Genetic characterization of autochthonous grapevine cultivars from Eastern Turkey by simple sequence repeats (SSRs)

Abstract

In this research, two well-recognized standard grape cultivars, Cabernet Sauvignon and Merlot, together with eight historical autochthonous grapevine cultivars from Eastern Anatolia in Turkey, were genetically characterized by using 12 pairs of simple sequence repeat (SSR) primers in order to evaluate their genetic diversity and relatedness. All of the used SSR primers produced successful amplifications and revealed DNA polymorphisms, which were subsequently utilized to evaluate the genetic relatedness of the grapevine cultivars. Allele richness was implied by the identification of 69 alleles in 8 autochthonous cultivars with a mean value of 5.75 alleles per locus. The average expected heterozygosity and observed heterozygosity were found to be 0.749 and 0.739, respectively. Taking into account the generated alleles, the highest number was recorded in VVC2C3 and VVS2 loci (nine and eight alleles per locus, respectively), whereas the lowest number was recorded in VrZAG83 (three alleles per locus). Two main clusters were produced by using the unweighted pair-group method with arithmetic mean dendrogram constructed on the basis of the SSR data. Only Cabernet Sauvignon and Merlot cultivars were included in the first cluster. The second cluster involved the rest of the autochthonous cultivars. The results obtained during the study illustrated clearly that SSR markers have verified to be an effective tool for fingerprinting grapevine cultivars and carrying out grapevine biodiversity studies. The obtained data are also meaningful references for grapevine domestication.

Genetic relationships of 34 grapevine varieties and construction of molecular fingerprints by SSR markers

“…There were 1-8, 1-8 and 1-7 alleles per locus of each group identified from the used 15 pairs SSR markers, which was consistent with the previously reported data of 4-16 alleles per locus in V. vinifera germplasms [3,9,12,24,25]. The average number of 3.6, 4.4 and 3.6 alleles per locus was a little lower than in contrast earlier reports of 10 autochthonous cultivars (5.75) from Eastern Turkey [4], 25 autochthonous cultivars (8.67) from northeastern Turkey [26], 33 Slovenian cultivars (8.00) [27], 11 Romanian cultivars (7.90) [28], 50 Greek cultivars (7.90) [29] and 51 accessions from Bosnia and Herzegovina (7.82) [30]. The reason may be that the groups we had chosen were small, the varieties were few in each population, and all the cultivars in each group had similar traits.…”

“…Genomic DNA was extracted from young leaf tissues by the method of Thomas and Scott [4] with minor modifications. DNA integrity was confirmed using 1% (w/v) agarose gel electrophoresis, and DNA concentration and purity were determined by Bio-Photometer (Eppendorf BioSpectrometer Germany).…”

“…In this work, we used 15 pairs SSR markers selected from 44 pairs, but still did not cover the different linkage groups of the whole grape genome [32]. Complete and irrefutable identification needs a larger number of loci [4]. The main purpose of our research was to perform a preliminary study of the genetic diversity and explore the molecular fingerprinting system of grape varieties.…”

“…The traditional field evaluation method had been considered an important approach for the grape variety identification, however, it is time-consuming, laborious and error-prone due to environmental factors, which poses great challenges [1]. As an alternative, SSR (simple sequence repeat) markers, also known as short tandem repeats, are now widely used and have become a rewarding tool in the construction of genetic maps, description of distinctive individuals and assessment of genetic relatedness of grapevine varieties, for their reproducibility, high polymorphism, openness and co-dominance [2][3][4]. Since 1993, when Thomas et al [5] first used SSR markers to identify multiple Eurasian grape varieties and several other representatives of genus Vitis, SSR markers became more and more widely used in the research of different species [6,7], cultigens and rootstock varieties [8,9], and in distinguishing and identification of homonym and synonym varieties [3,[10][11][12][13].…”

Associations between the α-terpineol synthase gene and α-terpineol content in different grapevine varieties

“…A relatively low rate of nucleotide variation in a-TPS was observed in the grapevine varieties considered. The frequency of SNPs in the a-TPS coding region found in study was slightly lower than that reported in other grapevine studies, wherein a frequency of one SNP per 47-64 bp was detected on average [28][29][30][31][32]. This might be due to differences in the sample size and uneven distribution of polymorphisms in the grapevine genome.…”