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Expression profiling of cotton (Gossypium hirsutum L. TM1) fiber transcriptome during the development

ABSTRACT: In order to study gene expression at the genomic level during elongation and secondary cell wall synthesis of upland cotton fiber, oligonucleotide microarrays were employed. RNA was isolated from fibers in 7 different time points beginning prior to peak fiber expansion, continuing through termination of fiber expansion and ending at peak cellulose synthesis (5, 8, 10, 14, 17, 21, and 24dpa). The arrays contained ~25,000 oligonucleotides representing ~12,200 genes designed from a fiber EST database during peak cell expansion. Dynamic changes in gene expression were analyzed in a developmental context to identify stage-specific biological processes and pathways likely to be crucial to cell polar elongation or cellulose biosynthesis and secondary cell wall biogenesis. Genes with significant changes in expression relative to any preceding time point were identified (moderated t-statistics, adjusted p-value <0.05) for each developmental time point with an expected false discovery rate for multiple testing <5%

ORGANISM(S): Gossypium arboreum Gossypium hirsutum

PROVIDER: GSE11693 | GEO | 2008/06/12

SECONDARY ACCESSION(S): PRJNA106099

REPOSITORIES: GEO

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Project description:exceptional example of evolutionary innovation is the single-celled seed trichome in Gossypium ("cotton fiber"). We have used fiber development in Gossypium as a system to understand how morphology can rapidly evolve. Fiber has undergone considerable morphological changes between the short, tightly adherent fibers of G. longicalyx and the derived long, spinable fibers of its closest relative, G. herbaceum, that facilitated cotton domestication. We conducted comparative gene expression profiling across a developmental time-course of fibers from G. longicalyx and G. herbaceum using microarrays with ~ 22,000 genes. Expression changes between stages were temporally protracted in G. herbaceum relative to G. longicalyx, reflecting a prolongation of the ancestral developmental program. Gene expression and GO analyses showed that many genes involved with stress responses were up-regulated early in G. longicalyx fiber development. Several candidate genes up-regulated in G. herbaceum have been implicated in regulating redox levels and cell elongation processes. Three genes previously shown to modulate hydrogen peroxide levels were consistently expressed in domesticated and wild cotton species with long fibers but expression was not detected by qRT-PCR in wild species with short fibers. Hydrogen peroxide is important for cell elongation, but at high concentrations it becomes toxic, activating stress processes that may lead to early onset of secondary cell wall synthesis and the end of cell elongation. These observations suggest that the evolution of long spinable fibers in cotton was accompanied by novel expression of genes assisting in the regulation of reactive oxygen species levels. Our data suggest a model for the evolutionary origin of a novel morphology through differential gene regulation causing prolongation of an ancestral developmental program. Keywords: Cotton, fiber, evolution, time-point, comparative genomic hybridization, stress response genes, H2O2 A balanced developmental loop design for microarray analysis was performed. For G. herbaceum (A1) and G. longicalyx (F), four fiber developmental time-points, 5, 10, 20 and 25 DPA were sampled. Within each species, hybridizations were performed between each pair of consecutive developmental stages by labeling one with Cy5 and the other with Cy3, and by closing the loop with a comparison of 25 and 5 dpa. In addition, 2 hybridizations were done between species at each time-point, using a dye swap for each pair. With three biological replications and 16 slides each, we generated gene expression data from a total of 48 microarrays.

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Expression profiling of cotton (Gossypium hirsutum L. TM1) fiber transcriptome during the development

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