scholarly journals Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 204 ◽  
Author(s):  
Simone Scalabrin ◽  
Michela Troggio ◽  
Marco Moroldo ◽  
Massimo Pindo ◽  
Nicoletta Felice ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Pinot Noir ◽  
Grapevine Cultivar ◽  
Contig Map

scholarly journals A Diverse Virome of Leafroll-Infected Grapevine Unveiled by dsRNA Sequencing

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1142
Author(s):  
Mamadou L. Fall ◽  
Dong Xu ◽  
Pierre Lemoyne ◽  
Issam E. Ben Moussa ◽  
Carole Beaulieu ◽  
...  
Keyword(s):  
Interspecific Hybrid ◽  
Pinot Noir ◽  
Grapevine Cultivar ◽  
Sequencing Method ◽  
Hop Stunt Viroid ◽  
Multiple Virus ◽  
Leafroll Disease ◽  
Different Strains ◽  
Hybrid Cultivar ◽  
Rupestris Stem Pitting

Quebec is the third-largest wine grape producing province in Canada, and the industry is constantly expanding. Traditionally, 90% of the grapevine cultivars grown in Quebec were winter hardy and largely dominated by interspecific hybrid Vitis sp. cultivars. Over the years, the winter protection techniques adopted by growers and climate changes have offered an opportunity to establish V. vinifera L. cultivars (e.g., Pinot noir). We characterized the virome of leafroll-infected interspecific hybrid cultivar and compared it to the virome of V. vinifera cultivar to support and facilitate the transition of the industry. A dsRNA sequencing method was used to sequence symptomatic and asymptomatic grapevine leaves of different cultivars. The results suggested a complex virome in terms of composition, abundance, richness, and phylogenetic diversity. Three viruses, grapevine Rupestris stem pitting-associated virus, grapevine leafroll-associated virus (GLRaV) 3 and 2 and hop stunt viroid (HSVd) largely dominated the virome. However, their presence and abundance varied among grapevine cultivars. The symptomless grapevine cultivar Vidal was frequently infected by multiple virus and viroid species and different strains of the same virus, including GLRaV-3 and 2. Our data show that viruses and viroids associated with the highest number of grapevines expressing symptoms included HSVd, GLRaV-3 and GLRaV-2, in gradient order. However, co-occurrence analysis revealed that the presence of GLRaV species was randomly associated with the development of virus-like symptoms. These findings and their implications for grapevine leafroll disease management are discussed.

Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage, and contig map quality

Genomics ◽  
2004 ◽  
Vol 84 (6) ◽  
pp. 941-951 ◽  
Author(s):  
Zhanyou Xu ◽  
Shuku Sun ◽  
Lina Covaleda ◽  
Kejiao Ding ◽  
Aimin Zhang ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Fingerprint Analysis ◽  
Genome Coverage ◽  
Contig Map

scholarly journals Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

2018 ◽  
Author(s):  
Michael J. Roach ◽  
Daniel L. Johnson ◽  
Joerg Bohlmann ◽  
Hennie J.J. van Vuuren ◽  
Steven J. M. Jones ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Clonal Selection ◽  
Pinot Noir ◽  
Genetic Mutations ◽  
Phenotypic Trait ◽  
Sequencing Data ◽  
High Quality ◽  
Asexual Propagation ◽  
Grapevine Cultivar

