Transcription profiling of barley albina and xantha mutants1
Ontology highlight
ABSTRACT:
ORGANISM(S): Hordeum vulgare
SUBMITTER: Livia Tommasini
PROVIDER: E-GEOD-10332 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip. Experiment Overall Design: Barley developing and germinating seeds were harvested at different time points after flowering (developing) and imbibition (germinating). To further disseect the influence of different tissues, seeds were dissecte and tissues were analyzed individually.
2008-06-16 | E-GEOD-9365 | biostudies-arrayexpress
Project description:Grain development in the Poaceae defines important end-use properties such as yield, quality and nutritive value. Microarray analyses have been performed on barley grain endosperm extracts from three to eight days after pollination (DAP), when cellularization of the syncytium occurs through the growth of cell walls around individual nuclei. Profiling of transcripts differentially expressed over time reveal 56 specific modules of genes that cluster into 15 groups. Expression patterns have been superimposed upon microscopy data, which identify the timing of key stages in grain development. Thus, cellularization is complete at six DAP, aleurone-related genes can be detected at seven to eight DAP, and starch synthase and hordein genes increase dramatically at seven and eight DAP, respectively. Genes known to be involved in cell wall metabolism are found predominantly in a single module, but analysis using a gene ontology approach splits these genes into four modules, which remain in a single cluster. Transcript levels of the cell wall-related genes peak at seven DAP and the developmental patterns of genes involved in arabinoxylan and (1,3;1,4)-β-glucan synthesis are defined. The transcript data are publicly available (www.etc.) and can be used to interrogate co-expression and differential expression patterns for other groups of genes. In addition, the examination of transcription factor genes that are co-expressed in modules of genes involved in specific processes, such as aleurone differentiation, can be used to identify candidate genes for the control of those particular processes during barley grain development.
2016-02-01 | E-MTAB-2728 | biostudies-arrayexpress
Project description:Some flowering plant and vertebrate genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon called genomic imprinting. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes, as well as by Polycomb group (PcG) proteins. Currently only eleven imprinted Arabidopsis genes are known. Here we use extensive sequencing of cDNA libraries to identify many new paternally and maternally imprinted genes in A. thaliana endosperm, including transcription factors, proteins involved in hormone signaling, and epigenetic regulators. The imprinted status of many maternally-expressed genes is not altered by mutations in the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1 or the core PcG protein FIE, indicating that these genes are regulated by novel mechanisms or deposited from maternal tissues. We did not find any imprinted genes in the embryo. Our results demonstrate that imprinted gene expression, particularly from the maternal genome, is an extensive, mechanistically complex phenomenon that likely affects multiple aspects of seed development. Epigenetics Examination of genomic imprinting in Arabidopsis endosperm
2011-03-10 | E-GEOD-24644 | biostudies-arrayexpress
Project description:Plants of different ploidy levels are separated by a strong postzygotic hybridization barrier that is established in the endosperm. Deregulated parent-of-origin specific genes are causal for the response to interploidy hybridizations, revealing an epigenetic basis of this phenomenon. In this study we present evidence that paternal hypomethylation can bypass the interploidy hybridization barrier by alleviating the requirement of the epigenetic Polycomb Repressive Complex 2 (PRC2) in the endosperm. Bypass of the barrier is mediated by suppressed expression of imprinted genes. We show that hypomethylated pollen causes redistribution of CHG methylation to PRC2 target genes, revealing that different epigenetic modifications can functionally substitute for each other. Our work presents a method and the underlying mechanism for the generation of viable triploids, providing an impressive example for the potential of epigenome manipulations for plant breeding. Examination of DNA methylation in Arabidopsis endosperm, embryo, and pollen, and gene expression in seeds
2014-09-22 | E-GEOD-53642 | biostudies-arrayexpress
