains of Group 1 (Class 1a and 1b) and the Group 2 (Class 2a and 2b) are different. Tandem and segmental duplication genes were found in Ru. idaeus, but not in R. chinensis, perhaps explaining the difference in HSP90 gene quantity in the two analyzed species. Analysis of cis-acting elements revealed abundant abiotic stress, photolight-response, and hormone-response elements in R. chinensis HSP90s. qRT-PCR analysis suggested that RcHSP90-1-1, RcHSP90-5-1 and RcHSP90-6-1 in Sweet Avalanche and Wangxifeng varieties played important regulatory roles under salt and drought stress. The analysis of protein structure and active sites indicate that the potential different roles of RcHSP90-1-1, RcHSP90-5-1, and RcHSP90-6-1 in salt and drought stresses may come from the differences of corresponding protein structures and activation sites. These data will provide information for the breeding of rose varieties with high stress resistance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04052-0.

Genome-wide identification of starch phosphorylase gene family in Rosa chinensis and expression in response to abiotic stress

Chinese rose (Rosa chinensis) is an important ornamental plant, with economic, cultural, and symbolic significance. During the application of outdoor greening, adverse environments such as high temperature and drought are often encountered, which affect its application scope and ornamental quality. The starch phosphorylase (Pho) gene family participate in the synthesis and decomposition of starch, not only related to plant energy metabolism, but also plays an important role in plant stress resistance. The role of Pho in combating salinity and high temperature stress in R. chinensis remains unknown. In this work, 4 Phos from R. chinensis were detected with Pfam number of Pho (PF00343.23) and predicted by homolog-based prediction (HBP). The Phos are characterized by sequence lengths of 821 to 997 bp, and the proteins are predicted to subcellularly located in the plastid and cytoplasm. The regulatory regions of the Phos contain abundant stress and phytohormone-responsive cis-acting elements. Based on transcriptome analysis, the Phos were found to respond to abiotic stress factors such as drought, salinity, high temperature, and plant phytohormone of jasmonic acid and salicylic acid. The response of Phos to abiotic stress factors such as salinity and high temperature was confirmed by qRT-PCR analysis. To evaluate the genetic characteristics of Phos, a total of 69 Phos from 17 species were analyzed and then classified into 3 groups in phylogenetic tree. The collinearity analysis of Phos in R. chinensis and other species was conducted for the first time. This work provides a view of evolution for the Pho gene family and indicates that Phos play an important role in abiotic stress response of R. chinensis.

Understanding the salt overly sensitive pathway in Prunus: Identification and characterization of NHX, CIPK, and CBL genes

Salinity is a major abiotic stress factor that can significantly impact crop growth, and productivity. In response to salt stress, the plant Salt Overly Sensitive (SOS) signaling pathway regulates the homeostasis of intracellular sodium ion concentration. The SOS1, SOS2, and SOS3 genes play critical roles in the SOS pathway, which belongs to the members of Na+/H+ exchanger (NHX), CBL-interacting protein kinase (CIPK), and calcineurin B-like (CBL) gene families, respectively. In this study, we performed genome-wide identifications and phylogenetic analyses of NHX, CIPK, and CBL genes in six Rosaceae species: Prunus persica, Prunus dulcis, Prunus mume, Prunus armeniaca, Pyrus ussuriensis × Pyrus communis, and Rosa chinensis. NHX, CIPK, and CBL genes of Arabidopsis thaliana were used as controls for phylogenetic analyses. Our analysis revealed the lineage-specific and adaptive evolutions of Rosaceae genes. Our observations indicated the existence of two primary classes of CIPK genes: those that are intron-rich and those that are intron-less. Intron-rich CIPKs in Rosaceae and Arabidopsis can be traced back to algae CIPKs and CIPKs found in early plants, suggesting that intron-less CIPKs evolved from their intron-rich counterparts. This study identified one gene for each member of the SOS signaling pathway in P. persica: PpSOS1, PpSOS2, and PpSOS3. Gene expression analyses indicated that all three genes of P. persica were expressed in roots and leaves. Yeast two-hybrid-based protein-protein interaction analyses revealed a direct interaction between PpSOS3 and PpSOS2; and between PpSOS2 and PpSOS1C-terminus region. Our findings indicate that the SOS signaling pathway is highly conserved in P. persica.

