Effect of salt-stress on gene expression in citrus roots revealed by RNA-seq

Calmodulin-Binding Transcription Factors: Roles in Plant Response to Abiotic Stresses

Plants face many abiotic stresses throughout their life cycle, such as drought, high temperature, low temperature, and salinity. To survive and reproduce, plants have evolved a complex and elaborate signal transduction network to sense stress signals and initiate corresponding defense mechanisms. Calcium ion (Ca2+), as a secondary messenger, plays an important role in mediating signal transduction in plant cells. Calmodulin (CaM) is an important class of Ca2+ receptors that sense changes in cellular calcium ion concentration and can interact with a range of proteins to regulate the activity of downstream target proteins. Calmodulin-binding transcription factors (CAMTAs) are a family of transcription factors (TFs) that are widely present in plants and can bind to CaM. The CAMTAs are regarded as the most characterized CaM-binding TF family in the plant Ca2+ signaling pathway. In recent years, studies have shown that CAMTAs play an important regulatory role in plant abiotic stress response and plant growth and development. Therefore, this review summarizes the recent progress in the discovery, structure, and role of CAMTAs under abiotic stresses, with a view to providing a reference for future CAMTA studies. Finally, the prospects and directions for further research on the potential mechanisms of CAMTAs in plants are also discussed.

Comparative transcriptomic analyses of diploid and tetraploid citrus reveal how ploidy level influences salt stress tolerance

Introduction

Citrus is an important fruit crop for human health. The sensitivity of citrus trees to a wide range of abiotic stresses is a major challenge for their overall growth and productivity. Among these abiotic stresses, salinity results in a significant loss of global citrus yield. In order to find straightforward and sustainable solutions for the future and to ensure citrus productivity, it is of paramount importance to decipher the mechanisms responsible for salinity stress tolerance. Thisstudy aimed to investigate how ploidy levels influence salt stress tolerance in citrus by comparing the transcriptomic responses of diploid and tetraploid genotypes. In a previous article we investigated the physiological and biochemical response of four genotypes with different ploidy levels: diploid trifoliate orange (Poncirus trifoliata [L.] Raf.) (PO2x) and Cleopatra mandarin (Citrus reshni Hort. Ex Tan.) (CL2x) and their respective tetraploids (PO4x, CL4x).

Methods

In this study, we useda multifactorial gene selection and gene clustering approach to finely dissect the influence of ploidy level on the salt stress response of each genotype. Following transcriptome sequencing, differentially expressed genes (DEGs) were identified in response to salt stress in leaves and roots of the different citrus genotypes.

Result and discussion

Gene expression profiles and functional characterization of genes involved in the response to salt stress, as a function of ploidy level and the interaction between stress response and ploidy level, have enabled us to highlight the mechanisms involved in the varieties tested. Saltstress induced overexpression of carbohydrate biosynthesis and cell wall remodelling- related genes specifically in CL4x Ploidy level enhanced oxidative stress response in PO and ion management capacity in both genotypes. Results further highlighted that under stress conditions, only the CL4x genotype up- regulated genes involved in sugar biosynthesis, transport management, cell wall remodelling, hormone signalling, enzyme regulation and antioxidant metabolism. These findings provide crucial insights that could inform breeding strategies for developing salt-tolerant citrus varieties.

Transcriptomic and metabolomic analyses reveal that ABA increases the salt tolerance of rice significantly correlated with jasmonic acid biosynthesis and flavonoid biosynthesis

