title: Genome wide expression profiling of two accession of G. herbaceum L. in response to drought.
abstract: BACKGROUND
  Genome-wide gene expression profiling and detailed physiological investigation were used for understanding the molecular mechanism and physiological response of Gossypium herbaceum, which governs the adaptability of plants in drought conditions. Recently, microarray-based gene expression analysis is commonly used to decipher genes and genetic networks controlling the traits of interest. However, the results of such an analysis are often plagued due to a limited number of genes (probe sets) on microarrays. On the other hand, pyrosequencing of a transcriptome has the potential to detect rare as well as a large number of transcripts in the samples quantitatively. We used Affymetrix microarray as well as Roche's GS-FLX transcriptome sequencing for a comparative analysis of cotton transcriptome in leaf tissues under drought conditions.
  
  
  RESULTS
  Fourteen accessions of Gossypium herbaceum were subjected to mannitol stress for preliminary screening; two accessions, namely Vagad and RAHS-14, were selected as being the most tolerant and most sensitive to osmotic stress, respectively. Affymetrix cotton arrays containing 24,045 probe sets and Roche's GS-FLX transcriptome sequencing of leaf tissue were used to analyze the gene expression profiling of Vagad and RAHS-14 under drought conditions. The analysis of physiological measurements and gene expression profiling showed that Vagad has the inherent ability to sense drought at a much earlier stage and to respond to it in a much more efficient manner than does RAHS-14. Gene Ontology (GO) studies showed that the phenyl propanoid pathway, pigment biosynthesis, polyketide biosynthesis, and other secondary metabolite pathways were enriched in Vagad under control and drought conditions as compared with RAHS-14. Similarly, GO analysis of transcriptome sequencing showed that the GO terms responses to various abiotic stresses were significantly higher in Vagad. Among the classes of transcription factors (TFs) uniquely expressed in both accessions, RAHS-14 showed the expression of ERF and WRKY families. The unique expression of ERFs in response to drought conditions reveals that RAHS-14 responds to drought by inducing senescence. This was further supported by transcriptome analysis which revealed that RAHS-14 responds to drought by inducing many transcripts related to senescence and cell death.
  
  
  CONCLUSIONS
  The comparative genome-wide gene expression profiling study of two accessions of G.herbaceum under drought stress deciphers the differential patterns of gene expression, including TFs and physiologically relevant processes. Our results indicate that drought tolerance observed in Vagad is not because of a single molecular reason but is rather due to several unique mechanisms which Vagad has developed as an adaptation strategy.
authors.affiliation: Council of Scientific and Industrial Research-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, UP, India.
authors.forename: Alok
authors.initials: A
authors.lastname: Ranjan
authors.forename: Deepti
authors.initials: D
authors.lastname: Nigam
authors.forename: Mehar H
authors.initials: MH
authors.lastname: Asif
authors.forename: Ruchi
authors.initials: R
authors.lastname: Singh
authors.forename: Sanjay
authors.initials: S
authors.lastname: Ranjan
authors.forename: Shrikant
authors.initials: S
authors.lastname: Mantri
authors.forename: Neha
authors.initials: N
authors.lastname: Pandey
authors.forename: Ila
authors.initials: I
authors.lastname: Trivedi
authors.forename: Krishan Mohan
authors.initials: KM
authors.lastname: Rai
authors.forename: Satya N
authors.initials: SN
authors.lastname: Jena
authors.forename: Bhupendra
authors.initials: B
authors.lastname: Koul
authors.forename: Rakesh
authors.initials: R
authors.lastname: Tuli
authors.forename: Uday V
authors.initials: UV
authors.lastname: Pathre
authors.forename: Samir V
authors.initials: SV
authors.lastname: Sawant
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D055864:Droughts; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D003368:Gossypium / Q000235:genetics* / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D013312:Stress, Physiological; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors