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: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: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
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:Murine ES cells of different Srf genotype (E14wt, E100-/-, E100-/- rescue (Srf transgene)) were stimulated with FBS for 0-180 min. RNA was harvested and hybridized to Affymetrix MGU74A arrays. Keywords: time-course
2004-11-15 | GSE1949 | GEO
Project description:Transcriptional profiling of cotton fibers during development. Time course at 6 days post anthesis (dpa), 10 dpa, 20 dpa, and 24 dpa. All referenced to 20 dpa.
2009-04-16 | GSE12202 | GEO
Project description:Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, a global assembly of cotton ESTs was constructed based on three Gossypium. Using that assembly as a template, we now describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of more than 150,000 cotton ESTs derived from 30 different cDNA libraries representing many different tissue types and tissue treatments. A total of 13,158 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome but also including previously studied cotton genes, duplicated gene pairs derived from a paleoduplication event, transcription factors, and homology to protein coding genes in Arabidopsis. About 10% of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the array has direct application for analysis of the fiber transcriptome. To illustrate the utility of the array, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results. The cotton microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info. Keywords: self vs. self; platform testing
2006-09-22 | GSE5875 | GEO