Expression profiling of cotton (Gossypium barbadense L. Pima S7) fiber transcriptome during the development

To gain novel insights into the molecular mechanisms underlying Pima cotton fiber quality, expression profiling of the Pima fiber transcriptome was performed as a function of development. The profiling was performed at 6 developmental time points: 8, 11, 14, 17, 21, and 24dpa. The expression profiling using long oligonucleotide microarray showed dynamic changes to the fiber transcriptome that correlate to morphogenesis, and biological cellular processes. Differentially expressed genes were identified by being differentially regulated at various stages of fiber development, and they were used to develop stage-specific regulation patterns that correlate the dynamics of gene expression to fiber morphogenesis. A bi-directional double loop hybridization (Kerr and Churchill, 2001) with dye swap experimental design encompassing a total of 28 hybridizations was employed to maximize discovery of significant changes between developmental stages. Self-hybridization controls were conducted to evaluate both within-array correlation and dye bias.