Abscisic acid (ABA) has been shown to mitigate the deleterious effects of abiotic stresses and to regulate plant growth and development. Salinity is one of the important abiotic stresses affecting plant cell metabolism and physiology, which causes serious damages to crops. In this study, we investigated the protective role of exogenous ABA on leaves in response to salinity stress using rice seedlings (two leaf-one heart) subjected to three treatments: ZCK (control), ZS (50 mM NaCl), and ZSA (5 mg L-1 ABA + 50 mM NaCl). We carried out transcriptomic and metabolomic analyses to identify the molecular mechanisms by which ABA protects plants against salt stress. Results showed that 1159 differentially expressed genes (DEGs) (916 up-regulated, 243 down-regulated) and 63 differentially accumulated metabolites (DAMs) (42 up-regulated, 21 down-regulated) were identified between the ZS and ZSA treatments, respectively. In addition, ABA pretreatment regulated the expression pattern of genes responsible for oxidation redox, starch and sucrose metabolism, and phenylpropanoid biosynthesis. The combined transcriptomic and metabolomic analysis revealed that 16 DEGs and 2 DAMs were involved in Flavonoid biosynthesis and 8 DEGs and 2 DAMs were involved alpha-Linolenic acid metabolism which are responsible for salinity stress tolerance through induced by exogenous ABA. Overall, ABA could enhance rice leaves growth and development mainly by regulating flavonoid biosynthesis and linoleic acid metabolism pathway.

Time-Course Transcriptome Analysis of Aquilegia vulgaris Root Reveals the Cell Wall's Roles in Salinity Tolerance

Salt stress has a considerable impact on the development and growth of plants. The soil is currently affected by salinisation, a problem that is becoming worse every year. This means that a significant amount of salt-tolerant plant material needs to be added. Aquilegia vulgaris has aesthetically pleasing leaves, unique flowers, and a remarkable tolerance to salt. In this study, RNA-seq technology was used to sequence and analyse the transcriptome of the root of Aquilegia vulgaris seedlings subjected to 200 mM NaCl treatment for 12, 24, and 48 h. In total, 12 Aquilegia vulgaris seedling root transcriptome libraries were constructed. At the three time points of salt treatment compared with the control, 3888, 1907, and 1479 differentially expressed genes (DEGs) were identified, respectively. Various families of transcription factors (TFs), mainly AP2, MYB, and bHLH, were identified and might be linked to salt tolerance. Gene Ontology (GO) analysis of DEGs revealed that the structure and composition of the cell wall and cytoskeleton may be crucial in the response to salt stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs showed a significant enrichment of the pentose and glucuronate interconversion pathway, which is associated with cell wall metabolism after 24 and 48 h of salt treatment. Based on GO and KEGG analyses of DEGs, the pentose and glucuronate interconversion pathway was selected for further investigation. AP2, MYB, and bHLH were found to be correlated with the functional genes in this pathway based on a correlation network. This study provides the groundwork for understanding the key pathways and gene networks in response to salt stress, thereby providing a theoretical basis for improving salt tolerance in Aquilegia vulgaris.

Combining Genetic and Transcriptomic Approaches to Identify Transporter-Coding Genes as Likely Responsible for a Repeatable Salt Tolerance QTL in Citrus

The excessive accumulation of chloride (Cl-) in leaves due to salinity is frequently related to decreased yield in citrus. Two salt tolerance experiments to detect quantitative trait loci (QTLs) for leaf concentrations of Cl-, Na+, and other traits using the same reference progeny derived from the salt-tolerant Cleopatra mandarin (Citrus reshni) and the disease-resistant donor Poncirus trifoliata were performed with the aim to identify repeatable QTLs that regulate leaf Cl- (and/or Na+) exclusion across independent experiments in citrus, as well as potential candidate genes involved. A repeatable QTL controlling leaf Cl- was detected in chromosome 6 (LCl-6), where 23 potential candidate genes coding for transporters were identified using the C. clementina genome as reference. Transcriptomic analysis revealed two important candidate genes coding for a member of the nitrate transporter 1/peptide transporter family (NPF5.9) and a major facilitator superfamily (MFS) protein. Cell wall biosynthesis- and secondary metabolism-related processes appeared to play a significant role in differential gene expression in LCl-6. Six likely gene candidates were mapped in LCl-6, showing conserved synteny in C. reshni. In conclusion, markers to select beneficial Cleopatra mandarin alleles of likely candidate genes in LCl-6 to improve salt tolerance in citrus rootstock breeding programs are provided.