Molecular cloning and characterization of farnesyl diphosphate synthase from Rosa rugosa Thunb associated with salinity stress

Rosa rugosa, a renowned ornamental plant, is cultivated for its essential oil containing valuable monoterpenes, sesquiterpenes, and other compounds widely used in the floriculture industry. Farnesyl diphosphate synthase (FPPS) is a key enzyme involved in the biosynthesis of sesquiterpenes and triterpenes for abiotic or biotic stress. In this study, we successfully cloned and characterized a full-length FPPS- encoding cDNA identified as RrFPPS1 using RT-PCR from R. rugosa. Phylogenetic analysis showed that RrFPPS1 belonged to the angiosperm-FPPS clade. Transcriptomic and RT-qPCR analyses revealed that the RrFPPS1 gene had tissue-specific expression patterns. Subcellular localization analysis using Nicotiana benthamiana leaves showed that RrFPPS1 was a cytoplasmic protein. In vitro enzymatic assays combined with GC-MS analysis showed that RrFPPS1 produced farnesyl diphosphate (FPP) using isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) as substrates to provide a precursor for sesquiterpene and triterpene biosynthesis in the plant. Additionally, our research found that RrFPPS1 was upregulated under salt treatment. These substantial findings contribute to an improved understanding of terpene biosynthesis in R. rugosa and open new opportunities for advancements in horticultural practices and fragrance industries by overexpression of the RrFPPS1 gene in vivo increased FPP production and subsequently led to elevated sesquiterpene yields in the future. The knowledge gained from this study can potentially lead to the development of enhanced varieties of R. rugosa with improved aroma, medicinal properties, and resilience to environmental stressors.

RcMYB8 enhances salt and drought tolerance in rose (Rosa chinensis) by modulating RcPR5/1 and RcP5CS1

Plant Myeloblastosis (MYB) proteins function crucially roles upon variegated abiotic stresses. Nonetheless, their effects and mechanisms in rose (Rosa chinensis) are not fully clarified. In this study, we characterized the effects of rose RcMYB8 under salt and drought tolerances. For induction of the RcMYB8 expression, NaCl and drought stress treatment were adopted. Rose plants overexpressing RcMYB8 displayed enhanced tolerance to salinity and drought stress, while silencing RcMYB8 resulted in decreased tolerance, as evidenced by lowered intra-leaf electrolyte leakage and callose deposition, as well as photosynthetic sustainment under stressed conditions. Here, we further show that RcMYB8 binds similarly to the promoters of RcPR5/1 and RcP5C51 in vivo and in vitro. Inhibiting RcP5CS1 by virus-induced gene silencing led to decreased drought tolerance through the reactive oxygen species (ROS) homeostatic regulation. RcP5CS1-silenced plants showed an increase in ion leakage and reduce of proline content, together with the content of malondialdehyde (MDA) increased, lowered activities of Catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD). Our study highlights the transcriptional modulator role of RcMYB8 in drought and salinity tolerances, which bridges RcPR5/1 and RcP5CS1 by promoting ROS scavenging. Besides, it is probably applicable to the rose plant engineering for enhancing their abiotic stress tolerances.

