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

ABSTRACT: 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.

ORGANISM(S): Gossypium hirsutum

SUBMITTER: Du Xiongming

PROVIDER: E-GEOD-70205 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

A reversible light and genotype dependent acquired thermolerance response protects the potato plant from excessive temperature (microarray data set 2).

Project description:'Potato is particularly vulnerable to increased temperature, considered to be the most important uncontrollable factor affecting growth and yield. Here we describe an acquired thermotolerance response in potato, whereby treatment at a mildly elevated temperature (''acclimated'') primes the plant for more severe heat stress compared to control (''non-acclimated'') plants. We define the time course for acquiring thermotolerance and demonstrate that light is essential for the process. Physiological, transcriptomic and metabolomic approaches were employed to elucidate potential mechanisms that underpin the acquisition of heat tolerance and indicate a role for cell wall modification, auxin and ethylene signalling, and chromatin remodelling in acclimatory priming. This experiment identifies changes in transcript level were measured over a time course (0, 2, 6, 12 h) during the period of acquisition of thermotolerance following transfer from 18 °C (non-acclimated) to 25 °C (acclimated). Related experiment (E-MTAB-5857) looks to understand the mechanisms by which acclimation results in protection of leaves at extreme temperature; gene expression patterns were determined in leaves from acclimated and non-acclimated plants which were subsequently transferred to 40 °C and compared during a 48 h time course (2, 6, 12, 24 h).'

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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

Gene expression profile from field-grown drought-stressed cotton

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2010-05-22 | E-GEOD-18253 | biostudies-arrayexpress

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2024-02-06 | GSE225085 | GEO

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2023-02-06 | GSE221132 | GEO

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Transcription profiling of Arabidopsis AtrbohB null mutant in response to heat

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2020-10-19 | PXD015721 | Pride

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