Evaluating the genotoxicity of salinity stress and secondary products gene manipulation in lime, Citrus aurantifolia, plants

Salinity is a significant abiotic stress that has a profound effect on growth, the content of secondary products, and the genotoxicity of cells. Lime, Citrus aurantifolia, is a popular plant belonging to the family Rutaceae. The interest in cultivating this plant is due to the importance of its volatile oil, which is included in many pharmaceutical industries, but C. aurantifolia plants are affected by the NaCl salinity levels. In the present study, a comet assay test has been applied to evaluate the genotoxic impact of salinity at 0, 50, 100, and 200 mM of NaCl on C. aurantifolia tissue-cultured plants. Furthermore, terpene gene expression was investigated using a semi-quantitative real-time polymerase chain reaction. Results from the two analyses revealed that 200 mM of NaCl stress resulted in high levels of severe damage to the C. aurantifolia plants' DNA tail 21.8%, tail length 6.56 µm, and tail moment 3.19 Unit. The relative highest expression of RtHK and TAT genes was 2.08, and 1.693, respectively, when plants were exposed to 200 mM of NaCl, whereas pv4CL2RT expressed 1.50 in plants subjected to 100 mM of NaCl. The accumulation of transcripts for the RTMYB was 0.951 when plants were treated with NaCl at 50 mM, and RtGPPS gene was significantly decreased to 0.446 during saline exposure at 100 mM. We conclude that the comet assay test offers an appropriate tool to detect DNA damage as well as RtHK, TAT, and pv4CL2RT genes having post-transcriptional regulation in C. aurantifolia plant cells under salinity stress. Future studies are needed to assess the application of gene expression and comet assay technologies using another set of genes that show vulnerability to different stresses on lime and other plants.

Transcriptome Analysis of Differentially Expressed Genes Associated with Salt Stress in Cowpea (Vigna unguiculata L.) during the Early Vegetative Stage

Cowpea (Vigna unguiculata (L.), 2n = 22) is a tropical crop grown in arid and semiarid regions that is tolerant to abiotic stresses such as heat and drought. However, in these regions, salt in the soil is generally not eluted by rainwater, leading to salt stress for a variety of plant species. This study was conducted to identify genes related to salt stress using the comparative transcriptome analysis of cowpea germplasms with contrasting salt tolerance. Using the Illumina Novaseq 6000 platform, 1.1 billion high-quality short reads, with a total length of over 98.6 billion bp, were obtained from four cowpea germplasms. Of the differentially expressed genes identified for each salt tolerance type following RNA sequencing, 27 were shown to exhibit significant expression levels. These candidate genes were subsequently narrowed down using reference-sequencing analysis, and two salt stress-related genes (Vigun_02G076100 and Vigun_08G125100) with single-nucleotide polymorphism (SNP) variation were selected. Of the five SNPs identified in Vigun_02G076100, one that caused significant amino acid variation was identified, while all nucleotide variations in Vigun_08G125100 was classified as missing in the salt-resistant germplasms. The candidate genes and their variation, identified in this study provide, useful information for the development of molecular markers for cowpea breeding programs.

Co-overexpression of AtSAT1 and EcPAPR improves seed nutritional value in maize

Maize seeds synthesize insufficient levels of the essential amino acid methionine (Met) to support animal and livestock growth. Serine acetyltransferase1 (SAT1) and 3'-phosphoadenosine-5'-phosphosulfate reductase (PAPR) are key control points for sulfur assimilation into Cys and Met biosynthesis. Two high-MET maize lines pRbcS:AtSAT1 and pRbcS:EcPAPR were obtained through metabolic engineering recently, and their total Met was increased by 1.4- and 1.57-fold, respectively, compared to the wild type. The highest Met maize line, pRbcS:AtSAT1-pRbcS:EcPAPR, was created by stacking the two transgenes, causing total Met to increase 2.24-fold. However, the pRbcS:AtSAT1-pRbcS:EcPAPR plants displayed progressively severe defects in plant growth, including early senescence, stunting, and dwarfing, indicating that excessive sulfur assimilation has an adverse effect on plant development. To explore the mechanism of correlation between Met biosynthesis in maize leaves and storage proteins in developing endosperm, the transcriptomes of the sixth leaf at stage V9 and 18 DAP endosperm of pRbcS:AtSAT1, pRbcS:AtSAT1-pRbcS:EcPAPR, and the null segregants were quantified and analyzed. In pRbcS:AtSAT1-pRbcS:EcPAPR, 3274 genes in leaves (1505 up- and 1769 downregulated) and 679 genes in the endosperm (327 up- and 352 downregulated) were differentially expressed. Gene ontology (GO) and KEGG (Kyoto encyclopedia of genes and genomes) analyses revealed that many genes were associated with Met homeostasis, including transcription factors and genes involved in cysteine and Met metabolism, glutathione metabolism, plant hormone signal transduction, and oxidation-reduction. The data from gene network analysis demonstrated that two genes, serine/threonine-protein kinase (CCR3) and heat shock 70 kDa protein (HSP), were localized in the core of the leaves and endosperm regulation networks, respectively. The results of this study provide insights into the diverse mechanisms that underlie the ideal establishment of enhanced Met levels in maize seeds.

