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Comparsion of gene expression profile in polaris (pola) mutant lines and its POLARIS (POLA) wild-type at meiotic and ripening stages

ABSTRACT: To assess the role of POLA in relation to ovule development, embryogenesis and endosperm development, we analyzed gene expression profiles by using microarray. Compared to the wild-type plants, several groups of transcription factors in the pola mutant plants and POLA RNAi lines showed up- or down-regulation at meiotic stage and ripening stages of floral development. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as biosynthesis, transport, signal transduction, and degeneration of hormone, sugar, starch, fatty and lipid, protein and amino acid. These results supported that MADS protein POLA could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes involved in developmental and hormonal pathways.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE25693 | GEO | 2010/12/01

SECONDARY ACCESSION(S): PRJNA135843

REPOSITORIES: GEO

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Comparsion of gene expression profile in polaris (pola) mutant lines and its POLARIS (POLA) wild-type at meiotic and ripening stages

Project description:To assess the role of POLA in relation to ovule development, embryogenesis and endosperm development, we analyzed gene expression profiles by using microarray. Compared to the wild-type plants, several groups of transcription factors in the pola mutant plants and POLA RNAi lines showed up- or down-regulation at meiotic stage and ripening stages of floral development. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as biosynthesis, transport, signal transduction, and degeneration of hormone, sugar, starch, fatty and lipid, protein and amino acid. These results supported that MADS protein POLA could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes involved in developmental and hormonal pathways. To perform microarray analysis, the samples were pooled by 20 panicles from 10 individual plants at meiotic and ripening stage. For meiotic stage RNA sample, panicle of pola mutant were prepared at early to late meiotic stage, and panicle of POLA RNAi line(T2) were prepared at ten to fifteen days after pollination stage for ripening stage RNA sample.

2010-12-01 | E-GEOD-25693 | biostudies-arrayexpress

Expression data from cynosure (cyn) mutant and its CYNOSURE (CYN) wild-type at before flowering and 5 days after pollination stage

Project description:To assess further the role of CYN in relation to integument morphogenesis, gametophytic cell fate specification, embryogenesis and endosperm development, we compared the expression profiles between the cyn mutant and wild-type at two different stages(before flowering and 5 days after pollination stage) of ovule development by microarray analysis. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as auxin efflux & polarity & cell differentiation, flower and embryonic development, signal transduction.These results supported that MADS protein CYN could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes (including MADS or non-MADS transcription factors) involved in developmental and hormonal pathways. Three independent biological replicates of cyn mutant and wild-type panicle mRNA at two different stages of ovule development were used for microarray experiments. To perform microarray analysis, the samples were pooled by 20 panicles from 10 individual plants at before flowering and 5 days after pollination stage.

2014-11-03 | E-GEOD-33441 | biostudies-arrayexpress

Expression data from cynosure (cyn) mutant and its CYNOSURE (CYN) wild-type at before flowering and 5 days after pollination stage

2014-11-03 | GSE33441 | GEO

Global gene expression analysis of normal and ripening inhibitor (rin) mutant tomatoes during ripening

Project description:Ripening is an important stage of fruit development to determine its quality as a diet. A tomato (Solanum lycopersicum) MADS-box transcription factor, RIPENING INHIBITOR (RIN), has been believed to serve as a regulator of ripening lying upstream of ethylene-dependent and ethylene-independent pathways. Here, we have conducted global gene expression analysis to comprehensively identify tomato genes whose expressions are affected by the rin mutation using microarray with RNA samples from the normal and rin mutant tomato fruits at the pre-ripening (mature green) and ripening (pink coloring) stages. By analysing this microarray data, we identified 342 of positively regulated and 473 negatively regulated genes by RIN, which showed >5 and <0.2 of the fold change ratio (FC) of normal fruits at the ripening stage relative to those at the pre-ripening stage, respectively, in a RIN-dependent manner. A chromatin immunoprecipitation (ChIP) analysis of the normal ripening tomatoes with the anti-RIN antibody revealed that the positively regulated gene set contained at least 13 direct RIN targets. We monitored global gene expression in normal (PK331 cultivar) and rin mutant (PK353 cultivar) tomatoes at the pre-ripening (mature green, G) and ripening (pink coloring, P) stages using microarray with three biological replicates for each sample.