AbstractChardonnay is the basis of some of the world’s most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propagation. However, the genetic variation that underlies these differences remains largely unknown. To address this knowledge gap, a high-quality, diploid-phased Chardonnay genome assembly was produced from single-molecule real time sequencing, and combined with re-sequencing data from 15 different commercial Chardonnay clones. There were 1620 markers identified that distinguish the 15 Chardonnay clones. These markers were reliably used for clonal identification of validation genomic material, as well as in identifying a potential genetic basis for some clonal phenotypic differences. The predicted parentage of the Chardonnay haplomes was elucidated by mapping sequence data from the predicted parents of Chardonnay (Gouais blanc and Pinot noir) against the Chardonnay reference genome. This enabled the detection of instances of heterosis, with differentially-expanded gene families being inherited from the parents of Chardonnay. Most surprisingly however, the patterns of nucleotide variation present in the Chardonnay genome indicate that Pinot noir and Gouais blanc share an extremely high degree of kinship that has resulted in the Chardonnay genome displaying characteristics that are indicative of inbreeding.Author SummaryPhenotypic variation within a grapevine cultivar arises from an accumulation of mutations from serial vegetative propagation. Old cultivars such as Chardonnay have been propagated for centuries resulting in hundreds of available ‘clones’ containing unique genetic mutations and a range of various phenotypic peculiarities. The genetic mutations can be leveraged as genetic markers and are useful in identifying specific clones for authenticity testing, or as breeding markers for new clonal selections where particular mutations are known to confer a phenotypic trait. We produced a high-quality genome assembly for Chardonnay, and using re-sequencing data for 15 popular clones, were able to identify a large selection of markers that are unique to at least one clone. We identified mutations that may confer phenotypic effects, and were able to identify clones from material independently sourced from nurseries and vineyards. The marker detection framework we describe for authenticity testing would be applicable to other grapevine cultivars or even other agriculturally important woody-plant crops that are vegetatively propagated such as fruit orchards. Finally, we show that the Chardonnay genome contains extensive evidence for parental inbreeding, such that its parents, Gouais blanc and Pinot noir, may even represent first-degree relatives.

scholarly journals Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 261 ◽  
Author(s):  
Silvia Laura Toffolatti ◽  
Gabriella De Lorenzis ◽  
Matteo Brilli ◽  
Mirko Moser ◽  
Vahid Shariati ◽  
...  
Keyword(s):  
De Novo ◽  
Susceptibility Gene ◽  
Plasmopara Viticola ◽  
Pinot Noir ◽  
Gene Encoding ◽  
Grapevine Cultivar ◽  
Gene Expression Dynamics ◽  
Plant Pathogen Interaction ◽  
First Time ◽  
Encoding Genes

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola.

scholarly journals A Diverse Virome of Leafroll-Infected Grapevine Unveil by dsRNA Sequencing

2020 ◽  
Author(s):  
Mamadou L. Fall ◽  
Dong Xu ◽  
Pierre Lemoyne ◽  
Issam E. Ben Moussa ◽  
Carole Beaulieu ◽  
...  
Keyword(s):  
Interspecific Hybrid ◽  
Pinot Noir ◽  
Grapevine Cultivar ◽  
Sequencing Method ◽  
Hop Stunt Viroid ◽  
Multiple Virus ◽  
Leafroll Disease ◽  
Different Strains ◽  
Hybrid Cultivar ◽  
Rupestris Stem Pitting

Quebec is the third-largest wine grape producing province in Canada, and the industry is constantly expanding. Traditionally, 90% of the grapevine cultivars grown in Quebec were rustic or semi-rustic and largely dominated by winter hardy interspecific hybrid Vitis sp. cultivars. Over the years, the winter protection techniques adopted by growers and climate changes have offered an opportunity to establish V. vinifera L. cultivars (e.g. Pinot Noir). We characterized the virome of leafroll-infected interspecific hybrid cultivar and compared it to the virome of V. vinifera cultivar to support and facilitate the transition of the industry. A dsRNA sequencing method was used to sequence symptomatic and asymptomatic grapevine leaves of different cultivars. The results suggested a complex virome in terms of composition, abundance, richness, and phylogenetic diversity. Three viruses, grapevine Rupestris stem pitting-associated virus, grapevine leafroll-associated virus (GLR) 3 and 2 and hop stunt viroid (HSVd) largely dominated the virome. However, their presence and abundance varied among grapevine cultivars. The symptomless grapevine cultivar Vidal was frequently infected by multiple virus and viroid species and different strains of the same virus, including GLR virus 3 and 2. Our data shows that viruses and viroids associated with the highest number of grapevines expressing symptoms included HSVd, GLR3 and GLR2, in gradient order. However, co-occurrence analysis revealed that the presence of GLR species was randomly associated with the development of virus-like symptoms. These findings and their implication for grapevine leafroll disease management were discussed.

scholarly journals Cloning, molecular and functional characterization by overexpression in Arabidopsis of MAPKK genes from grapevine (Vitis vinifera)

2020 ◽  
Author(s):  
Gang Wang ◽  
Ying-hai Liang ◽  
Ji-yu Zhang ◽  
Zong-Ming (Max) Cheng
Keyword(s):  
Salt Stress ◽  
Stress Tolerance ◽  
Functional Characterization ◽  
Pinot Noir ◽  
Transcriptional Level ◽  
Environmental Signals ◽  
Grapevine Cultivar ◽  
Drought And Salt Stress ◽  
Mitogen Activated Protein ◽  
And Function

