Genomics

Dataset Information

39

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


ABSTRACT: 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. Overall design: Leaf mRNA and miRNA profiles of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive during a 72-h NaCl exposure were generated by deep sequencing, using Illumina HiSeq 2000 system.

INSTRUMENT(S): Illumina HiSeq 2000 (Gossypium hirsutum)

SUBMITTER: Du Xiongming  

PROVIDER: GSE58655 | GEO | 2017-06-18

SECONDARY ACCESSION(S): PRJNA253112

REPOSITORIES: GEO

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Publications

Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes.

Peng Zhen Z   He Shoupu S   Gong Wenfang W   Sun Junling J   Pan Zhaoe Z   Xu Feifei F   Lu Yanli Y   Du Xiongming X  

BMC genomics 20140905


<h4>Background</h4>Cotton (Gossypium spp.) is one of the major fibre crops of the world. Although it is classified as salt tolerant crop, cotton growth and productivity are adversely affected by high salinity, especially at germination and seedling stages. 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-  ...[more]

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