Analysis of the origin of stenospermocarpy under the control of the major seedlessness locus in grapevine
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA418785 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6300210_1.fastq.gz | Fastqsanger.gz | |||
| SRR6300210_2.fastq.gz | Fastqsanger.gz | |||
| SRR6300211_1.fastq.gz | Fastqsanger.gz | |||
| SRR6300211_2.fastq.gz | Fastqsanger.gz | |||
| SRR6300212_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpy determined by the Seed Development Inhibitor (SDI) locus is the usual source of seedlessness in commercial grapevine cultivars, the sdi mutation underlying this locus remained unknown and we undertook an integrative approach to identify it. Quantitative genetics and fine mapping studies in two Crimson Seedless (CS)-derived F1 populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a region of 323 kb on chromosome 18. Transcriptomics comparing gene expression between seeds and seed traces in RG (Red Globe) × CS progeny identified processes triggered during sdi-determined seed abortion, including the activation of salicylic acid (SA)-dependent defenses. RNA-seq and NimbleGen microarray datasets were investigated for candidate genes and, while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide sequence changes in the seedless haplotype were predicted in two genes within the sdi fine mapping interval, VviPPAT2 and VviAGL11. Targeted re-sequencing of the two genes in a collection of 126 cultivars showed that only the point variation causing the Arg197Leu substitution in the seed morphogenesis regulator gene VviAGL11 was fully linked with seedlessness. Remarkably, this missense mutation was not detected in seeded clonal variants of Sultanina cultivar, the original donor of the sdi mutation, providing genetic evidence that this is the major cause of seedlessness in cultivated grapevines. The identification of the dominant effects of this amino acid substitution in seed abortion can be exploited to boost seedless grape breeding.
2018-07-31 | GSE107014 | GEO
Project description:One of the most economically important grapevine diseases is Downy mildew (DM) caused by the oomycete <i>Plasmopara viticola</i>. A strategy to reduce the use of fungicides to compensate for the high susceptibility of <i>V. vinifera</i> is the selection of grapevine varieties showing pathogen-specific resistance. We applied a metabolomics approach to evaluate the metabolic modulation in mono-locus resistant genotypes carrying one locus associated with <i>P. viticola</i> resistance (<i>Rpv</i>) (BC4- <i>Rpv1</i>, Bianca- <i>Rpv3-1</i>, F12P160- <i>Rpv12</i>, Solaris- <i>Rpv10</i>), as well as in pyramided resistant genotypes carrying more than one <i>Rpv</i> (F12P60- <i>Rpv3-1; Rpv12</i> and F12P127- <i>Rpv3-1, Rpv3-3; Rpv10</i>) taking as a reference the susceptible genotype Pinot Noir. In order to understand if different sources of resistance are associated with different degrees of resistance and, implicitly, with different responses to the pathogen, we considered the most important classes of plant metabolite primary compounds, lipids, phenols and volatile organic compounds at 0, 12, 48, and 96 h post-artificial inoculation (hpi). We identified 264 modulated compounds; among these, 22 metabolites were found accumulated in significant quantities in the resistant cultivars compared to Pinot Noir. In mono-locus genotypes, the highest modulation of the metabolites was noticed at 48 and 96 hpi, except for Solaris, that showed a behavior similar to the pyramided genotypes in which the changes started to occur as early as 12 hpi. Bianca, Solaris and F12P60 showed the highest number of interesting compounds accumulated after the artificial infection and with a putative effect against the pathogen. In contrast, Pinot Noir showed a less effective defense response in containing DM growth.
2021-07-07 | MTBLS2876 | MetaboLights
Project description:The chromatin at origins of replication is the template for DNA replication initiation in eukaryotic genomes. However, whether the chromatin composition instructs individual origins to fire early-efficiently (EE) or late-inefficiently (LI) remains to be investigated. Here, we used site-specific recombination and a single-locus chromatin isolation approach to purify selected EE and LI replication origins from chromosome III of Saccharomyces cerevisiae. Using mass spectrometry, we define the histone modification landscape and identify the protein composition of defined ~1kb native chromatin regions surrounding the EE and LI replication start sites. We confirm expected origin interactors but also find unexpected interactions, such as the Ask1 subunit of the kinetochore-associated DASH complex. Strikingly, we show that Ask1 is a critical factor in the replication timing control of specific origins in yeast. These results highlight that our unbiased approach can specifically identify the functionally-relevant proteome at a single-copy locus of interest and provide a detailed view of histone modification and protein interaction networks on replication origin chromatin. The current dataset contains proteomic data used for the histone PTM analysis.
