Ontology highlight
ABSTRACT:
PROVIDER: PRJNA751446 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15446684_1.fastq.gz | Fastqsanger.gz | |||
| SRR15446684_2.fastq.gz | Fastqsanger.gz | |||
| SRR15446685_1.fastq.gz | Fastqsanger.gz | |||
| SRR15446685_2.fastq.gz | Fastqsanger.gz | |||
| SRR15446686_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants. Waterlogging stress causes yield reductions in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging causes significant reductions in stem elongation, shoot mass, root mass, and leaf number. At the global gene expression level waterlogging significantly alters the expression of 1012 genes (4.2% of genes assayed) in root tissue as early as 4h after flooding. Many of these genes are associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global leaf gene expression, significantly changing the expression of 1305 genes (5.4% of genes assayed) after 24h of flooding. Genes associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism were affected in leaf tissues of waterlogged plants. Implications of these results for the development of waterlogging tolerant cotton are discussed. Keywords: Stress Response
2009-12-18 | GSE16467 | GEO
Project description:Cotton premature leaf senescence often occurred with an increasing frequency in many cotton growing areas and caused serious reduction in yield and quality of cotton has been one of the impontant factors that restrict severely the production of cotton.Our laboratory studies showed chilling stress is the key factor that induced A. alternatia infection, caused Alternaria disease and then lead to cotton leaf senescence, but the molecular mechanism of cotton premature leaf senscence is still unclear. We used microarrays to study molecular mechanism of chilling stress causing Alternaria alternata infection and leading to cotton leaf senescence and find the key genes during this process.
2015-10-28 | GSE74412 | GEO
Project description:Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants. Waterlogging stress causes yield reductions in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging causes significant reductions in stem elongation, shoot mass, root mass, and leaf number. At the global gene expression level waterlogging significantly alters the expression of 1012 genes (4.2% of genes assayed) in root tissue as early as 4h after flooding. Many of these genes are associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global leaf gene expression, significantly changing the expression of 1305 genes (5.4% of genes assayed) after 24h of flooding. Genes associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism were affected in leaf tissues of waterlogged plants. Implications of these results for the development of waterlogging tolerant cotton are discussed. Keywords: Stress Response Plants of cotton cultivar Sicot 71 were grown to the two-leaf stage in tubs. For stress treatments plants were either watered as normal or flooded with water to completely submerge the root system. At four and twenty-four hours post-flooding samples of root or leaf tissue were taken from control and flooded plants. Total RNA was extracted from each tissue sample and assayed on cotton Affymetrix chips. Two biological replications were used for each comparison.
2010-05-17 | E-GEOD-16467 | 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:Apple leaf spot caused by the Alternaria alternata f. sp. mali (ALT1) fungus is one of the most devastating diseases of apple (Malus × domestica). We identified a hairpin RNA (hpRNA)-mediated small RNAs, MdhpRNA277, from apple (cv. ‘Golden Delicious’) that is induced by infection with ALT1. MdhpRNA277 produces mdm-siR277-1 and mdm-siR277-2, which target five R genes, MdRNL1, MdRNL2, MdRNL3, MdRNL4, and MdRNL5, that are expressed at high levels in the resistant apple variety ‘Hanfu’ and at low levels in the susceptible variety ‘Golden Delicious’ following ALT1 infection. MdhpRNA277 is strongly induced in ‘Golden Delicious’ but was not induced in ‘Hanfu’ following ALT1 inoculation. The promoter activity of MdhpRNA277 was much stronger in ‘Golden Delicious’ than in ‘Hanfu’ after ALT1 inoculation. We identified a single nucleotide polymorphism (SNP) in the MdhpRNA277 promoter region between the susceptible variety ‘Golden Delicious’ (pMdhpRNA277-GD) and resistant variety ‘Hanfu’ (pMdhpRNA277-HF). The transcription factor MdWHy binds to pMdhpRNA277-GD, but not to pMdhpRNA277-HF. Transgenic ‘GL-3’ apple lines expressing pMdhpRNA277-GD: MdhpRNA277 were more susceptible to ALT1 infection than were those expressing pMdhpRNA277-HF:MdhpRNA277 due to induced mdm-siR277 accumulation and low levels of expression of the five target R genes. The failure of MdWHy to bind to pMdhpRNA277-HF might contribute to the low levels of MdhpRNA277 and mdm-siR277-1/-2 expression and the high levels of R gene expression and resistance to Alternaria leaf spot in resistant apple varieties. We confirmed that the SNP in pMdhpRNA277 is associated with Alternaria leaf spot resistance by analyzing the progeny of three additional crosses. The SNP identified in this study could be used as a marker to distinguish between apple varieties that are resistant or susceptible to Alternaria leaf spot.
