Series-temporal transcriptome profiling of cotton reveals the response mechanism of phosphatidylinositol signaling system in the early stage of drought stress
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ABSTRACT:
ORGANISM(S): Gossypium hirsutum
PROVIDER: GSE211298 | GEO | 2025/08/11
REPOSITORIES: GEO
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Project description:Structural and functional approaches were used to study cotton (Gossypium) genes implicated in water-deficit stress. A genetic map representing the hypothetical ancestral diploid genome (Consensus Map) was used to map 1,907 of 15,784 tentative consensus sequences (TCs). These TCs represent 25,119 cotton ESTs derived from various tissues under irrigated and water-limited condition. The correspondence of mapped TCs and 42 stress-related quantitative trait loci (QTLs) revealed that 391 of the initial 1907 TCs co-localized within a QTL interval. About 31% of these TCs were annotated as genes involved in plant responses to abiotic stress. By comparison, only 18% of the total annotated TCs mapped on the Consensus map were classified as abiotic stress genes. The enrichment of stress-related TCs that map to stress-related QTLs could not be explained by chance (P = 1.5 x 10-7). Gene expression profiling experiments were carried out using a microarray composed of 12,006 oligonucleotides. Transcriptional responses to imposed water-deficit stress in root and leaf tissue of 8-week old cotton plants revealed 1401 transcripts identified as drought responsive. A total of 158 (84 drought-induced and 74 drought-repressed) genes were mapped, of which 22 (8 induced and 14 repressed) genes co-localized with a QTL. A total of 539 unique genes were identified in the drought-stressed libraries. However, only 91 of these genes are contained on the array. Of these genes, 12 showed significant changes in transcript abundance between stressed and irrigated leaf and root. Forty-five candidate genes implicated in drought-stress response at some level of characterization were identified. Keywords: stress response
2007-10-03 | GSE8719 | 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.
2012-06-04 | GSE29567 | GEO
Project description:Drought-responsive genes were identified in leaf tissues of the cotton Acala 15-1799, a cotton genotype derived in the Southwest USA. Most of the identified genes such as the heat shock proteins have been described as responsive to drought and heat in other plant species. Microarray analysis was used to identify drought-responsive genes that might confer this cotton genotype with an improved tolerance to drought stress. Leaves from cotton plants watered or exposed to drought stress were used for RNA extraction and generarion of cRNA probes for hybridization of Affymetrix microarrays. Microarray technology was used to identify drought-responsive genes in cotton to assist in molecular breeding program. The supplementary file 'GSE18253_differentially_expressed.txt' lists the differentially expressed genes.
2010-05-22 | E-GEOD-18253 | biostudies-arrayexpress
Project description:To detect salt-tolerance-related miRNAs, comparative analysis of miRNA expression profiles was performed between the salt-tolerant and -sensitive cotton cultivars in control and salt-stressed conditions (treated with 300 mM NaCl for 24 h) using microRNA microarray Total RNA was extracted from (1) the seedling of salt-tolerant cotton cultivar in normal growth conditions, (2) the seedling of salt-tolerant cotton cultivar in salt-stressed growth conditions, (3) the seedling of salt-sensitive cotton cultivar in normal growth conditions, and (4) the seedling of salt-sensitive cotton cultivar in salt-stressed growth conditions. Then, the low-molecular-weight RNA (LMW-RNA) was isolated using the PEG solution precipitation method and used to hybridization.
