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ABSTRACT: RNA-seq for upland cotton abiotic stress treatments

PROVIDER: PRJNA631851 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR11774440_1.fastq.gz	Fastqsanger.gz
	SRR11774440_2.fastq.gz	Fastqsanger.gz
	SRR11774441_1.fastq.gz	Fastqsanger.gz
	SRR11774441_2.fastq.gz	Fastqsanger.gz

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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.

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Project description:Abiotic stress is a major environmental factor that limits cotton growth and yield, moreover, this problem has become more and more serious recently and multiple stresses often occur simultaneously due to the global climate change and environmental pollution. We used microarrays to analyze the crosstalk of responsive genes to multiple abiotic stresses including ABA, cold, drought, salinity and alkalinity in cotton. Cotton seedlings with different abiotic stress treatment were selected at 14-day after germination for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify genes involved in diverse stresses including abscisic acid (A), cold (C), drought (M), salinity (N) and alkalinity (P) by comparative microarray analysis (3 biological replicates for each abiotic stress treatment).

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Comparison of cotton fiber to ovule at 9 DPA

Project description:RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule. RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule.

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Project description:upland cotton RNA-seq for leaf

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Transcriptome analysis reveals crosstalk of responsive genes to multiple abiotic stresses in cotton (Gossypium hirsutum L.)

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Comparison of cotton fiber to ovule at 9 DPA

Project description:RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule. Keywords: tissue comparison

2006-04-12 | GSE4642 | GEO