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Transcriptome analysis of Upland Cotton revealed novel pathways to scavenge reactive oxygen species (ROS) responding to Na2SO4 tolerance

ABSTRACT: To explore the mechanisms of cotton response to Na2SO4 stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under the treatment of 300 mmol• L-1 Na2SO4 solution at 12 h and the control with water at 12 h. A total of 15,524, 20,409 and 12,146 differentially expressed genes (DEGs) were identified in cotton roots, stems and leaves between treatment and control, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs associated with plant hormone signal transduction, plant-pathogen interaction, and Starch and sucrose metabolites were regulated in response to the Na2SO4 stress. We further analyzed genes enriched in ROS (reactive oxygen species) scavenging system including osmotic stress and ion toxicity were significantly up-regulated. In addition, analysis for sulfur metabolism, results in to identification of two rate limiting enzymes APR and OASTL during synthesis of GSH from SO42-. The analysis of the expression profiles of diverse tissues under Na2SO4 stress and identification of relevant key hub genes in a network crosstalk will provide a strong foundation and valuable clues for genetic improvements of cotton in response to various salt stresses.

ORGANISM(S): Gossypium hirsutum

PROVIDER: GSE167109 | GEO | 2021/08/05

REPOSITORIES: GEO

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Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress

Project description:To explore the mechanisms of cotton response to this alkaline stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under NaHCO3 alkaline stress. A total of 18,230 and 11,177 differentially expressed genes (DEGs) were identified in cotton roots and leaves, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs associated with plant hormone signal transduction, amino acid biosynthesis, and biosynthesis of secondary metabolites were regulated in response to the NaHCO3 stress. We further analyzed genes enriched in secondary metabolic pathways and found that secondary metabolites were regulated to eliminate the reactive oxygen species (ROS) and improve the cotton tolerance to the NaHCO3 stress. In this study, we learned that the toxic effect of NaHCO3 was more profound than that of NaOH at the same pH. Thus, Na+, HCO3- and pH had a great impact on the growth of cotton plant. The novel biological pathways and candidate genes for the cotton tolerance to NaHCO3 stress identified from the study would be useful in the genetic improvement of the alkaline tolerance in cotton.

2022-01-26 | GSE165472 | GEO

Identification of candidate thermotolerance genes during early seedling stage in upland cotton (Gossypium hirsutum L.) revealed by comparative transcriptome analysis

Project description:High temperature (HT) stress is a major environmental stress that limits cotton growth, metabolism, and yield worldwide. The identification and characterization of thermotolerance is restricted by the plant growth environment and growth stage. In this study, four genotypes of upland cotton (Gossypium hirsutum L.) with known field thermotolerance were evaluated under normal and HTs at the seedlings stage in a growth cabinet with 11 physiological, biochemical, and phenotypic assays. Consistent with previous field observations, the thermotolerance could be identified by genotype differences at the seedling stage under HT in a growth cabinet. Comparative transcriptome analysis was performed on seedlings of two contrasting cotton genotypes after 4 and 8 hours of HT exposure. Gene ontology analysis combined with BLAST annotations revealed a large number of HT-induced differentially expressed genes (4,698) that either exhibited higher expression levels in the heat-tolerant genotype (Nan Dan Ba Di Da Hua) compared with the heat-sensitive genotype (Earlistaple 7), or were differentially expressed only in Nan Dan Ba Di Da Hua. These genes encoded mainly protein kinases, transcription factors, and heat shock proteins, which were considered to play key roles in thermotolerance in upland cotton. Two heat shock transcription factor genes (homologs of AtHsfA3, AtHsfC1) and AP2/EREBP family genes (homologs of AtERF20, AtERF026, AtERF053, and AtERF113) were identified as possible key regulators of thermotolerance in cotton. Some of the differentially expressed genes were validated by quantitative real-time PCR analysis. Our findings provide candidate genes that could be used to improve thermotolerance in cotton cultivars.

2016-06-30 | GSE70205 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Differentially Expressed Genes and Transcriptional Regulation Induced by Salt Stress in Upland Cotton

Project description:Purpose:Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology. And quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods:We investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics approach was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions. Results:During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype. Conclusions:Our comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance.

2017-06-18 | GSE58655 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Differentially Expressed Genes and Transcriptional Regulation Induced by High Temprature Stress in Upland Cotton

Project description:Purpose: Identification and characterization of thermotolerance candidate genes during early seedling stage by comparative transcriptome analysis. We performed transcriptome sequencing (mRNA-seq) of cotton leaves under high temprature stress using Illumina sequencing technology. And quantitative reverse transcription polymerase chain reaction (qRTâPCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: A comparative transcriptomics approach was used to monitor gene differential expression at two time points (4 and 8 h) in leaves of the two cotton genotypes under high temprature conditions. Results: During a 8-h salt exposure,among 9,777 differentially expressed unigenes (DEUs) were identified during at least one time point, 7,296 DEUs representing different classes of protein kinases, transcription factors, and heat shock proteins as well as downstream thermotolerance-related genes are reported. Gene ontology enrichment and biochemical pathway analyses showed these DEUs were mainly related to carbohydrate metabolism, secondary metabolites, and plant hormone signalling. Conclusions: Our findings offer high efficiency technique for early charactering thermotolerance in cotton and provide the information for the candidate genes to improve thermotolerance of cotton cultivars. Leaf mRNA profiles of 20-day-old seedlings of two cotton genotypes, one heat tolerant and the other heat sensitive during a 8-h high-temperature exposure were generated by deep sequencing, using Illumina HiSeq 2000 system.

