Identification of genes associated with Egyptian cotton fiber development using combination of SSH, microarrays and real time RT-PCR

ABSTRACT

One of the major limitations in the application of genetic engineering or conventional breeding methods in improving cotton fiber is the paucity of information about fiber related genes. Availability of Gossypium barbedense Giza 88 extra-long staple cotton fiber traits provides a unique opportunity to study fiber-associated genes because of its high-quality fiber compared to Giza 90 long staple fiber. To understand the molecular basis of cotton fiber development, we used the combination of suppression subtractive hybridization [SSH], microarrays and real-time reverse transcription-polymerase chain reaction [RT-PCR] technologies to identify the potential genes related to cotton fiber development. Utilizing mRNAs from 15 days post anthesis [dpa] fibers, we constructed a SSH cDNA library from Giza 88 extra long staple fiber as the tester and Giza 90 long staple fiber as the driver. The SSH cDNA library was then screened using microarrays. Microarrays analysis showed that 20 genes were differentially expressed in Giza 88 15-dpa fiber compared to Giza 90 as confirmed by real time RT-PCR. These genes include two beta-tubulins, an actin, a putative kinesin light chain, a cellulose synthase, glycosyl hydrolase family protein, pyruvate decarboxylase, glycoside hydrolase family, GDP-mannose pyrophosphorylase, dynaminlike protein, annexin and a number of genes involved in signal transduction, and protein, nucleic acid metabolism and lipid metabolisms