2011-05-03 | E-GEOD-19009 | 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. 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:Transcriptome analysis in cotton under drought stress. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out in leaf tissue. Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Leaf 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 | GSE29566 | GEO
Project description:Cotton productivity is affected by water deficit and little is known about the molecular basis of drought tolerance in cotton. In this study, microarray analysis was carried out to identify drought responsive genes in functional leaves of the field-grown drought stressed cotton (Gossypium hirsutum L.) Acala 1517-99. The water stress was imposed after withholding irrigation for 9 days in the early squaring stage, which resulted in 10-15% reduction in plant growth compared to the well watered plants. A total of 110 drought responsive genes (0.5% of the total genes represented in the microarray) were identified, 79% (88 genes) of which were down-regulated and 21% (22 genes) were up-regulated by water stress. The responsiveness of 19 selected drought responsive genes was validated by real time PCR. The drought inducible genes were grouped into six functional categories only including stress related (10 genes, 9 of which are heat shock proteins), metabolism (3) and one each for transcription factor, proline biosynthesis and cellular transport. The down-regulated genes were classified into 14 functional categories including metabolism (20 genes), cellular transport (12), stress related (12), and regulation of gene expression (9) and transcription factor (4), signal transduction (7) and 2 genes each for biosynthesis of secondary compounds, cell wall, fatty acids/lipids and chlorophyll, and protein degradation. Most of the genes have been reported in other plants as drought tolerant/responsive and only 21 drought responsive genes (19%) were functionally unknown. The genes identified provides the first glimpse into the molecular basis of drought response in cotton.
2009-09-25 | GSE18253 | GEO
Project description:Cotton (Gossypium hirsutum L) is an important crop world wide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. These reserves are not available to produce seed and fiber when cotton is usually grown as an annual crop. Analysis of developing cotton plants indicated that starch levels peaked about the time of first anthesis then began to decline. An earlier peak of levels of starch was occasionally observed and in some greenhouse-grown samples starch increased 2 week after first bloom. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with carbohydrate metabolism, transcription activity and the proteasome. Genes associated with starch synthesis, starch degradation, sucrose metabolism, hexose metabolism, raffinose synthesis and trehalose synthesis increased in expression in starch accumulating tissues. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in relevant tissues. We propose that altering expressions of genes and pathways identified in this work could be used to more efficiently mobilize stored carbohydrate to fiber production. Keywords: starch accumulating, stem, root Genes expression was compared between cotton stems that were low in starch and accumulating starch. Gene expression was also compared between cotton roots that were low in starch and accumulating starch. A total of three microarrays were used. One dye swap was used. Material from the field were harvested 2 weeks apart. Greenhouse grown material were planted at two week intervals and harvested at the same time. NOTE that the channel representing the low starch material only gave about half of the total signal than the high starch samples. QPCR of 9 genes confirmed differential expression of 8 of them. QPCR also confirmed similar expression of two genes not predicted to be differentially expressed by the microarray analysis. Therefore no correction was made for the apparent difference in the hybridization of high and low starch samples.
2010-06-24 | E-GEOD-8973 | biostudies-arrayexpress
Project description:Cotton (Gossypium hirsutum L) is an important crop world wide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. These reserves are not available to produce seed and fiber when cotton is usually grown as an annual crop. Analysis of developing cotton plants indicated that starch levels peaked about the time of first anthesis then began to decline. An earlier peak of levels of starch was occasionally observed and in some greenhouse-grown samples starch increased 2 week after first bloom. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with carbohydrate metabolism, transcription activity and the proteasome. Genes associated with starch synthesis, starch degradation, sucrose metabolism, hexose metabolism, raffinose synthesis and trehalose synthesis increased in expression in starch accumulating tissues. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in relevant tissues. We propose that altering expressions of genes and pathways identified in this work could be used to more efficiently mobilize stored carbohydrate to fiber production. Keywords: starch accumulating, stem, root
2009-01-04 | GSE8973 | GEO
Project description:To identify potential miRNAs involved in fiber development and elucidate their expression differences between G. barbadense and G. hirsutum, we constructed two small RNA libraries, Gb10 and Gh10, prepared from fibers of 3-79 (G. barbadense) and TM-1 (G. hirsutum) collected at 10 days post-anthesis (DPA). We identified 28 conserved miRNA families, including 24 that exactly match known plant miRNA families in miRBase. With MIREAP and newly developed software miRsearcher, 7 candidate-novel miRNAs were found. 5 candidate-novel miRNAs were expressed in both species, 2 candidate-novel miRNAs were expressed only in one species. Moreover, 4 miRNA families showed significant expression differences between sea-island cotton and upland cotton in 10 DPA fibers.
2010-12-03 | GSE25773 | GEO