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Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources.

De Lorenzis G, Chipashvili R, Failla O, Maghradze D - BMC Plant Biol. (2015)

Bottom Line: The number of loci successfully amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted polymorphic.Our results demonstrated a moderate differentiation between sativa and sylvestris compartments, even though a connection between several samples of both subspecies may be assumed for the occurrence of cross hybridization events among native wild populations and the cultivated accessions.Nevertheless, first degree relationships have not been discovered between wild and cultivated individuals.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy. gabriella.delorenzis@unimi.it.

ABSTRACT

Background: Georgia, in the Caucasian region, is considered the first domestication centre of grapevine. This country is characterized by high morphological variability of cultivated (Vitis vinifera L. subsp. sativa (DC.) Hegi) and wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi) compartments. The main objective of this study was to investigate the level of genetic diversity obtained by the novel custom Vitis18kSNP array, in order to analyse 71 grapevine accessions representative of wild and cultivated Georgian germplasms.

Results: The number of loci successfully amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted polymorphic. Sixty-eight unique profiles were identified, 42 for the sativa and 26 for the sylvestris compartment. Cluster analysis highlighted two main groups, one for cultivars and another for wild individuals, while a genetic structure according to accession taxonomic status and cultivar geographical origin was revealed by multivariate analysis, differentiating clearly the genotypes into 3 main groups, two groups including cultivars and one for wild individuals, even though a considerable overlapping area was observed.

Conclusions: Pattern of genetic diversity structure presented an additional proof that grapevine domestication events took place in the Caucasian region contributing to the crop evolution. Our results demonstrated a moderate differentiation between sativa and sylvestris compartments, even though a connection between several samples of both subspecies may be assumed for the occurrence of cross hybridization events among native wild populations and the cultivated accessions. Nevertheless, first degree relationships have not been discovered between wild and cultivated individuals.

No MeSH data available.


Relationships between wild and cultivated Georgian samples as represented by the first two principal coordinates of PCoA using SNP profiles. C1: Western cultivars; C2: Southern cultivars; W1: wild individuals
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Fig3: Relationships between wild and cultivated Georgian samples as represented by the first two principal coordinates of PCoA using SNP profiles. C1: Western cultivars; C2: Southern cultivars; W1: wild individuals

Mentions: In order to identify the structure of populations and the correlations among samples, two different methods were performed. The first method was the PCoA analysis [29], computed based on the genetic distance matrix obtained by SNP profiles. Two dimensional projections of PCoA analysis per each sample were plotted in a 2-D dimension scattered plot (Fig. 3). The first two principal components (PCs), accounting for 25.63 and 18.29 % of the total variation, differentiated clearly the genotypes into 3 main groups, despite the presence of overlapping areas: two groups including cultivars (C1 and C2) and one for wild individuals (W1). In the overlapping areas, several cultivated samples appeared borderline with W1 samples. Along the PC1, a separation between C2 and W1 groups was highlighted, while the discrimination of C1 group was highlighted by the PC2.Fig. 3


Study of genetic variability in Vitis vinifera L. germplasm by high-throughput Vitis18kSNP array: the case of Georgian genetic resources.

De Lorenzis G, Chipashvili R, Failla O, Maghradze D - BMC Plant Biol. (2015)

Relationships between wild and cultivated Georgian samples as represented by the first two principal coordinates of PCoA using SNP profiles. C1: Western cultivars; C2: Southern cultivars; W1: wild individuals
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4477415&req=5

Fig3: Relationships between wild and cultivated Georgian samples as represented by the first two principal coordinates of PCoA using SNP profiles. C1: Western cultivars; C2: Southern cultivars; W1: wild individuals
Mentions: In order to identify the structure of populations and the correlations among samples, two different methods were performed. The first method was the PCoA analysis [29], computed based on the genetic distance matrix obtained by SNP profiles. Two dimensional projections of PCoA analysis per each sample were plotted in a 2-D dimension scattered plot (Fig. 3). The first two principal components (PCs), accounting for 25.63 and 18.29 % of the total variation, differentiated clearly the genotypes into 3 main groups, despite the presence of overlapping areas: two groups including cultivars (C1 and C2) and one for wild individuals (W1). In the overlapping areas, several cultivated samples appeared borderline with W1 samples. Along the PC1, a separation between C2 and W1 groups was highlighted, while the discrimination of C1 group was highlighted by the PC2.Fig. 3

Bottom Line: The number of loci successfully amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted polymorphic.Our results demonstrated a moderate differentiation between sativa and sylvestris compartments, even though a connection between several samples of both subspecies may be assumed for the occurrence of cross hybridization events among native wild populations and the cultivated accessions.Nevertheless, first degree relationships have not been discovered between wild and cultivated individuals.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Milano, Milan, Italy. gabriella.delorenzis@unimi.it.

ABSTRACT

Background: Georgia, in the Caucasian region, is considered the first domestication centre of grapevine. This country is characterized by high morphological variability of cultivated (Vitis vinifera L. subsp. sativa (DC.) Hegi) and wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi) compartments. The main objective of this study was to investigate the level of genetic diversity obtained by the novel custom Vitis18kSNP array, in order to analyse 71 grapevine accessions representative of wild and cultivated Georgian germplasms.

Results: The number of loci successfully amplified was 15,317 out of 18,775 SNP and 79 % of loci resulted polymorphic. Sixty-eight unique profiles were identified, 42 for the sativa and 26 for the sylvestris compartment. Cluster analysis highlighted two main groups, one for cultivars and another for wild individuals, while a genetic structure according to accession taxonomic status and cultivar geographical origin was revealed by multivariate analysis, differentiating clearly the genotypes into 3 main groups, two groups including cultivars and one for wild individuals, even though a considerable overlapping area was observed.

Conclusions: Pattern of genetic diversity structure presented an additional proof that grapevine domestication events took place in the Caucasian region contributing to the crop evolution. Our results demonstrated a moderate differentiation between sativa and sylvestris compartments, even though a connection between several samples of both subspecies may be assumed for the occurrence of cross hybridization events among native wild populations and the cultivated accessions. Nevertheless, first degree relationships have not been discovered between wild and cultivated individuals.

No MeSH data available.