2012-04-01 | E-GEOD-28564 | biostudies-arrayexpress

Global gene expression analysis of normal and ripening inhibitor (rin) mutant tomatoes during ripening

2012-04-02 | GSE28564 | GEO

Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit

Project description:[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes. Three chronological stages of tomato (Solanum lycopersicon) fruit ripening were compared between wild type and rin mutant

2012-02-29 | E-GEOD-20720 | biostudies-arrayexpress

Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit

2012-02-29 | GSE20720 | GEO

Single and double mutations in tomato ripening transcription factors have distinct effects on fruit development and quality traits

Project description:The study of climacteric fruit ripening in tomato has been facilitated by the spontaneous ripening mutants Colorless non-ripening (Cnr), non-ripening (nor), and ripening inhibitor (rin). These mutants effect the genes encoding ripening transcription factors (TFs) SPL-CNR, NAC-NOR, and MADS-RIN causing pleiotropic defects to the ripening program. Here, we demonstrate that some ripening processes occur in the mutant fruit but at later stages of development compared to the wild type. The rin and nor mutant fruit exhibit similar quality traits to wildtype at later stages of ripening and senescence and delayed expression of ripening-associated genes. In addition, we propose that the Cnr mutant has a broader range of effects to fruit development than just fruit ripening. Cnr fruit show distinct differences from wild type in ripening phenotypic traits and gene expression profiles prior to the initiation of ripening. We provide new evidence that some mutants can produce more ethylene than basal levels and demonstrate ABA accumulation is also affected by the mutations. Studies have examined the relationship between the CNR, RIN, and NOR TFs based on protein-protein interactions and transcriptional regulation during fruit ripening. We describe the genetic interactions affecting specific fruit traits by using homozygous double mutants. Cnr predominantly influences the phenotype of the Cnr/nor and Cnr/rin double mutants but additional defects beyond either single mutation is evident in the transcriptome of the Cnr/nor double mutant. Our reevaluation of the Cnr, nor, and rin mutants provides new insights the utilization of the mutants in breeding and studying fruit development.

2020-12-24 | GSE163745 | GEO

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

Project description:DNA methylation is a conserved epigenetic mark important for genome integrity, development and environmental responses in plants and mammals. Active DNA demethylation in plants is initiated by a family of 5mC DNA glycosylases/lyases (i.e. DNA demethylases). The role of DNA demethylases in transposon regulation, pathogen responses, and gene imprinting and other developmental processes have been studied extensively in the model plant Arabidopsis thaliana. Recent studies suggested a role of active DNA demethylation in fruit ripening in tomato. In this study, we generated loss-of-function mutant alleles of a tomato gene, SlROS1/SlDML1/2, which is a close homolog of the Arabidopsis DNA demethylase gene ROS1. In the fruits of the tomato mutants, increased DNA methylation was found in thousands of genes. These genes include not only hundreds of ripening induced genes but also many ripening repressed genes. Our results show that SlROS1 is critical for tomato fruit ripening, and suggest that active DNA demethylation is required for both the activation of ripening induced genes and inhibition of ripening repressed genes.

2017-05-02 | GSE94903 | GEO

Expression data in individual grape berries during ripening initation

Project description:We used Affymetrix microarray analyses of thirty-two individual Vitis vinifera cv. Cabernet Sauvignon berries sampled from two clusters at fifty-percent ripening initiation. By delineating four developmental stages of ripening initiation, we demonstrate that color is a statistically significant indicator of transcriptional state during ripening initiation. We report on clustered gene expression patterns which were mined for genes annotated with signal transduction functions in order to advance regulatory network modeling of ripening initiation in grape berries. We also demonstrated that gene expression does not differ statistically significantly at a global level in berries sampled from different plants or different positions in a cluster. Keywords: time course (berry development series)

2008-07-15 | GSE11406 | GEO

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