Use of SSR markers to identify grapevine cultivars registered in the Czech Republic

In this study we analyzed 51 grapevine cultivars registered in the Czech Republic using six highly informative SSR loci, and determined SSR profiles typical for each cultivar. All cultivars were easily distinguished on the basis of SSR allele length, except for berry color mutants (Pinot and Chasselas group). The average number of detected alleles per locus was 13.2, while observed heterozygosity is between 0.745 (VrZAG 79) and 0.922 (VVMD 7). The lengths of the alleles were compared with results from other laboratories; lengths were either the same or different by 1-3 bp. We also tested a new approach to microsatellite data comparison using a coding system based on reference alleles as a size standard (THIS et al., 2004). The obtained profiles were mostly in accordance with profiles of reference cultivars (THIS et al., 2004); we discuss the possible reasons for observed discrepancies. A third allele in the microsatellite spectrum was observed in five samples where template DNA originated from leaves. Additional analyses with DNA isolated from phloem-enriched samples (L2 meristem layer) were performed and typical diallelic profiles obtained. The reason for the detected triallelism is assumed to be a periclinal chimerism

The group of variants analysed by MSAP.

<p>The system used to identify individual variants in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126638#pone.0126638.t001" target="_blank">Table 1</a> is as follows: the cultivar abbreviation (MT = Müller Thurgau or R = Riesling) is followed by identification number of the cutting. Meaning of the suffixes: M-NI = maternal, non-infected plants; M-I = maternal, GFLV-infected plants; IV-NI = <i>in vitro</i> cultivated, non-infected plants; IV-I = <i>in vitro</i> cultivated, infected plants; TIV-NI = <i>in vitro</i> thermotherapy, non-infected plants; and TIV-HAI = <i>in vitro</i> thermotherapy, plants healed after GFLV infection. The notes “(1 year)” and “(8 weeks)” indicate the time interval elapsed since the transfer of plants from <i>in vitro</i> to non-sterile conditions.</p><p>The group of variants analysed by MSAP.</p

Comparison of average mutual epigenetic similarities between groups represented by individuals with the same attributes (time elapsed since exposure to stress and the nature of conditions during <i>in vitro</i> cultivation).

<p>The first column clearly shows a decreasing tendency of similarity of DNA methylation landscape, when compared with state in maternal plants. It is also noticeable that the most similar DNA methylation states for each group of variants were usually recorded when individuals from the same group were compared (i.e., values on the diagonal of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126638#pone.0126638.t002" target="_blank">Table 2</a>).</p><p>Comparison of average mutual epigenetic similarities between groups represented by individuals with the same attributes (time elapsed since exposure to stress and the nature of conditions during <i>in vitro</i> cultivation).</p