Study of Intra-Varietal Genetic Variability in Grapevine Cultivars by PCR-Derived Molecular Markers and Correlations with the Geographic Origins

Abstract

The genetic grapevine intravarietal variability will be analyzed by PCR-derived marker systems. In particular, the object of the investigation will be the clonal variations of Malvasia nera di Brindisi/Lecce, Negroamaro and Primitivo, also known as Zinfandel, which are three grapevine varieties cultivated in Apulia region (Italy). In order to assess varietal identity of the samples, 132 DNA tests were performed by amplifying 16 SSR loci. The study of the intravarietal variability was performed using AFLPs, SAMPLs, ISSRs, and M-AFLPs. The application of the above-mentioned techniques allowed both to discriminate all genotypes of the three cultivars and to distinguish the accessions of each cultivar sampled from different geographic cultivation areas. Furthermore, the study of biotypes cultivated in different geographical environments of Salento (i.e., Apulia region) allowed important correlations between molecular marker variability and phenotypic traits. These results are suggesting both to focus our attention on the effects of the environment on the genotype and to consider, as a practical consequence, the importance of preserving autochthon grapevine biotypes found in different areas to truly preserve the richness of the germplasm. Thus, more accurate DNA studies give new information that can be extremely useful to the vine nurseries for the correct choice (i.e., supported by more accurate intravarietal variability analysis) of the grape multiplication materials.

Inter- and Intra-Varietal Genetic Variability in Vitis vinifera L.

“…The PCR was performed in a GeneAmp PCR System 9700 (Applied Biosystems) and SSR polymorphisms were resolved on an ABI-3130XL capillary sequencer (Applied Biosystems) using GeneMapper version 4.1 (Applied Biosystems) with a Vitis vinifera microsatellite BinSet of 11 SSR standard loci. The important molecular polymorphisms were checked by the Sequi-Gen GT Sequencing Cell electrophoresis (Biorad) (Meneghetti, 2012a). …”

“…The morphological traits of the five biotypes (i.e., leaves, bunch, and berry) were maintained after repeated propagation of these biotypes in experimental vineyards. Thus, the morphological traits could have been fixed and stabilized during several centuries of cultivation at Gioia del Colle (Meneghetti, 2012a). …”

“…It represents an important variety in the Apulia region. In the past, Malvasia nera of Brindisi and Malvasia nera of Lecce were considered two different cultivars, but this presumed synonymy has been ascertained with SSR markers and therefore these two Malvasia nera would be considered to be the same variety (Meneghetti, 2012a). Morphological analysis allows to differentiate accessions of this cultivar when we compare biotypes cultivated from the Lecce region with others from the Brindisi region.…”

“…Biotype A was similar to biotype AA with smaller sized bunches and wings. Biotypes B has smaller, shorter, less compact bunches than biotypes AA and A. Biotype AB showed bunch with intermediary characteristics between biotypes A and B. AFLP, M-AFLP, and SAMPL molecular markers were used to analyze the intra-varietal genetic variability (Meneghetti, 2012a). Cluster analyses showed a correlation between molecular profile and morphological traits of bunches relating to Malvasia di Candia biotypes ( Figure 13).…”

“…Molecular markers have been used on Vitis vinifera in several studies to distinguish among clones of the same cultivars as RAPD random amplified polymorphic DNA, PCR specific analysis ISSR (intermicrosatellites), SNP (single nucleotide polymorphism), S-SAP (specific sequence amplified polymorphism), IRAP (inter-retrotransposon amplified polymorphism), REMAP (retrotransposon microsatellite amplified polymorphism), M-SAP (methylsensitive amplified length polymorphism), chloroplast DNA polymorphisms, SSCP (single-strand conformation polymorphism) (Moreno, 1995 A molecular strategy to obtain DNA polymorphisms of Vitis vinifera genotypes from the same cultivar to study the intra-and inter-varietal genetic variability, to discriminate accessions, clones, and biotypes of a same grape variety, and to analyze the relationships between molecular profiles and some environmental parameters (i.e., geographic site) or morphological traits was reported by Meneghetti et al (2012a;2012b;2012c). This approach uses four different molecular marker systems (i.e., AFLP amplified fragment length polymorphism, SAMPL selective amplification of microsatellite polymorphic loci, M-AFLP microsatellites amplified fragment length polymorphism, and ISSR inter simple sequence repeat).…”