Gossypium hirsutum
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ABSTRACT:
PROVIDER: PRJNA117515 | ENA |
REPOSITORIES: ENA
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Project description:Sea-island cotton (Gossypium barbadense L.) has superior fiber quality properties such as length, fineness and strength, while Upland cotton (Gossypium hirsutum L.) is characterized by high yield. To reveal features of Upland cotton and Sea-island cotton fiber cells, differential genes expression profiles during fiber cell elongation and in secondary wall deposits were established using cDNA microarray technology. This research provides a valuable genomic resource to deepen our understanding of the molecular mechanisms of cotton fiber development, and may ultimately lead to improvements in cotton fiber quality and yield.
2012-05-24 | GSE18028 | GEO
Project description:A cDNA library from 0-10 day post anthesis cotton ovules was established to study genes expressed in cotton ovule during initiation and quickly elongation period. We randomly sequenced over 100,000 ESTs from this library and acquired a gene pool of more than 28,000 UniESTs. The cotton UniESTs were then PCR-amplified and printed onto microarray. This array is comprised of about 28000 high-quality cotton cDNAs (with average length>750bp) and external controls. To study the different growth potential of cotton fibers in a one-year cycle, we then hybridized the array with RNA samples derived from +7 DPA wild-type upland cotton fibers in four different seasons, respectively.
2010-06-01 | GSE16802 | 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:Upland cotton (Gossypium hirsutum L.) is one of the world’s most important fiber crops, accounting for more than 90% of all cotton production. While their wild progenitors have relatively short and coarse, often tan-colored fibers, modern cotton cultivars possess longer, finer, stronger, and whiter fiber. In this study, the wild and cultivated cottons (YU-3 and TM-1) selected show significant differences on fibers at 10 day post-anthesis (DPA), 20 DPA and mature stages at the physiological level. In order to explore the effects of domestication, reveal molecular mechanisms underlying these phenotypic differences and better inform our efforts to further enhance cotton fiber quality, an iTRAQ-facilitated proteomic methods were performed on developing fibers. There were 6990 proteins identified, among them 336 were defined as differentially expressed proteins (DEPs) between fibers of wild versus domesticated cotton. The down- or up-regulated proteins in wild cotton were involved in Phenylpropanoid biosynthesis, Zeatin biosynthesis, Fatty acid elongation and other processes. Association analysis between transcroptome and proteome showed positive correlations between transcripts and proteins at both 10 DPA and 20 DPA. The difference of proteomics had been verified at the mRNA level by qPCR, also at physiological and biochemical level by POD activity determination and ZA content estimation. This work corroborate the major pathways involved in cotton fiber development and demonstrate that POD activity and zeatin content have a great potential related to fiber elongation and thickening.
2017-08-28 | PXD006604 | Pride
Project description:Sea-island cotton (Gossypium barbadense L.) has superior fiber quality properties such as length, fineness and strength, while Upland cotton (Gossypium hirsutum L.) is characterized by high yield. To reveal features of Upland cotton and Sea-island cotton fiber cells, differential genes expression profiles during fiber cell elongation and in secondary wall deposits were established using cDNA microarray technology. This research provides a valuable genomic resource to deepen our understanding of the molecular mechanisms of cotton fiber development, and may ultimately lead to improvements in cotton fiber quality and yield. 15 samples were prepared for microarray slides hybridized with three biological replicate samples including a swap-dye experiment for each growth stage. Each spot had a repeat in the microarray slideM-oM-<M-^Ltherefore, data for six replicate experiments performed with biologically independent samples.
2012-05-23 | E-GEOD-18028 | biostudies-arrayexpress
Project description:Transcriptomes fiber and ovules were compared by applying serial analysis of gene expression (SAGE). Keywords: Tissue Comparison We constructed three SAGE libraries and sequenced 57321, 64188, and 69104 tags from fiber, Xu-142 ovule (ovule) and fl mutant ovules (fl) respectively of Upland Cotton, Gossypium hirsutum L. cv. Xu-142.
2007-02-17 | E-GEOD-6103 | biostudies-arrayexpress
Project description:Cotton is one of the most commercially important Fiber crops in the world and used as a source for natural textile Fiber and cottonseed oil. The fuzzless-lintless ovules of cotton mutants are ideal source for identifying genes involved in Fiber development by comparing with Fiber bearing ovules of wild-type. To decipher molecular mechanisms involved in Fiber cell development, transcriptome analysis has been carried out by comparing G. hirsutum cv. MCU5 (wild-type) with its fuzzless-lintless mutant (MUT). Cotton bolls were collected at Fiber initiation (0 dpa/days post anthesis), elongation (5, 10 and 15 dpa) and secondary cell wall synthesis stage (20 dpa) and gene expression profiles were analyzed in wild-type and MUT using Affymetrix cotton GeneChip Genome array.
