Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0754-z) contains supplementary material, which is available to authorized users.

Assessing the impact of plant genetic diversity in shaping the microbial community structure of Vitis vinifera phyllosphere in the Mediterranean

“…Considering that the microbial diversity present in phyllosphere could be relevant for plant health (Lugtenberg et al 2002;Compant et al 2005;Vorholt 2012), a better understanding of how the microbiota associated with grapevine phyllosphere is structured according to the grapevine genetic diversity available at a particular geographic location may provide unexpected opportunities to develop innovative and natural biocontrol methods or phytostimulators against plant pathogen or new breeding scheme for the creation of innovative resistant cultivars. As a first step towards this goal, we explored the bacterial and fungal diversity in the phyllosphere of leaf and berry samples from a set of rather diverse grapevine cultivars that belongs to the three genetic pools of the cultivated grapevine (Nicolas et al 2016), in the French Mediterranean region. These experiments led us to address two major questions: (i) What microbial diversity is present in the phyllosphere of our Mediterranean vineyards and (ii) how this microbiome structure itself according to the grapevine genetic diversity and plant organs.…”

Towards an open grapevine information system

“…This could include the use of mutants or individuals carrying extreme phenotypes to decipher physiological mechanisms, progenies derived from controlled crosses or diversity panels to determine the genetic control of trait variation, individuals collected in situ for the study of the adaptation of populations to environments, the evaluation of wild relatives and so on. In the grapevine community association studies, exploiting natural diversity through large-scale sequencing and phenotyping, have enormous potential to compensate for the lack of large mutant collections and are widely implemented to complement other approaches to support the identification of candidate genes for traits in physiological processes (for example, Fournier-Level et al, 21 Nicolas et al 39 ). Importantly, many studies not only involve diverse genotypes of Vitis vinifera (the most widely cultivated species), but also related wild species, which are especially interesting in the context of improving tolerance to biotic and abiotic stresses (for example, Venuti et al 40 ).…”

Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms

“…LD, the non-random association of alleles at different loci and germplasm panels that represent genome-wide cultivar diversity (power of association panel), plays an integral role in GWAS and determines the density of SNPs required for GWAS (Flint-Garcia et al, 2003; Nicolas et al, 2016). Low to moderate LD (decay within 100 kb) such as that observed for the C. baccatum panel in our study must utilize high SNP density (Kovi et al, 2015).…”