Transcriptional signatures in contrasting cultivars of Barley during early reproductive development of meristem
Ontology highlight
ABSTRACT:
ORGANISM(S): Hordeum vulgare
PROVIDER: GSE218882 | GEO | 2023/11/28
REPOSITORIES: GEO
Similar Datasets
Project description:Existence of potent in vitro regeneration system is a prerequisite for efficient genetic transformation and functional genomics of crop plants. Little is known why only some cultivars in crop plants are tissue culture friendly? In this study, contrasting barley cultivars Golden Promise (GP) and DWRB91 (D91) were utilized for digging the molecular basis of regeneration efficiency. Multiomics studies involving transcriptomics, proteomics, metabolomics, and biochemical analysis were performed using GP and D91 callus to unravel the regulatory mechanisms. Transcriptomics analysis revealed 1487 differentially expressed genes (DEGs), in which 795 DEGs were upregulated and 692 DEGs were downregulated in the GP-D91 transcriptome. Genes encoding proteins localized in chloroplast and involved in ROS generation were upregulated in the embryogenic calli of GP. Moreover, proteome analysis by LC-MS revealed 3062 protein groups and 16989 peptide groups, out of these 1586 protein groups were differentially expressed proteins (DEPs). Eventually, GC-MS based metabolomics analysis also revealed the higher activity of plastids and alterations in key metabolic processes such as sugar metabolism, fatty acid biosynthesis, and secondary metabolism. Higher accumulation of sugars, amino acids and metabolites corresponding to lignin biosynthesis were observed in GP as compared to D91.
2022-07-31 | GSE206271 | GEO
Project description:Wheat panicle development is a coordinated process of proliferation and differentiation with distinctive phase and architecture changes. However, the multiple genes involved networks controlling this process remain enigmatic. Here, we characterized and dissected common wheat panicles in the stages of vegetative stage before elongation, elongation, single ridge, double ridge, glume primodium differentiation and floret differentiation, respectively, followed by RNA-seq and bioinformatics analysis to study genome-wide mRNA transcriptome profiling in wheat early spike development. High gene expression correlations between any two stages (R2>0.97) and only 4000 Differentially Expressed Genes (DEGs) out of 49624 expressed transcripts in all stages indicated that wheat early panicle development is just controlled by an small proportion of important genes. Three subgenomes (A, B and D) contribute equally to this process. K-means clustering analysis revealed the dynamic expression patterns of DEGs and Hierarchical Clustering analysis demonstrated that single bridge stage and double bridge stage are most important for wheat panicle development. Interestingly, 306 transcription factors (TFs) with various functions from different families were identified and the spatial-temporal expression patterns of some were verified by quantitative PCR or in situ hybridization. At early stages, repressing flowering TFs combined with AP2/ERF TFs and cytokinin promote inflorescence meristem development and repress meristem differentiation. At single ridge and double ridge stages, highly expressed stress-response TFs balance the interaction between stress response and development. During reproductive stages, crosstalk between auxin and cytokinin coordinate the meristem proliferation and differentiation, and promoting flowering TFs with polarity establishment TFs and MADS-box TFs promote floral meristem generation and floral organ identity and development. This dataset provided an ideal resource for wheat panicle developmental research. Our study uncovered the regulatory network for coordinated wheat early spike development and would eventually contribute to the improvement of grain number and crop yield.
2018-10-25 | GSE83287 | GEO
Project description:Transcriptional signatures in contrasting cultivars of Barley during early reproductive development of meristem
| PRJNA906074 | ENA
Project description:gnp07_regeneome_transdifferenciation - microdissection - Study of the moleculars mecanism during transdifferenciation of Root ApicalMeristem to Shoot Apical Meristem - middle of growth permits to induce transdifferenciation of root apical meristem to shoot apical meristem
2012-06-01 | GSE30259 | GEO
Project description:DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we found that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also found that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs.
