The cotton fiber,as a single-celled trichome,is a biological model system for studying cell differentiation and elongation.However,the complexity of gene expression and regulation in the fiber complicates genetic research.In this study,we investigated the genome-wide transcriptome profiling in Texas Marker-1(TM-1)and five naked seed or fuzzless mutants(three dominant and two recessive)during the fuzz initial development stage.More than three million clean tags were generated from each sample representing the expression data for 27,325 genes,which account for 72.8%of the annotated Gossypium raimondii primary transcript genes.