Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1020818 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26163225_1.fastq.gz | Fastqsanger.gz | |||
| SRR26163226_1.fastq.gz | Fastqsanger.gz | |||
| SRR26163227_1.fastq.gz | Fastqsanger.gz | |||
| SRR26163228_1.fastq.gz | Fastqsanger.gz | |||
| SRR26163229_1.fastq.gz | Fastqsanger.gz |
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Project description:Grapes are a valuable fruit and an important economic crop in the world, where wine production is a major industry. In grapevine, the environmental regulation of bud dormancy varies among its diverse genotypes. Certain grapevine genotypes become dormant in response to decreasing photoperiod and others require low temperature or both environmental cues to induce dormancy. This study used a proteomic approach to gain an understanding of the underlying molecular events involved in bud dormancy commitment.
2018-06-29 | PXD001627 | Pride
Project description:Hydrogen cyanamide (HC) is an agrochemical compound frequently used to break bud dormancy in grapevine grown under mild winter conditions all over the world. The present study was carried out to get a better understanding of the molecular mechanism associated with HC to release bud dormancy in grapevine using RNA-seq based transcriptomic and tandem mass tag (TMT) based proteomic analysis.
2019-12-19 | GSE127322 | GEO
Project description:Somatic variants spontaneously appear during the vegetative multiplication of woody crops. The new white-berried grapevine cultivar Tempranillo Blanco (TB) originally appeared as a bud sport of the black skin-berried Tempranillo Tinto (TT) cultivar. To understand the origin of this variation, TT and TB genomes were sequenced. Structural variation and genetic segregation analyses uncovered that complex chromosome rearrangements consistent with chromothripsis, a catastrophic phenomenon recently described in human cancer, generated the variant genome of TB and the deletion of the color locus functional allele. Loss of heterozygosity and decreased copy number delimited alternating monosomic and disomic fragments in the distal arms of TB’s linkage groups 2 and 5. Hemizygous fragments collectively extended over 8.1 Mb and comprised 313 annotated genes. Clustered breakpoints for complex chromosome rearrangements disrupting linkage groups 2 and 5 were identified and junctions involved unbalanced inter- and intra-chromosome translocations and one unbalanced inversion. Signatures of blunt fusions or microhomology-mediated end joining mechanisms were detected at breakpoint junction flanks. Segregation distortion in TB-derived selfed progeny indicated linkage of rearrangements in a single copy of the affected chromosomes that was barely transmitted. Additionally to berry color loss, these dramatic changes have further viticultural consequences in TB associated to a decreased sexual fitness. Our findings show that chromothripsis spontaneously arise during mitotic multiplication of grapevine, evidencing that this phenomenon could contribute to clonal variation in woody crops and to the evolution of plant genomes. Grapevine GrapeGen GeneChips(R) were used for partial comparative genome hybridization between black-berried cultivars and their respective white-berried somatic variants. Differences in copy number were used to estimate chromosome deletions associated to the loss of berry color.
2017-04-01 | GSE80801 | GEO
Project description:Taste and color, which are important organoleptic qualities of grape berry, undergo rapid and substantial changes during development and ripening. In this study, we use two cultivars ‘Sanbenti’ and its bud sport ‘11-06-25’ to explore expression profiles differences and identify genes associated with total soluble solid (TSS) and total anthocyanins during grape berry development stages using RNA sequencing.
