scholarly journals Comprehensive analysis of transcriptional regulation and functional genes induced by alkaline salt stress in roots of two switchgrass (Panicum virgatum L.) genotypes

2020 ◽  
Author(s):  
Pan Zhang ◽  
Tianqi Duo ◽  
Fengdan Wang ◽  
Xunzhong Zhang ◽  
Zouzhuan Yang ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Ion Homeostasis ◽  
Comprehensive Analysis ◽  
Functional Genes ◽  
Antioxidant Systems ◽  
Limiting Factor ◽  
Rna Seq ◽  
Alkaline Salt

Abstract Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here, we investigated the physiological responses and transcriptome changes in the roots of two switchgrass genotypes under alkaline salt stress.Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1,480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1,718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.Conclusions: The alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene transcription and regulation induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

scholarly journals De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

2020 ◽  
Author(s):  
Pan Zhang ◽  
Tianqi Duo ◽  
Fengdan Wang ◽  
Xunzhong Zhang ◽  
Zouzhuan Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Salt Tolerance ◽  
De Novo ◽  
Ion Homeostasis ◽  
Antioxidant Systems ◽  
Limiting Factor ◽  
Rna Seq ◽  
Alkaline Salt ◽  
Gene Expression Dynamic

Abstract Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here, we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkali-tolerant genotype) and AM-314/MS-155 (alkali-sensitive genotype) under alkaline salt stress.Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1,480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1,718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.Conclusions: The alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

scholarly journals De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pan Zhang ◽  
Tianqi Duo ◽  
Fengdan Wang ◽  
Xunzhong Zhang ◽  
Zouzhuan Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Salt Tolerance ◽  
De Novo ◽  
Ion Homeostasis ◽  
Antioxidant Systems ◽  
Limiting Factor ◽  
Rna Seq ◽  
Alkaline Salt ◽  
Gene Expression Dynamic

Abstract Background Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress. Results Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes. Conclusions Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

scholarly journals De novo transcriptome in roots of switchgrass (Panicum virgatum L.) reveals gene expression dynamic and act network under alkaline salt stress

2021 ◽  
Author(s):  
Pan Zhang ◽  
Tianqi Duo ◽  
Fengdan Wang ◽  
Xunzhong Zhang ◽  
Zouzhuan Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Salt Tolerance ◽  
De Novo ◽  
Ion Homeostasis ◽  
Antioxidant Systems ◽  
Limiting Factor ◽  
Rna Seq ◽  
Alkaline Salt ◽  
Gene Expression Dynamic

Abstract Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM-314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress.Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1,480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1,718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes.Conclusions: Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

scholarly journals The RNA-seq transcriptomic analysis reveals genes mediating salt tolerance through rapid triggering of ion transporters in a mutant barley

2019 ◽  
Author(s):  
Sareh Yousefirad ◽  
Hassan Soltanloo ◽  
Sayad Sanaz Ramezanpour ◽  
Khalil Zaynalinezhad ◽  
Vahid Shariati
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Ion Homeostasis ◽  
High Ratio ◽  
Rna Seq ◽  
Ion Transporters ◽  
Wild Type ◽  
Specific Expression ◽  
Mutant Genotype ◽  
In The Wild

Abstract Regarding the complexity of the mechanisms of salinity tolerance, the use of isogenic lines or mutants that have the same genetic background but show different tolerance to salinity is a suitable method to reduce the analytical complexity to study these mechanisms. In the current study, whole transcriptome analysis was evaluated using RNA-seq method between a salt-tolerant mutant line “73-M4-30” and its wild-type “Zarjou” cultivar at a seedling stage after six hours of exposure to salt stress (300 mM NaCl). Transcriptome sequencing yielded 20 million reads for each genotype. A total number of 7116 transcripts with differential expression were identified, 1586 and 1479 of which were obtained with significantly increased expression in the mutant and the wild-type, respectively. In addition, the families of WRKY, ERF, AP2/EREBP, NAC, CTR/DRE, AP2/ERF, MAD, MIKC, HSF, and bZIP were identified as the important transcription factors with specific expression in the mutant genotype. The RNA-seq results were confirmed in several time points using qRT-PCR of some important salt-responsive genes. In general, the results revealed that the mutant compared to its wild-type via fast stomach closure and consequently transpiration reduction under the salt stress, saved more sodium ion in the root and decreased its transfer to the shoot, and increased the amount of potassium ion leading to the maintenance a high ratio [K+]/­[Na+] in the shoot. Moreover, it caused a reduction in photosynthesis and respiration, resulting in the use of the stored energy and the carbon for maintaining the plant tissues, which is a mechanism of salt tolerance in plants. Up-regulation of catalase, peroxidase, and ascorbate peroxidase genes, which was probably due to the more accumulation of H2O2 in the wild-type compared to the mutant. Therefore, the wild-type initiated rapid ROS signals lead to less oxidative scavenging than the mutant. The mutant increased expression in the ion transporters and the channels related to the salinity to retain the ion homeostasis. Totally, the results demonstrated that the mutant responded better to the salt stress under both the osmotic and the ionic stress phases. Less damage was observed in the mutant compared to its wild-type under the salt stress.