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

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

RcbHLH59-RcPRs module enhances salinity stress tolerance by balancing Na+/K+ through callose deposition in rose (Rosa chinensis)

Basic helix-loop-helix (bHLH) proteins play pivotal roles in plant growth, development, and stress responses. However, the molecular and functional properties of bHLHs have not been fully characterized. In this study, a novel XI subgroup of the bHLH protein gene RcbHLH59 was isolated and identified in rose (Rosa sp.). This gene was induced by salinity stress in both rose leaves and roots, and functioned as a transactivator. Accordingly, silencing RcbHLH59 affected the antioxidant system, Na ⁺/K ⁺ balance, and photosynthetic system, thereby reducing salt tolerance, while the transient overexpression of RcbHLH59 improved salinity stress tolerance. Additionally, RcbLHLH59 was found to regulate the expression of sets of pathogenesis-related (PR) genes in RcbHLH59-silenced (TRV-RcbHLH59) and RcbHLH59-overexpressing (RcbHLH59-OE) rose plants. The RcPR4/1 and RcPR5/1 transcript levels showed opposite changes in the TRV-RcbHLH59 and RcbHLH59-OE lines, suggesting that these two genes are regulated by RcbHLH59. Further analysis revealed that RcbHLH59 binds to the promoters of RcPR4/1 and RcPR5/1, and that the silencing of RcPR4/1 or RcPR5/1 led to decreased tolerance to salinity stress. Moreover, callose degradation- and deposition-related genes were impaired in RcPR4/1- or RcPR5/1-silenced plants, which displayed a salt tolerance phenotype by balancing the Na⁺/K⁺ ratio through callose deposition. Collectively, our data highlight a new RcbLHLH59-RcPRs module that positively regulates salinity stress tolerance by balancing Na⁺/K⁺ and through callose deposition in rose plants.

GT Transcription Factors of Rosa rugosa Thunb. Involved in Salt Stress Response

Rosa rugosa was a famous aromatic plant while poor salt tolerance of commercial cultivars has hindered its culture in saline-alkali soil. In many plants, the roles of GT (or trihelix) genes in salt stresses responses have been emerging. In the wild R. rugosa, a total of 37 GTs (RrGTs) were grouped into GT-1, GT-2, GTγ, SH4, and SIP1 lineages. SIP1 lineage expanded by transposition. The motifs involved in the binding of GT cis-elements were conserved. Four RrGTs (RrGT11/14/16/18) significantly differentially expressed in roots or leaves under salt stress. The responsive patterns within 8 h NaCl treatment indicated that RrGTγ-4 (RrGT18) and RrGT-1 (RrGT16) were significantly induced by salt in roots of R. rugosa. Subcellular localizations of RrSIP1 (RrGT11) and RrGTγ-4 were on chloroplasts while RrGT-1 and RrSIP2 (RrGT14) located on cell nucleus. Regulation of ion transport could be the most important role of RrSIPs and RrGTγ-4. And RrGT-1 could be a halophytic gene with higher transcription abundance than glycophytic GT-1. These results provide key clue for further investigations of roles of RrGTs in salt stress response and would be helpful in the understanding the salt tolerance regulation mechanism of R. rugosa.

Comparative Transcriptomic Analysis of Root and Leaf Transcript Profiles Reveals the Coordinated Mechanisms in Response to Salinity Stress in Common Vetch

Owing to its strong environmental suitability to adverse abiotic stress conditions, common vetch (Vicia sativa) is grown worldwide for both forage and green manure purposes and is an important protein source for human consumption and livestock feed. The germination of common vetch seeds and growth of seedlings are severely affected by salinity stress, and the response of common vetch to salinity stress at the molecular level is still poorly understood. In this study, we report the first comparative transcriptomic analysis of the leaves and roots of common vetch under salinity stress. A total of 6361 differentially expressed genes were identified in leaves and roots. In the roots, the stress response was dominated by genes involved in peroxidase activity. However, the genes in leaves focused mainly on Ca²⁺ transport. Overexpression of six salinity-inducible transcription factors in yeast further confirmed their biological functions in the salinity stress response. Our study provides the most comprehensive transcriptomic analysis of common vetch leaf and root responses to salinity stress. Our findings broaden the knowledge of the common and distinct intrinsic molecular mechanisms within the leaves and roots of common vetch and could help to develop common vetch cultivars with high salinity tolerance.

