Identification of differentially expressed genes associated with semigamy in Pima cotton
Ontology highlight
ABSTRACT:
ORGANISM(S): Gossypium raimondii Gossypium arboreum Gossypium barbadense Gossypium hirsutum
PROVIDER: GSE27242 | GEO | 2011/02/12
SECONDARY ACCESSION(S): PRJNA137169
REPOSITORIES: GEO
Similar Datasets
Project description:The comparative analysis between 57-4 and Pima S-1 identified 284 genes in anthers and 1,864 genes in ovules as being differentially expressed in the semigametic genotype. Based on gene functions, 127 differentially expressed genes were common to both semigametic anthers and ovules, with 115 being consistently differentially expressed in both tissues. Nine of those genes were selected for qRT-PCR analysis, seven of which were confirmed. Furthermore, several well characterized metabolic pathways including glycolysis/gluconeogenesis, carbon fixation in photosynthetic organisms, sesquiterpenoid biosynthesis, and the biosynthesis of and response to plant hormones were shown to be affected by differentially expressed genes in the semigametic tissues. Anther and ovule tissues from 10 flowers of 57-4 and Pima S-1 was collected at zero days postanthesis (0 DPA) and placed in liquid nitrogen and stored at -80 °C. Total RNA was isolated using a hot borate method and cRNA was hybridized to the Affymetrix Cotton Genome GeneChips.
2011-02-12 | E-GEOD-27242 | biostudies-arrayexpress
Project description:Identification of differentially expressed genes associated with semigamy in Pima cotton
| PRJNA137169 | ENA
Project description:To gain novel insights into the molecular mechanisms underlying Pima cotton fiber quality, expression profiling of the Pima fiber transcriptome was performed as a function of development. The profiling was performed at 6 developmental time points: 8, 11, 14, 17, 21, and 24dpa. The expression profiling using long oligonucleotide microarray showed dynamic changes to the fiber transcriptome that correlate to morphogenesis, and biological cellular processes. Differentially expressed genes were identified by being differentially regulated at various stages of fiber development, and they were used to develop stage-specific regulation patterns that correlate the dynamics of gene expression to fiber morphogenesis.
2008-06-12 | GSE11689 | GEO
Project description:To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. Our aims were to: 1) identify genes expressed in a tissue-specific and temporal-specific manner; 2) define clusters of genes showing similar patterns of spatial and temporal expression; and 3) identify stage-specific or transition-specific candidate genes for further functional genomic analyses.We analyzed gene expression during S. chacoense embryogenesis in a series of experiments with probes derived from ovules isolated before and after fertilization (from 0 to 22 days after pollination), and from leaves, anthers, and styles. From the 6374 unigenes present in our array, 1024 genes were differentially expressed (≥ ±2 fold change, p value ≤ 0.01) in fertilized ovules and only limited expression overlap was observed between these genes and the genes expressed in the other tissues tested, with more than three quarters of the fertilization-regulated genes specifically or predominantly expressed in ovules. During embryogenesis three major expression profiles corresponding to early, middle and late stages of embryo development were identified. From the early and middle stages, a large number of genes corresponding to cell cycle, DNA processing, signal transduction, and transcriptional regulation were found. Defense and stress response-related genes were found in all stages of embryo development. Protein biosynthesis genes, genes coding for ribosomal proteins and other components of the translation machinery were highly expressed in embryos during the early stage. Genes for protein degradation were overrepresented later in the middle and late stages of embryo development. As expected, storage protein transcripts accumulated predominantly in the late stage of embryo development. Our analysis provides the first study in a solanaceous species of the transcriptional program that takes place during the early phases of plant reproductive development, including all embryogenesis steps during a comprehensive time-course. Our comparative expression profiling strategy between fertilized and unfertilized ovules identified a subset of genes specifically or predominantly expressed in ovules while a closer analysis between each consecutive time points allowed the identification of a subset of stage-specific and transition-specific genes.
