scholarly journals Over-expression of poplar NAC15 gene enhances wood formation in transgenic tobacco

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Wenjing Yao ◽  
Dawei Zhang ◽  
Boru Zhou ◽  
Jianping Wang ◽  
Renhua Li ◽  
...  
Keyword(s):  
Transgenic Tobacco ◽  
Wood Formation ◽  
Potential Candidate ◽  
Rna Seq ◽  
Populus Simonii ◽  
Over Expression ◽  
Potential Candidate Gene ◽  
Relative Expression Level ◽  
Transgenic Lines ◽  
Highly Expressed Genes

Abstract Background NAC (NAM/ATAF/CUC) is one of the largest plant-specific transcription factor (TF) families known to play significant roles in wood formation. Acting as master gene regulators, a few NAC genes can activate secondary wall biosynthesis during wood formation in woody plants. Results In the present study, firstly, we screened 110 differentially expressed NAC genes in the leaves, stems, and roots of di-haploid Populus simonii×P. nigra by RNA-Seq. Then we identified a nucleus-targeted gene, NAC15 gene, which was one of the highly expressed genes in the stem among 110 NAC family members. Thirdly, we conducted expression pattern analysis of NAC15 gene, and observed NAC15 gene was most highly expressed in the xylem by RT-qPCR. Moreover, we transferred NAC15 gene into tobacco and obtained 12 transgenic lines overexpressing NAC15 gene (TLs). And the relative higher content of hemicellulose, cellulose and lignin was observed in the TLs compared to the control lines containing empty vector (CLs). It also showed darker staining in the culms of the TLs with phloroglucinol staining, compared to the CLs. Furthermore, the relative expression level of a few lignin- and cellulose-related genes was significantly higher in the TLs than that in the CLs. Conclusions The overall results indicated that NAC15 gene is highly expressed in the xylem of poplar and may be a potential candidate gene playing an important role in wood formation in transgenic tobacco.

scholarly journals Over-expression of poplar NAC15 gene enhances wood formation in transgenic tobacco

2019 ◽  
Author(s):  
Wenjing Yao ◽  
Dawei Zhang ◽  
Boru Zhou ◽  
Jianping Wang ◽  
Renhua Li ◽  
...  
Keyword(s):  
Transgenic Tobacco ◽  
Wood Formation ◽  
Potential Candidate ◽  
Rna Seq ◽  
Populus Simonii ◽  
Over Expression ◽  
Potential Candidate Gene ◽  
Relative Expression Level ◽  
Transgenic Lines ◽  
Highly Expressed Genes

Abstract Background NAC (NAM/ATAF/CUC) is one of the largest plant-specific transcription factor (TF) families known to play significant roles in wood formation. Acting as master gene regulators, a few NAC genes can activate secondary wall biosynthesis during wood formation in woody plants. Results In the present study, firstly, we screened 110 differentially expressed NAC genes in the leaves, stems, and roots of di-haploid Populus simonii×P. nigra by RNA-Seq. Then we identified a nucleus-targeted gene, NAC15 gene, which was one of the highly expressed genes in the stem among 110 NAC family members. Thirdly, we conducted expression pattern analysis of NAC15 gene, and observed NAC15 gene was most highly expressed in the xylem by RT-qPCR. Moreover, we transferred NAC15 gene into tobacco and obtained 12 transgenic lines overexpressing NAC15 gene (TLs). And the relative higher content of hemicellulose, cellulose and lignin was observed in the TLs compared to the control lines containing empty vector (CLs). It also showed darker staining in the culms of the TLs with phloroglucinol staining, compared to the CLs. Furthermore, the relative expression level of a few lignin- and cellulose-related genes was significantly higher in the TLs than that in the CLs. ConclusionsThe overall results indicated that NAC15 gene is highly expressed in the xylem of poplar and may be a potential candidate gene playing an important role in wood formation in transgenic tobacco.

scholarly journals Over-expression of poplar NAC15 gene enhances wood formation in transgenic tobacco

2019 ◽  
Author(s):  
Wenjing Yao ◽  
Dawei Zhang ◽  
Boru Zhou ◽  
Jianping Wang ◽  
Renhua Li ◽  
...  
Keyword(s):  
Transgenic Tobacco ◽  
Wood Formation ◽  
Potential Candidate ◽  
Rna Seq ◽  
Populus Simonii ◽  
Over Expression ◽  
Potential Candidate Gene ◽  
Relative Expression Level ◽  
Transgenic Lines ◽  
Highly Expressed Genes