Screening of Key Indices and the Gene Transcriptional Regulation Analysis Related to Salt Tolerance in Salix matsudana Seedlings

Pot experiments were performed to comparatively study the differences in 16 salt tolerance indices between the seedlings of six Salix matsudana clones under the stress of various concentrations of NaCl (0, 0.1%, 0.3%, 0.5%, and 0.7%), including the salt injury index, shoot fresh weight, root fresh weight, leaf water content, relative conductivity, malondialdehyde content, and antioxidant enzyme activity. The salt-tolerant clones and key indices of salt tolerance were selected. Transcriptome sequencing analysis was performed on the selected salt-tolerant and salt-sensitive clones under salt stress, and the links between the physiological indices of salt tolerance and gene expression were analyzed. Results: (1) Superoxide dismutase (SOD), peroxidase (POD), chlorophyll, and net photosynthetic rate were closely related to the salt tolerance of Salix matsudana at the seedling stage. The regression equation was constructed as follows: salt tolerance index (y) = 0.224x10 + 0.216x11 + 0.127x12 + 0.191x7 − 0.187 (x10 = chlorophyll, x11 = SOD, x12 = POD, x7 = net photosynthetic rate). (2) The number of differentially expressed genes between the seedlings of salt-tolerant and salt-sensitive clones varied with the time of exposure (0 h, 4 h, 12 h, and 24 h) to 200 mmol·L−1 NaCl stress. The most differentially expressed genes in Sm172 were detected upon 24 h vs. 4 h of salt treatment, while the most in Sm6 were in the 24 h vs. 0 h comparison. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis showed that several differentially expressed genes were involved in carotenoid biosynthesis and plant mitogen-activated protein kinase signaling pathways. The nine highly expressed transcription factor genes (Sm172-f2p30-2392, Sm172-f2p28-2386, Sm6-f8p60-2372, Sm6-f2p39-2263, Sm6-f16p60-2374, Sm6-f3p60-931, Sm6-f2p60-1067, Sm172-f3p54-1980, and Sm172-f3p54-1980) were closely correlated with the four key indices of salt tolerance. These genes could become genetic resources for salt tolerance breeding of Salix matsudana.

Genome-wide analysis of the rose (Rosa chinensis) NAC family and characterization of RcNAC091

A genome-wide analysis identified 116 NAC genes in rose, including stress-related ones with different expression patterns under drought and salt stress. Silencing of RcNAC091, a member of the ATAF subfamily, decreased dehydration tolerance in rose. The NAC (NAM, ATAF, and CUC) transcription factors (TFs) are plant-specific proteins that regulate various developmental processes and stress responses. However, knowledge of the NAC TFs in rose (Rosa chinensis), one of the most important horticultural crops, is limited. In this study, 116 NAC genes were identified from the rose genome and classified into 16 subfamilies based on protein phylogenetic analysis. Chromosomal mapping revealed that the RcNAC genes were unevenly distributed on the seven chromosomes of rose. Gene structure and motif analysis identified a total of ten conserved motifs, of which motifs 1-7 were highly conserved and present in most rose NACs, while motifs 8-10 were present only in a few subfamilies. Further study of the stress-related RcNACs based on the transcriptome data showed differences in the expression patterns among the organs, at various floral developmental stages, and under drought and salt stress in rose leaves and roots. The stress-related RcNACs possessed cis-regulatory elements (CREs) categorized into three groups corresponding to plant growth and development, phytohormone response, and abiotic and biotic stress response. Reverse transcription-quantitative real-time PCR (RT-qPCR) analysis of 11 representative RcNACs revealed their differential expression in rose leaves and roots under abscisic acid (ABA), polyethylene glycol (PEG), and sodium chloride (NaCl) treatments. Furthermore, the silencing of RcNAC091 verified its role in positively regulating the dehydration stress response. Overall, the present study provides valuable insights into stress-related RcNACs and paves the way for stress tolerance in rose.

