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The dominant mutation not only delayed the process of fiber cell formation and elongation but also reduced the total number of fiber cells, resulting in sparsely distributed short fibers. Gene expression changes in TM-1 and N1N1 mutant lines among four tissues were analyzed using spotted cotton oligo-gene microarrays. Using the Arabidopsis genes, we selected and designed 1,334 70-mer oligos from a subset of cotton fiber ESTs. Statistical analysis of the microarray data indicates that the number of significantly differentially expressed genes was 856 in the leaves compared to the ovules (3 days post-anthesis, DPA), 632 in the petals relative to the ovules (3 DPA), and 91 in the ovules at 0 DPA compared to 3 DPA, all in TM-1. Moreover, 117 and 30 genes were expressed significantly different in the ovules at three and 0 DPA, respectively, between TM-1 and N1N1. Quantitative RT-PCR analysis of 23 fiberassociated genes in seven tissues including ovules, fiber-bearing ovules, fibers, and non-fiber tissues in TM-1 and N1N1 indicates a mode of temporal regulation of the genes involved in transcriptional and translational regulation, signal transduction, and cell differentiation during early stages of fiber development. Suppression of the fiber-associated genes in the mutant may suggest that the N1N1 mutation disrupts temporal regulation of gene expression, leading to a defective process of fiber cell elongation and development.Cotton fiber development is a fundamental biological phenomenon, yet the molecular basis of fiber cell initiation is poorly understood. We examined molecular and cellular events of fiber cell development in the naked seed mutant (N1N1) and its isogenic line of cotton (Gossypium hirsutum L. cv. Texas Marker-1, TM-1). The dominant mutation not only delayed the process of fiber cell formation and elongation but also reduced the total number of fiber cells, resulting in sparsely distributed short fibers. Gene expression changes in TM-1 and N1N1 mutant lines among four tissues were analyzed using spotted cotton oligo-gene microarrays. Using the Arabidopsis genes, we selected and designed 1,334 70-mer oligos from a subset of cotton fiber ESTs. Statistical analysis of the microarray data indicates that the number of significantly differentially expressed genes was 856 in the leaves compared to the ovules (3 days post-anthesis, DPA), 632 in the petals relative to the ovules (3 DPA), and 91 in the ovules at 0 DPA compared to 3 DPA, all in TM-1. Moreover, 117 and 30 genes were expressed significantly different in the ovules at three and 0 DPA, respectively, between TM-1 and N1N1. Quantitative RT-PCR analysis of 23 fiberassociated genes in seven tissues including ovules, fiber-bearing ovules, fibers, and non-fiber tissues in TM-1 and N1N1 indicates a mode of temporal regulation of the genes involved in transcriptional and translational regulation, signal transduction, and cell differentiation during early stages of fiber development. Suppression of the fiber-associated genes in the mutant may suggest that the N1N1 mutation disrupts temporal regulation of gene expression, leading to a defective process of fiber cell elongation and development.enUniversity of Cotton (Gossypium hirsutum L); Fiberless mutant; Fiber cell initiation; Microarray; Gene regulation; ArabidopsisArticlehttps://doi.org/10.1007/s00425-005-0098-7