Dodder-transmitted mobile systemic signals activate a salt-stress response characterized by a transcriptome change in Citrus sinensis

Citrus is an essential horticultural fruit whose yield and quality are affected by salinity all over the world. The recognition and adaptive regulation of citrus against salt stress are important areas for cultivar improvement, but the vascular system signal transduction mechanism of the plant response to salt stress remains elusive. In this study, we constructed a dodder (Cuscuta spp.) linked Hamlin sweet orange (Citrus sinensis) plant community in which deliver a vascular signal through the dodder in response to salt stress. RNA-seq technology was used to analyze the gene expression profile of citrus leaves after salt treatment. The results showed that a vascular signal was transmitted to a dodder-linked host plant, triggering a transcriptional response to salt stress. However, the phenotypic and transudative ability of the dodder changed after 24 h. The salt treatment group (Group S) and the dodder-linked group (Group D) respectively contained 1,472 and 557 differentially expressed genes (DEGs). 454 of which were common to both groups. The results of our analysis revealed that the gene expression categories in Group D represented a highly consistent trend compared to the group S plants, indicating that the dodder-bridged vascular signals activated the stress-response of citrus leaves for transcriptomic reconfiguration. The KEGG pathway database and an analysis of key drivers revealed that phenylpropanoid biosynthesis, photosynthesis-antenna proteins, starch and sucrose metabolism, plant hormone signal transduction, circadian rhythm, and MAPK signaling pathways were significantly enriched as the critical genes during salt stress. A systemic signal in the dodder-bridged host significantly regulated abiotic stress-related secondary metabolic pathways, including those for phenylpropanoids, lignin, and lignans. The physiological indexes of photosynthetic intensity, respiration, and attractiveness among communities supported the transcriptional changes. Thus, our results indicate that salt stress-induced vascular system signals can be transmitted through the vascular system of a dodder linking citrus plants, revealing the genetic regulation and physiological changes of citrus leaves responding to plant stress signal transmission.

Comparative transcriptome analysis unveiling reactive oxygen species scavenging system of Sonneratia caseolaris under salinity stress

Many mangrove forests have undergone major changes as a result of human activity and global climate change. Sonneratia caseolaris is a common tree located in inner mangroves, and its range extends inland along tidal creeks, as far as the influence of salinity extends. This study investigated the physiological and molecular response mechanisms of S. caseolaris by analyzing its antioxidant defense capacity, including its differentially expressed genes (DEGs) under similar salt stress conditions. Salt treatment significantly affected the osmoprotectants and lipid peroxidation in S. caseolaris seedlings, which increased proline (Pro) content by 31.01-54.90% during all sample periods and decreased malonaldehyde (MDA) content by 12.81 and 18.17% at 25 and 40 days under 3.0% NaCl treatment. Antioxidant enzyme activities increased significantly following 3.0% NaCl treatment. Transcriptome analysis following De novo assembly showed 26,498 matched unigenes. The results showed that 1,263 DEGs responded to transcription factors (TFs) and plant phytohormones and mediated oxidoreductase activity to scavenge reactive oxygen species (ROS) in the control vs. 3.0% NaCl comparison. In addition, the transcription levels of genes associated with auxin and ethylene signal transduction also changed. Under salt stress, ROS scavenging genes (POD, CAT, and APX) and part of AP2, MYB, NAC, C2C2, bHLH, and WRKY TFs were upregulated. This study identified important pathways and candidate genes involved in S. caseolaris salinity tolerance and provided suggestions for further research into the mechanisms of salt tolerance in S. caseolaris.