2023-05-10 | PXD031984 | Pride
Project description:Analysis of the origin of stenospermocarpy under the control of the major seedlessness locus in grapevine
2020-04-27 | E-GEOD-107014 | ExpressionAtlas
Project description:European grapevine cultivars (Vitis vinifera spp.) are highly susceptible to the downy mildew pathogen Plasmopara viticola. Breeding of resistant V. vinifera cultivars is a promising strategy to reduce the impact of disease management. Most cultivars that have been bred for resistance to downy mildew, rely on resistance mediated by the Rpv3 (Resistance to P. viticola) locus. However, despite the extensive use of this locus, little is known about the mechanism of Rpv3-mediated resistance. In this study, Rpv3-mediated defense responses were studied in Rpv3+ and Rpv3ˉ grapevine cultivars following inoculation with two distinct P. viticola isolates avrRpv3+ and avrRpv3ˉ, with the latter being able to overcome Rpv3 resistance. Based on comparative microscopic, metabolomic and transcriptomic analyses, our results show that the Rpv3-mediated resistance is associated with a defense mechanism that triggers synthesis of fungi-toxic stilbenes and programmed cell death (PCD), resulting in reduced but not suppressed pathogen growth and development. Functional annotation of the encoded protein sequence of genes significantly upregulated during the Rpv3-mediated defense response revealed putative roles in pathogen recognition, signal transduction and defense responses.
2019-08-21 | GSE128865 | GEO
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:Mapping major QTL for grapevine anthocyanin coloration in variety 'Chasselas violet'
| PRJEB106606 | ENA
Project description:Seedlessness is greatly prized by consumers of fresh grapes. While stenospermocarpy determined by the Seed Development Inhibitor (SDI) locus is the usual source of seedlessness in commercial grapevine cultivars, the sdi mutation underlying this locus remained unknown and we undertook an integrative approach to identify it. Quantitative genetics and fine mapping studies in two Crimson Seedless (CS)-derived F1 populations confirmed the major effect of the SDI locus and delimited the sdi mutation to a region of 323 kb on chromosome 18. Transcriptomics comparing gene expression between seeds and seed traces in RG (Red Globe) × CS progeny identified processes triggered during sdi-determined seed abortion, including the activation of salicylic acid (SA)-dependent defenses. RNA-seq and NimbleGen microarray datasets were investigated for candidate genes and, while no evidence for causal cis-acting regulatory mutations was detected, deleterious nucleotide sequence changes in the seedless haplotype were predicted in two genes within the sdi fine mapping interval, VviPPAT2 and VviAGL11. Targeted re-sequencing of the two genes in a collection of 126 cultivars showed that only the point variation causing the Arg197Leu substitution in the seed morphogenesis regulator gene VviAGL11 was fully linked with seedlessness. Remarkably, this missense mutation was not detected in seeded clonal variants of Sultanina cultivar, the original donor of the sdi mutation, providing genetic evidence that this is the major cause of seedlessness in cultivated grapevines. The identification of the dominant effects of this amino acid substitution in seed abortion can be exploited to boost seedless grape breeding.
2018-07-31 | GSE106668 | GEO
Project description:Genetic mapping of the grapevine veraison locus
| PRJEB75005 | ENA
Project description:Grapevine red blotch is a recently identified viral disease that was first recognized in the Napa Valley of California. Infected plants showed foliar symptoms similar to leafroll, another grapevine viral disease, on vines testing negative for known grapevine leafroll-associated virus. Later, the Grapevine red blotch virus (GRBV) was independently discovered in the US states of California and New York and was demonstrated to be the causal agent of red blotch disease. Due to its wide occurrence in the US, vector transmission and impacts on grape industry, this virus has the potential to cause serious economic losses. Despite numerous attempts, it was not possible to isolate or visualize viral particles from GRBV infected plants. Consequently, this has hampered the development of a serological assay that would facilitate GRBV detection in grapevine. We therefore decided to explore mass spectrometry approaches in order to quantify GRBV in infected plants and to identify potential biomarkers for viral infection. We present for the first time the physical detection on the protein level of the two GRBV genes V1 (coat protein) and V2 in grapevine tissue lysates. The GRBV coat protein load in leaf petioles was determined to be in the range of 100 to 900 million copies per milligram wet weight by using three heavy isotope labeled reference peptides as internal standards. The V1 copy number per unit wet tissue weight in leaves appeared to be about six times lower, and about 200-times lower in terms of protein concentration in the extractable protein mass than in petioles. We found a consistent upregulation of several enzymes involved in flavonoid biosynthesis in leaf and petiole extracts of GRBV-infected plants by label-free shotgun proteomics, indicating the activation of a defense mechanism against GRBV, a plant response already described for grapevine leafroll associated virus infection on the transcriptome level. Last but not least, we identified some other microorganisms belonging to the grapevine leaf microbiota, two bacterial species (Novosphingobium sp. Rr 2-17 and Methylobacterium) and one virus, Grapevine rupestris stem pitting associated virus.
2018-12-19 | PXD011002 | Pride