title: Functional genomics of fuzzless-lintless mutant of Gossypium hirsutum L. cv. MCU5 reveal key genes and pathways involved in cotton fibre initiation and elongation.
abstract: BACKGROUND
  Fuzzless-lintless cotton mutants are considered to be the ideal material to understand the molecular mechanisms involved in fibre cell development. Although there are few reports on transcriptome and proteome analyses in cotton at fibre initiation and elongation stages, there is no comprehensive comparative transcriptome analysis of fibre-bearing and fuzzless-lintless cotton ovules covering fibre initiation to secondary cell wall (SCW) synthesis stages. In the present study, a comparative transcriptome analysis was carried out using G. hirsutum L. cv. MCU5 wild-type (WT) and it's near isogenic fuzzless-lintless (fl) mutant at fibre initiation (0 dpa/days post anthesis), elongation (5, 10 and 15 dpa) and SCW synthesis (20 dpa) stages.
  
  
  RESULTS
  Scanning electron microscopy study revealed the delay in the initiation of fibre cells and lack of any further development after 2 dpa in the fl mutant. Transcriptome analysis showed major down regulation of transcripts (90%) at fibre initiation and early elongation (5 dpa) stages in the fl mutant. Majority of the down regulated transcripts at fibre initiation stage in the fl mutant represent calcium and phytohormone mediated signal transduction pathways, biosynthesis of auxin and ethylene and stress responsive transcription factors (TFs). Further, transcripts involved in carbohydrate and lipid metabolisms, mitochondrial electron transport system (mETS) and cell wall loosening and elongation were highly down-regulated at fibre elongation stage (5-15 dpa) in the fl mutant. In addition, cellulose synthases and sucrose synthase C were down-regulated at SCW biosynthesis stage (15-20 dpa). Interestingly, some of the transcripts (~50%) involved in phytohormone signalling and stress responsive transcription factors that were up-regulated at fibre initiation stage in the WT were found to be up-regulated at much later stage (15 dpa) in fl mutant.
  
  
  CONCLUSIONS
  Comparative transcriptome analysis of WT and its near isogenic fl mutant revealed key genes and pathways involved at various stages of fibre development. Our data implicated the significant role of mitochondria mediated energy metabolism during fibre elongation process. The delayed expression of genes involved in phytohormone signalling and stress responsive TFs in the fl mutant suggests the need for a coordinated expression of regulatory mechanisms in fibre cell initiation and differentiation.
authors.affiliation: Plant Transformation Group, International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
authors.forename: Kethireddy Venkata
authors.initials: KV
authors.lastname: Padmalatha
authors.forename: Deepak P
authors.initials: DP
authors.lastname: Patil
authors.forename: Krishan
authors.initials: K
authors.lastname: Kumar
authors.forename: Gurusamy
authors.initials: G
authors.lastname: Dhandapani
authors.forename: Mogilicherla
authors.initials: M
authors.lastname: Kanakachari
authors.forename: Mullapudi L V
authors.initials: ML
authors.lastname: Phanindra
authors.forename: Saravanan
authors.initials: S
authors.lastname: Kumar
authors.forename: T C
authors.initials: TC
authors.lastname: Mohan
authors.forename: Neha
authors.initials: N
authors.lastname: Jain
authors.forename: Arkalgud H
authors.initials: AH
authors.lastname: Prakash
authors.forename: Hiremath
authors.initials: H
authors.lastname: Vamadevaiah
authors.forename: Ishwarappa S
authors.initials: IS
authors.lastname: Katageri
authors.forename: Sadhu
authors.initials: S
authors.lastname: Leelavathi
authors.forename: Malireddy K
authors.initials: MK
authors.lastname: Reddy
authors.forename: Polumetla Ananda
authors.initials: PA
authors.lastname: Kumar
authors.forename: Vanga Siva
authors.initials: VS
authors.lastname: Reddy
mesh_terms: D020013:Calcium Signaling / Q000235:genetics; D050260:Carbohydrate Metabolism / Q000235:genetics; D002473:Cell Wall / Q000378:metabolism; D032561:Cotton Fiber; D004579:Electron Transport / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics; D005227:Fatty Acids / Q000378:metabolism; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics*; D023281:Genomics; D003368:Gossypium / Q000033:anatomy & histology / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D006706:Homeostasis / Q000235:genetics; D008928:Mitochondria / Q000378:metabolism; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D009995:Osmosis; D010937:Plant Growth Regulators / Q000378:metabolism; D055550:Protein Stability; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D005227:Fatty Acids; D010937:Plant Growth Regulators; D012333:RNA, Messenger; D014157:Transcription Factors