scholarly journals Transcriptome analysis reveals gene expression associated with fuzz fiber initiation regulated by high-temperature in Gossypium barbadense

2020 ◽  
Author(s):  
Gongmin Cheng ◽  
Longyan Zhang ◽  
Hengling Wei ◽  
Hantao Wang ◽  
Jianhua Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Temperature ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Fiber Quality ◽  
Expression Patterns ◽  
Gossypium Barbadense ◽  
Fiber Development ◽  
Potential Candidate ◽  
Fiber Initiation

Abstract Background: Gossypium barbadense L. is the most important renewable source of textile fiber. Cotton fiber cell initiation and elongation are often affected by various environmental stimulus, such as high temperature. However, little is known about the underlying mechanisms of temperature regulating the fuzz fiber initiation.Results: In the present study, phenotypic observation revealed that high temperature (HT) accelerated the fiber development, improved fiber quality and induced fuzz fiber initiation. It has been proved that the fuzz fiber initiation was inhibited by low temperature (LT), and 4 days post-anthesis (DPA) was the key stage for fuzz fiber initiation. Based on comparative transcriptome analysis, a total of 43,826 differentially expressed genes (DEGs) were identified, of which 9,667 were involved in both fiber development and temperature response with 901 transcription factor genes and 189 genes related to plant hormone signal transduction. Further analysis of gene expression patterns revealed that 240 genes were involved in fuzz fiber initiation. Functional annotation revealed that the candidate genes related to fuzz initiation were significantly involved in asparagine biosynthetic process, cell wall biosynthesis and stress response. Furthermore, the expression trends of sixteen selected genes from the RNA-seq data were almost consistent with the results of qRT-PCR results.Conclusions: Our study revealed several potential candidate genes and pathways that related to fuzz fiber initiation induced by high-temperature and provided a new view of temperature-induced tissue and organ development in Gossypium barbadense.

scholarly journals Transcriptome Analysis Reveals a Gene Expression Pattern Associated with Fuzz Fiber Initiation Induced by High Temperature in Gossypium barbadense

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1066
Author(s):  
Gongmin Cheng ◽  
Longyan Zhang ◽  
Hengling Wei ◽  
Hantao Wang ◽  
Jianhua Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Temperature ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Gossypium Barbadense ◽  
Fiber Development ◽  
Potential Candidate ◽  
Fiber Initiation

Gossypium barbadense is an important source of natural textile fibers, as is Gossypium hirsutum. Cotton fiber development is often affected by various environmental factors, such as abnormal temperature. However, little is known about the underlying mechanisms of temperature regulating the fuzz fiber initiation. In this study, we reveal that high temperatures (HT) accelerate fiber development, improve fiber quality, and induced fuzz initiation of a thermo-sensitive G. barbadense variety L7009. It was proved that fuzz initiation was inhibited by low temperature (LT), and 4 dpa was the stage most susceptible to temperature stress during the fuzz initiation period. A total of 43,826 differentially expressed genes (DEGs) were identified through comparative transcriptome analysis. Of these, 9667 were involved in fiber development and temperature response with 901 transcription factor genes and 189 genes related to plant hormone signal transduction. Further analysis of gene expression patterns revealed that 240 genes were potentially involved in fuzz initiation induced by high temperature. Functional annotation revealed that the candidate genes related to fuzz initiation were significantly involved in the asparagine biosynthetic process, cell wall biosynthesis, and stress response. The expression trends of sixteen genes randomly selected from the RNA-seq data were almost consistent with the results of qRT-PCR. Our study revealed several potential candidate genes and pathways related to fuzz initiation induced by high temperature. This provides a new view of temperature-induced tissue and organ development in Gossypium barbadense.

scholarly journals Validation of suitable genes for normalization of diurnal gene expression studies in Chenopodium quinoa

2020 ◽  
Author(s):  
Nathaly Maldonado-Taipe ◽  
Dilan Sarange ◽  
Sandra Schmöckel ◽  
Christian Jung ◽  
Nazgol Emrani
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Reference Genes ◽  
Expression Patterns ◽  
Data Normalization ◽  
Potential Candidate ◽  
Polypyrimidine Tract Binding Protein ◽  
Expression Studies ◽  
Diurnal Expression ◽  
Gene Expression Studies

AbstractQuinoa depicts high nutritional quality and abiotic stress resistance attracting strong interest in the last years. To unravel the function of candidate genes for agronomically relevant traits, studying their transcriptional activities by RT-qPCR is an important experimental approach. The accuracy of such experiments strongly depends on precise data normalization. To date, validation of potential candidate genes for normalization of diurnal expression studies has not been performed in C. quinoa. We selected eight candidate genes based on transcriptome data and literature survey, including conventionally used reference genes. We used three statistical algorithms (BestKeeper, geNorm and NormFinder) to test their stability and added further validation by a simulation-based strategy. We demonstrated that using different reference genes, including those top ranked by stability, causes significant differences among the resulting diurnal expression patterns, and that our novel approach overcomes failures related to stability-based selection of reference genes. Our results show that isocitrate dehydrogenase enzyme (IDH-A) and polypyrimidine tract-binding protein (PTB) are suitable genes to normalize diurnal expression data of two different quinoa accessions. The validated reference genes obtained in this study will improve the accuracy of RT-qPCR data normalization and facilitate gene expression studies in quinoa.

scholarly journals Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiangtao Yang ◽  
Lihua Gao ◽  
Xiaojing Liu ◽  
Xiaochun Zhang ◽  
Xujing Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gossypium Hirsutum ◽  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Cotton Fiber ◽  
Upland Cotton ◽  
Fiber Quality ◽  
Fiber Development ◽  
Comparative Transcriptome

AbstractCotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.

Gene Expression Changes in Bone Marrow of MDS Patients with Del(5q) During Lenalidomide Treatment.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2622-2622
Author(s):  
Esther Natalie Oliva ◽  
Maria Cuzzola ◽  
Roberto Latagliata ◽  
Francesca Ronco ◽  
D'Errigo Maria Grazia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Candidate Genes ◽  
Reference Values ◽  
Expression Patterns ◽  
Genetic Alterations ◽  
Chromosome 1 ◽  
Potential Candidate ◽  
Long Term Effects ◽  
Repeated Testing

Abstract Abstract 2622 Poster Board II-598 Introduction: Genetic alterations reported in myelodysplastic syndromes (MDS) are not disease-specific and the underlying molecular causes of the disease remain poorly understood. It has been suggested that one or more of the genes mapping within the commonly deleted region of the 5q syndrome, together with other distant genes, may be critical to the development of the 5q syndrome. Potential candidate genes have been identified including the tumor suppressor gene SPARC, and the ribosomial protein gene, RPS14. Haploinsufficiency of RPS14 has been demonstrated and recent evidence indicates RPS14 as a causal gene for the 5q syndrome. Lenalidomide has proven efficacy in MDS patients with del(5q). Rapid and durable responses include transfusion-independence, with a rise in Hb, suppression of the 5q-deletion clone and improvement in bone marrow morphologic features. Methods: In a multicenter Italian phase II trial to evaluate safety, changes in quality of life and efficacy of lenalidomide in primary MDS patients with del(5q) and low or Int-1 risk IPSS, we investigate changes in bone marrow cytogenetics and gene expression patterns during treatment. The starting dose of lenalidomide is 10 mg p.o once daily on a continuous daily schedule for a maximum of 12 months. Dosing is based upon clinical and laboratory findings. Bone marrow cytogenetics and gene expression profiling are performed on study entry and every 12 weeks up to end of study (week 52). Gene expression assays of 51 candidate genes from the published literature and genomic databases have been selected and are carried out with TaqMan® Low Density Array Fluidic card (TaqMan® Human Array, Applied Biosystems, Foster City, CA, USA) based on Applied Biosystems PRISM® 7900HT comparative dd CT method, according to manufacturer's instructions. Using an 18S mRNA gene pre-designed assay from Applied Biosystems to detect the expression of the housekeeping gene 18S in each sample, target gene expression is normalized with 18S gene expression derived from a bone marrow pool of normal healthy subjects and for each sample the ratio between the target and 18S are expressed. Results: Baseline values for 23 patients (mean age 73 ± 10 years) are available and 16 have been re-evaluated after 12 weeks. Mean Hb was 8.6 ± 0.9 g/dL and 20 patients were transfusion-dependent. Seven patients had additional cytogenetic abnormalities. At baseline, RPS14 was under-expressed in 19 out of 21 patients evaluated. After 12 weeks RPS14 was re-evaluated in 13 patients: all had erythroid responses and RPS14 increased significantly from 0.07 (IQ Range 0.03–0.13) to 76.1 (0.73– 304.0, p=0.002). SPARC expression was under-expressed in 15/23 patients and variations during treatment were not significant. Baseline FAS gene was under-expressed in all patients and increased above reference values (p=0,006) after 12 weeks in 7/14 cases. IL7R was over-expressed in all patients at baseline (median 3263.3, IQ range 1998.3–5027.1) and was significantly reduced after 12 weeks (median 0.17, IQ range 0.05–2.20, p<0.0001). TINAGL1 gene expression was very high at baseline (mean 5214 ± 3661) and significantly reduced below normal values during treatment (0.63±0.87, p<0.0001). WTI was over-expressed in almost all patients (median 3246, IQ range 1590–7785) and, though reduced during treatment, still remained highly over reference values at 12 weeks (p=0.148). The expression of the other genes did not vary significantly during treatment. Conclusions: A preliminary study evaluating short-term effects of lenalidomide in low and Int-1 IPSS risk MDS and del(5q) demonstrates that gene expression is abnormal and varies during treatment. RPS14 is down-expressed and a significant increase in its expression is observed during treatment with lenalidomide in responsive patients. There is also an increase in FAS expression; the protein encoded by FAS gene is a member of the TNF-receptor superfamily and its interaction with its ligand leads to apoptosis.The IL7R gene on chromosome 5 (5p13) codifies for the IL7 receptor, which blocks apoptosis during differentiation and activation of T lymphocytes. TINAGL1 gene on chromosome 1 codifies for a Cathepsin B-like protein implicated in a number of human diseases such as cancer. During lenalidomide treatment, the expression of IL7R and TINAGL1 are reduced. Further results and repeated testing during this trial may develop new insights in the pathogenesis of MDS with del(5q) and in long-term effects of lenalidomide on bone marrow changes. Disclosures: Oliva: Celgene: Consultancy. Balleari:Celgene: Consultancy. Finelli:Celgene: Consultancy.

