Cotton fiber development is a fundamental biological phenomenon. In spite of its economical importance, a large proportion of cotton fiber initiation is unknown. A naked seed mutant (N1N1) was compared with its isogenic lines of cotton (Gossypium hirsutum, TM-1) using a 70-mer oligonucleotide microarray that contained 1,536 features designed from a subset of cotton fiber ESTs. Statistical analysis and quantitative RT-PCR identified 23 "fiber-associated" genes. The annotation suggested that the temporal regulation of genes involved in transcriptional and translational regulation, signal transduction, and cell differentiation during early stages of fiber development. To get a large view of fiber initiation, a new cotton oligonucleotide microarray was developed containing sequences from an ovule EST library from Gossypium hirsutum L. T̲M̲-1 immature o̲vules (GH_TMO), a set from Jonathan Wendel's lab at Iowa State University, and the pilot set of oligos used for previous study. Global gene expression studies were performed with microdissected fiber initials (or epidermis) and inner ovules to investigate fiber preferentially expressed genes. Laser capture microdissection and antisense RNA (aRNA) amplification allowed us to collect fiber initials (0 DPA and 2 DPA) or epidermal layers (-2 DPA) from whole ovule tissues. The gene expression profiles of fiber initials showed up-regulation of fiber proteins, myb transcription factors, and hormonal regulators as well as trichome related factors during fiber initiation. In each developmental stage, different sets of gene categories in molecular function or biological processes were over- or under-represented, suggesting temporal regulation of genes during fiber development. One of the possible "fiber associated genes" found in microarray analyses, RD22 like gene (GhRDL), was highly enriched in the epidermis of cotton ovules during fiber initiation. The function of GhRDL was studied with the Arabidopsis trichome system which shares many similarities with fiber development. Overexpression of 35S::GhRDL into Arabidopsis thaliana Columia-0 induced seed hairs (or seed trichomes) and pRDL:GUS was localized in Arabidopsis seeds. This suggests that GhRDL plays an important role in the seed trichome development and can be a key player in cell differentiation and fiber development. / text