Abstract Abstract Background NAC (NAM/ATAF/CUC) family is one of the largest plant-specific transcription factor (TF) families known to play significant roles in wood formation. Acting as master gene regulators, a few NAC genes can activate secondary wall biosynthesis during wood formation in woody plants. Results In the present study, firstly, we screened 110 differentially expressed NAC genes in the leaves, stems, and roots of di-haploid Populus simonii×P. nigra by RNA-Seq. Then we identified a nucleus-targeted gene, NAC15 gene, which was one of the highly expressed genes in the stem among 110 NAC family members. Thirdly, we conducted expression pattern analysis of NAC15 gene, and observed NAC15 gene was most highly expressed in the xylem by RT-qPCR. Moreover, we transferred NAC15 gene into tobacco and obtained 12 transgenic lines overexpressing NAC15 gene (TLs). And the relative higher content of hemicellulose, cellulose and lignin was observed in the TLs compared to the control lines containing empty vector (CLs). It also showed darker staining in the culms of the TLs with phloroglucinol staining, compared to the CLs. Furthermore, the relative expression level of a few lignin- and cellulose-related genes was significantly higher in the TLs than that in the CLs. Conclusions The overall results indicated that NAC15 gene is highly expressed in the xylem of poplar and may be a potential candidate gene playing an important role in wood formation in transgenic tobacco.

scholarly journals Over-expression of poplar NAC15 gene enhances wood formation in transgenic tobacco

2019 ◽  
Author(s):  
Wenjing Yao ◽  
Dawei Zhang ◽  
Boru Zhou ◽  
Jianping Wang ◽  
Renhua Li ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Transgenic Tobacco ◽  
Wood Formation ◽  
Significant Implication ◽  
Rna Seq ◽  
Populus Simonii ◽  
Over Expression ◽  
Relative Expression Level ◽  
Highly Expressed Genes ◽  
Nac Family

Abstract BackgroundNAC (NAM/ATAF/CUC) family is one of the largest plant-specific TF families known to play significant roles in wood formation. Acting as master gene regulators, a few NAC genes can activate secondary wall biosynthesis during wood formation in woody plants.ResultsIn the present study, firstly, we screened 110 differentially expressed NAC genes in the leaves, stems, and roots of di-haploid Populus simonii×P. nigra by RNA-Seq. Then we identified a nucleus-targeted gene, NAC15 gene, which was one of the most highly expressed genes in the stem among NAC family members. Thirdly, we conducted expression pattern analysis of NAC15 gene, and proved NAC15 gene was most highly expressed in the xylem. Moreover, we transferred NAC15 gene into tobacco and obtained 12 transgenic tobacco lines overexpressing the gene. And the relative content of hemicellulose, cellulose and lignin was determined to be higher in the transgenic plants than that in the control plants. It also showed darker staining in the culms of the transgenic plants with phloroglucinol staining, compared to the control plants. Furthermore, the relative expression level of a few lignin- and cellulose-related genes was significantly higher in the TLs than that in the CLs.ConclusionsThe overall results indicated that NAC15 gene is highly expressed in the xylem of poplar and plays an important role in wood formation in transgenic tobacco, which provides a foundation for the identification of wood-associated downstream genes and has significant implication in tree biology and biotechnology.

GDP-D-mannose pyrophosphorylase from Pogonatherum paniceum enhances salinity and drought tolerance of transgenic tobacco

2016 ◽  
Vol 71 (7-8) ◽  
pp. 243-252 ◽  
Author(s):  
Taobo Ai ◽  
Xuehong Liao ◽  
Rui Li ◽  
Linhong Fan ◽  
Fengxue Luo ◽  
...  
Keyword(s):  
Drought Stress ◽  
Transgenic Tobacco ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Germination Rate ◽  
Crop Improvement ◽  
Potential Candidate ◽  
Sod Activity ◽  
Potential Candidate Gene ◽  
Pogonatherum Paniceum

Abstract Pogonatherum paniceum is a highly drought- and salt-tolerant plant species that is typically used for ecological restoration and the conservation of soil and water in many countries. Understanding the molecular mechanisms underlying plant abiotic stress responses, especially to salinity and drought stresses, in species such as P. paniceum could be important to broader crop improvement efforts. GDP-D-mannose pyrophosphorylase (GMPase) is the limiting enzyme in the synthesis of L-ascorbic acid (AsA), which plays a crucial role in the detoxification of reactive oxygen species (ROS). We have cloned and characterized the cDNA of the PpGMP gene of P. paniceum encoding a GMPase. The full-length cDNA sequence contains 1411 nucleotides encoding a putative protein with 361 amino acid residues and an approximate molecular mass of 39.68 kDa. The GMPase transcript was up-regulated in P. paniceum plants subjected to salinity and drought stress, respectively. Transgenic tobacco expressing PpGMPase exhibited enhanced salinity and drought resistance, a higher seed germination rate, better growth performance, a higher AsA content, a more stable redox state, higher superoxide dismutase (SOD) activity, and lower levels of malonaldehyde (MDA) and H2O2 under drought and salinity stress. Taken together, expression of PpGMPase in tobacco conferred salinity and drought stress tolerance by increasing the content of AsA, thereby enhancing ROS-detoxifying functions. Thus, PpGMP is a potential candidate gene for crop improvement.