Abstract Background : The mitogen-activated protein kinases (MAPKs), as a part of the MAPKKK-MAPKK-MAPK cascade, play crucial roles in plant development as an intracellular signal transduction pathways to respond various environmental signals. However, few MAPKK have been functionally characterized in grapevine. Results : In the study, five MAPKK (MKK) members were identified in grapevine (cultivar ‘Pinot Noir’), cloned and designated as VvMKK1-VvMKK5. A phylogenetic analysis grouped them into four sub-families based on the similarity of their conserved motifs and gene structure to Arabidopsis MAPKK members. qRT-PCR results indicated that the expression of VvMKK1, VvMKK2, VvMKK4, and VvMKK5 were up-regulated in mature leaf and young blades, and roots, but exhibited low expression in leaf petioles. VvMKK2, VvMKK3, and VvMKK5 genes were differentially up-regulated when grapevine leaves were inoculated with spores of Erisyphe necator , or treated with salicylic acid (SA), ethylene (ETH), H 2 O 2, or exposed to drought, indicating that these genes may be involved in a variety of signaling pathways. Over expression of VvMKK2 and VvMKK4 genes in transgenic Arabidopsis plants resulted in the production of seeds with a significantly higher germination and survival rate, and better seedling growth under stress conditions than wild-type plants. Overexpression of VvMKK2 in Arabidopsis improved salt and drought stress tolerance while overexpression of VvMKK4 only improved salt stress tolerance. Conclusions: Results of the present investigation provide a better understanding of the interaction and function of MAPKKK-MAPKK-MAPK genes at the transcriptional level in grapevine and led to the identification of candidate genes for drought and salt stress in grapes.

scholarly journals Cloning, molecular and functional characterization by overexpression in Arabidopsis of MAPKK genes from grapevine (Vitis vinifera)

2020 ◽  
Author(s):  
Gang Wang ◽  
Ying-hai Liang ◽  
Ji-yu Zhang ◽  
Zong-Ming (Max) Cheng
Keyword(s):  
Salt Stress ◽  
Stress Tolerance ◽  
Functional Characterization ◽  
Pinot Noir ◽  
Transcriptional Level ◽  
Environmental Signals ◽  
Grapevine Cultivar ◽  
Drought And Salt Stress ◽  
Mitogen Activated Protein ◽  
And Function

Abstract Background: The mitogen-activated protein kinases (MAPKs), as a part of the MAPKKK-MAPKK-MAPK cascade, play crucial roles in plant development as an intracellular signal transduction pathways to respond various environmental signals. However, few MAPKK have been functionally characterized in grapevine.Results: In the study, five MAPKK (MKK) members were identified in grapevine (cultivar ‘Pinot Noir’), cloned and designated as VvMKK1-VvMKK5. A phylogenetic analysis grouped them into four sub-families based on the similarity of their conserved motifs and gene structure to Arabidopsis MAPKK members. qRT-PCR results indicated that the expression of VvMKK1, VvMKK2, VvMKK4, and VvMKK5 were up-regulated in mature leaf and young blades, and roots, but exhibited low expression in leaf petioles. VvMKK2, VvMKK3, and VvMKK5 genes were differentially up-regulated when grapevine leaves were inoculated with spores of Erisyphe necator, or treated with salicylic acid (SA), ethylene (ETH), H2O2, or exposed to drought, indicating that these genes may be involved in a variety of signaling pathways. Over expression of VvMKK2 and VvMKK4 genes in transgenic Arabidopsis plants resulted in the production of seeds with a significantly higher germination and survival rate, and better seedling growth under stress conditions than wild-type plants. Overexpression of VvMKK2 in Arabidopsis improved salt and drought stress tolerance while overexpression of VvMKK4 only improved salt stress tolerance.Conclusions: Results of the present investigation provide a better understanding of the interaction and function of MAPKKK-MAPKK-MAPK genes at the transcriptional level in grapevine and led to the identification of candidate genes for drought and salt stress in grapes.

scholarly journals A Diverse Virome of Leafroll-Infected Grapevine Unveil by dsRNA Sequencing