Transcriptomic, proteomic, metabolomic, and functional genomic approaches of Brassica napus L. during salt stress

Environmental abiotic stresses limit plant growth, development, and reproduction. This study aims to reveal the response of Brassica napus to salt stress. Here, transcriptomics, metabolomics, and proteomics analysis were performed on 15 Brassica napus leave samples treated with salt at different times. Through functional enrichment analyzing the differentially expressed genes (DEGs), differential metabolites (DMs) and differentially expressed proteins (DEPs), the key factors that dominate Brassica napus response to salt stress were identified. The results showed that the two key hormones responding to salt stress were Abscisic acid (ABA) and jasmonic acid (JA). Salt stress for 24h is an important milestone. Brassica napus adjusted multiple pathways at 24h to avoid over-response to salt stress and cause energy consumption. The increased expression in BnPP2C is tangible evidence. In response to salt stress, JA and ABA work together to reduce the damage caused by salt stress in Brassica napus. The increased expression of all BnJAZs after salt stress highlighted the function of JA that cannot be ignored responding to salt stress. In addition, some metabolites, such as N-acetyl-5-hydroxytryptamine, L-Cysteine and L-(+)-Arginine, play a critical role in maintaining the balance of ROS. Proteins like catalase-3, cysteine desulfurase, HSP90 and P450_97A3 were the most critical differential proteins in response to salt stress. These findings of this study provide data support for Brassica napus breeding.

Transcriptome analysis and functional identification of GmMYB46 in soybean seedlings under salt stress

Salinity is one of the major abiotic stress that limits crop growth and productivity. We investigated the transcriptomes of salt-treated soybean seedlings versus a control using RNA-seq to better understand the molecular mechanisms of the soybean (Glycine max L.) response to salt stress. Transcriptome analysis revealed 1,235 differentially expressed genes (DEGs) under salt stress. Several important pathways and key candidate genes were identified by KEGG enrichment. A total of 116 differentially expressed transcription factors (TFs) were identified, and 17 TFs were found to belong to MYB families. Phylogenetic analysis revealed that these TFs may be involved in salt stress adaptation. Further analysis revealed that GmMYB46 was up-regulated by salt and mannitol and was localized in the nucleus. The salt tolerance of transgenic Arabidopsis overexpressing GmMYB46 was significantly enhanced compared to wild-type (WT). GmMYB46 activates the expression of salt stress response genes (P5CS1, SOD, POD, NCED3) in Arabidopsis under salt stress, indicating that the GmMYB46 protein mediates the salt stress response through complex regulatory mechanisms. This study provides information with which to better understand the molecular mechanism of salt tolerance in soybeans and to genetically improve the crop.

Analysis of the thaumatin-like genes of Rosa chinensis and functional analysis of the role of RcTLP6 in salt stress tolerance

A total of 27 rose thaumatin-like protein (TLP) genes were identified from the rose genome through bioinformatics analyses. RcTLP6 was found to confer salinity stress tolerance in rose. Thaumatin-like proteins (TLPs) play critical roles in regulating many biological processes, including abiotic and biotic stress responses in plants. Here, we conducted a genome-wide screen of TLPs in rose (Rosa chinensis) and identified 27 RcTLPs. The identified RcTLPs, as well as other TLPs from six different plant species, were placed into nine groups based on a phylogenetic analysis. An analysis of the intron-exon structures of the TLPs revealed a high degree of similarity. RcTLP genes were found on all chromosomes except for chromosome four. Cis-regulatory elements (CEs) were identified in the promoters of all RcTLPs, including CEs associated with growth, development and hormone-responsiveness, as well as abiotic and biotic responses, indicating they play diverse roles in rose. Transcriptomics analysis revealed that RcTLPs had tissue-specific expression patterns, and several root-preferential RcTLPs were responsive to drought and salinity stress. Quantitative PCR analysis of six RcTLPs under ABA, PEG and NaCl treatment confirmed the differentially expressed genes identified in the transcriptomics experiment. In addition, silencing RcTLP6 in rose leaves led to decreased tolerance to salinity stress. We also screened proteins which may interact with RcTLP6 to understand its biological roles. This study represents the first report of the TLP gene family in rose and expands the current understanding of the role that RcTLP6 plays in salt tolerance. These findings lay a foundation for future utilization of RcTLPs to improve rose abiotic stress tolerance.