2016-06-30 | E-GEOD-70205 | biostudies-arrayexpress

Histone H3 lysine 27 trimethylation (H3K27me3) modulates the fiber initiation in upland cotton

Project description:Histone methylation is one of the most significant epigenetic modifications in plants because it is responsible for regulating and controlling the expression of many important functional genes. Although there have been many studies concerning histone methylation, its specific functions and mechanisms in cotton fiber initiation remain unclear. To determine if the H3K27me3 modification had regulated cotton fiber initiation in upland cotton (Gossypium hirsutum), we performed a comparative analysis on the cleavage under targets and tagmentation (CUT&Tag) between the wild-type cultivar Xu142 and its fibreless mutant Xu142 fl. This research was carried out three time points during the initiation period of cotton fibers, which were -1, 0 and 1 days post-anthesis (DPA). We also used the H3K27me3 antibody in Xu142 and Xu142 fl to examine the differential deposition of H3K27me3. Combing these results with RNA-seq analysis, we discovered a negative correlation between transcription and H3K27me3. We identified 336 genes with opposing trends in H3K27me3 deposition and expression. These genes are involved in various metabolic pathways, including fatty acid biosynthesis, galactose metabolism, plant hormone signal transduction, plant-pathogen interaction, glycolysis-/-gluconeogenesis, phenylpropanoid biosynthesis, and cutin, suberin and wax biosynthesis. Further physiological research revealed that in vitro ovule culture with an RDS 3434 inhibitor could alters the level of H3K27me3 in ovules, thus influencing the process of cotton fiber development. Taken together, these results indicate that H3K27me3 plays an important role in the fiber initiation process of cotton, and demonstrates the H3K27me3 network involved in fiber initiation in cotton ovules. The study also provides a foundation for the future study of genes involved in fiber development.

2024-03-14 | GSE227870 | GEO

Comparison of upland li mutant with normal fibers

Project description:The G. hirsutum mutant li1 is caused by a dominant mutation which has pleiotropic effects on plant development. To get information for molecular effects by li1 mutation on cotton fiber development, we examined expression patterns of over 5000 genes by cDNA array from 6 to 18 DPA in a 3-day interval between li1 mutant and normal fibers. RNAs from li1 mutant fibers at 6-, 9-, 12-, 15-, and 18-DPA were compared to normal fiber RNA at each corresponding time points. Four biological repeats were carried out including two dye-swap ones.

2010-07-01 | E-GEOD-4643 | biostudies-arrayexpress

Transcriptome and metabolome profiling reveals key pathways and metabolites involved in defense response of upland cotton against Verticillium dahliae

Project description:Cotton is the main source of natural fiber in the textile industry, making it one of the most economically important fiber crops in the world. Verticillium wilt, caused by the pathogenic fungus Verticillium dahlia, is one of the most damaging biotic factors limiting cotton production. Mechanistic details of cotton defense responses to verticillium wilt remain unclear. In this study, GFP-labeled strain of V. dahlia was used to track colonization in cotton roots, and clear conidial germination could be observed at 48 hours post-inoculation (hpi), marking this as a crucial time point during infection. Transcriptome analysis identified 1,523 and 8,270 differentially expressed genes (DEGs) at 24 hpi and 48 hpi, respectively. Metabolomic screening found 78 differentially accumulated metabolites (DAMs) at 48 hpi. Conjoint analysis indicated that the phenylpropanoid biosynthesis pathway was activated in cotton infected with V. dahliae. The five metabolites in the phenylpropanoid biosynthesis pathway, including caffeic acid, coniferyl alcohol, coniferin, scopoletin and scopolin, could significantly inhibit V. dahlia growth in vitro, implicating their roles in cotton resistance to Verticillium wilt. The findings expand our understanding of molecular mechanisms underlying the pathogen defense response against V. dahlia infection in upland cotton, which may lead to future insights into controlling Verticillium wilt disease.

2023-12-26 | GSE221845 | GEO

Comparison of upland li mutant with normal fibers

2006-04-12 | GSE4643 | GEO

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2006-01-01 | GSE2851 | GEO

Comparative expression among organs between upland cotton species upland cotton CKG (Coker312-gland) and CKN (Coker312-glandless)

Project description:To investigate the gossypol synthasis between distinct cotton species CKG and CKN We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 organs betweeen two species

2022-06-29 | GSE206663 | GEO

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