Co-expression of AGPS and AGPL genes encoded for AGPase from cassava to enhance starch accumulation in transgenic tobacco

2016 ◽  
Vol 14 (2) ◽  
pp. 287-293
Author(s):  
Nguyễn Văn Đoài ◽  
Nguyễn Minh Hồng ◽  
Lê Thu Ngọc ◽  
Nguyễn Thị Thơm ◽  
Nguyễn Đình Trọng ◽  
...  
Keyword(s):  
Transgenic Tobacco ◽  
Higher Plants ◽  
Starch Content ◽  
Genetically Modified Crops ◽  
Starch Accumulation ◽  
35S Promoter ◽  
Effective Strategies ◽  
Plant Expression Vector ◽  
Transgenic Lines ◽  
Cassava Varieties

The AGPase (ADP-Glucose pyrophosphorylase) is one of the ubiquitous enzymes catalyzing the first step in starch biosynthesis. It plays an important role in regulation and adjusts the speed of the entire cycle of glycogen biosynthesis in bacteria and starch in plants. In higher plants, it is a heterotetramer and tetrameric enzyme consisting two large subunits (AGPL) and two small subunits (AGPS) and encoded by two genes. In this paper, both AGPS and AGPL genes were sucessfully isolated from cassava varieties KM140 and deposited in Genbank with accession numbers KU243124 (AGPS) and KU243122 (AGPL), these two genes were fused with P2a and inserted into plant expression vector pBI121 under the control of 35S promoter. The efficient of this construct was tested in transgenic N. tabacum. The presence and expression of AGPS and AGPL in transgenic plants were confirmed by PCR and Western hybridization. The starch content was quantified by the Anthrone method. Transgenic plant analysis indicated that that two targeted genes were expressed simultaneously in several transgenic tobacco lines under the control of CaMV 35S promoter.  The starch contents in 4 analyzed tobacco transgenic lines displays the increase 13-116%  compared to WT plants. These results indicated that the co-expression of AGPS and AGPL is one of effective strategies for enhanced starch production in plant. These results can provide a foundation for developing other genetically modified crops to increase starch accumulation capacity.

scholarly journals Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yuxin Yang ◽  
Xueying Zhang ◽  
Lifen Wu ◽  
Lichao Zhang ◽  
Guoxiang Liu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Flowering Time ◽  
Heading Date ◽  
Yield Component ◽  
Potential Candidate ◽  
Rna Seq ◽  
Nucleotide Synthesis ◽  
Light Reaction ◽  
Grain Number Per Spike ◽  
Double Ridge

Abstract Background Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in terms of grain number per spike. Results In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-Seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. Based on MapMan metabolic analysis, the DEGs are mainly involved in the light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors closely related to flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs have biological connections with Vrn1-5 A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 encodes a MADS-MIKC transcription factor and is co-expressed with Vrn1-5 A, which indicates that this gene may be related to flowering time. Conclusions RNA-Seq analysis provided transcriptome data for the wheat heading date at key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs identified, co-expression networks of key flowering time genes in Vrn1-5 A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene, TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of the wheat heading date.

Over-expression of the rice OsAMT1-1 gene increases ammonium uptake and content, but impairs growth and development of plants under high ammonium nutrition

2006 ◽  
Vol 33 (2) ◽  
pp. 153 ◽  
Author(s):  
Mohammad S. Hoque ◽  
Josette Masle ◽  
Michael K. Udvardi ◽  
Peter R. Ryan ◽  
Narayana M. Upadhyaya
Keyword(s):  
Transgenic Plants ◽  
Ammonium Assimilation ◽  
Ammonium Transporter ◽  
Ammonium Uptake ◽  
Vegetative Stage ◽  
Over Expression ◽  
Transgenic Lines ◽  
Ammonium Nutrition ◽  
Maize Ubiquitin Promoter

