ArticleBMC plant biology2008
A SNP transferability survey within the genus Vitis.
Article in BMC plant biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Mapping and identification of QTLs for low light tolerance traits in grapevine.BMC plant biology · 2025Article
- Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing.Biomolecules · 2021Article
- Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.Nature communications · 2020Article
- A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine.Horticulture research · 2016Article
- Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip.BMC plant biology · 2015Article
- Article
- Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine.PloS one · 2015Article
- A small XY chromosomal region explains sex determination in wild dioecious V. vinifera and the reversal to hermaphroditism in domesticated grapevines.BMC plant biology · 2014Article
- A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change.BMC evolutionary biology · 2013Article
- Article
- Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls.PloS one · 2013Article
- Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data.BMC genomics · 2012Article
- Pinot blanc and Pinot gris arose as independent somatic mutations of Pinot noir.Journal of experimental botany · 2012Article
- SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping.BMC genomics · 2012Article
- Development of marker sets useful in the early selection of Ren4 powdery mildew resistance and seedlessness for table and raisin grape breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
- Article
- SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.BMC bioinformatics · 2011Article
- High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species.BMC plant biology · 2011Article
- High throughput analysis of grape genetic diversity as a tool for germplasm collection management.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions.BMC plant biology · 2010Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEfforts to sequence the genomes of different organisms continue to increase. The DNA sequence is usually decoded for one individual and its application is for the whole species. The recent sequencing of the highly heterozygous Vitis vinifera L. cultivar Pinot Noir (clone ENTAV 115) genome gave rise to several thousand polymorphisms and offers a good model to study the transferability of its degree of polymorphism to other individuals of the same species and within the genus.
resultsThis study was performed by genotyping 137 SNPs through the SNPlex Genotyping System (Applied Biosystems Inc.) and by comparing the SNPlex sequencing results across 35 (of the 137) regions from 69 grape accessions. A heterozygous state transferability of 31.5% across the unrelated cultivars of V. vinifera, of 18.8% across the wild forms of V. vinifera, of 2.3% among non-vinifera Vitis species, and of 0% with Muscadinia rotundifolia was found. In addition, mean allele frequencies were used to evaluate SNP informativeness and develop useful subsets of markers.
conclusionUsing SNPlex application and corroboration from the sequencing analysis, the informativeness of SNP markers from the heterozygous grape cultivar Pinot Noir was validated in V. vinifera (including cultivars and wild forms), but had a limited application for non-vinifera Vitis species where a resequencing strategy may be preferred, knowing that homology at priming sites is sufficient. This work will allow future applications such as mapping and diversity studies, accession identification and genomic-research assisted breeding within V. vinifera.
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