Comparative Transcriptome Analysis of Leaves of Sour Jujube Seedlings under Salt Stress

2021 ◽  
Author(s):  
Ruiheng Lyu ◽  
Rui Wang ◽  
Cuiyun Wu ◽  
Yajing Bao ◽  
Peng Guo
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Enrichment Analysis ◽  
Northwest China ◽  
Scientific Basis ◽  
Control Group ◽  
Molecular Response ◽  
Raffinose Family Oligosaccharides ◽  
Ecological Value ◽  
Significant Differential Expression

Abstract Sour jujube ( Ziziphus jujuba Mill. var. spinosa ) is a native tree species in China. It is often used as the rootstock of jujube, its fruit can also be used as medicine. So it has high scientific and ecological value. Sour jujube is mostly planted in Northwest China and has extremely high salt tolerance. But the molecular mechanism of its salt tolerance is rarely studied. This study was carried out in the laboratory of Environment and Resources College of Dalian Nationalities University, two treatments were performed on the leaves of sour jujuba seedlings, the experimental group (H3): 300 mM Nacl for 3 h, and the control group (CK): sterile water for 3 h. A total of 47.02GB of valid data and 32730 annotated genes were obtained. Based on the analysis of gene expression in the comparison group, a total of 2295 genes with significant differential expression were obtained, of which 807 were up-regulated and 1488 were down-regulated. According to gene function annotation and enrichment analysis, we finally screened 148 genes. These genes were mainly involved in signal transduction of plant hormones (38), homeostasis of cell walls (27), secondary metabolism of organic matter (32), redox reactions (20) in leaves of sour jujuba seedlings under salt stress. It was also accompanied by some stress-related transcription factors (31). In addition, under salt stress, raffinose family oligosaccharides (RFO) metabolism of sour jujube seedlings was accelerated. Studying the molecular response of sour jujuba seedlings under salt stress provides a scientific basis for its cultivation in saline areas and is beneficial to further improve the salt tolerance of grafted jujube trees.

scholarly journals Comprehensive transcriptome and metabolome profiling reveal metabolic mechanisms of Nitraria sibirica Pall. to salt stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huanyong Li ◽  
Xiaoqian Tang ◽  
Xiuyan Yang ◽  
Huaxin Zhang
Keyword(s):  
Salt Stress ◽  
Amino Acid ◽  
Salt Tolerance ◽  
Metabolic Pathways ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Sulfur Metabolism ◽  
Enrichment Analysis ◽  
Extracellular Region ◽  
Nitraria Sibirica

AbstractNitraria sibirica Pall., a typical halophyte that can survive under extreme drought conditions and in saline-alkali environments, exhibits strong salt tolerance and environmental adaptability. Understanding the mechanism of molecular and physiological metabolic response to salt stress of plant will better promote the cultivation and use of halophytes. To explore the mechanism of molecular and physiological metabolic of N. sibirica response to salt stress, two-month-old seedlings were treated with 0, 100, and 400 mM NaCl. The results showed that the differentially expressed genes between 100 and 400 mmol L−1 NaCl and unsalted treatment showed significant enrichment in GO terms such as binding, cell wall, extemal encapsulating structure, extracellular region and nucleotide binding. KEGG enrichment analysis found that NaCl treatment had a significant effect on the metabolic pathways in N. sibirica leaves, which mainly including plant-pathogen interaction, amino acid metabolism of the beta alanine, arginine, proline and glycine metabolism, carbon metabolism of glycolysis, gluconeogenesis, galactose, starch and sucrose metabolism, plant hormone signal transduction and spliceosome. Metabolomics analysis found that the differential metabolites between the unsalted treatment and the NaCl treatment are mainly amino acids (proline, aspartic acid, methionine, etc.), organic acids (oxaloacetic acid, fumaric acid, nicotinic acid, etc.) and polyhydric alcohols (inositol, ribitol, etc.), etc. KEGG annotation and enrichment analysis showed that 100 mmol L−1 NaCl treatment had a greater effect on the sulfur metabolism, cysteine and methionine metabolism in N. sibirica leaves, while various amino acid metabolism, TCA cycle, photosynthetic carbon fixation and sulfur metabolism and other metabolic pathways have been significantly affected by 400 mmol L−1 NaCl treatment. Correlation analysis of differential genes in transcriptome and differential metabolites in metabolome have found that the genes of AMY2, BAM1, GPAT3, ASP1, CML38 and RPL4 and the metabolites of L-cysteine, proline, 4-aminobutyric acid and oxaloacetate played an important role in N. sibirica salt tolerance control. This is a further improvement of the salt tolerance mechanism of N. sibirica, and it will provide a theoretical basis and technical support for treatment of saline-alkali soil and the cultivation of halophytes.

