Clonal variation in grape
Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L.
Through numerous vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity of grape. Clonal diversity provided clones such as Cabernet-Sauvignon Clone N°470, Chardonnay Clone N°548 and Pinot noir Clone N ° 777 which produce wines of superior quality. The economic impact of clonal selection is very high: for example 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 in the context of vegetative propagation. Genome sequencing was performed using 454 sequencing 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 available sequence of Pinot noir ENTAV-INRA® 115 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 mobile elements displayed the highest activity with respect to clonal variation. Mobile elements active in the genome of Pinot noir were identified and classified and a list is presented in this study. Among these, the dynamics of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.