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

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.

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

10.21203/rs.3.rs-57429/v1 ◽

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.

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

10.21203/rs.3.rs-57429/v2 ◽

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.

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

BMC Genomics ◽

10.1186/s12864-021-07368-w ◽

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.

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

10.21203/rs.3.rs-57429/v3 ◽

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.

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Marker-assisted identification of potential fertility restorers for the development of three-line hybrids in rice (Oryza sativa L.)

ORYZA- An International Journal on Rice ◽

10.35709/ory.2020.57.3.2 ◽

2020 ◽

Vol 57 (3) ◽

pp. 181-189

Author(s):

Asma Majid ◽

GA Parray ◽

NR Sofi ◽

Gazala H Khan ◽

Showkat A Waza ◽

...

Keyword(s):

Oryza Sativa L ◽

Chromosome 1 ◽

Limiting Factor ◽

Kashmir Valley ◽

Fertility Restorer ◽

Yield And Quality ◽

Restorer Genes ◽

Increase Productivity ◽

Fertility Restorers ◽

Selection Of

Rice being a staple food crop of Kashmir valley, the focus is on enhancement of yield in order to meet the needs of ever-growing population.Identification of new parental lines is crucial for developing ecology-specific hybrids with ideal agronomic performance. Exploitation of heterosis in the form of hybrid rice technology can be one of the approaches to increase productivity in this crop, especially exploiting diversity among japonica lines can serve as an excellent route.A number of CMS lines suitable formountainous areas of Kashmir have been developed, however, the availability of promising restorer lines remains to be the major limitation for utilization of these lines.Identification of potential restorers acts as the main limiting factor for hybrid development in the Kashmir valley. Marker based screening for Rf3 and Rf4 fertility restorer genes can be helpful in rapid selection of restorer lines while dealing with the large quantity of genetic materials. In the present study, 100 rice germplasm were screened with the help of SSR markers, RM3148 and RM6100linked to Rf3 and Rf4 genes on chromosome 1 and 10, respectively. In total, 19 lines revealed the presence of both Rf3 and Rf4 genes. These lines amplified fertility restorer specific alleles for both the genes and may serve as potential restorers for obtaining heterotic rice hybrids. Further the germplasm lines were also evaluated for yield and quality traits.The present results would help in selection of suitable restorers along with preferred grain shape/size.

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