Studies of wax genes in cotton (Gossypium arboreum)
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ABSTRACT:
ORGANISM(S): Gossypium arboreum
PROVIDER: GSE15279 | GEO | 2015/03/08
SECONDARY ACCESSION(S): PRJNA116503
REPOSITORIES: GEO
Similar Datasets
Project description:Studies of wax genes in cotton (Gossypium arboreum)
| PRJNA116503 | ENA
Project description:Mature green fruits of the tomato (Solanum lycopersicum L.) cultivar MicroTom were investigated (fruit developmental category II). For removal of the epicuticular wax layer a thin film of 1 g ml-1 aqueous gum arabic (Roth, Karlsruhe, Germany) as a fixative was applied to the fruit surface. After 1 h the dried polymer including the outermost epicuticular waxes was mechanically removed. This procedure was repeated once. During this experiment the tomato fruits remained on the tomato plant. Untreated (0 days) and gum arabic stripped tomato fruits harvested 2 days after treatment were compared. Samples contained exclusively the fruit peel, which was removed with a scalpel to a depth of approximately 1 mm. After sampling point the plant material was immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2163 | biostudies-arrayexpress
Project description:Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter. Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. Results from RNA-seq were combined with non-targeted metabolomics. Results: Approximately 38,000 transcripts were expressed (RPKM>2) in each fiber type and approximately 2,000 of these transcripts were differentially expressed in a cross-species comparison at each timepoint. Enriched Gene Ontology biological processes in differentially expressed transcripts suggested that Gh fibers were more stressed. Conclusions: Both metabolomic and transcriptomic data suggest that better mechanisms for managing reactive oxygen species contribute to the increased fiber length in Gossypium barbadense. This appears to result from enhanced ascorbate biosynthesis via gulono-1,4-lactone oxidase and ascorbate recycling via dehydroascorbate reductase. See Bioproject PRJNA263926 and SRA accession SRP049330 for study design and raw sequencing data and Bioproject PRJNA269608 and TSA accession GBYK00000000 for Gossypium arboreum assembled contig sequences used for transcriptome mapping - Cotton fiber mRNA from 10,15,18,21 and 28 day post anthesis fiber from either Gossypium hirusutm or Gossypium barbadense was sequenced and differential gene expression analysis was conducted between species for each timepoint and between adjacent timepoints. Each timepoint was representative of fiber from 9 individual plants processed as 3 biological replicate pools (material from 3 individual plants per pool).
2015-06-26 | E-GEOD-64958 | 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
Project description:Drought is one of the primary limiting factors affecting the growth and yield of cotton. Studying the genotypic drought response of plant towards stress stimuli necessitates the development of a standardized, comprehensive and cohesive system that specifically captures information regarding the focal purpose. In-house development of drought specific microarray using drought specific oligonucleotide probes was carried out and the leaf and root tissue of the two-important species Gossypium arboreum and Gossypium hirsutum were tested for genetic traits responses under 10 days’ drought stress. Further the response of these tissue under control and drought stress were studied via inhouse developed oligonucleotide chip.
2021-06-03 | GSE116908 | GEO
Project description:Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter. Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. Results from RNA-seq were combined with non-targeted metabolomics. Results: Approximately 38,000 transcripts were expressed (RPKM>2) in each fiber type and approximately 2,000 of these transcripts were differentially expressed in a cross-species comparison at each timepoint. Enriched Gene Ontology biological processes in differentially expressed transcripts suggested that Gh fibers were more stressed. Conclusions: Both metabolomic and transcriptomic data suggest that better mechanisms for managing reactive oxygen species contribute to the increased fiber length in Gossypium barbadense. This appears to result from enhanced ascorbate biosynthesis via gulono-1,4-lactone oxidase and ascorbate recycling via dehydroascorbate reductase.
2015-06-26 | GSE64958 | GEO
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. Cotton plants were grown under field condition. Flowers were tagged and cotton bolls were collected during fibre development stages. Total RNA was isolated from fibre bearing ovules of wild-type (WT) and fuzzy-lintless ovules of mutant (ANOI 1960) collected at various (0 and 10 dpa) fibre 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).
2014-11-01 | E-GEOD-52432 | biostudies-arrayexpress
Project description:This study was initiated with the objective of identifying the anther/tapetum specific promoters from cotton floral buds. Cotton is an important commercial crop. Hybrid cotton varieties are developed to obtain improved yield and fiber quality. Most of the hybrid seed production in cotton is carried out by hand emasculation, which requires large amount of manpower, resulting in high cost of hybrid seed. We are developing barnase-barstar based male sterility system, which would be a better alternative for hybrid development. The tapetum specific promoters are main requirement for such a system. The study was thus carried out to identify genes expressed in the anthers.
2013-10-31 | GSE51779 | GEO
Project description:Histone methylation is one of the most significant epigenetic modifications in plants because it is responsible for regulating and controlling the expression of many important functional genes. Although there have been many studies concerning histone methylation, its specific functions and mechanisms in cotton fiber initiation remain unclear. To determine if the H3K27me3 modification had regulated cotton fiber initiation in upland cotton (Gossypium hirsutum), we performed a comparative analysis on the cleavage under targets and tagmentation (CUT&Tag) between the wild-type cultivar Xu142 and its fibreless mutant Xu142 fl. This research was carried out three time points during the initiation period of cotton fibers, which were -1, 0 and 1 days post-anthesis (DPA). We also used the H3K27me3 antibody in Xu142 and Xu142 fl to examine the differential deposition of H3K27me3. Combing these results with RNA-seq analysis, we discovered a negative correlation between transcription and H3K27me3. We identified 336 genes with opposing trends in H3K27me3 deposition and expression. These genes are involved in various metabolic pathways, including fatty acid biosynthesis, galactose metabolism, plant hormone signal transduction, plant-pathogen interaction, glycolysis-/-gluconeogenesis, phenylpropanoid biosynthesis, and cutin, suberin and wax biosynthesis. Further physiological research revealed that in vitro ovule culture with an RDS 3434 inhibitor could alters the level of H3K27me3 in ovules, thus influencing the process of cotton fiber development. Taken together, these results indicate that H3K27me3 plays an important role in the fiber initiation process of cotton, and demonstrates the H3K27me3 network involved in fiber initiation in cotton ovules. The study also provides a foundation for the future study of genes involved in fiber development.
2024-03-14 | GSE227870 | GEO
Project description:Cotton fiber were used for the expression analysis at different developmental stages Affymetrix Cotton Genome array were used for the global profiling of gene expression of cotton fiber at different developmental stages
2012-03-20 | GSE36228 | GEO