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Gossypium hirsutum

ABSTRACT: Identification of candidate thermotolerance genes during early seedling stage in upland cotton (Gossypium hirsutum L.) revealed by comparative transcriptome analysis

PROVIDER: PRJNA287839 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2075740_1.fastq.gz	Fastqsanger.gz
	SRR2075740_2.fastq.gz	Fastqsanger.gz
	SRR2075741_1.fastq.gz	Fastqsanger.gz
	SRR2075741_2.fastq.gz	Fastqsanger.gz
	SRR2075736_1.fastq.gz	Fastqsanger.gz

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Identification of candidate thermotolerance genes during early seedling stage in upland cotton (Gossypium hirsutum L.) revealed by comparative transcriptome analysis

Project description:High temperature (HT) stress is a major environmental stress that limits cotton growth, metabolism, and yield worldwide. The identification and characterization of thermotolerance is restricted by the plant growth environment and growth stage. In this study, four genotypes of upland cotton (Gossypium hirsutum L.) with known field thermotolerance were evaluated under normal and HTs at the seedlings stage in a growth cabinet with 11 physiological, biochemical, and phenotypic assays. Consistent with previous field observations, the thermotolerance could be identified by genotype differences at the seedling stage under HT in a growth cabinet. Comparative transcriptome analysis was performed on seedlings of two contrasting cotton genotypes after 4 and 8 hours of HT exposure. Gene ontology analysis combined with BLAST annotations revealed a large number of HT-induced differentially expressed genes (4,698) that either exhibited higher expression levels in the heat-tolerant genotype (Nan Dan Ba Di Da Hua) compared with the heat-sensitive genotype (Earlistaple 7), or were differentially expressed only in Nan Dan Ba Di Da Hua. These genes encoded mainly protein kinases, transcription factors, and heat shock proteins, which were considered to play key roles in thermotolerance in upland cotton. Two heat shock transcription factor genes (homologs of AtHsfA3, AtHsfC1) and AP2/EREBP family genes (homologs of AtERF20, AtERF026, AtERF053, and AtERF113) were identified as possible key regulators of thermotolerance in cotton. Some of the differentially expressed genes were validated by quantitative real-time PCR analysis. Our findings provide candidate genes that could be used to improve thermotolerance in cotton cultivars.

2016-06-30 | GSE70205 | GEO

cDNA microarray expression profile during fiber elongation between G. hirsutum and G. barbadense

2012-05-24 | GSE18028 | GEO

Cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation

Project description:As an initial step to explore the cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation, conventional heirloom G. hirsutum (Gh) cultivars [susceptible Acala SJ-2 (SJ2), moderately resistant Upland Wild Mexico Jack Jones (WMJJ), and resistant Acala NemX] that have been shown to be useful as an informative genetic model for detecting and introgressing RKN resistance genes into commercial Upland cotton were used to enlighten the molecular mechanisms and gene expression of RKN resistance. Using the next generation sequencing (NGS) Illumina MiSeq and HiSeq, we performed RNA-seq profiling in roots with disease progression of 10 days and collected from 23 days old plants of SJ2, WMJJ, and NemX. With three biological replicates of each treatment from each cultivar, plants were subjected to RKN-infestation and non-infested control developing a total of 18 RNA-seq libraries

2022-04-01 | GSE190503 | GEO

Transcriptome profiling of Gossypium hirsutum in response to NO by high-throughput tag-sequencing

Project description:Nitric oxide(NO) is emerging as an important signaling molecule with diverse physiological functions in plants, leading to a necessity to discover the downstream genes and signal transduction network modulated by NO. In the current study, changes in gene expression in response to NO were studied in upland cotton(Gossypium hirsutum) using Solexa/Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing method. After mapping to an integrated reference sequence database, we obtained about 30,000 genes per library, and yielded 2,393 differential expressed genes in total.

2015-12-01 | GSE53674 | GEO

cDNA microarray expression profile during fiber elongation between G. hirsutum and G. barbadense

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

Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue and during fibre development stages.

Project description:This SuperSeries is composed of the following subset Series: GSE29566: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue. GSE29567: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress during fibre development stages. Refer to individual Series

2012-06-03 | E-GEOD-29810 | biostudies-arrayexpress

Transcriptomics and Metabolomics of 10 - 28 day post anthesis cotton fiber from Gossypium hirsutum and Gossypium barbadense

2015-06-26 | GSE64958 | GEO

Transcriptomics and Metabolomics of 10 - 28 day post anthesis cotton fiber from Gossypium hirsutum and Gossypium barbadense

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

Transcriptome of Gossypium hirsutum floral and extrafloral nectaries

Project description:Comparative RNA-Seq study of expression in Gossypium hirsutum nectaries

2018-04-19 | GSE113373 | GEO

Gossypium hirsutum strain:upland cotton

Project description:Gossypium hirsutum strain:upland cotton Raw sequence reads

| PRJNA670627 | ENA