2018-12-25 | GSE115664 | GEO
Project description:Five allotetraploid cotton species have adapted, through their transcriptional responses, to unique environments with distinct levels of inherent abiotic stresses. The transcriptional responses of leaf and root tissue in five allotetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) under salt stress have been investigated in this study using cotton long oligonucleotide microarrays. Physiological responses to salinity such as stomatal conductance, ion and osmoprotectant contents were also measured as indicators of imposed stress. Accessions from these five cotton species were hydroponically grown and gradually introduced to a NaCl treatment (15 dS m-1). The microarray results identified 2721 and 2460 differentially expressed genes under salt stress that were significant in leaf and root tissue, respectively. Many of these genes were classified under gene ontology (GO) categories that suggest abiotic stress. These allotetraploid cottons shared transcriptional responses to salinity, but also showed responses that were species-specific. No consistent differences in transcriptional response among the previously estimated phylogenetic branches were found. Stomatal conductance, ion accumulation, and betaine, trigonelline, and trehalose contents also indicated salt stress. This global assessment of transcriptional and physiological responses to salt stress of these cotton species may identify possible gene targets for crop improvement and evolutionary studies of cotton. Keywords: CEGC Cotton oligo salt stress
2010-01-21 | GSE19966 | GEO
Project description:Five allotetraploid cotton species have adapted, through their transcriptional responses, to unique environments with distinct levels of inherent abiotic stresses. The transcriptional responses of leaf and root tissue in five allotetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) under salt stress have been investigated in this study using cotton long oligonucleotide microarrays. Physiological responses to salinity such as stomatal conductance, ion and osmoprotectant contents were also measured as indicators of imposed stress. Accessions from these five cotton species were hydroponically grown and gradually introduced to a NaCl treatment (15 dS m-1). The microarray results identified 2721 and 2460 differentially expressed genes under salt stress that were significant in leaf and root tissue, respectively. Many of these genes were classified under gene ontology (GO) categories that suggest abiotic stress. These allotetraploid cottons shared transcriptional responses to salinity, but also showed responses that were species-specific. No consistent differences in transcriptional response among the previously estimated phylogenetic branches were found. Stomatal conductance, ion accumulation, and betaine, trigonelline, and trehalose contents also indicated salt stress. This global assessment of transcriptional and physiological responses to salt stress of these cotton species may identify possible gene targets for crop improvement and evolutionary studies of cotton. Keywords: CEGC Cotton oligo salt stress The transcriptional responses of leaf and root tissue in five allotetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum, and G. darwinii) under salt stress have been investigated in this study using cotton long oligonucleotide microarrays. Physiological responses to salinity such as stomatal conductance, ion and osmoprotectant contents were also measured as indicators of imposed stress. Accessions from these five cotton species were hydroponically grown and gradually introduced to a NaCl treatment (15 dS m-1).
2010-01-20 | E-GEOD-19966 | biostudies-arrayexpress
Project description:Transcriptional profiling comparing gut tissue from fifth instar larvae exposed to five different diets, namely cotton fruit or boll (B), cotton flower bud or square (SQ), cotton leaf (L), pinto bean-based artificial diet (PB) and wheat-based artificial Lepidoptera diet (BIO). The generalist lepidopteran herbivore Helicoverpa armigera can consume host plants in more than 40 plant families, and often utilizes several different tissues on the same plant. It is believed that generalists owe their success to the deployment of various members of multigene families of detoxicative and digestive enzymes, a strategy that may also be responsible for rapid evolution of insecticide resistance. However studies of generalist adaptations have been limited to specific genes or gene families, and an overview of how these adaptations are orchestrated at the transcriptional level is lacking. To investigate the previously-shown CBW preferences for different cotton plant structures, we measured net weight gain of larvae that fed on different cotton organs and compared the transcript profiles of larval guts in response to these organs and towards two different artificial diets commonly used for laboratory rearing of this species, using a two-color alternating loop design microarray experiment.
2011-12-12 | GSE34344 | GEO