Identification of differentially expressed genes during bud stage of cotton boll development using suppression subtractive hybridization and cDNA macroarray

Cotton boll development is the result of a genetically programmed process influenced by environmental factors. Sequence information derived from advanced EST sequencing is an essential resource for functional genomics studies. The present study was undertaken to understand the gene expression profile of the early boll development stage. PCR select cDNA subtraction was employed to obtain subtracted library using cDNA prepared from ?5 Days Post Anthesis stage of bud as a tester and cDNA from leaves as a driver. Differential screening of 868 positive single inserts by cDNA macroarray resulted in 170 ESTs from ?5 days post anthesis bud which were further assembled into 64 contigs. Obtained results were validated by quantitative PCR for selected genes. Functional annotation showed the presence of majority of genes involved in transport processes, stress, nucleotide binding and cytoskeleton. The role of carbohydrate metabolism in bud and role of tubulin6 in fibre cell initiation were discussed.