2013-06-14 | GSE38490 | GEO
Project description:This experiment was designed to investigate the molecular basis of cotton fiber cell initiation. 32,000 ESTs were sequenced from Gossypium hirsutum L. TM-1 immature ovules (GH_TMO) and developed cotton oligonucleotide microarrays containing ~23,000 unigenes. Transcriptome analyses were performed to compare gene expression changes in laser capture microdissected fiber cell initials (or epidermis) and inner ovules. The gene expression profiles of the fiber cell initials were compared with those of the inner ovules in each developmental stage prior to, right at, and shortly after the initiation of fiber cells. Many genes in various molecular function or biological processes were over- or under-represented between fibers and non-fiber tissues in each developmental stage, suggesting temporal regulation of gene expression during early stages of fiber development. For gene expression studies using a large set cotton oligo-microarray, 4 developmental stages were chosen. To study differential expression during fiber initiation, ovules at -2 DPA, 0 DPA, and 2 DPA were used. One of the fiber elongation stage tissues (7 DPA) was included. In each developmental stage, epidermis was separated from inner ovules and subjected to the hybridization. In addition, epidermis and ovule comparisons were performed individually with 0 DPA as a control point for comparison.
2011-11-02 | E-GEOD-17378 | biostudies-arrayexpress
Project description:The chip of cotton oligonucleotide microarrrays, which contain ~23,000 UniGenes from our own ESTs sequence project (Gossypium hirsutum L. TM-1 immature ovules (GH_TMO) ) and open resources, was developed. Transcriptome analyses were performed to compare gene expression changes in laser capture microdissected (LCM) fiber cell initials (or epidermis) and inner ovules. The gene expression profiles of the fiber cell initials were compared with those of the inner ovules in each developmental stage prior to (-2DPA), right at (0DPA), and shortly after the initiation of fiber cells (2DAP and 7DPA). Many genes in various molecular functions or biological processes were over- or under-represented between fibers and non-fiber tissues in each developmental stage, suggesting temporal regulation of gene expression during early stages of fiber development. For gene expression studies using a large set cotton oligo-microarray, 4 developmental stages were chosen. To study differential expression during fiber initiation, ovules at -2 DPA, 0 DPA, and 2 DPA were used. One of the fiber elongation stage tissues (7 DPA) was included. In each developmental stage, epidermis was separated from inner ovules and subjected to the hybridization. In addition, epidermis and ovule comparisons were performed individually with 0 DPA as a control point for comparison.
2011-05-06 | E-GEOD-27506 | biostudies-arrayexpress
Project description:Cotton is one of the most commercially important Fiber crops in the world and used as a source for natural textile Fiber and cottonseed oil. The fuzzless-lintless ovules of cotton mutants are ideal source for identifying genes involved in Fiber development by comparing with Fiber bearing ovules of wild-type. To decipher molecular mechanisms involved in Fiber cell development, transcriptome analysis has been carried out by comparing G. hirsutum cv. MCU5 (wild-type) with its fuzzless-lintless mutant (MUT). Cotton bolls were collected at Fiber initiation (0 dpa/days post anthesis), elongation (5, 10 and 15 dpa) and secondary cell wall synthesis stage (20 dpa) and gene expression profiles were analyzed in wild-type and MUT using Affymetrix cotton GeneChip Genome array. Cotton plants were grown under field condition. Flowers were tagged and cotton bolls were collected during Fiber development stages. Total RNA was isolated from Fiber bearing ovules of wild-type (WT) and fuzzless-lintless ovules of mutant (MUT) collected at various (0, 5, 10, 15 and 20 dpa) Fiber development stages using SpectrumTM Plant Total RNA kit (Sigma, USA) according to the manufacturerM-bM-^@M-^Ys protocol. Affymetrix cotton GeneChip Genome array (Affymetrix, USA) having 23,977 probe sets representing 21,854 cotton transcripts was used for transcriptome analysis. Three biological replicates were maintained to test the reproducibility and quality of the chip hybridization. cDNA labeling, array hybridization, staining and washing procedures were carried out as described in the Affymetrix protocols. CEL files having estimated probe intensity values were analyzed with GeneSpring GX-11.5 software (Agilent Technologies, USA) to get differentially expressed transcripts. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).
2013-06-14 | E-GEOD-38490 | biostudies-arrayexpress