Transcriptomic Profile Analysis of Populus talassica × Populus euphratica Response and Tolerance under Salt Stress Conditions

A new Populus variety with a strong salt tolerance was obtained from cross breeding P. talassica as the female parent and P. euphratica as the male parent. In order to elucidate the molecular mechanism and find out the major differentially expressed genes of salt tolerance of P. talassica × P. euphratica, after being subjected to salt stress, at 0, 200, and 400 mmol/L NaCl, the root, stem, and leaf transcriptomes (denoted as R0, S0, and L0; R200, S200, and L200; and R400, S400, and L400, respectively) of P. talassica × P. euphratica were sequenced. In total, 41,617 differentially expressed genes (DEGs) were identified in all the comparison groups with 21,603 differentially upregulated genes and 20,014 differentially downregulated genes. Gene Ontology analysis showed that DEGs were significantly enriched in biological processes that may be involved in salt stress, such as ‘cell communication’, ‘ion transport’, ‘signaling’, and signal ‘transmission’. Kyoto Encyclopedia of Genes and Genomes analysis showed that DEGs were mainly enriched in pathways of ‘plant–pathogen interaction’, ‘carbon metabolism’, and ‘plant hormone signal transmission’. The pathways and related gene information formed a basis for future research on the mechanisms of salt stress, the development of molecular markers, and the cloning of key genes in P. talassica × P. euphratica.

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.

Meta-QTL analysis and candidate genes identification for various abiotic stresses in maize (Zea mays L.) and their implications in breeding programs

Global climate change leads to the concurrence of a number of abiotic stresses including moisture stress (drought, waterlogging), temperature stress (heat, cold), and salinity stress, which are the major factors affecting maize production. To develop abiotic stress tolerance in maize, many quantitative trait loci (QTL) have been identified, but very few of them have been utilized successfully in breeding programs. In this context, the meta-QTL analysis of the reported QTL will enable the identification of stable/real QTL which will pave a reliable way to introgress these QTL into elite cultivars through marker-assisted selection. In this study, a total of 542 QTL were summarized from 33 published studies for tolerance to different abiotic stresses in maize to conduct meta-QTL analysis using BiomercatorV4.2.3. Among those, only 244 major QTL with more than 10% phenotypic variance were preferably utilised to carry out meta-QTL analysis. In total, 32 meta-QTL possessing 1907 candidate genes were detected for different abiotic stresses over diverse genetic and environmental backgrounds. The MQTL2.1, 5.1, 5.2, 5.6, 7.1, 9.1, and 9.2 control different stress-related traits for combined abiotic stress tolerance. The candidate genes for important transcription factor families such as ERF, MYB, bZIP, bHLH, NAC, LRR, ZF, MAPK, HSP, peroxidase, and WRKY have been detected for different stress tolerances. The identified meta-QTL are valuable for future climate-resilient maize breeding programs and functional validation of candidate genes studies, which will help to deepen our understanding of the complexity of these abiotic stresses.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01294-9.

Physiological, biochemical, and molecular aspects of grafting in fruit trees

Grafting is a widely used practice for asexual propagation of fruit trees. Many physiological, biochemical, and molecular changes occur upon grafting that can influence important horticultural traits. This technology has many advantages, including avoidance of juvenility, modifying the scion architecture, improving productivity, adapting scion cultivars to unfavourable environmental conditions, and developing traits in resistance to insect pests, bacterial and fungal diseases. A limitation of grafting is scion-rootstock incompatibility. It may be caused by many factors, including insufficient genetic proximity, physiological or biochemical factors, lignification at the graft union, poor graft architecture, insufficient cell recognition between union tissues, and metabolic differences in the scion and the rootstock. Plant hormones, like auxin, ethylene (ET), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), and jasmonic acid (JA) orchestrate several crucial physiological and biochemical processes happening at the site of the graft union. Additionally, epigenetic changes at the union affect chromatin architecture by DNA methylation, histone modification, and the action of small RNA molecules. The mechanism triggering these effects likely is affected by hormonal crosstalk, protein and small molecules movement, nutrients uptake, and transport in the grafted trees. This review provides an overview of the basis of physiological, biochemical, and molecular aspects of fruit tree grafting between scion and rootstock.