scholarly journals Molecular response of canola to salt stress: insights on tolerance mechanisms

2018 ◽  
Author(s):  
Reza Shokri-Gharelo ◽  
Pouya Motie-Noparvar
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Edible Oils ◽  
Biodiesel Fuel ◽  
Molecular Response ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Brassica Napus L ◽  
Salt Response ◽  
The Many

Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests where researchers should focus future studies.

scholarly journals Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks

2021 ◽  
Vol 12 ◽  
Author(s):  
Pajaree Sonsungsan ◽  
Pheerawat Chantanakool ◽  
Apichat Suratanee ◽  
Teerapong Buaboocha ◽  
Luca Comai ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Time Course ◽  
Rice Variety ◽  
Enrichment Analysis ◽  
Normal Growth ◽  
Growth Conditions ◽  
Pathway Enrichment Analysis ◽  
Key Genes

Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of ‘Luang Pratahn’ rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.

scholarly journals Transcriptomic profile analysis of the halophyte Suaeda rigida response and tolerance under NaCl stress

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhan-Jiang Han ◽  
Yang Sun ◽  
Min Zhang ◽  
Jun-Tuan Zhai
Keyword(s):  
Cell Wall ◽  
Salt Tolerance ◽  
Protein Transport ◽  
Profile Analysis ◽  
Nitrogen Compound ◽  
Enrichment Analysis ◽  
Plant Type ◽  
Ecological Value ◽  
Annotation Database ◽  
Cell Wall Biogenesis

Abstract Suaeda rigida is a lignified, true haplotype that predominantly grows in the Tarim basin, China. It has significant economic and ecological value. Herein, with aim to determine the genes associated with salt tolerance, transcriptome sequencing was performed on its stem, leaves and root over three set NaCl gradients regimens at treatment intervals of 3 h and 5 days. From our findings, we identified 829,095 unigenes, with 331,394 being successfully matched to at least one annotation database. In roots, under 3 h treatment, no up-regulated DEGs were identified in 100 and 500 mM NaCl treated samples. Under 5 days treatment, 97, 60 and 242 up-regulated DEGs were identified in 100, 300, 500 mM NaCl treated samples, respectively. We identified 50, 22 and 255 down-regulated DEGs in 100, 300, 500 mM NaCl treated samples, respectively. GO biological process enrichment analysis established that down-regulated DEGs were associated with nitrogen compound transport, organic substance transport and intracellular protein transport while the up-regulated genes were enriched in cell wall biogenesis, such as plant-type cell wall biogenesis, cell wall assembly, extracellular matrix organization and plant-type cell wall organization. These findings provide valuable knowledge on genes associated with salt tolerance of Suaeda rigida, and can be applied in other downstream haplotype studies.

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

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Chaohong Deng ◽  
Zhibin Zhang ◽  
Guorong Yan ◽  
Fan Wang ◽  
Lianjia Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
De Novo ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Time Points

AbstractTriticale 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.

scholarly journals RNA-Seq And WGCNA Analysis Identifies Salt-Responsive Genes In Pear (Pyrus Ussuriensis Maxim)

2021 ◽  
Author(s):  
Qiming Chen ◽  
Huizhen Dong ◽  
Zhihua Xie ◽  
Kaijie Qi ◽  
Xiaosan Huang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Plant Hormone ◽  
Enrichment Analysis ◽  
Salt Resistance ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Signal Transduction Pathways ◽  
Rna Seq

Abstract Background: Pear is one of the most abundant fruit crops and has been cultivated world-wide. However, the salt injury events caused by increased salinity limited the distribution and sustainable production of pear crops. Therefore, it is needed to take further efforts to understand the genetics and mechanisms of salt tolerance to improved salt resistance and productivity.Results: In this work, we analyzed the dynamic transcriptome of pear (Pyrus ussuriensis Maxim) under salt stress by using RNA-Seq and WGCNA. A total of 3540, 3831, 8374, 6267 and 5381 genes were identified that were differentially expressed after exposure to 200mM NaCl for 4, 6, 12, 24 and 48 hours, respectively, and 1163 genes were shared among the five comparisons. KEGG enrichment analysis of these DEGs (differentially expressed genes) revealed that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly enriched. Meanwhile, 622 DEGs identified from WGCNA were highly correlated with these pathways, and some of them were able to indicate the salt tolerance of pear varieties. In addition, we provide a network to demonstrate the time-sequence of these co-expressed MAPK and hormone related genes.Conclusion: A comprehensive analysis about salt-responsive pear transcriptome were performed by using RNA-Seq and WGCNA. We demonstrated that “MAPK signaling” and “Plant hormone signal transduction” pathways were highly recruited during salt stress, and provided new insights into the metabolism of plant hormones related signaling at transcriptome level underlying salt resistance in pear. The dynamic transcriptome data obtained from this study and these salt-sensitive DEGs may provide potential genes as suitable targets for further biotechnological manipulation to improve pear salt tolerance.

