Identification of differentially expressed genes associated with semigamy in Pima cotton

The comparative analysis between 57-4 and Pima S-1 identified 284 genes in anthers and 1,864 genes in ovules as being differentially expressed in the semigametic genotype. Based on gene functions, 127 differentially expressed genes were common to both semigametic anthers and ovules, with 115 being consistently differentially expressed in both tissues. Nine of those genes were selected for qRT-PCR analysis, seven of which were confirmed. Furthermore, several well characterized metabolic pathways including glycolysis/gluconeogenesis, carbon fixation in photosynthetic organisms, sesquiterpenoid biosynthesis, and the biosynthesis of and response to plant hormones were shown to be affected by differentially expressed genes in the semigametic tissues. Anther and ovule tissues from 10 flowers of 57-4 and Pima S-1 was collected at zero days postanthesis (0 DPA) and placed in liquid nitrogen and stored at -80 °C. Total RNA was isolated using a hot borate method and cRNA was hybridized to the Affymetrix Cotton Genome GeneChips.