Within and between-species transcript profiling during cotton fibre development
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PROVIDER: PRJNA105625 | ENA |
REPOSITORIES: ENA
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Project description:A gene expression profiling study on two major cotton species that are cultivated for fibre, Gossypium hirsutum (L.) and Gossypium barbadense (L.), at different stages during fibre development using a printed cDNA microarray was undertaken to identify potential candidate genes for manipulation to improve fibre quality. Keywords: Species comparison, development
2009-07-21 | GSE10363 | GEO
Project description:A gene expression profiling study on two major cotton species that are cultivated for fibre, Gossypium hirsutum (L.) and Gossypium barbadense (L.), at different stages during fibre development using a printed cDNA microarray was undertaken to identify potential candidate genes for manipulation to improve fibre quality. Keywords: Species comparison, development Three-condition experiment: 7, 11 and 21 day post anthesis. Biological replicates: 3, Two species compared at each condition: Gossypium.hirsutum and Gossypium.barbadense. One replicate per array, dye swap, one rep per array.
2010-05-16 | E-GEOD-10363 | biostudies-arrayexpress
Project description:Transcriptome analysis in cotton during fibre development stages. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out at fibre development stages (0, 5, 10 and 20 dpa/Days post anthesis). Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. Gene expression profiles in drought induced and their respective control samples were analyzed using Affymertix cotton Genechip Genome arrays to study the global changes in the expression of genome.
2012-06-04 | GSE29567 | GEO
Project description:0dpa Fibre vs epidermal laser capture microdisection comparison Keywords: Development
2006-06-27 | GSE5133 | GEO
Project description:Transcriptome analysis in cotton during fibre development stages. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out at fibre development stages (0, 5, 10 and 20 dpa/Days post anthesis). Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. Gene expression profiles in drought induced and their respective control samples were analyzed using Affymertix cotton Genechip Genome arrays to study the global changes in the expression of genome. Total RNA was isolated from 0 dpa, 5 dpa, fibre bearing ovules of 10 dpa, and fibre bearing ovules of 20 dpa. Samples were collected from both drought induced and control plants. Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following the Affymetrix protocols. Three biological replicates were maintained.
2012-06-03 | E-GEOD-29567 | biostudies-arrayexpress
Project description:0dpa Fibre vs epidermal laser capture microdisection comparison Total RNA was isolated from each cell type (fibre initial or non-fibre epidermal pavement cell) from both Plant 1 and Plant 2. Hence, there were two biological replicates of each cell-type. Sub-samples of each cell type, designated here as technical replicates, were taken as separate batches of cells from different groups of ovules, but each from the same pair of plants. In particular, there were four sub-samples of fibre initial cells from plant 1 and two from plant 2 and two sub-samples of non-fibre epidermal from plant 1 and four from plant 2. The complete experiment involved three dye-swap pairs using a total of 6 arrays.
2006-06-26 | E-GEOD-5133 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE29566: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue. GSE29567: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress during fibre development stages. Refer to individual Series
2012-06-03 | E-GEOD-29810 | biostudies-arrayexpress
Project description:Comparative transcriptome profiles of cotton (G. hirsutum L. cv. Bikaneri narma) during boll development stages (0, 2, 5 and 10 dpa) under bollworm infested biotic stress. Cotton is one of the most commercially important fibre crops in the world and used as a source for natural textile fibre and cottonseed oil. The biotic stress is one of the major constraints for crop production. Cotton bollworm (Helicoverpa armigera) is one the major insect pest in cotton and drastically damages the cotton boll. To decipher the molecular mechanisms involved in cotton boll/fibre cell development, transcriptome analysis has been carried out by comparing G. hirsutum L cv. Bikaneri narma cotton boll samples induced by biotic stress (bollworm infested) and that their respective control cotton bolls collected under field conditions. Cotton bolls were collected at fibre initiation (0, 2 dpa/days post anthesis) and elongation (5, 10 dpa) stages for both control and biotic stress condition and gene expression profiles were analyzed by Affymetrix cotton GeneChip Genome array.
2015-03-01 | GSE55511 | GEO
Project description:Cotton (Gossypium hirsutum L.) fibres are specialised trichomes that extend from the seedcoat. To date only a few genes directly involved in the differentiation of these epidermal cells have been identified. We have identified a HD-ZIP transcription factor, GhHD-1, expressed in trichomes and early fibres that might play a role in cotton fibre initiation. Here we characterise GhHD-1 from G. hirsutum and show, using reporter constructs and qRT-PCR, that they are expressed predominantly in epidermal tissues during early fibre development and in other tissues bearing epidermal trichomes. GhHD-1 silencing caused reduced trichome formation and delayed the timing of fibre initiation whereas constitutive over-expression of GhHD-1 increased the number of fibres initiating on the seed, but did not affect leaf trichomes. Expression of GhHD-1 in transgenic cotton silenced for different fibre MYBs suggest that in ovules it acts downstream of GhMYB25-like. Microarray analysis of silencing and over-expression lines of GhHD-1 indicated that it potentially functions through a WRKY transcription factor and calcium-signalling pathway genes that are shared with some biotic stress reactions. Microarray analysis of 2 biological replicates each of GhHD-1 silenced and over-expression transgenic lines relative to wild-type were used to identify downstream targets of this transcription factor during early fibre development. 0 dpa (Days post anthesis) ovules from GhHD-1 silenced and over-expression lines and wild-type cotton plants were selected for RNA extraction and hybridisation on Affymetrix cotton arrays. Cotton fibre development initiates on the epidermal surface of each ovule within a cotton boll on the day of flowering and GhHD-1 has been shown to be most highly expressed at this stage (0 dpa). Ovules were obtained from 0dpa flowers for hybridisation to cotton arrays to identify genes that may be regulated by GhHD-1 during this early fibre development stage (initiation).
2012-05-31 | E-GEOD-36021 | biostudies-arrayexpress
Project description:Comparative analysis of transcriptome profiles of G. arboreum L. cv. and its fuzzy-lintless mutant (ANOI 1960) at 0 and 10 dpa. Cotton is one of the most commercially important fibre crops in the world and used as a source for natural textile fibre and cottonseed oil. The fuzzy-lintless ovules of cotton mutants are ideal source for identifying genes involved in fibre development by comparing with fibre bearing ovules of wild-type. To decipher molecular mechanisms involved in fibre cell development, transcriptome analysis has been carried out by comparing G. arboreum cv. (wild-type) with its fuzzy-lintless mutant (ANOI 1960). Fuzzed-lintless mutant line was generated by back cross breeding between FL and Fl (recurrent parent) lines (personal communication by Dr. I. S. Katageri). Basically Fibre less type was a RIL, first recovered from cross between G.arboreum (linted) and G. anomalum (lint less). This RIL was used as donor parent and crossed with normal arboreum (as recurrent parent) to develop G. arboreum FL and G. arboreum Fl isogenic lines. This G. arboreum Fl line is named as ANOI 1960. Cotton bolls were collected at fibre initiation (0 dpa/days post anthesis) and elongation (10 dpa) and gene expression profiles were analyzed in wild-type and ANOI 1960 mutant using Affymetrix cotton GeneChip Genome array.
2014-11-01 | GSE52432 | GEO