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

ABSTRACT: 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.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE33441 | GEO | 2014/11/03

SECONDARY ACCESSION(S): PRJNA148695

REPOSITORIES: GEO

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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

Transcription profiling of pistils from Arabidopsis wild type, ant-4 mutant and ino-1mutant plants at different developmental stages

Project description:This experiment was designed to identify genes expressed preferentially in the two integuments of the Arabidopsis ovule. Pistils from wild type and two ovule mutants were compared against each aintegumenta-4 (ant-4) which lacks both integuments and inner no outer (ino-1) which lacks the outer integument. Genes that are highly expressed only in the integuments were expected to be reduced in expression in the mutants, as compared with wild type. Pistils containing ovules through all stages of ovule development prior to pollination were pooled for one experiment (FULL arrays), and for two separate experiments, a set of early differentiation stages (EARLY arrays) and a set of later differentiation stages (LATE ARRAYS) were pooled. Wild type and mutant lines are in the ecotype Landsberg erecta.

2009-06-01 | E-MEXP-1920 | biostudies-arrayexpress

Next Generation Sequencing Analysis of Wild Type and fl3 Transcriptomes in 10DAP(day after pollination) endosperm

Project description:Maize floury3 (fl3) is a classic semi-dominant mutant that shows severe defects in the endosperm but appears normal in the plant.The goals of this study are to compare WT to fl3 transcriptomes in 10DAP(day after pollination) endosperm by Next Generation Sequencing.

2017-07-22 | GSE95039 | GEO

H3K27me3 ChIP-seq on 16 days after pollination endosperm of cultivated barley

Project description:To provide comprehensive spatiotemporal information about biological processes in developing grains of cultivated barley (Hordeum vulgare subsp. vulgare), we performed a chromatin immunoprecipitation of H3K27me3 followed by high-throughput sequencing (ChIP-seq) in barley endosperm at 16 days after pollination.

2023-07-26 | GSE238237 | GEO

Expression analysis of barley glumes vs. endosperm between 0-24 days after pollination

Project description:During grain filling in barley reserves are remobilized from vegetative organs like glumes. In this expression analysis values from glumes and endosperm material were compared from 0 - 24 day after pollination (DAP). This study showed that glumes metabolism and development is adjusted to changing grain demands. Candidate genes are potentially involved in assimilate conversion and translocation.

2015-01-30 | E-MTAB-3040 | biostudies-arrayexpress

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

2015-12-01 | E-GEOD-33441 | ExpressionAtlas

Gene expression in B73 maize aleurone and starchy endosperm at 18 and 22 day after pollination

Project description:The cereal endosperm consists of starchy endosperm (ST) cells, which accumulate storage proteins and starch, the peripheral aleurone (AL) cells, which mobilize these storage compounds during germination, and transfer cells in contact with the maternal vascular tissues, and the embryo-surrounding region. We conducted RNA-sequencing and analyzed transcript profiles of AL and ST tissues at 18 and 22 days after pollination (DAP), when storage compounds such as proteins, starch, triacylglycerols, specialized metabolites, and minerals are actively synthesized in the maize endosperm. We combined published RNA-seq datasets from other kernel tissues at different developmental stages to analyze gene expression connected to synthesis and accumulation of storage compounds and metabolites. Using weighted correlation network analysis (WGCNA), we identified gene modules associated with metabolic pathways related to nutritional properties of the maize endosperm. We also provide information of novel marker genes specifically expressed in AL and ST, at either early or late developmental stages. This study is important for understanding maize endosperm development and for developing strategies to improve nutritional quality of maize kernels.

2017-05-02 | GSE95678 | GEO

Transcription profiling of maize endoderm from plants 17 days after pollination in Genotype: B73 and Mo17 hybrids

Project description:The nuclear content of the plant endosperm is the result of the contribution two maternal genomes and a single paternal genome. This 2:1 dosage relationship provides a unique system for studying the additivity of gene expression levels in reciprocal hybrids. A combination of microarray profiling and allele-specific expression analysis was performed using RNA isolated from endosperm tissues of maize inbred lines B73 and Mo17 and their reciprocal hybrids at two developmental stages, 13 and 19 days after pollination. By assessing the relative levels of expression in the reciprocal hybrids it was possible to determine the prevalence of additive and non-additive expression patterns. While the majority of differentially expressed genes displayed additive expression patterns in the endosperm, approximately 10% of the genes displayed non-additive expression patterns including maternal-like, paternal-like, dominant high-parent, dominant low-parent and expression patterns outside the range of the inbreds. The frequency of hybrid expression patterns outside of the parental range in maize endosperm tissue is much higher than that observed for vegetative tissues. For a set of 90 genes allele-specific expression assays were employed to monitor allelic bias and regulatory variation. Eight of these genes exhibited evidence for maternally or paternally biased expression at multiple stages of endosperm development and are potential examples of differential imprinting. Collectively, our data indicate that parental effects on gene expression are much stronger in endosperm than in vegetative tissues, and that endosperm imprinting may be far more common than previously estimated. Experiment Overall Design: Gene expression levels were profiled in 19 day after pollination endosperm tissue from four maize genotypes; B73, Mo17, Mo17xB73 and B73xMo17.

2008-06-16 | E-GEOD-8278 | biostudies-arrayexpress

DNA demethylation activates genes in seed maternal integument development in rice (Oryza sativa L.)

Project description:DNA methylation is an important epigenetic modification that regulates various plant developmental processes. Rice seed integument determines the seed size. However, the role of DNA methylation in its development remains largely unknown. Here, we report the first dynamic DNA methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. Analysis of DNA methylation patterns identified 4238 differentially methylated regions underpin 4112 differentially methylated genes, including GW2, DEP1, RGB1 and numerous other regulators participated in maternal integument development. Bisulfite sanger sequencing and qRT-PCR of six differentially methylated genes revealed extensive occurrence of DNA hypomethylation triggered by double fertilization at IAP compared with IBP, suggesting that DNA demethylation might be a key mechanism to activate numerous maternal controlling genes. These results presented here not only greatly expanded the rice methylome dataset, but also shed novel insight into the regulatory roles of DNA methylation in rice seed maternal integument development.

2017-10-10 | GSE95107 | GEO

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