A transgenic approach was undertaken to investigate the role of a rice ammonium transporter (OsAMT1-1) in ammonium uptake and consequent ammonium assimilation under different nitrogen regimes. Transgenic lines overexpressing OsAMT1-1 were produced by Agrobacterium-mediated transformation of two rice cultivars, Taipei 309 and Jarrah, with an OsAMT1-1 cDNA gene construct driven by the maize ubiquitin promoter. Transcript levels of OsAMT1-1 in both Taipei 309 and Jarrah transgenic lines correlated positively with transgene copy number. Shoot and root biomass of some transgenic lines decreased during seedling and early vegetative stage compared to the wild type, especially when grown under high (2 mm) ammonium nutrition. Transgenic plants, particularly those of cv. Jarrah recovered in the mid-vegetative stage under high ammonium nutrition. Roots of the transgenic plants showed increased ammonium uptake and ammonium content. We conclude that the decreased biomass of the transgenic lines at early stages of growth might be caused by the accumulation of ammonium in the roots owing to the inability of ammonium assimilation to match the greater ammonium uptake.

scholarly journals RgCop-A regularized copula based method for gene selection in single cell rna-seq data

2021 ◽  
Vol 17 (10) ◽  
pp. e1009464
Author(s):  
Snehalika Lall ◽  
Sumanta Ray ◽  
Sanghamitra Bandyopadhyay
Keyword(s):  
Single Cell ◽  
Gene Selection ◽  
Real Life ◽  
Classification Performance ◽  
Rna Seq ◽  
Scale Invariant ◽  
Dependence Measure ◽  
Highly Expressed Genes ◽  
The Stability ◽  
Downstream Analysis

Gene selection in unannotated large single cell RNA sequencing (scRNA-seq) data is important and crucial step in the preliminary step of downstream analysis. The existing approaches are primarily based on high variation (highly variable genes) or significant high expression (highly expressed genes) failed to provide stable and predictive feature set due to technical noise present in the data. Here, we propose RgCop, a novel regularized copula based method for gene selection from large single cell RNA-seq data. RgCop utilizes copula correlation (Ccor), a robust equitable dependence measure that captures multivariate dependency among a set of genes in single cell expression data. We raise an objective function by adding a l1 regularization term with Ccor to penalizes the redundant co-efficient of features/genes, resulting non-redundant effective features/genes set. Results show a significant improvement in the clustering/classification performance of real life scRNA-seq data over the other state-of-the-art. RgCop performs extremely well in capturing dependence among the features of noisy data due to the scale invariant property of copula, thereby improving the stability of the method. Moreover, the differentially expressed (DE) genes identified from the clusters of scRNA-seq data are found to provide an accurate annotation of cells. Finally, the features/genes obtained from RgCop can able to annotate the unknown cells with high accuracy.

scholarly journals Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression

2021 ◽  
Vol 8 ◽  
Author(s):  
Andrew Marete ◽  
Olivier Ariel ◽  
Eveline Ibeagha-Awemu ◽  
Nathalie Bissonnette
Keyword(s):  
Neural Networks ◽  
Logistic Regression ◽  
Differential Expression Analysis ◽  
Johne's Disease ◽  
Classification Systems ◽  
Johne’S Disease ◽  
Potential Candidate ◽  
Rna Seq ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Mycobacterium avium ssp. paratuberculosis (MAP) causes chronic enteritis in most ruminants. The pathogen MAP causes Johne's disease (JD), a chronic, incurable, wasting disease. Weight loss, diarrhea, and a gradual drop in milk production characterize the disease's clinical phase, culminating in death. Several studies have characterized long non-coding RNA (lncRNA) in bovine tissues, and a previous study characterizes (lncRNA) in macrophages infected with MAP in vitro. In this study, we aim to characterize the lncRNA in macrophages from cows naturally infected with MAP. From 15 herds, feces and blood samples were collected for each cow older than 24 months, twice yearly over 3–5 years. Paired samples were analyzed by fecal PCR and blood ELISA. We used RNA-seq data to study lncRNA in macrophages from 33 JD(+) and 33 JD(–) dairy cows. We performed RNA-seq analysis using the “new Tuxedo” suite. We characterized lncRNA using logistic regression and multilayered neural networks and used DESeq2 for differential expression analysis and Panther and Reactome classification systems for gene ontology (GO) analysis. The study identified 13,301 lncRNA, 605 of which were novel lncRNA. We found seven genes close to differentially expressed lncRNA, including CCDC174, ERI1, FZD1, TWSG1, ZBTB38, ZNF814, and ZSCAN4. None of the genes associated with susceptibility to JD have been cited in the literature. LncRNA target genes were significantly enriched for biological process GO terms involved in immunity and nucleic acid regulation. These include the MyD88 pathway (TLR5), GO:0043312 (neutrophil degranulation), GO:0002446 (neutrophil-mediated immunity), and GO:0042119 (neutrophil activation). These results identified lncRNA with potential roles in host immunity and potential candidate genes and pathways through which lncRNA might function in response to MAP infection.

Sign in / Sign up

Export Citation Format

Share Document