De novo transcriptome analysis provides insights into the salt tolerance of Podocarpus macrophyllus under salinity stress

BACKGROUND

Soil salinization is causing ecosystem degradation and crop yield reduction worldwide, and elucidation of the mechanism of salt-tolerant plants to improve crop yield is highly significant. Podocarpus macrophyllus is an ancient gymnosperm species with a unique environmental adaptation strategy that may be attributed to its lengthy evolutionary process. The present study investigated the physiological and molecular responses of P. macrophyllus plants to salt stress by analyzing its photosynthetic system and antioxidant enzyme activity. We also analyzed the differentially expressed genes (DEGs) in P. macrophyllus under salt stress using RNA sequencing and de novo transcriptome assembly.

RESULTS

Salt treatment significantly affected the photosynthetic system in P. macrophyllus seedlings, which decreased chlorophyll content, altered chloroplast ultrastructure, and reduced photosynthesis. The activities of antioxidant enzymes increased significantly following salt stress treatment. Transcriptome analysis showed that salt stress induced a large number of genes involved in multiple metabolic and biological regulation processes. The transcription levels of genes that mediate phytohormone transport or signaling were altered. K⁺ and Ca²⁺ transporter-encoding genes and the MYB transcription factor were upregulated under salt stress. However, the genes involved in cell wall biosynthesis and secondary metabolism were downregulated.

CONCLUSION

Our research identified some important pathways and putative genes involved in salt tolerance in P. macrophyllus and provided clues for elucidating the mechanism of salt tolerance and the utilization of the salt tolerance genes of P. macrophyllus for crop improvement.

Regulation of Plant Responses to Salt Stress

Salt stress is a major environmental stress that affects plant growth and development. Plants are sessile and thus have to develop suitable mechanisms to adapt to high-salt environments. Salt stress increases the intracellular osmotic pressure and can cause the accumulation of sodium to toxic levels. Thus, in response to salt stress signals, plants adapt via various mechanisms, including regulating ion homeostasis, activating the osmotic stress pathway, mediating plant hormone signaling, and regulating cytoskeleton dynamics and the cell wall composition. Unraveling the mechanisms underlying these physiological and biochemical responses to salt stress could provide valuable strategies to improve agricultural crop yields. In this review, we summarize recent developments in our understanding of the regulation of plant salt stress.

Genome-Wide Analysis of Dof Genes and Their Response to Abiotic Stress in Rose (Rosa chinensis)

Dof (DNA binding with one finger) proteins play important roles in plant development and defense regulatory networks. In the present study, we report a genome-wide analysis of rose Dof genes (RchDof), including phylogenetic inferences, gene structures, chromosomal locations, gene duplications, and expression diversity. A total of 24 full-length RchDof genes were identified in Rosa chinensis, which were assigned to nine distinct subgroups. These RchDof genes were unevenly distributed on rose chromosomes. The genome-scale analysis of synteny indicated that segmental duplication events may have played a major role in the evolution of the RchDof gene family. Analysis of cis-acting elements revealed putative functions of Dofs in rose during development as well as under numerous biotic and abiotic stress conditions. Moreover, the expression profiles derived from qRT-PCR experiments demonstrated distinct expression patterns in various tissues, and gene expression divergence existed among the duplicated RchDof genes, suggesting a fundamentally functional divergence of the duplicated Dof paralogs in rose. The gene expression analysis of RchDofs under drought and salt stress conditions was also performed. The present study offered novel insights into the evolution of RchDofs and can aid in the further functional characterization of its candidate genes.

