Vitis vinifera
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA248771 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Seedless varieties are of particular importance to the table-grape and raisin industries. Gibberellin (GA) application is widely used in the early stages of seedless berry development to increase berry size and economic value. However, the underlying mechanism of GA induction of berry enlargement is not well understood. Here, RNA-sequencing analysis of âCentennial Seedlessâ (Vitis vinifera L.) berries treated with GA3 12 days after flowering is reported.
2014-12-05 | E-MTAB-4247 | biostudies-arrayexpress
Project description:Genomic differences between seeded and seedless grapes
| PRJNA512210 | ENA
Project description:Bud endodormancy induction response of two genotypes (Seyval, a hybrid white wine grape and Vitis riparia, PI588259, a native North American grape species) was compared under long (15 h) and short (13 h) photoperiods. Proteins were extracted from both genotypes for all time points and experimental conditions. The proteins were separaed by 2D-PAGE, trypsin digested, and the peptides identified with a MALDI-TOF-TOF mass spectrometer. A master gel was made and mapped with all proteins from both genotypes. The proteins were identified by matching the peptide sequences against the 8X Vitis vinifera grape genome in NCBI. This study was funded by NSF grant DBI064755 and is the result of a collaboration between Dr. Anne Fennell at South Dakota State University and Dr. Grant R. Cramer at the University of Nevada, Reno.
2010-08-09 | PRD000169 | Pride
Project description:We report the application of Illumina mRNA sequencing technology for high-throughput profiling of the transcriptome of a seeded wine cultivar (wild-type) and its seedless somatic variant (mutant), sampled at three key growth stages of grapevine:Â E-L 15 (single flowers in compact groups), E-L 27 (young berries enlarging) and E-L 38 (berries harvest-ripe). By obtaining over 126 to 143 million and 102 to 127 million reads of 100-bp in length for the wild-type and mutant respectively, we have for the first time provided a holistic view of the transcriptional landscape during seed development in both phenotypes. We found that comparison of differentially expressed (DE) genes, gene patterns and gene enrichment between the wild-type and mutant distinguished transcriptional events in the two lines. For example, differential expression analysis in the pairwise comparison between developmental stages identified DE genes specific to the wild-type background, DE genes specific to the mutant background and DE genes commonly shared in both backgrounds. The analysis of differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have lead to the identification of candidate genes for seedlessness that have altered expression in wild-type and mutant. In conclusion, we have shown here a logical approach to identify possible regulators and processes required for normal seed development that may be altered in the seedless phenotype, and highlighted the importance of somatic variants as a resources. Examination of absolute expression count for every gene at three key time-points in a seeded grapevine variety and its seedless somatic variant.
2014-12-31 | E-GEOD-58061 | biostudies-arrayexpress
Project description:Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue.
2021-08-27 | GSE164586 | GEO
Project description:Transcriptome analysis for shoot of Japanese wine grape cultivar "Koshu"
| PRJDB5807 | ENA
Project description:White grape (Vitis vinifera cv. Furmint) berry samples subjected to natural noble rot were collected in a vineyard in Mád, Hungary (Tokaj wine region). Raw data include grapevine and Botrytis cinerea sequence reads.
2021-11-25 | E-MTAB-11205 | biostudies-arrayexpress
Project description:Plasticity of the berry ripening program in a white grape variety
| PRJNA304607 | ENA
Project description:We report the application of Illumina mRNA sequencing technology for high-throughput profiling of the transcriptome of a seeded wine cultivar (wild-type) and its seedless somatic variant (mutant), sampled at three key growth stages of grapevine: E-L 15 (single flowers in compact groups), E-L 27 (young berries enlarging) and E-L 38 (berries harvest-ripe). By obtaining over 126 to 143 million and 102 to 127 million reads of 100-bp in length for the wild-type and mutant respectively, we have for the first time provided a holistic view of the transcriptional landscape during seed development in both phenotypes. We found that comparison of differentially expressed (DE) genes, gene patterns and gene enrichment between the wild-type and mutant distinguished transcriptional events in the two lines. For example, differential expression analysis in the pairwise comparison between developmental stages identified DE genes specific to the wild-type background, DE genes specific to the mutant background and DE genes commonly shared in both backgrounds. The analysis of differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have lead to the identification of candidate genes for seedlessness that have altered expression in wild-type and mutant. In conclusion, we have shown here a logical approach to identify possible regulators and processes required for normal seed development that may be altered in the seedless phenotype, and highlighted the importance of somatic variants as a resources.
2014-12-31 | GSE58061 | GEO
Project description:itis vinifera cv. Tannat is largely cultivated in Uruguay for the production of high quality red wines. Its most notable characteristic is an elevated content of polyphenolic compounds, which provide an intense purple color and remarkable antioxidant properties to the wine. To characterize the genetic components encoding this important phenotypic characteristic, the genome of the Uruguayan Tannat clone UY11 was sequenced to 134X coverage using the Illumina technology and assembled with a mixed approach of de novo assembly and iterative mapping on the PN40024 reference genome. An approach based on both reference-guided annotation and de novo transcript assembly of RNA-Seq data allowed the definition of 3,673 genes not previously annotated in PN40024 that we consider novel, and the discovery of 2,228 genes not shared with the grapevine reference genome that we consider private to Tannat. Expression analysis showed that private genes contributed substantially (more than 50%) to the overall expression of enzymes involved in phenol and polyphenol biosynthesis indicating that the dispensable portion of the grapevine genome contains many private genes which are likely to contribute to the peculiar phenotypic characteristics of this grapevine variety.
2014-01-09 | E-MTAB-4278 | biostudies-arrayexpress