Project description:Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development or seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed and renewal resources. However, little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. As a first step towards understanding these processes, we have profiled all mRNAs in kernel and endosperm of maize at eight successive stages during the first 12 days after pollination. Analysis of these gene sets has identified temporal programs of gene expression including hundreds of transcription-factor genes. We also show a close correlation of these sequentially expressed gene sets with distinct spatial programs of expression in distinct compartments of the developing endosperm. The results constitute a preliminary atlas of spatiotemproal patterns of endosperm gene expression in support of future efforts for understanding the underlying mechanisms that control seed yield and quality. The unpollinated kernels (0 DAP), the kernels of 2, 3, 4, 6 DAP and hand dissected endosperms of 8, 10, 12 DAP from the B73 were used to perform high-throughput sequencing using the SOLiD platform
2014-01-17 | E-GEOD-54131 | biostudies-arrayexpress
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
Project description:In Arabidopsis mature seeds, the onset of the embryo-to-seedling transition is nonautonomously controlled, being blocked by endospermic abscisic acid (ABA) release under unfavorable conditions. Mature embryos lack an impermeable cuticle, unlike seedlings, consistent with their endospermic ABA uptake capability. Seedling cuticle formation occurs after germination rather than during embryogenesis. Mature endosperm removal prevents seedling cuticle formation and seed reconstitution by endosperm grafting onto embryos shows that the endosperm promotes seedling cuticle development. Grafting different endosperm and embryo mutant combinations, together with biochemical, microscopy and mass spectrometry approaches, reveals that endospermic release of Tyrosyl Sulfate Transferase (TPST)-sulfated CIF2 and PSY1 peptides promotes seedling cuticle development. Endosperm-deprived embryos produced nonviable seedlings bearing numerous developmental defects, in a manner unrelated to embryo nourishment, all restored by exogenously provided endosperm. Hence, seedling establishment is nonautonomous, requiring the mature endosperm.
2021-11-10 | PXD028576 | Pride
Project description:Transcriptome analysis in tobacco mutant plants using tomato Genechip Genome array Tobacco (Nicotiana tabacum cv. Petit Havanna) psaA and psbA deletion mutants were constructed through a targeted deletion of 767 and 1152 nucleotides of coding regions, respectively with two gene cassettes: psbAproR:uidA:psbterR and rrnR:aadA:rbcLterR coding for GUS reporter and spectinomycin selectable marker genes, respectively. Standard established procedures were followed for chloroplast transformation to generate the psaA and psbA deletion mutants based on the homologous recombination. Gene expression profiles in psaA and psbA tobacco mutant plants were analyzed using tomato Genechip Genome array to study the global changes in the expression of genome. Total RNA was isolated from psaA and psbA tobacco mutant plants along with the wild type plants. Biotin labeled cRNA was hybridized on tomato GeneChip Genome Array following the Affymetrix protocols. Two independent biological replicates were maintained.
2011-08-01 | E-GEOD-23626 | biostudies-arrayexpress
Project description:In this study, we compared the transcriptome map of maize and sorghum using PacBio single-molecule long-read sequencing from multiple matched tissues in each species. Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the transcriptional profiles of both protein-coding and non-coding transcripts in matched tissues using large-scale single-molecule sequencing from 130 RSII cells and 5 Sequel cells, as well as deep short-read RNA sequencing. The use of multiple size-fractionated libraries (<1 kb, 12 kb, 23 kb, 35 kb, and >5 kb) enhanced our capture of non-redundant transcripts in these tissues.
2018-04-05 | E-MTAB-5957 | biostudies-arrayexpress
Project description:The phytohormone gibberellic acid (GA) is well known to promote seed germination in plants. One of its functions is to stimulate the production of hydrolytic enzymes in the aleurone and their secretion to the adjacent endosperm. The storage in the endosperm is thus degraded by these hydrolases into small molecules, which are utilized as nutrients for embryo growth to establish the young seedling. ABA in contrast plays antagonistic role to GA to keep seed in dormancy. Cereal aleurone has been established as a model system to investigate giberrellin (GA) and abscisic acid (ABA) responses. Using Barley 1 GeneChip, we examined the mRNA accumulation of over 22 000 genes in barley aleurone treated with GA, ABA, GA plus ABA, and sln1 mutant. Barley aleurone tissues were separated from half-seed without embryo. Three independent RNA samples for each treatment including the control without any hormone were extracted and hybridized onto Affymetrix microarrays. We also did microarray in three replications for sln1 mutant aleurone without hormone treatment.
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