scholarly journals Melatonin: A Small Molecule but Important for Salt Stress Tolerance in Plants

2019 ◽  
Vol 20 (3) ◽  
pp. 709 ◽  
Author(s):  
Haoshuang Zhan ◽  
Xiaojun Nie ◽  
Ting Zhang ◽  
Shuang Li ◽  
Xiaoyu Wang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Ion Homeostasis ◽  
Free Radical Scavenger ◽  
Limiting Factors ◽  
Polyamine Metabolism ◽  
Antioxidant Systems ◽  
Radical Scavenger ◽  
Salt Stress Tolerance

Salt stress is one of the most serious limiting factors in worldwide agricultural production, resulting in huge annual yield loss. Since 1995, melatonin (N-acetyl-5-methoxytryptamine)—an ancient multi-functional molecule in eukaryotes and prokaryotes—has been extensively validated as a regulator of plant growth and development, as well as various stress responses, especially its crucial role in plant salt tolerance. Salt stress and exogenous melatonin lead to an increase in endogenous melatonin levels, partly via the phyto-melatonin receptor CAND2/PMTR1. Melatonin plays important roles, as a free radical scavenger and antioxidant, in the improvement of antioxidant systems under salt stress. These functions improve photosynthesis, ion homeostasis, and activate a series of downstream signals, such as hormones, nitric oxide (NO) and polyamine metabolism. Melatonin also regulates gene expression responses to salt stress. In this study, we review recent literature and summarize the regulatory roles and signaling networks involving melatonin in response to salt stress in plants. We also discuss genes and gene families involved in the melatonin-mediated salt stress tolerance.

A barley mutant with improved salt tolerance through ion homeostasis and ROS scavenging under salt stress

2017 ◽  
Vol 39 (3) ◽  
Author(s):  
Davood Kiani ◽  
Hassan Soltanloo ◽  
Seyyede Sanaz Ramezanpour ◽  
Ali Asghar Nasrolahnezhad Qumi ◽  
Ahad Yamchi ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Ion Homeostasis ◽  
Ros Scavenging ◽  
Barley Mutant

scholarly journals Melatonin Improves Cotton Salt Tolerance by Regulating ROS Scavenging System and Ca2 + Signal Transduction

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuexin Zhang ◽  
Yapeng Fan ◽  
Cun Rui ◽  
Hong Zhang ◽  
Nan Xu ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Signal Molecules ◽  
Protective Mechanism ◽  
Rna Seq ◽  
Ros Scavenging ◽  
Exogenous Melatonin ◽  
Endogenous Melatonin

As one of the cash crops, cotton is facing the threat of abiotic stress during its growth and development. It has been reported that melatonin is involved in plant defense against salt stress, but whether melatonin can improve cotton salt tolerance and its molecular mechanism remain unclear. We investigated the role of melatonin in cotton salt tolerance by silencing melatonin synthesis gene and exogenous melatonin application in upland cotton. In this study, applicating of melatonin can improve salt tolerance of cotton seedlings. The content of endogenous melatonin was different in cotton varieties with different salt tolerance. The inhibition of melatonin biosynthesis related genes and endogenous melatonin content in cotton resulted in the decrease of antioxidant enzyme activity, Ca2+ content and salt tolerance of cotton. To explore the protective mechanism of exogenous melatonin against salt stress by RNA-seq analysis. Melatonin played an important role in the resistance of cotton to salt stress, improved the salt tolerance of cotton by regulating antioxidant enzymes, transcription factors, plant hormones, signal molecules and Ca2+ signal transduction. This study proposed a regulatory network for melatonin to regulate cotton’s response to salt stress, which provided a theoretical basis for improving cotton’s salt tolerance.

