New insights on the genetic basis of Portuguese grapevine and on grapevine domestication

Genome ◽  
2009 ◽  
Vol 52 (9) ◽  
pp. 790-800 ◽  
Author(s):  
M. S. Lopes ◽  
D. Mendonça ◽  
M. Rodrigues dos Santos ◽  
J. E. Eiras-Dias ◽  
A. da Câmara Machado
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Vitis Vinifera ◽  
Ssr Markers ◽  
Genetic Basis ◽  
Genetic Resource ◽  
Putative Parent ◽  
Last Glaciation ◽  
Wild Grapevine ◽  
Nuclear Ssr

As the ancestor of cultivated grape, Vitis vinifera subsp. sylvestris represents a unique, invaluable genetic resource for the improvement of cultivated grapevines. Recently, five populations of wild grapevines were identified in Portugal. Sixty vines were characterized with 11 nuclear SSR markers and further compared with 70 genotypes of Portuguese Vitis vinifera subsp. sativa. The obtained data demonstrate moderate genetic differentiation between wild grapevine populations and moderate to high genetic differentiation between wild and cultivated grapevines. However, the identification of high degrees of similarity between wild and cultivated grapes (up to 87%) and a putative parent–progeny relationship between wild and cultivated grapes with 17 additional SSR markers is indicative of gene flow between local wild grapevine populations and Portuguese domesticated vines. Also, the ancestry of some Azorean cultivars was ascertained. The obtained data further support the hypothesis of several domestication centres, with Portugal, Spain, and Italy playing a particular role after the last glaciation, giving rise to many of the Western European cultivars.

scholarly journals Low Level of Pollen-Mediated Gene Flow from Cultivated to Wild Grapevine: Consequences for the Evolution of the Endangered Subspecies Vitis vinifera L. subsp. silvestris

2008 ◽  
Vol 100 (1) ◽  
pp. 66-75 ◽  
Author(s):  
Manuel Di Vecchi-Staraz ◽  
Valérie Laucou ◽  
Gérard Bruno ◽  
Thierry Lacombe ◽  
Sophie Gerber ◽  
...  
Keyword(s):  
Gene Flow ◽  
Vitis Vinifera ◽  
Vitis Vinifera L ◽  
Low Level ◽  
Wild Grapevine

scholarly journals Genome-wide sampling suggests island divergence accompanied by cryptic epigenetic plasticity in Canada lynx

2018 ◽  
Author(s):  
J.B. Johnson ◽  
D.L. Murray ◽  
A.B.A. Shafer
Keyword(s):  
Dna Methylation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Markers ◽  
Phenotypic Variation ◽  
Lynx Canadensis ◽  
Functional Plasticity ◽  
Canada Lynx ◽  
Last Glaciation ◽  
Genome Wide

ABSTRACTDetermining the molecular signatures of adaptive differentiation is a fundamental component of evolutionary biology. A key challenge remains for identifying such signatures in wild organisms, particularly between populations of highly mobile species that undergo substantial gene flow. The Canada lynx (Lynx canadensis) is one species where mainland populations appear largely undifferentiated at traditional genetic markers, despite inhabiting diverse environments and displaying phenotypic variation. Here, we used high-throughput sequencing to investigate both neutral genetic structure and epigenetic differentiation across the distributional range of Canada lynx. Using a customized bioinformatics pipeline we scored both neutral SNPs and methylated nucleotides across the lynx genome. Newfoundland lynx were identified as the most differentiated population at neutral genetic markers, with diffusion approximations of allele frequencies indicating that divergence from the panmictic mainland occurred at the end of the last glaciation, with minimal contemporary admixture. In contrast, epigenetic structure revealed hidden levels of differentiation across the range coincident with environmental determinants including winter conditions, particularly in the peripheral Newfoundland and Alaskan populations. Several biological pathways related to morphology were differentially methylated between populations, with Newfoundland being disproportionately methylated for genes that could explain the observed island dwarfism. Our results indicate that epigenetic modifications, specifically DNA methylation, are powerful markers to investigate population differentiation and functional plasticity in wild and non-model systems.SIGNIFICANCEPopulations experiencing high rates of gene flow often appear undifferentiated at neutral genetic markers, despite often extensive environmental and phenotypic variation. We examined genome-wide genetic differentiation and DNA methylation between three interconnected regions and one insular population of Canada lynx (Lynx canadensis) to determine if epigenetic modifications characterized climatic associations and functional molecular plasticity. Demographic approximations indicated divergence of Newfoundland during the last glaciation, while cryptic epigenetic structure identified putatively functional differentiation that might explain island dwarfism. Our study suggests that DNA methylation is a useful marker for differentiating wild populations, particularly when faced with functional plasticity and low genetic differentiation.

scholarly journals Shallow evolutionary divergence between two Andean hummingbirds: Speciation with gene flow?

