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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.


Admixture proportions of wild and cultivated Georgian groups, as estimated by fastSTRUCTURE at K = 3, displayed in a barplot. Each sample is represented as a vertical bar, reflecting assignment probabilities to each of the three groups. G1: red bars; G2: purple bars; G3: green bars
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Fig4: Admixture proportions of wild and cultivated Georgian groups, as estimated by fastSTRUCTURE at K = 3, displayed in a barplot. Each sample is represented as a vertical bar, reflecting assignment probabilities to each of the three groups. G1: red bars; G2: purple bars; G3: green bars

Mentions: The second method used to infer the relationship among genotypes was the clustering algorithm implemented in the fastSTRUCTURE program [30]. In order to uncover the hierarchical population structure, different numbers of K populations were explored (Fig. 4). Optimal K estimated the most likely number of populations at K = 3. Using a >0.75 % threshold for group assignation, 48 samples (68 %) were assigned to a cluster at K = 3 (Additional file 2: Table S2). Structure clustering highlighted 3 groups: two groups for sativa samples (G1 and G2) and one for sylvestris individuals (G3), including 25, 42 and 33 % of the entire genetic pool, respectively. In G3, only putative wild accessions (89 %) were included. The inbreeding coefficient (Fst) within three subpopulations identified by STRUCTURE analysis ranged from 0.076 (G1-G2 pairwise) to 0.064 (G2-G3).Fig. 4


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)

Admixture proportions of wild and cultivated Georgian groups, as estimated by fastSTRUCTURE at K = 3, displayed in a barplot. Each sample is represented as a vertical bar, reflecting assignment probabilities to each of the three groups. G1: red bars; G2: purple bars; G3: green bars
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Admixture proportions of wild and cultivated Georgian groups, as estimated by fastSTRUCTURE at K = 3, displayed in a barplot. Each sample is represented as a vertical bar, reflecting assignment probabilities to each of the three groups. G1: red bars; G2: purple bars; G3: green bars
Mentions: The second method used to infer the relationship among genotypes was the clustering algorithm implemented in the fastSTRUCTURE program [30]. In order to uncover the hierarchical population structure, different numbers of K populations were explored (Fig. 4). Optimal K estimated the most likely number of populations at K = 3. Using a >0.75 % threshold for group assignation, 48 samples (68 %) were assigned to a cluster at K = 3 (Additional file 2: Table S2). Structure clustering highlighted 3 groups: two groups for sativa samples (G1 and G2) and one for sylvestris individuals (G3), including 25, 42 and 33 % of the entire genetic pool, respectively. In G3, only putative wild accessions (89 %) were included. The inbreeding coefficient (Fst) within three subpopulations identified by STRUCTURE analysis ranged from 0.076 (G1-G2 pairwise) to 0.064 (G2-G3).Fig. 4

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.