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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.

The present study deals with the resequencing of cultivars, Suvin and BCS-23-18-7 belonging to Gossypium barbadense which are distinctly differing in fiber qualities and seed cotton yield using Illumina Hiseq2500 sequencer. A total of 2,604,107 single nucleotide polymorphism (SNP) and 592,364 insertion and deletions (INDELs) were identified when compared with G. barbadense reference genome. Among the 14,075 preferentially expressed genes of agronomically important traits of cotton, we have identified 33,637 markers in the genic regions. Comparing between the variants of Suvin and BCS-23-18-7, among the 4,929 preferentially expressed genes in fiber, only 1,128 genes have 2,453 variants and of these 1,512 variants are non-synonymous types, leading to change at the protein level. In order to validate the presence of these markers in the expressed genes could tag the expression and/or phenotypic variation bought by alleles of Suvin/BCS-23-18-7, among 51 fiber elongation genes, ten genes that had high effect SNPs were utilized for real-time PCR, which showed an extended period of expression up to 15 days post-anthesis (DPA) in Suvin. Hence, utilization of such markers for the construction of SNP array / linkage maps would provide greater value to quantitative trait loci (QTL) mapping instead of random genomic markers. [ABSTRACT FROM AUTHOR]

The complex allotetraploid nature of the cotton genome makes genetic, genomic and functional analyses extremely challenging. Until now, several methods have been published for the purpose, but none is found to be universally applicable. To overcome these difficulties, we have designed protocol for the isolation of high quality and quantity genomic DNA from young as well as older leaves, which is suitable for molecular biology applications. We modified and optimized the CTAB method for plant genomic DNA extraction in large quantity and described protocol takes less than 80 min and does not require RNase treatment and purification step. The DNA yield ranged between 700-800 μg per gram of leaf tissue. Quantification of isolated DNA from spectral (A260/A280) measurements as well as agarose gel electrophoresis showed negligible polysaccharide and protein contamination. Thus the extracted DNA was very much suitable for southern hybridization and PCR based applications. [ABSTRACT FROM AUTHOR]