How do Pinot noir clones develop genetic differences despite being propagated as clones?

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Through repeated cycles of vegetative propagation, grapevine clones accumulate mutations in somatic cells that give rise to differences in their observable traits. Clonal diversity has yielded Cabernet-Sauvignon N°470, Chardonnay N°548 and Pinot noir N°777, all of which produce wines of superior quality. Clonal selection has a very large economic impact: approximately 95% of grapevines produced in French nurseries originate from French clonal selection.

This comparative genomic sequencing study provides the first broad description of genetic polymorphism—differences in DNA—among clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. The researchers used 454 GS-FLX genome sequencing without an a priori approach to identify and quantify, for the first time, molecular polymorphisms responsible for grapevine clonal variability. New generation sequencing (NGS) compared a large portion of the genomes of three Pinot noir clones selected for their differences in observable traits. The NGS reads and the sequence of Pinot noir ENTAV-INRA® 115, sequenced by Velasco and colleagues, were aligned to the PN40024 reference sequence. The researchers then searched for molecular polymorphisms between clones.

They found three types of polymorphism: single-nucleotide polymorphisms (SNPs), insertions and deletions (Indels), and mobile elements. Of these, insertion polymorphisms generated by mobile elements from many families showed the highest number of mutational events related to clonal variation. The researchers identified and classified mobile elements inducing insertion polymorphisms in the Pinot noir genome and presented a list of them as potential markers for studying clonal variation. They also analyzed the dynamics of four mobile elements with high levels of polymorphism and confirmed insertion polymorphism in all Pinot clones registered in France.