2020-08-14 | PXD020608 | Pride
Project description:When Arabidopsis seedlings are grown in the dark, their shoot meristem remains in a repressed state and does not develop leaves. The tight control of leaf development by light provides the opportunity to analyse a fundamental plant developmental process in its very early stages. We have observed that activation of photoreceptors in dark-grown seedlings leads to a rapid and dramatic increase in mitotic activity in and around the shoot meristem. Cotyledons also exhibit an induction of cell cycle activity by light, but this consists of endoreduplication and occurs later. Many other processes take place upon induction by light, including the development of the photosynthetic apparatus and the synthesis of sunscreens, but these processes are expected to take place in both the leaf primordia and the cotyledons. We have used this information to carry out a whole transcriptome analysis of shoot meristem activation and early stages of leaf development by light. For this we dissected the shoot apical regions from seedlings grown in the dark or 1, 2, 6, 24, 48 or 72 h after transfer to light. We also dissected cotyledons from equivalent seedlings grown in the dark or 1 or 6 h after transfer to light. From these samples we obtained RNA used for hybridisations against the ATH1 GenChip. 16 samples were used in this experiment.
2009-12-04 | E-GEOD-19261 | biostudies-arrayexpress
Project description:When Arabidopsis seedlings are grown in the dark, their shoot meristem remains in a repressed state and does not develop leaves. The tight control of leaf development by light provides the opportunity to analyse a fundamental plant developmental process in its very early stages. We have observed that activation of photoreceptors in dark-grown seedlings leads to a rapid and dramatic increase in mitotic activity in and around the shoot meristem. Cotyledons also exhibit an induction of cell cycle activity by light, but this consists of endoreduplication and occurs later. Many other processes take place upon induction by light, including the development of the photosynthetic apparatus and the synthesis of sunscreens, but these processes are expected to take place in both the leaf primordia and the cotyledons. We have used this information to carry out a whole transcriptome analysis of shoot meristem activation and early stages of leaf development by light. For this we dissected the shoot apical regions from seedlings grown in the dark or 1, 2, 6, 24, 48 or 72 h after transfer to light. We also dissected cotyledons from equivalent seedlings grown in the dark or 1 or 6 h after transfer to light. From these samples we obtained RNA used for hybridisations against the ATH1 GenChip.
2009-12-05 | GSE19261 | GEO
Project description:we used soybean genome chips to investigate the expression pattern of about 37,500 unique ESTs locating on soybean Affymetrix chips (Affymetrix Inc.). KEYWORDS: Tissue comparison we compared soybean root meristem samples with non-meristematic tissues in 10 days old vegetative stage seedlings to define a unique set of root meristem enriched genes.
2011-05-31 | E-GEOD-27894 | biostudies-arrayexpress
Project description:Knowledge about an organism’s cell and tissue-specific transcriptional repertoire is essential for understanding the gene regulatory circuits that control key developmental events. The shoot apical meristem (SAM) is responsible for development of all the above ground parts of plants. Our understanding of SAM at the molecular level is far from complete. The present work investigates the global gene expression repertoire of SAMs in the garden pea (Pisum sativum). To this end, 10,346 EST sequences representing 7611 unique genes were generated from pea SAM cDNA libraries. These sequences, together with previously reported ESTs, were used to construct a 12K oligonucleotide array used to identify genes exhibiting differential SAM expression, as compared to the axillary meristem, root apical meristem, and non-meristematic tissues. We identified a number of genes that are predominantly expressed in specific cell layers or domains of the SAM, and thus are likely components of the gene networks involved in stem cell maintenance and initiation of lateral organ primordial cells. In situ hybridization confirmed the spatial localisation of some of these key genes within the SAM. Our data also indicate the diversification of some gene expression patterns and functions in legume crop plants.
2009-10-26 | GSE13451 | GEO
Project description:gnp07_regeneome_transdifferenciation - microdissection - Study of the moleculars mecanism during transdifferenciation of Root ApicalMeristem to Shoot Apical Meristem - middle of growth permits to induce transdifferenciation of root apical meristem to shoot apical meristem 6 dye-swap - time course
2012-05-31 | E-GEOD-30259 | biostudies-arrayexpress