In order to answer the new challenges faced by viticulture, the objective of breeding in grapevine is to create new cultivars accumulating both resistance to pathogens and adaptation to climatic changes while still offering a high quality of final product. These traits have to be accumulated from different sources, several Vitis species for resistance to biotic and abiotic stresses and V. vinifera for quality.
However, the genetic bases of the variability of these complex traits are still poorly known in grapevine compared to other crops, in particular because searching for QTLs in long-cycled woody species is very long, tedious and costly. Applying association genetics at the whole genome scale ("genome-scan" technique) will permit to much more rapidly and efficiently make the inventory of the main genetic factors underlying the variation of these agronomically important traits, by taking advantage of the high variability and large number of recombinations accumulated within the available genetic resources.
However, precise knowledge of the structure of genetic diversity and of linkage disequilibrium in analysed samples is crucial to design
and perform association genetics studies. Since this knowledge is scarce in Vitis, we propose to produce this knowledge for several
Vitis species of interest for breeding, mainly Vitis vinifera, V. riparia, V. cinerea and V. aestivalis.
For Vitis vinifera, whose population structure is already known, the project will focus on the analysis of the extent of LD in 5 populations,
in 4 regions of interest (underlying QTLs) using SNPs well spread in the regions.
For the other Vitis species, after in situ collection of
seeds in the USA, we will analyse the structure of the populations and define non-structured sample. The extent of LD will also be analyzed in these species for the same 4 regions after some confirmation of synteny between species.
Finally, local association genetics for downy mildew resistance and berry size will be performed on the samples of the four species in order to test the methodology.
The project has 3 main scientific objectives:
The project also has more technical objectives:
- to characterize the structure of genetic diversity within populations of 3 wild Vitis species which are sources of interesting agronomic traits for breeding
- to characterize linkage disequilibrium between SNPs in 4 genomic regions in 5 populations of V. vinifera and 1 population of each of 3 wild Vitis species
- to test the genome-scan method for two important traits, resistance to downy mildew and berry size.
- to enlarge French grapevine germplasm collection by introducing new populations of wild Vitis species
- to install populations well suited for genome-scan for many traits in replicated field trials for reliable phenotyping
- to start reliable phenotyping of populations for resistance to downy mildew and berry weight
Coordinator: Patrice This
Bioinformatics tool: SNiPlay