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.

经过多轮无性繁殖循环后，葡萄克隆体的体细胞会积累突变，这些突变正是葡萄克隆表型多样性的成因。克隆多样性衍生出了如赤霞珠（Cabernet-Sauvignon）470号克隆、霞多丽（Chardonnay）548号克隆以及黑皮诺（Pinot noir）777号克隆等优质酿酒克隆，其所酿造的葡萄酒品质上乘。克隆选育的经济影响极为显著：例如法国苗圃产出的葡萄植株中，约95%均源自法国的克隆选育体系。
本研究首次针对无性繁殖背景下单一葡萄品种的不同克隆间的多态性展开系统性描述。研究采用无先验假设的454测序技术进行全基因组测序，首次对导致葡萄克隆变异的分子多态性进行鉴定与定量分析。本研究利用新一代测序（Next Generation Sequencing, NGS）技术，对3株因表型差异而被筛选出的黑皮诺克隆的大片段基因组进行比对分析。将NGS获得的测序读段与已公开的黑皮诺ENTAV-INRA® 115的序列，比对至PN40024参考基因组序列上，随后对克隆间的分子多态性进行筛查。
本研究共发现三类分子多态性：单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）、插入缺失多态性（Insertion-Deletion, Indels）以及转座元件（mobile elements）多态性，其中转座元件在克隆变异中表现出最高的活性。研究人员对黑皮诺基因组中具有活性的转座元件进行了鉴定与分类，并在本研究中列出了相关清单。在此基础上，本研究对4个多态性水平较高的转座元件的动态变化进行了分析，并证实法国注册的所有黑皮诺克隆中均存在这些转座元件的插入多态性。