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The mechanisms of cotton fiber development and somatic embryogenesis have been explored systematically with microarray and suppression subtractive hybridization. Real-time RT-PCR provides the simultaneous measurement of gene expression in many different samples, with which the data from microarray or others can be confirmed in detail. To achieve accurate and reliable gene expression results, normalization of real-time PCR data against one or several internal control genes is required, which should not fluctuate in different tissues during various stages of development. We assessed the gene expression of 7 frequently used housekeeping genes, including 18S rRNA, Histone3, UBQ7, Actin, Cyclophilin, Gbpolyubiquitin-1 and Gbpolyubiquitin-2, in a diverse set of 21 cotton samples. For fiber developmental series the expression of all housekeeping genes had the same down tendency after 17 …