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.

Comparative transcriptome analyses of maize seedling root responses to salt stress

Salt stress affects crop yield by limiting growth and delaying development. In this study, we constructed 16 transcriptome libraries from maize seedling roots using two maize lines, with contrasting salt tolerance, that were exposed to salt stress for 0, 6, 18 and 36 h. In total, 6,584 differential expression genes (DEGs; 3,669 upregulated, 2,915 downregulated) were induced in the salt-sensitive line and 6,419 DEGs (3,876 upregulated, 2,543 downregulated) were induced in the salt-tolerant line. Several DEGs common to both lines were enriched in the ABA signaling pathway, which was presumed to coordinate the process of maize salt response. A total of 459 DEGs were specifically induced in the salt-tolerant line and represented candidate genes responsible for high salt-tolerance. Expression pattern analysis for these DEGs indicated that the period between 0 and 6 h was a crucial period for the rapid response of the tolerant genes under salt stress. Among these DEGs, several genes, Aux/IAA, SAUR, and CBL-interacting kinase have been reported to regulate salt tolerance. In addition, the transcription factors WRKY, bZIP and MYB acted as regulators in the salt-responsive regulatory network of maize roots. Our findings will contribute to understanding of the mechanism on salt response and provide references for functional gene revelation in plants.

Comparative transcriptome profile analysis of rice varieties with different tolerance to zinc deficiency

Zinc (Zn) is an indispensable element for rice growth. Zn deficiency results in brown blotches and streaks 2-3 weeks after transplanting, as well as stunting, reduced tillering, and low productivity of rice plants. These processes are controlled by different families of expressed genes. A comparative transcriptome profile analysis was conducted using the roots of two Zn deficiency tolerant varieties (UCP122 and KALIBORO26) and two sensitive varieties (IR26 and IR64) by merging data from untreated control (CK) and Zn deficiency treated samples. Results revealed a total of 4,688 differentially expressed genes (DEGs) between the normal Zn and deficient conditions, with 2,702 and 1,489 unique DEGs upregulated and downregulated, respectively. Functional enrichment analysis identified transcription factors (TFs), such as WRKY, MYB, ERF, and bHLH which are important in the regulation of the Zn deficiency response. Furthermore, chitinases, jasmonic acid, and phenylpropanoid pathways were found to be important in the Zn deficiency response. The metal tolerance protein (MTP) genes also appeared to play an important role in conferring tolerance to Zn deficiency. A heavy metal-associated domain-containing protein 7 was associated with tolerance to Zn deficiency and negatively regulated downstream genes. Collectively, our findings provide valuable expression patterns and candidate genes for the study of molecular mechanisms underlying the response to Zn deficiency and for improvements in breeding for tolerance to Zn deficiency in rice.

Salt-responsive transcriptome analysis of triticale reveals candidate genes involved in the key metabolic pathway in response to salt stress

Triticale is tolerant of many environmental stresses, especially highly resistant to salt stress. However, the molecular regulatory mechanism of triticale seedlings under salt stress conditions is still unclear so far. In this study, a salt-responsive transcriptome analysis was conducted to identify candidate genes or transcription factors related to salt tolerance in triticale. The root of salt-tolerant triticale cultivars TW004 with salt-treated and non-salt stress at different time points were sampled and subjected to de novo transcriptome sequencing. Total 877,858 uniquely assembled transcripts were identified and most contigs were annotated in public databases including nr, GO, KEGG, eggNOG, Swiss-Prot and Pfam. 59,280, 49,345, and 85,922 differentially expressed uniquely assembled transcripts between salt treated and control triticale root samples at three different time points (C12_vs_T12, C24_vs_T24, and C48_vs_T48) were identified, respectively. Expression profile and functional enrichment analysis of DEGs found that some DEGs were significantly enriched in metabolic pathways related to salt tolerance, such as reduction–oxidation pathways, starch and sucrose metabolism. In addition, several transcription factor families that may be associated with salt tolerance were also identified, including AP2/ERF, NAC, bHLH, WRKY and MYB. Furthermore, 14 DEGs were selected to validate the transcriptome profiles via quantitative RT-PCR. In conclusion, these results provide a foundation for further researches on the regulatory mechanism of triticale seedlings adaptation to salt stress in the future.

