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Grapevine breeding requires renewed efforts to meet the challenge of the ongoing climate change and the societal demand for low input viticulture. A breeding program supported by Bordeaux wine professional committee (CIVB) aims at generating new cultivars that should meet these two objectives by improving traits such as disease resistance (downy and powdery mildew, black rot), while retaining the typicality of Bordeaux wines. As part of this program, two V. vinifera bi-parental mapping populations were generated by crossing, on the one hand, 'Petit Verdot' (PV) and 'Cabernet Franc' (CF) (n = 202) and, on the other hand, 'Ugni blanc' (UB) and 'Sauvignon blanc' (SB) (n = 214). These two mapping populations were investigated for quantitative trait loci (QTLs) detection of relevant segregating traits such as phenology or aromatic potential with GC-MS and LC-MS analyses. Genotyping by sequencing (GBS) by Illumina HiSeq 3000 of both mapping populations was performed on GET-plage platform (Toulouse, France). After bioinformatics treatments, the construction of the related genetic maps was achieved using JoinMap 4.1. High-density genetic maps, based on single nucleotide polymorphism (SNPs), allowed the detection of 25 QTLs related with phenology, berry quality, aroma composition and aroma precursors, as well as the identification of some relevant candidate genes. The QTLs identified typically accounted for 7-27% of the trait variation. The molecular markers identified in this project will be used for marker-assisted selection in current and future grapevine breeding programs. The project will provide the basis of the genetic architecture of useful traits for the production of red and white wines with emblematic Bordeaux typicality and will thus contribute to the design of new ideotypes. [ABSTRACT FROM AUTHOR]

Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay Nu 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France. [ABSTRACT FROM AUTHOR]