Overexpression of A Biotic Stress-Inducible Pvgstu Gene Activates Early Protective Responses in Tobacco under Combined Heat and Drought

Drought and heat stresses are major factors limiting crop growth and productivity, and their effect is more devastating when occurring concurrently. Plant glutathione transferases (GSTs) are differentially expressed in response to different stimuli, conferring tolerance to a wide range of abiotic stresses. GSTs from drought-tolerant Phaseolus vulgaris var. "Plake Megalosperma Prespon" is expected to play an important role in the response mechanisms to combined and single heat and drought stresses. Herein, we examined wild-type N. tabacum plants (cv. Basmas Xanthi) and T1 transgenic lines overexpressing the stress-induced Pvgstu3-3 and Pvgstu2-2 genes. The overexpression of Pvgstu3-3 contributed to potential thermotolerance and greater plant performance under combined stress. Significant alterations in the primary metabolism were observed in the transgenic plants between combined stress and stress-free conditions. Stress-responsive differentially expressed genes (DEGs) and transcription factors (TFs) related to photosynthesis, signal transduction, starch and sucrose metabolism, osmotic adjustment and thermotolerance, were identified under combined stress. In contrast, induction of certain DEGs and TF families under stress-free conditions indicated that transgenic plants were in a primed state. The overexpression of the Pvgstu3-3 is playing a leading role in the production of signaling molecules, induction of specific metabolites and activation of the protective mechanisms for enhanced protection against combined abiotic stresses in tobacco.

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

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

Salt-Induced Differences During the Gene Expression of Telomerase Enzyme in Sunflower

Background:

Salinity is one of the most important environmental stresses which reduces the nutrient uptake, growth and yield of crops including sunflower.

Objectives:

The aim of this study was evaluating the expression pattern of telomerase gene, TERT, in sunflower plants under salinity stress.

Materials and Methods:

Sunflower plants of both sensitive and resistant lines were grown in greenhouse and treated with different levels of NaCl (2, 5 and 8 dSm^-1). The expression pattern of TERT gene was evaluated at 8^th leaf stage 6, 12 and 24 hours post salt treatment using real time-PCR, since the effects of salt stress are eventually manifested in the leaves.

Results:

In both lines, salt-subjected plants showed reduced size and dried leaves, due to breakthrough of the growth. Compared to the control group, treated groups tended to indicate downregulated pattern of TERT gene expression.

Conclusions:

This study offers TERT as a new gene affected by salt stress when growth is arrested.

Uncovering candidate genes responsive to salt stress in Salix matsudana (Koidz) by transcriptomic analysis

Salix matsudana, a member of Salicaceae, is an important ornamental tree in China. Because of its capability to tolerate high salt conditions, S. matsudana also plays an important ecological role when grown along Chinese coastal beaches, where the salinity content is high. Here, we aimed to elucidate the mechanism of higher salt tolerance in S. matsudana variety ‘9901’ by identifying the associated genes through RNA sequencing and comparing differential gene expression between the S. matsudana salt-tolerant and salt-sensitive samples treated with 150 mM NaCl. Transcriptomic comparison of the roots of the two samples revealed 2174 and 3159 genes responsive to salt stress in salt-sensitive and salt-tolerant sample, respectively. Real-time polymerase chain reaction analysis of 9 of the responsive genes revealed a strong, positive correlation with RNA sequencing data. The genes were enriched in several pathways, including carbon metabolism pathway, plant-pathogen interaction pathway, and plant hormone signal transduction pathway. Differentially expressed genes (DEGs) encoding transcription factors associated with abiotic stress responses and salt stress response network were identified; their expression levels differed between the two samples in response to salt stress. Hub genes were also revealed by weighted gene co-expression network (WGCNA) analysis. For functional analysis of the DEG encoding sedoheptulose-1,7-bisphosphatase (SBPase), the gene was overexpressed in transgenic Arabidopsis, resulting in increased photosynthetic rates, sucrose and starch accumulation, and enhanced salt tolerance. Further functional characterization of other hub DEGs will reveal the molecular mechanism of salt tolerance in S. matsudana and allow the application of S. matsudana in coastal afforestation.

In the name of the rose: a roadmap for rose research in the genome era

The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: 'Now that we have "the" genome, what's next?'. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.