Gossypium hirsutum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA196402 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR800610.fastq.gz | Fastqsanger.gz | |||
| SRR800611.fastq.gz | Fastqsanger.gz | |||
| SRR800612.fastq.gz | Fastqsanger.gz | |||
| SRR800613.fastq.gz | Fastqsanger.gz | |||
| SRR800614.fastq.gz | Fastqsanger.gz |
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Project description:Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton
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Project description:We used a next-generation sequencing approach, Illumina Digital Gene Expression II (DGEII) technology, to Genome-wide profiling of gene expression during somatic (SE) and zygotic embryo (ZE) development. As a result, 4242 differentially expressed genes (DEGs) were identified between SE and ZE. Expression pattern cluster and functional classification analysis of the differentially expressed genes revealed that large number of genes indicative of response to stress highly expressed in somatic embryos. Combined with KEGG analysis and BLAST annotation, genes related to stress response in DEGs have been comprehensively analyzed, mainly including: ABA biosynthesis, ABA and JA (jasmonic acid) response, LEA (late embryogenesis abundant protein) family members, RD (responsive to dehydration) and ERD (early responsive to dehydration) family members, Hot Shock Proteins, WRKY family members and NAC family members. Semi-quantitative Reverse Transcriptase-PCR (RT-PCR) analysis was performed on 27 selected genes and and the results enhance that genes related to stress response were involved in SE development. Our main goal is to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. This is a systematical expression analysis focusing on somatic embryo development, and also a global comparison between somatic and zygotic embryo at transcript level. Therefore, this study might bring new insights into the regulation of somatic embryo development. An analysis of differentially expressed genes at 3 parallel stages during somatic and zygotic embryo development in cotton by next-generation sequencing, using Illumina Digital Gene Expression II (DGE II) .
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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: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. Cotton bud sizes were correlated with tapetum development. RNA was isolated from following tissues: • Anther tissues from buds at pre-meiotic stage of development (Tapetum absent) • Buds without anther tissues at pre-meiotic stage of development • Anther tissues from buds during meiosis (Tapetum present) • Buds without anther tissues during meiosis • Anther tissues from buds at post-meiotic stage of development (Tapetum degenerated) • Buds without anther tissues at post-meiotic stage of development • Leaf tissues • Seedling 5 days after germination Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following Affymetrix protocols. Three biological replicates were maintained.
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Project description:Genome-wide profiling of miRNAs and their target genes during somatic embryogenesis in cotton by small RNA and degradome sequencing
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Project description:Cotton is the most important economic crop that provides natural fibre and by-products such as oil and protein. The global gene expression could provide insight into the biological processes underlying growth and development, which involving suites of genes expressed with temporal and spatial controls by regulatory networks. Improvement of cotton fiber in yield and quality is the main goal for molecular breeding, but many previous research have been largely focused on identifying genes only in fibres, so that we ignore seed which may play an important role in the development of fibers. In this study, we constructed and systematically analyzed twenty-one strand-specific RNA-Seq libraries on Gossypium hirsutum L. covering different tissues, organs and development stages, of which approximately 970 million reads were generated. In total, 5,6754 transcripts derived from 2,9541 unigenes were obtained to provide a global view of gene expression for cotton development. Hierarchical clustering of transcriptional profiles suggests that transcriptomes among tissues or organs corresponded well to their developmental relatedness. The organ (tissue)-specific gene expressions were investigated efficiently and provided further insight into the dynamic programming of the transcriptome, in particularly for coordinating development between fiber cell and seed (ovule). We identified series of transcription factors and seed-specific genes, which as the candidate genes should help elucidate key mechanisms and regulatory networks that underlie fiber and seed development. This report identified comprehensive transcriptome changes in different stage of cotton development and will serves as a valuable genome-wide transcriptome resource for cotton breeding.
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Project description:Cotton (Gossypium hirsutum) is widely distributed worldwide, and improving the quality of its fiber is one of the most important tasks in cotton breeding. Cotton fibers are primarily composed of cellulose, which is synthesized and regulated by cellulose synthase (CesAs). However, the molecular mechanism of CesA genes in cotton is unclear. In this study, the cotton transcriptome and metabolome were used to investigate the significant function of CesA genes in fiber development. Finally, 321 metabolites were obtained, 84 of which were associated with the corresponding genes. Interestingly, a target gene named Gh_A08G144300, one of the CesA gene family members, was closely correlated with the development of cotton fibers. Then, identification and functional analysis were conducted. The target CesA gene Gh_A08G144300 was selected and analysed to determine its specific function in cotton fiber development. High-level gene expression of Gh_A08G144300 was found at different fiber development stages by RNA-seq analysis, and the silencing of Gh_A08G144300 visibly inhibited the growth of cotton fibers, showing that it is critical for their growth. This study provides an important reference for research on the gene function of Gh_A08G144300 and the regulatory mechanism of fiber development in cotton.
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Project description:Cotton Fiber Development Time-course Analysis
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