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.

Identification and characterization of differentially expressed genes in the rice root following exogenous application of spermidine during salt stress

Salinity is a major limiting factor in crop production. Exogenous spermidine (spd) effectively ameliorates salt injury, though the underlying molecular mechanism is poorly understood. We have used a suppression subtractive hybridization method to construct a cDNA library that has identified up-regulated genes from rice root under the treatment of spd and salt. Total 175 high-quality ESTs of about 100-500 bp in length with an average size of 200 bp are isolated, clustered and assembled into a collection of 62 unigenes. Gene ontology analysis using the KEGG pathway annotation database has classified the unigenes into 5 main functional categories and 13 subcategories. The transcripts abundance has been validated using Real-Time PCR. We have observed seven different types of post-translational modifications in the DEPs. 44 transmembrane helixes are predicted in 6 DEPs. This above information can be used as first-hand data for dissecting the administrative role of spd during salinity.

Nitric oxide modulating ion balance in Hylotelephium erythrostictum roots subjected to NaCl stress based on the analysis of transcriptome, fluorescence, and ion fluxes

Soil salinization is one of the main stress factors that affect both growth and development of plants. Hylotelephium erythrostictum exhibits strong resistance to salt, but the underlying genetic mechanisms remain unclear. In this study, hydroponically cultured seedlings of H. erythrostictum were exposed to 200 mM NaCl. RNA-Seq was used to determine root transcriptomes at 0, 5, and 10 days, and potential candidate genes with differential expression were analyzed. Transcriptome sequencing generated 89.413 Gb of raw data, which were assembled into 111,341 unigenes, 82,081 of which were annotated. Differentially expressed genes associated to Na+ and K+ transport, Ca2+ channel, calcium binding protein, and nitric oxide (NO) biosynthesis had high expression levels in response to salt stress. An increased fluorescence intensity of NO indicated that it played an important role in the regulation of the cytosolic K+/Na+ balance in response to salt stress. Exogenous NO donor and NO biosynthesis inhibitors significantly increased and decreased the Na+ efflux, respectively, thus causing the opposite effect for K+ efflux. Moreover, under salt stress, exogenous NO donors and NO biosynthesis inhibitors enhanced and reduced Ca2+ influx, respectively. Combined with Ca2+ reagent regulation of Na+ and K+ fluxes, this study identifies how NaCl-induced NO may function as a signaling messenger that modulates the K+/Na+ balance in the cytoplasm via the Ca2+ signaling pathway. This enhances the salt resistance in H. erythrostictum roots.

Tissue-specific respiratory burst oxidase homolog-dependent H2O2 signaling to the plasma membrane H+-ATPase confers potassium uptake and salinity tolerance in Cucurbitaceae

Potassium (K+) is a critical determinant of salinity tolerance, and H2O2 has been recognized as an important signaling molecule that mediates many physiological responses. However, the details of how H2O2 signaling regulates K+ uptake in the root under salt stress remain elusive. In this study, salt-sensitive cucumber and salt-tolerant pumpkin which belong to the same family, Cucurbitaceae, were used to answer the above question. We show that higher salt tolerance in pumpkin was related to its superior ability for K+ uptake and higher H2O2 accumulation in the root apex. Transcriptome analysis showed that salinity induced 5816 (3005 up- and 2811 down-) and 4679 (3965 up- and 714 down-) differentially expressed genes (DEGs) in cucumber and pumpkin, respectively. DEGs encoding NADPH oxidase (respiratory burst oxidase homolog D; RBOHD), 14-3-3 protein (GRF12), plasma membrane H+-ATPase (AHA1), and potassium transporter (HAK5) showed higher expression in pumpkin than in cucumber under salinity stress. Treatment with the NADPH oxidase inhibitor diphenylene iodonium resulted in lower RBOHD, GRF12, AHA1, and HAK5 expression, reduced plasma membrane H+-ATPase activity, and lower K+ uptake, leading to a loss of the salinity tolerance trait in pumpkin. The opposite results were obtained when the plants were pre-treated with exogenous H2O2. Knocking out of RBOHD in pumpkin by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9] editing of coding sequences resulted in lower root apex H2O2 and K+ content and GRF12, AHA1, and HAK5 expression, ultimately resulting in a salt-sensitive phenotype. However, ectopic expression of pumpkin RBOHD in Arabidopsis led to the opposite effect. Taken together, this study shows that RBOHD-dependent H2O2 signaling in the root apex is important for pumpkin salt tolerance and suggests a novel mechanism that confers this trait, namely RBOHD-mediated transcriptional and post-translational activation of plasma membrane H+-ATPase operating upstream of HAK5 K+ uptake transporters.

Physiological and Transcriptomic Analysis Reveals Distorted Ion Homeostasis and Responses in the Freshwater Plant Spirodela polyrhiza L. under Salt Stress

Duckweeds are a family of freshwater angiosperms with morphology reduced to fronds and propagation by vegetative budding. Unlike other angiosperm plants such as Arabidopsis and rice that have physical barriers between their photosynthetic organs and soils, the photosynthetic organs of duckweeds face directly to their nutrient suppliers (waters), therefore, their responses to salinity may be distinct. In this research, we found that the duckweed Spirodela polyrhiza L. accumulated high content of sodium and reduced potassium and calcium contents in large amounts under salt stress. Fresh weight, Rubisco and AGPase activities, and starch content were significantly decreaseded in the first day but recovered gradually in the following days and accumulated more starch than control from Day 3 to Day 5 when treated with 100 mM and 150 mM NaCl. A total of 2156 differentially expressed genes were identified. Overall, the genes related to ethylene metabolism, major CHO degradation, lipid degradation, N-metabolism, secondary metabolism of flavonoids, and abiotic stress were significantly increased, while those involved in cell cycle and organization, cell wall, mitochondrial electron transport of ATP synthesis, light reaction of photosynthesis, auxin metabolism, and tetrapyrrole synthesis were greatly inhibited. Moreover, salt stress also significantly influenced the expression of transcription factors that are mainly involved in abiotic stress and cell differentiation. However, most of the osmosensing calcium antiporters (OSCA) and the potassium inward channels were downregulated, Na⁺/H⁺ antiporters (SOS1 and NHX) and a Na⁺/Ca²⁺ exchanger were slightly upregulated, but most of them did not respond significantly to salt stress. These results indicated that the ion homeostasis was strongly disturbed. Finally, the shared and distinct regulatory networks of salt stress responses between duckweeds and other plants were intensively discussed. Taken together, these findings provide novel insights into the underlying mechanisms of salt stress response in duckweeds, and can be served as a useful foundation for salt tolerance improvement of duckweeds for the application in salinity conditions.

Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as "photosynthesis" and "starch and sucrose metabolism," were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai rice

Khao Dawk Mali 105 (KDML105) rice is one of the most important crops of Thailand. It is a challenging task to identify the genes responding to salinity in KDML105 rice. The analysis of the gene co-expression network has been widely performed to prioritize significant genes, in order to select the key genes in a specific condition. In this work, we analyzed the two-state co-expression networks of KDML105 rice under salt-stress and normal grown conditions. The clustering coefficient was applied to both networks and exhibited significantly different structures between the salt-stress state network and the original (normal-grown) network. With higher clustering coefficients, the genes that responded to the salt stress formed a dense cluster. To prioritize and select the genes responding to the salinity, we investigated genes with small partners under normal conditions that were highly expressed and were co-working with many more partners under salt-stress conditions. The results showed that the genes responding to the abiotic stimulus and relating to the generation of the precursor metabolites and energy were the great candidates, as salt tolerant marker genes. In conclusion, in the case of the complexity of the environmental conditions, gaining more information in order to deal with the co-expression network provides better candidates for further analysis.