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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.

Project description:Stem internodes of grasses function in mechanical support, transport, and, in some species are a major sink organ for carbon in the form of cell wall polymers. To establish the rice elongating internode as a model for secondary cell wall development, we conducted cell wall composition, proteomic and metabolomic analyses of the second rice internode at booting stage. We measured major secondary cell wall components along eight segments of an elongating internode. Cellulose, lignin, and xylose increase as a percentage of cell wall material from the younger to the older internode segments, indicating active cell wall synthesis. With the whole elongating internode, we measured peptides via liquid-chromatography mass spectrometry (LC-MS) following trypsin digestion of size fractionated proteins. This identified a total of 3249 protein groups with at least two unique peptides, including many glycosyltransferases, acyltransferases, glycohyrolases, cell wall-localized proteins, and protein kinases that have or may have functions in cell wall biosynthesis or remodeling. In addition, GO over-representation analysis and KO pathway analysis indicate many proteins involved in biosynthetic processes, especially the synthesis of secondary metabolites such as phenylpropanoids, flavonoids, and tepenoids. Therefore, we also used LC-MS to measure methanol-extracted secondary metabolites from the whole internode at the elongation stage and three post-elongation stages, and from leaf and root at the second post-elongation stage. The results indicate secondary metabolites in stems are distinct from those of roots and leaves, and show different profiles during stem development. This study fills a void of knowledge of proteomics and metabolomics data for grass stems, especially of rice, and provides baseline knowledge for more detailed studies of cell wall synthesis and other biological processes during internode development. This and future work is aimed at optimizing stem development and cell wall composition of grasses to improve agronomic properties and biofuel production.

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

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