scholarly journals Validation of suitable genes for normalization of diurnal gene expression studies in Chenopodium quinoa

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0233821
Author(s):  
Nathaly Maldonado-Taipe ◽  
Dilan S. R. Patirange ◽  
Sandra M. Schmöckel ◽  
Christian Jung ◽  
Nazgol Emrani
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Reference Genes ◽  
Expression Patterns ◽  
Data Normalization ◽  
Potential Candidate ◽  
Polypyrimidine Tract Binding Protein ◽  
Expression Studies ◽  
Diurnal Expression ◽  
Gene Expression Studies

Quinoa depicts high nutritional quality and abiotic stress resistance, attracting strong interest in the last years. To unravel the function of candidate genes for agronomically relevant traits, studying their transcriptional activities by RT-qPCR is an important experimental approach. The accuracy of such experiments strongly depends on precise data normalization. To date, validation of potential candidate genes for normalization of diurnal expression studies has not been performed in C. quinoa. We selected eight candidate genes based on transcriptome data and literature survey, including conventionally used reference genes. We used three statistical algorithms (BestKeeper, geNorm and NormFinder) to test their stability and added further validation by a simulation-based strategy. We demonstrated that using different reference genes, including those top ranked by stability, causes significant differences among the resulting diurnal expression patterns. Our results show that isocitrate dehydrogenase enzyme (IDH-A) and polypyrimidine tract-binding protein (PTB) are suitable genes to normalize diurnal expression data of two different quinoa accessions. Moreover, we validated our reference genes by normalizing two known diurnally regulated genes, BTC1 and BBX19. The validated reference genes obtained in this study will improve the accuracy of RT-qPCR data normalization and facilitate gene expression studies in quinoa.

scholarly journals Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq

2020 ◽  
Vol 7 (11) ◽  
pp. 201081
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Zhiqiang Chen ◽  
Ruiying Wang ◽  
Lanming Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bulked Segregant Analysis ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Chilling Tolerance ◽  
Pathway Enrichment Analysis ◽  
Potential Candidate ◽  
Rice Varieties ◽  
Booting Stage ◽  
F2 Population

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

scholarly journals Regional heterogeneity in rat Peyer’s patches through whole transcriptome analysis

2020 ◽  
pp. 153537022097301
Author(s):  
Charles L Phillips ◽  
Bradley A Welch ◽  
Michael R Garrett ◽  
Bernadette E Grayson
Keyword(s):  
Gene Expression ◽  
Small Intestine ◽  
Transcriptome Analysis ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Peyer's Patches ◽  
Peyer’S Patches ◽  
Junction Protein ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Peyer’s patches are gut-associated lymphoid tissue located throughout the intestinal wall. Peyer’s patches consist of highly organized ovoid-shaped follicles, classified as non-encapsulated lymphatic tissues, populated with B cells, T cells, macrophages, and dendritic cells and function as an organism’s intestinal surveillance. Limited work compares the gene profiles of Peyer’s patches derived from different intestinal regions. In the current study, we first performed whole transcriptome analysis using RNAseq to compare duodenal and ileal Peyer’s patches obtained from the small intestine of Long Evans rats. Of the 12,300 genes that were highly expressed, 18.5% were significantly different between the duodenum and ileum. Using samples obtained from additional subjects ( n = 10), we validated the novel gene expression patterns in Peyer’s patches obtained from the three regions of the small intestine. Rats had a significantly reduced number of Peyer’s patches in the duodenum in comparison to either the jejunum or ileum. Regional differences in structural, metabolic, and immune-related genes were validated. Genes such as alcohol dehydrogenase 1, gap junction protein beta 2, and serine peptidase inhibitor clade b, member 1a were significantly reduced in the ileum in comparison to other regions. On the other hand, genes such as complement C3d receptor type, lymphocyte cytosolic protein 1, and lysozyme C2 precursor were significantly lower in the duodenum. In summary, the gene expression pattern of Peyer’s patches is influenced by intestinal location and may contribute to its role in that segment.

scholarly journals Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Pibiao Shi ◽  
Minfeng Gu
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Plant Hormone ◽  
Stress Factors ◽  
Soil Conditions ◽  
Regulation Mechanism

Abstract Background Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance. Results The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. One hundred seventeen DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. Conclusions We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.

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