Ontology highlight
ABSTRACT:
PROVIDER: PRJNA700799 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13664376_1.fastq.gz | Fastqsanger.gz | |||
| SRR13664376_2.fastq.gz | Fastqsanger.gz | |||
| SRR13664377_1.fastq.gz | Fastqsanger.gz | |||
| SRR13664377_2.fastq.gz | Fastqsanger.gz | |||
| SRR13664378_1.fastq.gz | Fastqsanger.gz |
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Project description:P1 is the major QTL for maysin and chlorogenic acid accumulation in silk. Both compounds were important for plant defenses. Silk is an important reproductive organ that is critical for good seed setting in corn ear and needs to be protected against various stresses, therefore, metabolics compounds (ex: phenolics) were highly enriched in silk. Here we characterize transcriptome changes in maize protoplast, and natural variants of P1 silks, and pericards to characterize the regulatory landscape. Also we evaluated profiles of silk in B73 x A632 hybrids in order to cis and trans specific effect driven by P1 in maize. Our study identifies new P1 targets in the silk and protoplast. Together with the RNA-seq data (P1-rr vs P1-ww in silk and pericarp and protoplast 35S:P1 vs empty vector control), we observed new P1 functions in silk that were not observed in pericarp. Also, Protoplast and silk ChIP-seq in F1 silk, as well as DAP-seq analysis of P1 - shows specific P1 targets with highlight cis and trans effect on the F1 hybrids.
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Project description:P1 encodes an R2R3-MYB transcription factor responsible for the accumulation of insecticidal flavones in maize silks and red phlobaphene pigments in pericarps and other floral tissues, which contributed to making P1 an important visual marker since the dawn of modern genetics. We conducted RNA-Seq using pericarps at two different stages, 14 and 25 days after pollination (DAP). High-throughput sequencing using the Illumina platform resulted in the generation of ~20 million high quality reads, from which ~90% aligned to the recently completed maize genome sequence corresponding to ~5 million reads for each one of the four samples. Examination of two different RNA samples from two different stages of maize pericarp tissues.
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Project description:Endoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programs that are characteristic to each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types and especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of genes differentially expressed when comparing ploidy levels at a specific developmental stage. We found that non-endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome-based predictions were validated by quantifying ploidy levels within the pericarp tissue. This in situ ploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation, and gene expression patterns in the tomato pericarp.
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Project description:At 35 DAP whole kernels (pericarp + endosperm + embryo) without glumes of green house grown ears of heterozygous (+/bt2-H2328), self-pollinated plants were visually divided into pools of phenotypically normal looking kernels (small indentation, slightly smaller than mutant kernels, genotype +/+ or +/bt2-H2328) and pools of phenotypically mutant kernels (plump, round kernels, slightly larger than normal kernels, genotype bt2-H2328/bt2-H2328). Pools consisted of 4 kernels. 3 different ears were used for a biological duplicate. Experiment Overall Design: 4 arrays - maize
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Project description:To determine which of the genes differentially expressed between P1-rr and P1-ww pericarps were immediate (direct) targets of P1, we conducted chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) using P1 polyclonal antibodies (alphaP1344) that recognize the non-conserved C-terminal region of P1 (Falcone Ferreyra et al., 2010), on pericarp chromatin. Comparison of pericarp chromatin inmunoprecipitated material P-rr_14DAP (P1 expressed) vs P-ww_14DAP (P1 not expressed) to determine P1 direct targets
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