Ph. D. Juan OCAÑA

Epigenetic diversity of grapevine (Vitis vinifera L.) clones and somaclones: identification of stable and unstable MSAP markers.

Under the supervision of Bernard WALTER and

Co-supervised by Paul Schellenbaum

Thesis defended in September 2014

Grapevine is one of the most economically important fruit productions in the world. It can be consumed as fresh fruit (table grapes), dried fruit (raisins) or beverage (juice, spirits and wine). Most of the vine varieties belong to the European species Vitis vinifera, intended for the production of high-quality wines.

For the identification of Vitis vinifera cultivars, molecular markers such as SSRs (simple sequence repeats) or AFLPs (amplified fragment length polymorphisms) have been used. Epigenetic variation as a source of diversity is being studied in several plant species. In grapevine, MSAP (methylation-sensitive amplified polymorphism) markers have been used to detect differences between somaclones and their mother clones (Schellenbaum et al, 2008).

In our study, a set of Vitis vinifera cv Pinot Noir clones were analyzed using the MSAP technique, generating two categories of polymorphic fragments, some “stable” and others “unstable”. Only the stable polymorphisms were used for the robust distinction of 92.5% of the clones studied (Ocaña et al, 2013). Ten stable polymorphic fragments were isolated and sequenced. After bisulfite treatment and fragment amplification, cytosine methylation profiles of four converted sequences were compared for 40 Pinot noir clones. The results show that SNP (single-nucleotide polymorphisms) markers are absent in these converted sequences and that most of the methylated cytosines are found in a CG context.

Stable MSAP markers could be useful to exploit epigenetic differences in clonal populations and to increase vine variability. They would then allow the development of specific cytosine methylation profiles, and the distinction of phenotypically identical clones. In addition, the MSAP approach could be useful to study the clonal origins of Pinot noir based on clone methylation profiles. Finally, characterizing clones with specific cytosine methylation profiles in several geographical areas could allow the study of grapevine adaptation to environmental changes and agricultural practices.

 

References:

Ocaña, J., Walter, B., & Schellenbaum, P. (2013) Stable MSAP Markers for the Distinction of Vitis vinifera cv Pinot Noir Clones. Molecular Biotechnology, 55:236-248.

Schellenbaum, P., Mohler, V., Wenzel, G., & Walter, B. (2008). Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.). BMC Plant Biology, 8:78.