2010-05-13 | GSE21552 | GEO
Project description:To provide a broad analysis of gene expression changes in developing embryos from a solanaceous species, we produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. Our aims were to: 1) identify genes expressed in a tissue-specific and temporal-specific manner; 2) define clusters of genes showing similar patterns of spatial and temporal expression; and 3) identify stage-specific or transition-specific candidate genes for further functional genomic analyses.We analyzed gene expression during S. chacoense embryogenesis in a series of experiments with probes derived from ovules isolated before and after fertilization (from 0 to 22 days after pollination), and from leaves, anthers, and styles. From the 6374 unigenes present in our array, 1024 genes were differentially expressed (? ±2 fold change, p value ? 0.01) in fertilized ovules and only limited expression overlap was observed between these genes and the genes expressed in the other tissues tested, with more than three quarters of the fertilization-regulated genes specifically or predominantly expressed in ovules. During embryogenesis three major expression profiles corresponding to early, middle and late stages of embryo development were identified. From the early and middle stages, a large number of genes corresponding to cell cycle, DNA processing, signal transduction, and transcriptional regulation were found. Defense and stress response-related genes were found in all stages of embryo development. Protein biosynthesis genes, genes coding for ribosomal proteins and other components of the translation machinery were highly expressed in embryos during the early stage. Genes for protein degradation were overrepresented later in the middle and late stages of embryo development. As expected, storage protein transcripts accumulated predominantly in the late stage of embryo development. Our analysis provides the first study in a solanaceous species of the transcriptional program that takes place during the early phases of plant reproductive development, including all embryogenesis steps during a comprehensive time-course. Our comparative expression profiling strategy between fertilized and unfertilized ovules identified a subset of genes specifically or predominantly expressed in ovules while a closer analysis between each consecutive time points allowed the identification of a subset of stage-specific and transition-specific genes. We produced amplicon-derived microarrays with 7741 ESTs isolated from Solanum chacoense ovules bearing embryos from all developmental stages. To monitor the expression pattern from genes involved in fertilization and embryogenesis processes, flowers were hand-pollinated and ovules were isolated every two days during a 22 days period after pollination. Four independent biological replicates were produced from each time points. In addition, to isolate genes specifically or predominantly expressed in ovules, four biological replicates of leaf, anther, and style tissue mRNA preparations were individually hybridized against unfertilized ovule mRNAs and compared with the data obtained from unfertilized and fertilized ovules at various time points after pollination. To estimate reproducibility and to produce control data for statistical analysis, a large number of unfertilized ovules were isolated and separated between seven independent control groups. RNA from randomly selected pairs of control was hybridized on six microarrays. 6374 unigenes present in our array in duplicate.
2010-05-13 | E-GEOD-21552 | biostudies-arrayexpress
Project description:To gain novel insights into the molecular mechanisms underlying Pima cotton fiber quality, expression profiling of the Pima fiber transcriptome was performed as a function of development. The profiling was performed at 6 developmental time points: 8, 11, 14, 17, 21, and 24dpa. The expression profiling using long oligonucleotide microarray showed dynamic changes to the fiber transcriptome that correlate to morphogenesis, and biological cellular processes. Differentially expressed genes were identified by being differentially regulated at various stages of fiber development, and they were used to develop stage-specific regulation patterns that correlate the dynamics of gene expression to fiber morphogenesis. A bi-directional double loop hybridization (Kerr and Churchill, 2001) with dye swap experimental design encompassing a total of 28 hybridizations was employed to maximize discovery of significant changes between developmental stages. Self-hybridization controls were conducted to evaluate both within-array correlation and dye bias.
2010-05-26 | E-GEOD-11689 | biostudies-arrayexpress
Project description:Gossypium barbadense is widely cultivated because of its extra-long staple cotton with superior luster, silkiness and high yield. These economically important traits were selected during initial domestication of an agronomically inferior wild ancestor, followed by millennia of human- mediated selection. To reveal the effects of this history on the cotton fiber transcriptome, we conducted comparative expression profiling on mechanically isolated fiber cells at three different stages encompassing early, mid, and late fiber elongation in wild (K101) and domesticated (Pima S-7) accessions, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes across developmental stages was different in the two accessions, with a shift toward greater change earlier in cultivated than in wild G. barbadense. Approximately 4200 genes were differentially expressed between wild and domesticated accessions at one or more of the stages studied. Domestication appears to have led to enhanced modulation of cellular redox levels and the avoidance or delay of stress-like processes. Prolonged fiber growth in cultivated relative to wild G. barbadense is associated with upregulation of signal transduction and hormone signaling genes and down-regulation of cell wall maturation genes. Clues are provided into the processes and genes that may unwittingly have been selected by humans during domestication and development of modern elite lines. Several of the transcriptomic differences between wild and domesticated G. barbadense described here appear to have parallels in a second domesticated cotton species, Gossypium hirsutum, suggesting that replicated domestication of two different species has resulted in overlapping, parallel, metabolic transformations. Two accessions of G. barbadense were studied, the elite cultivar, Pima S-7, and a wild accession from Bolivia, K101. Seeds of both accessions were sown in sterilized potting mix in the Pohl Conservatory at Iowa State University, Ames, IA, and three biological replicates were grown for 3-5 months. Flowers were tagged at anthesis and harvested at three time points, 2, 10, and 20 days postanthesis. For each of three biological replicates, ovules were excised, frozen in liquid nitrogen, and stored at -80C.
2008-11-13 | E-GEOD-13022 | biostudies-arrayexpress
Project description:Global transcript profiling to identify differentially expressed skeletal muscle genes in insulin resistance, a major risk factor for Type II (non-insulin-dependent) diabetes mellitus. Compared gene expression profiles of skeletal muscle tissues from 18 insulin-sensitive versus 17 insulin-resistant equally obese, non-diabetic Pima Indians. Keywords: other
2002-12-17 | GSE121 | GEO
Project description:Our results showed that hundreds of differentially expressed genes (DEGs) were detected in floral sex initiation period, but thousands of DEGs were involved in stamens and ovules development process. Moreover, the DEGs were mainly showed up-regulation in male floral initiation, but mainly down-regulation in female floral initiation. Male floral initiation was associated with the flavonoid biosynthesis pathway while female floral initiation was related to the phytohormone signal transduction pathway. In addition, the floral organ identity genes played important roles in floral sex differentiation process and displayed a general conservation of the ABCDE model in J. curcas.
2018-03-21 | GSE102894 | GEO