title: Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes.
abstract: BACKGROUND
  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-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology.
  
  
  RESULTS
  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 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. The expression patterns of differentially co-expressed unigenes were divided into six groups using short time-servies expression miner software. 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. We further analyzed the predicted target genes of these miRNAs along with the transcriptome for each time point. Important expressed genes encoding membrane receptors, transporters, and pathways involved in biosynthesis and signal transduction of calcium-dependent protein kinase, mitogen-activated protein kinase, and hormones (abscisic acid and ethylene) were up-regulated. We also analyzed the salt stress response of some key miRNAs and their target genes and found that the expressions of five of nine target genes exhibited significant inverse correlations with their corresponding miRNAs. On the basis of these results, we constructed molecular regulatory pathways and a potential regulatory network for these salt-responsive miRNAs.
  
  
  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.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Peng
authors.forename: Shoupu
authors.initials: S
authors.lastname: He
authors.forename: Wenfang
authors.initials: W
authors.lastname: Gong
authors.forename: Junling
authors.initials: J
authors.lastname: Sun
authors.forename: Zhaoe
authors.initials: Z
authors.lastname: Pan
authors.forename: Feifei
authors.initials: F
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000 Anyang, Henan, China. yanli.lu82@hotmail.com.
authors.forename: Yanli
authors.initials: Y
authors.lastname: Lu
authors.forename: Xiongming
authors.initials: X
authors.lastname: Du
mesh_terms: D016000:Cluster Analysis; D019295:Computational Biology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D008040:Genetic Linkage; D005838:Genotype; D003368:Gossypium / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics; D058977:Molecular Sequence Annotation; D012333:RNA, Messenger / Q000235:genetics; D054712:Salinity; D055049:Salt Tolerance / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics*; D013997:Time Factors; D014157:Transcription Factors; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D014157:Transcription Factors