title: Transcriptome dynamics during fibre development in contrasting genotypes of Gossypium hirsutum L.
abstract: Understanding the contribution of genetic background in fibre quality traits is important for the development of future cotton varieties with superior fibre quality. We used Affymetrix microarray (Santa Clara, CA) and Roche 454 GSFLX (Branford, CT) for comparative transcriptome analysis between two superior and three inferior genotypes at six fibre developmental stages. Microarray-based analysis of variance (ANOVA) for 89 microarrays encompassing five contrasting genotypes and six developmental stages suggests that the stages of the fibre development have a more pronounced effect on the differentially expressed genes (DEGs) than the genetic background of genotypes. Superior genotypes showed enriched activity of cell wall enzymes, such as pectin methyl esterase, at early elongation stage, enriched metabolic activities such as lipid, amino acid and ribosomal protein subunits at peak elongation, and prolonged combinatorial regulation of brassinosteroid and auxin at later stages. Our efforts on transcriptome sequencing were focused on changes in gene expression at 25 DPA. Transcriptome sequencing resulted in the generation of 475 658 and 429 408 high-quality reads from superior and inferior genotypes, respectively. A total of 24 609 novel transcripts were identified manually for Gossypium hirsutum with no hits in NCBI 'nr' database. Gene ontology analyses showed that the genes for ribosome biogenesis, protein transport and fatty acid biosynthesis were over-represented in superior genotype, whereas salt stress, abscisic acid stimuli and water deprivation leading to the increased proteolytic activity were more pronounced in inferior genotype.
authors.affiliation: Plant Molecular Biology Laboratory, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, India.
authors.forename: Deepti
authors.initials: D
authors.lastname: Nigam
authors.forename: Palacharla
authors.initials: P
authors.lastname: Kavita
authors.forename: Rajiv K
authors.initials: RK
authors.lastname: Tripathi
authors.forename: Alok
authors.initials: A
authors.lastname: Ranjan
authors.forename: Ridhi
authors.initials: R
authors.lastname: Goel
authors.forename: Mehar
authors.initials: M
authors.lastname: Asif
authors.forename: Alpika
authors.initials: A
authors.lastname: Shukla
authors.forename: Gunjita
authors.initials: G
authors.lastname: Singh
authors.forename: Debashis
authors.initials: D
authors.lastname: Rana
authors.forename: Samir V
authors.initials: SV
authors.lastname: Sawant
mesh_terms: D001483:Base Sequence; D002473:Cell Wall / Q000378:metabolism; D016000:Cluster Analysis; D032561:Cotton Fiber; D015536:Down-Regulation; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D005838:Genotype; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D010940:Plant Proteins; D012333:RNA, Messenger
keywords: GSE36228; SRA050044; cotton; fibre; microarray; transcriptome