scholarly journals Molecular response of canola to salt stress: insights on tolerance mechanisms

2018 ◽  
Author(s):  
Reza Shokri-Gharelo ◽  
Pouya Motie-Noparvar
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Edible Oils ◽  
Biodiesel Fuel ◽  
Molecular Response ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Brassica Napus L ◽  
Salt Response ◽  
The Many

Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests where researchers should focus future studies.

scholarly journals Molecular response of canola to salt stress: insights on tolerance mechanisms

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4822 ◽  
Author(s):  
Reza Shokri-Gharelo ◽  
Pouya Motie Noparvar
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Edible Oils ◽  
Biodiesel Fuel ◽  
Molecular Response ◽  
Salt Tolerant ◽  
Tolerance Mechanisms ◽  
Brassica Napus L ◽  
Salt Response ◽  
The Many

Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests what researchers should focus on in future studies.

scholarly journals The Effects of Saline Stress on the Growth of Two Shrub Species in the Qaidam Basin of Northwestern China

2019 ◽  
Vol 11 (3) ◽  
pp. 828 ◽  
Author(s):  
Tan Zhang ◽  
Zhenzhong Zhang ◽  
Yuanhang Li ◽  
Kangning He
Keyword(s):  
Salt Tolerance ◽  
Qaidam Basin ◽  
Northwest China ◽  
Scientific Basis ◽  
Soil Salinization ◽  
Saline Stress ◽  
Photosynthetic Parameters ◽  
Lycium Barbarum ◽  
Use Efficiency ◽  
Selection Of

Soil salinization is a serious issue in the Qaidam Basin and significantly limits economic development. To explore the salt tolerance of two shrubs in this area, we determined several parameters, including the Soil and Plant Analyzer Development (SPAD), net photosynthetic rate (Pn), transpiration rate (Tr), intercellular carbon dioxide (Ci, μmol mol−1), stomatal conductance (Gs, umol m−2s−1), and water use efficiency (WUE) under different salt concentrations (0, 100, 200, 300, and 400 mmol·L−1). In addition, the shrubs of Elaeagnus angustifolia and Lycium barbarum of salt tolerance were evaluated. The photosynthetic parameters of E. angustifolia were more sensitive to salinity than those of L. barbarum, and SPAD, Pn, Tr, and WUE of E. angustifolia decreased significantly with increasing salt concentrations (P < 0.05), while in L. barbarum, SPAD, Pn, and Tr decreased significantly with increasing salt concentrations (P < 0.05), but the WUE of L. barbarum showed no significantly variation under the salt concentration gradient. The results of correlation matrix of photosynthetic index also indicated that the minimum salt tolerance of E. angustifolia and L. barbarum were 108.4 and 246.3 mmol·L−1, respectively. Our results provide a scientific basis for the selection of salt-tolerant plant species in of northwest China.

scholarly journals Comparison Of Tolerant And Susceptible Cultivars Revealed The Roles of Circular RNAs In Rice Responding To Salt Stress

2021 ◽  
Author(s):  
Junliang Yin ◽  
Yike Liu ◽  
Lin Lu ◽  
Jian Zhang ◽  
Shaoyu Chen ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Plant Stress ◽  
Enrichment Analysis ◽  
Introgression Line ◽  
Circular Rnas ◽  
Ion Transportation ◽  
Different Response

Abstract As a newly characterized class of noncoding RNAs, circular RNAs (circRNAs) have been identified in many plant species, and play important roles in plant stress responses. However, little is known about how salt stress mediates the expression of circRNAs in rice. In this study, we identified circRNAs from root tissues of salt-susceptible recipient cultivar 93-11 and salt-tolerant introgression line 9L136. A total of 190 circRNAs were identified. Among them, 93 circRNAs were differentially expressed under salt stress in 93-11 (36 up- and 57 down-regulated) and 95 in 9L136 (46 up- and 49 down-regulated). Salt stress significantly decreased the average expression level of circRNAs in 93-11, but circRNA expression levels were slightly increased in 9L136, suggesting that circRNAs had different response patterns in these two cultivars. Function annotation and enrichment analysis indicated that, through cis-regulation and circRNA-miRNA-mRNA network regulation, those induced circRNAs were commonly involved in transcription, signal transduction, ion transportation, and secondary metabolism. Compared to 93-11, salt-induced circRNAs in line 9L136 targeted more stress response genes participating in transcription regulation, ion transportation, and signal transduction, which may contribute to the salt tolerance of 9L136. Summarily, this study revealed the common response of rice circRNAs to salt stress, and the possible circRNA-related salt tolerance mechanisms of 9L136.

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