2020 ◽  
Author(s):  
Mamadou L. Fall ◽  
Dong Xu ◽  
Pierre Lemoyne ◽  
Issam E. Ben Moussa ◽  
Carole Beaulieu ◽  
...  
Keyword(s):  
Interspecific Hybrid ◽  
Pinot Noir ◽  
Grapevine Cultivar ◽  
Sequencing Method ◽  
Hop Stunt Viroid ◽  
Multiple Virus ◽  
Leafroll Disease ◽  
Different Strains ◽  
Hybrid Cultivar ◽  
Rupestris Stem Pitting

Quebec is the third-largest wine grape producing province in Canada, and the industry is constantly expanding. Traditionally, 90% of the grapevine cultivars grown in Quebec were rustic or semi-rustic and largely dominated by winter hardy interspecific hybrid Vitis sp. cultivars. Over the years, the winter protection techniques adopted by growers and climate changes have offered an opportunity to establish V. vinifera L. cultivars (e.g. Pinot Noir). We characterized the virome of leafroll-infected interspecific hybrid cultivar and compared it to the virome of V. vinifera cultivar to support and facilitate the transition of the industry. A dsRNA sequencing method was used to sequence symptomatic and asymptomatic grapevine leaves of different cultivars. The results suggested a complex virome in terms of composition, abundance, richness, and phylogenetic diversity. Three viruses, grapevine Rupestris stem pitting-associated virus, grapevine leafroll-associated virus (GLR) 3 and 2 and hop stunt viroid (HSVd) largely dominated the virome. However, their presence and abundance varied among grapevine cultivars. The symptomless grapevine cultivar Vidal was frequently infected by multiple virus and viroid species and different strains of the same virus, including GLR virus 3 and 2. Our data shows that viruses and viroids associated with the highest number of grapevines expressing symptoms included HSVd, GLR3 and GLR2, in gradient order. However, co-occurrence analysis revealed that the presence of GLR species was randomly associated with the development of virus-like symptoms. These findings and their implication for grapevine leafroll disease management were discussed.

scholarly journals Cloning, molecular and functional characterization by overexpression in Arabidopsis of MAPKK genes from grapevine (Vitis vinifera)

2020 ◽  
Author(s):  
Gang Wang ◽  
Ying-hai Liang ◽  
Ji-yu Zhang ◽  
Zong-Ming (Max) Cheng
Keyword(s):  
Salt Stress ◽  
Stress Tolerance ◽  
Functional Characterization ◽  
Pinot Noir ◽  
Transcriptional Level ◽  
Environmental Signals ◽  
Grapevine Cultivar ◽  
Drought And Salt Stress ◽  
Mitogen Activated Protein ◽  
And Function

Abstract Background : The mitogen-activated protein kinases (MAPKs), as a part of the MAPKKK-MAPKK-MAPK cascade play crucial roles in plant development as an intracellular signal transduction pathways to respond various environmental signals. However, few MAPKK have been functionally characterized in grapevine. Results : In the study, five MAPKK (MKK) members were identified in grapevine (cultivar ‘Pinot Noir’), cloned and designated as VvMKK1-VvMKK5. A phylogenetic analysis grouped them into four sub-families based on the similarity of their conserved motifs and gene structure to Arabidopsis MAPKK members. qRT-PCR results indicated that the expression of VvMKK1, VvMKK2, VvMKK4, and VvMKK5 were up-regulated in mature leaf and young blades, and roots, but exhibited low expression in leaf petioles. VvMKK2, VvMKK3, and VvMKK5 genes were differentially up-regulated when grapevine leaves were inoculated with spores of Erisyphe necator , or treated with salicylic acid (SA), ethylene (ETH), H 2 O 2, or exposed to drought, indicating that these genes may be involved in a variety of signaling pathways. Over expression of VvMKK2 and VvMKK4 genes in transgenic Arabidopsis plants resulted in the production of seeds with a significantly higher germination and survival rate, and better seedling growth under stress conditions than wild-type plants. Overexpression of VvMKK2 in Arabidopsis improved salt and drought stress tolerance while overexpression of VvMKK4 only improved salt stress tolerance. Conclusions: Results of the present investigation provide a better understanding of the interaction and function of MAPKKK-MAPKK-MAPK genes at the transcriptional level in grapevine and led to the identification of candidate genes for drought and salt stress in grapes.

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