2019-12-25 | GSE142313 | GEO
Project description:Bud mutation (bud sport) is mutation occurred in one branch in a tree and the mutant branch shows different phenotype from normal branches. Because bud mutation occurs in a part of plant body, genomic backgrounds of mutant branch and normal branches are the same, except some mutations. Therefore bud mutants are ideal material to identify key genes for important traits of crops. We studied ‘Giant Laf’, a bud mutant setting large fruit, which generated spontaneously in European pear ‘La France’ tree. In ‘Giant Laf’, increase of cell size and DNA reduplication occurred specifically in fruit flesh. The DNA reduplication in ‘Giant Laf’ was observed at 1 week before full bloom stage. This suggested that DNA reduplication observed in ‘Giant Laf’ fruit is not endoreduplication, but endomitosis or nuclear fusion. To identify genes expressed differentially between in ‘Giant Laf’ and in ‘La France’, microarray analysis was performed with RNA from receptacle (fruit flesh) at 1 week before full bloom stage. To isolate the receptacle, laser microdissection was applied. Genes encoding proteins localized in nucleus and cytoskeleton were up-regulated in ‘Giant Laf’. Among these genes, we found several genes which shared homology with previously described DNA reduplication related genes. These are candidates of responsible gene of ‘Giant Laf’ mutation.
2012-12-31 | GSE38550 | GEO
Project description:Bud mutation (bud sport) is mutation occurred in one branch in a tree and the mutant branch shows different phenotype from normal branches. Because bud mutation occurs in a part of plant body, genomic backgrounds of mutant branch and normal branches are the same, except some mutations. Therefore bud mutants are ideal material to identify key genes for important traits of crops. We studied M-bM-^@M-^XGiant LafM-bM-^@M-^Y, a bud mutant setting large fruit, which generated spontaneously in European pear M-bM-^@M-^XLa FranceM-bM-^@M-^Y tree. In M-bM-^@M-^XGiant LafM-bM-^@M-^Y, increase of cell size and DNA reduplication occurred specifically in fruit flesh. The DNA reduplication in M-bM-^@M-^XGiant LafM-bM-^@M-^Y was observed at 1 week before full bloom stage. This suggested that DNA reduplication observed in M-bM-^@M-^XGiant LafM-bM-^@M-^Y fruit is not endoreduplication, but endomitosis or nuclear fusion. To identify genes expressed differentially between in M-bM-^@M-^XGiant LafM-bM-^@M-^Y and in M-bM-^@M-^XLa FranceM-bM-^@M-^Y, microarray analysis was performed with RNA from receptacle (fruit flesh) at 1 week before full bloom stage. To isolate the receptacle, laser microdissection was applied. Genes encoding proteins localized in nucleus and cytoskeleton were up-regulated in M-bM-^@M-^XGiant LafM-bM-^@M-^Y. Among these genes, we found several genes which shared homology with previously described DNA reduplication related genes. These are candidates of responsible gene of M-bM-^@M-^XGiant LafM-bM-^@M-^Y mutation. The gene expression profiles between European pear (Pyrus communis) M-bM-^@M-^XLa FranceM-bM-^@M-^Y and its bud mutant M-bM-^@M-^XGiant LafM-bM-^@M-^Y were compared. RNA was extracted from receptacle which was isolated from flower bud at 1 week before full bloom stage by using laser microdissection. Three biological replications were analyzed.
2012-12-31 | E-GEOD-38550 | biostudies-arrayexpress
Project description:The first genome-wide transcriptomic atlas of grapevine (Vitis vinifera) is based on 54 diverse samples expressing ~93% of predicted grapevine genes. Pollen and senescent leaves have unique transcriptomes but microarray analysis grouped all other samples into vegetative/green or mature/woody categories based on maturity rather than organ identity. This fundamental transcriptome reprograming during maturation was highlighted by three distinct statistical approaches supported by gene coexpression analysis. The shift to the mature/woody developmental program results from the reiterative coactivation of pathways that are largely inactive in vegetative/green tissues, often involving the coregulation of neighboring genes and global regulation based on codon preference. A total of 54 grapevine samples, covering most of the Grape organs at different stages, were collected. Three biological replicates were taken for each sample, resulting in a total of 162 observations. The collected plant organs were: bud, inflorescence, tendril, leaf, stem, root, developing berry, withering berry, seed, rachis, anther, carpel, petal, pollen, and seedling.
2012-09-10 | E-GEOD-36128 | biostudies-arrayexpress