Genetic diversity, structure, and patterns of differentiation in the genus Vitis

Aradhya, Mallikarjuna K.; Wang, Y.; Walker, Michael; Prins, Bernard; Koehmstedt, Anne; Velasco, Dianne; Gerrath, Jean M.; Dangl, Gerald S.; Preece, John E.

doi:10.1007/s00606-012-0723-4

Cited by 44 publications

(60 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The extensive ancestral reticulations revealed by the network and analysis of individual genes suggested well connected ancestral populations and species throughout the distribution followed by increasing range-wide fragmentation, isolation, and differentiation. The ancestral area analysis and the recurring distributional trend of American paraphyly with Eurasia in this study suggested a progression from North America to Asia to Europe consistent with previous studies [17,29,33,36]. However, Péros et al [23] concluded that their analysis may support an Asian origin of Vitis .…”

Section: Discussionsupporting

confidence: 90%

“…Studies most similar in goals and pertinent to the present study were conducted by Aradhya et al [33], Nie et al [34], Liu et al [35], and Zecca et al [36]. Aradhya et al [33] obtained a taxon sample similar to the present study and used SSR and AFLP markers to study genetic diversity within Vitis . These markers have limited value for phylogeny reconstruction [37] and dating divergences was not attempted.…”

Section: Introductionmentioning

confidence: 66%

See 1 more Smart Citation

A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

et al. 2013

View full text Add to dashboard Cite

BackgroundGrapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations.ResultsVitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 – 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 – 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species.ConclusionsPhylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.

show abstract

Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 66%

A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

et al. 2013

View full text Add to dashboard Cite

show abstract

“…It is interesting to notice that these chromosome similarities observed among species, strengthen the hypothesis about Vitis origin as an ancient secondary polyploid (paleoallohexaploid) firstly proposed by Patel and Olmo (1955). Recent comparative studies focusing on nuclear and chloroplast DNA sequences (ZECCA et al, 2012;ARADHYA et al, 2013) supported a monophyletic origin of Vitis, probably in the Eurasian lands, despite two different chromosome numbers, i.e., 2n=38 and 2n=40.…”

supporting

confidence: 61%

Karyotype Analysis in Grapevines

Pierozzi

Moura

2016

Rev. Bras. Frutic.

View full text Add to dashboard Cite

-Seven species of Vitis L., V. champinii Planchon, V. cinerea (Engelm in Gray) Engelm, V. girdiana Munson, V. labrusca L., V. rotundifolia Michaux, V. rupestres Scheels and V. vinifera L. were studied with the purpose of complementing the karyomorphometric information for further comparative analyses. Based on ideograms and on chromosome measures obtained it was possible to see several differences among the species, which were enough to distinguish at least V. champinii and V. girdiana from the others as well as V. labrusca for the lowest measures and V. rotundifolia for the highest mean value of arm ratio. It seems that during the species diversification process the most crucial differences among them did not involve drastic changes in chromosome morphometry. Index terms: Vitis, ideogram, Vitaceae, mitosis, satellite segment. ANÁLISE DE CARIÓTIPOS EM VIDEIRAS RESUMO -Sete espécies de Vitisrupestres Scheels e V. vinifera L. foram estudadas com o propósito de complementar as informações cariomorfométricas para posteriores análises comparativas. Baseado nos ideogramas e nas medidas cromossômicas obtidas foi possível distinguir pelo menos V. champinii e V. girdiana das demais espécies pelas maiores medidas, bem como V. labrusca pelas menores medidas e V. rotundifolia pelo maior valor médio da razão de braços. Parece que durante o processo de diversificação das espécies as diferenças mais cruciais entre elas não envolveram mudanças drásticas na morfometria cromossômica. Termos para indexação: Vitis, ideograma, Vitaceae, mitose, segmento satélite.

show abstract

“…STRUCTURE allocates individuals into a number of clusters (K) independent of population information based on multilocus genotypic data, so as to minimize deviations from Hardy-Weinberg and linkage equilibrium (Aradhya et al 2013). Structure analysis revealed that the log posterior probabilities (LnP[D]) increased sharply from K = 1[LnP(D) = -9324.66] to K = 3 [LnP(D) = -4681.18], followed by a gradual decline from K = 3 to K = 10 (Fig.…”

Section: Population Structure Analysismentioning

confidence: 99%

Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers

Rebaa¹,

Abid²,

Aouida³

et al. 2017

Physiol Mol Biol Plants

View full text Add to dashboard Cite

The genetic diversity of 21 faba bean populations was examined using morphological and molecular markers. DNA was extracted from 189 individuals and 8 microsatellite markers were genotyped individually in these 21 populations. A total of 53 alleles were obtained in all populations, with an average of 6.62 alleles per locus. The expected and observed heterozygosity was 0.38 and 0.62 respectively. The average polymorphism index content of SSR markers was 0.61, ranging from 0.31 to 0.81. The unweighted pair group method with arithmetic mean dendrogram clustered all the populations into two groups, each for them subdivided into 3 sub-groups according to geographical origin. Morphological variation showed that the populations were not grouped according to their geographical origin. Therefore, patterns of differentiation of morphological traits did not coincide with molecular differentiation, indicating that morphological variation does not reflect genetic subdivision in studied faba bean populations. Analysis of molecular variance revealed high levels of genetic variation (83%) within population and provides a good base for designing genetic improvement programs. The result of Principal Component Analysis (PCA) revealed that three dimensional principal components (PC1, PC2 and PC3) contributed 40.56% of the total variability and accounted with values of 20.64, 11.22 and 8.70%, respectively. Cluster analysis based on PCA indicated three separate groups of populations. The genetic relationships found between the 21 populations samples were the same in both the PCA and STRUCTURE analysis which support the results observed. These data may serve as a foundation for the development of faba bean breeding programs.

show abstract

Genetic diversity, structure, and patterns of differentiation in the genus Vitis

Cited by 44 publications

References 44 publications

A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

Karyotype Analysis in Grapevines

Genetic variability in Tunisian populations of faba bean (Vicia faba L. var. major) assessed by morphological and SSR markers

Contact Info

Product

Resources

About