Design of grapevine (Vitis vinifera L.) cultivar-specific SCAR primers for PCR fingerprinting

Abstract 

Among 34 grapevine cultivars (Vitis vinifera L.), eight putative genotype-specific RAPD markers, from ’Albariño’, ’Caíño blanco’, ’Chardonnay’, ’Folle blanche’, ’Grenache blanc’, ’Malvasía Sitges’, ’Torrontés’ and ’Treixadura’ respectively, were selected to transform into SCAR markers. Of these, seven markers were cloned and then five which showed a positive specific hybridization signal were sequenced. For these five markers, 30 sequence-specific primers ranging from 14 to 29 bases were designed to amplify genomic DNA from 64 grapevine cultivars under more-stringent PCR conditions. Only, two primer pairs, OpA11₁₁₇₅p17R/ p17F and OpD10₈₀₀p14R/p14F, still produced a specific SCAR marker, the ’Folle blanche’ ScA11₁₁₇₅ and the ’Malvasía Sitges’ ScD10₈₀₀ respectively. Moreover, the ScA11₁₁₇₅ marker was amplified only in ’Folle blanche’ among the 64 cultivars tested with a large annealing temperature range using either two different Taq DNA polymerases or two separate thermocyclers. In addition, we discuss the initial polymorphism originated by the RAPD technique and suggest a new design of SCAR primers to obtain reliable cultivar-specific SCAR markers from single PCR-based bands for identification purposes.