Molecular tools for clone identification: the case of the grapevine cultivar ‘Traminer’

Abstract

In viticulture, biotype identification problems have traditionally been solved using ampelography, ampelometry and chemical traits analysis. However, these tools have resulted in several false attributions, in particular when used at the clonal level. The availability of relatively cheap, reliable and reproducible tools to identify genetic differences at the clonal level would greatly facilitate the work of clonal patenting. In this work, 24 accessions of ‘Traminer’ cultivars were characterized using molecular markers. Three different approaches were applied: simple sequence repeats (SSR), amplified fragment length polymorphism (AFLP) and methyl‐sensitive amplified length polymorphism (MSAP). Results showed that SSRs were not a powerful tool for clonal distinction. In contrast, the AFLP technique was able to distinguish 16 out of the 24 cultivars, even though the average similarity was high (97.1%). The MSAP technique was used to evaluate qualitative differences in the degree of DNA methylation among clones. Results suggest that morphological differences among clones are probably due to the synergetic effect of genetic and epigenetic modifications, and that clonal identification could be greatly improved using molecular tools such as AFLP and MSAP.

The characterisation of Vitis vinifera ’Refošk’ with AFLP and SSR molecular markers and ampelographic traits

“…Kozjak et al (2003) tested some selected accessions from the collection vineyard in Komen with 6 microsatellite loci, also known as simple sequence repeats (SSR), and found that two Refošk samples are probably different from cultivar Refošk, showed different patterns, while other accessions revealed identical SSR allelic profiles. The insufficient clone discrimination ability of SSR molecular markers was also stated in other papers (Imazio et al, 2002;Laucou et al, 2011), although microsatellite markers have been widely used for grapevine cultivar identification, defining synonyms and homonyms, and for pedigree reconstruction (Cipriani et al, 2010;Laucou et al, 2011;Rusjan et al, 2012). Molecular markers that have been used on grapevine in several studies to detect intravarietal variability are the inter simple sequence repeats (ISSR) (Regner et al, 2000), amplified fragment length polymorphism (AFLP) (Cervera et al, 1998;Fanizza et al, 2003;Imazio et al, 2002;Konradi et al, 2007;Meneghetti et al, 2012), selective amplification of microsatellite polymorphic loci (SAMPL) (Cretazzo et al, 2010;Meneghetti et al, 2012), microsatellite amplified fragment length polymorphism (M-AFLP) (Cretazzo et al, 2010;Meneghetti et al, 2012) and specific sequence amplified polymorphism (S-SAP) (Carrier et al, 2012;Stajner et al, 2009).…”

Amplified fragment length polymorphism analysis of grapevine rootstock genotypes in Turkey

“…However, in order to display the capacity of AFLP markers and to recommend a minimum primer number for genetic analysis in rootstock discrimination, similarity ratios of single-and double-combination primers were determined. While Cervera et al (1998) defined the genotypes showing similarity higher than 0.900 as identical, Imazio et al (2002) identified 0.910 similarity between two different varieties, Pinot noir and Elbing. Also, Fossati et al (2001) found 0.920 similarity between two different varieties, Rossera and Urban.…”

Ampelographic and Genetic Characterization of Grapevine Varieties (Vitis vinifera L.) of the ‘Mavroudia’ Group Cultivated in Greece

“…Although the molecular method AFLP has been successfully used for the identification and discrimination of grapevine cultivars and the determination of the degree of genetic similarity between varieties, clones and rootstocks (Vignani et al, 2002;Imazio et al, 2002;Fanizza et al, 2005;Blaich et al, 2007;Stenkamp et al, 2009;Alba et al, 2011;Anhalt et al, 2011;Meneghetti et al, 2012;Shinde et al, 2013), the combined use of the ampelographic description for the selection of the proper sample, especially in the case of heterogeneous groups of grapevine varieties, as is the 'Mavroudia' group, is deemed necessary.…”