ArticleBMC plant biology2016
Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies.
Article in BMC plant biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Unveiling the genetic architecture of stripe rust resistance in wheat: a region-specific GWAS in Xinjiang, China.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Optimizing core collections for genetic studies: a worldwide flax germplasm case study.Frontiers in plant science · 2025Article
- Single nucleotide polymorphism (SNP) analysis reveals ancestry and genetic diversity of cultivated and wild grapevines in Croatia.BMC plant biology · 2024Article
- Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization.Biochemistry and biophysics reports · 2024Article
- Enhancing grapevine breeding efficiency through genomic prediction and selection index.G3 (Bethesda, Md.) · 2024Article
- The genetic characterization of grapevines prospected in old Serbian vineyards reveals multiple relationships between traditional varieties of the Balkans.Frontiers in plant science · 2024Article
- A super-pangenome of the North American wild grape species.Genome biology · 2023Article
- Ripening dynamics revisited: an automated method to track the development of asynchronous berries on time-lapse images.Plant methods · 2023Article
- Exploring genetic diversity and population structure of a large grapevine (Frontiers in plant science · 2023Article
- Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics.Frontiers in plant science · 2023Review
- Interest of phenomic prediction as an alternative to genomic prediction in grapevine.Plant methods · 2022Article
- A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs.G3 (Bethesda, Md.) · 2022Article
- Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).Scientific reports · 2022Article
- Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine.G3 (Bethesda, Md.) · 2021Article
- Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops.Plants (Basel, Switzerland) · 2021Review
- Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing.Biomolecules · 2021Article
- Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis.BMC plant biology · 2021Article
- Molecular Tools for Adapting Viticulture to Climate Change.Frontiers in plant science · 2021Review
- Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm.Genes · 2020Article
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAs for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. However, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. Genome wide association studies in germplasm panels is an alternative method of choice, since it allows identifying the main quantitative trait loci with high resolution by exploiting past recombination events between cultivars. Such studies require adequate panel design to represent most of the available genetic and phenotypic diversity. Assessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies.
resultsStarting from the largest grapevine collection worldwide maintained in Vassal (France), we designed a diversity panel of 279 cultivars with limited relatedness, reflecting the low structuration in three genetic pools resulting from different uses (table vs wine) and geographical origin (East vs West), and including the major founders of modern cultivars. With 20 simple sequence repeat markers and five quantitative traits, we showed that our panel adequately captured most of the genetic and phenotypic diversity existing within the entire Vassal collection. To assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. Linkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 Kb depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. This panel achieved reasonable power to detect associations between traits with high broad-sense heritability (> 0.7) and causal loci with intermediate allelic frequency and strong effect (explaining > 10 % of total variance).
conclusionsOur association panel constitutes a new, highly valuable resource for genetic association studies in grapevine, and deserves dissemination to diverse field and greenhouse trials to gain more insight into the genetic control of many agronomic traits and their interaction with the environment.
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