scholarly journals Comparative Transcriptome Analysis of Two Contrasting Chinese Cabbage (Brassica rapa L.) Genotypes Reveals That Ion Homeostasis Is a Crucial Biological Pathway Involved in the Rapid Adaptive Response to Salt Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Na Li ◽  
Zhihuan Zhang ◽  
Zijing Chen ◽  
Bili Cao ◽  
Kun Xu
Keyword(s):  
Salt Stress ◽  
Chinese Cabbage ◽  
Chlorophyll Biosynthesis ◽  
Ion Homeostasis ◽  
Limiting Factor ◽  
Galactinol Synthase ◽  
Yield And Quality ◽  
Comprehensive Comparison ◽  
Suitable Treatment ◽  
Treatment Concentration

Salt is the most important limiting factor in plant yield and quality. Different Chinese cabbage cultivars appeared different salt tolerances, but there are few studies attempting to elucidate the mechanism underlying this phenomenon. In this study, 100 mmol L–1 NaCl was found to be the most suitable treatment concentration according to a sprouting bag test of 39 Chinese cabbage cultivars, and through comprehensive comparison and analysis, the relative values of fresh weight and electrolyte leakage in leaves proved to be convenient indicators for the identification of salt tolerance in Chinese cabbage. We analyzed the physiological responses of Qinghua45 (salt-tolerant) and Biyuchunhua (salt-sensitive) in terms of the growth indexes, ion homeostasis and Photosynthesis, the results indicated that Qinghua45 could ensure osmotic regulation, ion homeostasis and photosynthesis under salt stress. Next, we compared the transcriptome dynamics of the two cultivars. Overall, 2,859 differentially expressed genes (DEGs) were identified, and the number of DEGs in Qinghua45 was significantly less than that in Biyuchunhua. VDAC promoted the release of Ca2+, which indirectly promoted the transport of Na+ to vacuoles through the SOS2 pathway. Cation/H (+) antiporter 17 and V-H + -ATPase improve the exchange of Na+ and H+ and maintain Na+ in the vacuoles, thereby reducing the injury affected by salt stress. Increases in galactinol synthase and soluble protein synthesis helped relieve osmotic stress caused by salt, together, they regulated the Na+ content and chlorophyll biosynthesis of the plant and enabled the plant to adapt to salt stress over time.

scholarly journals OXS2 is Required for Salt Tolerance Mainly through Associating with Salt Inducible Genes, CA1 and Araport11, in Arabidopsis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ying Jing ◽  
Lin Shi ◽  
Xin Li ◽  
Han Zheng ◽  
Jianwei Gao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Abiotic Stresses ◽  
Growth And Yield ◽  
Functional Screening ◽  
Rna Seq ◽  
Salt Tolerant ◽  
Promoter Regions ◽  
Inducible Genes ◽  
Chip Analysis

AbstractSalt stress is one of the abiotic stresses affecting crop growth and yield. The functional screening and mechanism investigation of the genes in response to salt stress are essential for the development of salt-tolerant crops. Here, we found that OXIDATIVE STRESS 2 (OXS2) was a salinity-induced gene, and the mutant oxs2-1 was hypersensitive to salt stress during seed germination and root elongation processes. In the absence of stress, OXS2 was predominantly localized in the cytoplasm; when the plants were treated with salt, OXS2 entered the nuclear. Further RNA-seq analysis and qPCR identification showed that, in the presence of salt stress, a large number of differentially expressed genes (DEGs) were activated, which contain BOXS2 motifs previously identified as the binding element for AtOXS2. Further ChIP analysis revealed that, under salt stress, OXS2 associated with CA1 and Araport11 directly through binding the BOXS2 containing fragments in the promoter regions. In conclusion, our results indicate that OXS2 is required for salt tolerance in Arabidopsis mainly through associating with the downstream CA1 and Araport11 directly.

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