2018 ◽  
Author(s):  
Catalina Palacios ◽  
Silvana García-R ◽  
Juan Luis Parra ◽  
Andrés M. Cuervo ◽  
F. Gary Stiles ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Basis ◽  
Flow Model ◽  
Evolutionary Divergence ◽  
Phenotypic Differences ◽  
Adaptive Mechanisms ◽  
The Face ◽  
Divergence With Gene Flow ◽  
Neutral Markers

AbstractEcological speciation can proceed despite genetic interchange when selection counteracts homogeneizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, two parapatric Andean hummigbirds with marked plumage divergence. We sequenced neutral markers (mtDNA and nuclear ultra conserved elements) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Glogers’ rule that darker forms occur in more humid environments, and compared ecomorphological variables to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was very low and coalescent estimates of migration were consistent with divergence with gene flow. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in ecomorphology. Although we reject adaptation to variation in humidity as the cause of divergence, we hypothesize that speciation likely occurred in the face of gene flow, driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

scholarly journals High levels of gene flow and genetic diversity in Irish populations of Salix capreaL. inferred from chloroplast and nuclear SSR markers

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Aude C Perdereau ◽  
Colin T Kelleher ◽  
Gerry C Douglas ◽  
Trevor R Hodkinson
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Ssr Markers ◽  
Nuclear Ssr

scholarly journals Evaluation of breeding potential of wild grape originating from Armenia

2019 ◽  
Vol 15 ◽  
pp. 01006
Author(s):  
K. Margaryan ◽  
E. Maul ◽  
Z. Muradyan ◽  
A. Hovhannisyan ◽  
G. Melyan ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Allelic Variation ◽  
Resistance Breeding ◽  
Crop Wild Relatives ◽  
Breeding Programs ◽  
Genetic Traits ◽  
Breeding Potential ◽  
Wild Grape ◽  
Wild Grapevine ◽  
The Future

Crop wild relatives provide a useful source of genetic variation and represent a large pool of genetic diversity for new allelic variation required in breeding programs. Armenia is an important center of origin both for cultivated Vitis vinifera ssp. sativa and wild Vitis vinifera ssp. sylvestris. Owing to recent prospection in Armenian woods and river floodplains many forms of wild grapevine were discovered and inventoried, which is an important prerequisite to unlock their breeding potential in the future. The fact that some genotypes of V. sylvestris can withstand the diseases is likely to be due to a more efficient basal immunity. The overall goal of the proposed research was to characterize the diversity of V. sylvestris from Armenia with respect to its capacity for stilbene biosynthesis, which might be exploited as genetic resource for resistance breeding. The realized research stimulates the recovery, characterization and preservation of wild grape germplasm, presently at risk of extinction. The recovery and characterization of wild genotypes will be the base of selection of genetic traits important in breeding programs for the generation of biotic and changing climate tolerant grapevine varieties and rootstocks, both necessary for the future of viticulture in Armenia and in Europe.

Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?

The Auk ◽  
2019 ◽  
Vol 136 (4) ◽  
Author(s):  
Catalina Palacios ◽  
Silvana García-R ◽  
Juan Luis Parra ◽  
Andrés M Cuervo ◽  
F Gary Stiles ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Incomplete Lineage Sorting ◽  
Lineage Sorting ◽  
Phenotypic Differences ◽  
Adaptive Mechanisms ◽  
The Face ◽  
Gloger’S Rule ◽  
Divergence With Gene Flow ◽  
Neutral Markers

Abstract Ecological speciation can proceed despite genetic interchange when selection counteracts the homogenizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, 2 parapatric Andean hummingbirds with marked plumage divergence. We sequenced putatively neutral markers (mitochondrial DNA [mtDNA] and nuclear ultraconserved elements [UCEs]) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Gloger’s rule that darker forms occur in more humid environments, and examined morphological variation to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was low in both ND2 and UCEs. Coalescent estimates of migration were consistent with divergence with gene flow, but we cannot reject incomplete lineage sorting reflecting recent speciation as an explanation for patterns of genetic variation. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in morphology. Although we reject adaptation to variation in macroclimatic conditions as a cause of divergence, speciation may have occurred in the face of gene flow driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

The Use of Protein Electrophoresis for Determining Species Boundaries in Amphipods

Crustaceana ◽  
1993 ◽  
Vol 65 (2) ◽  
pp. 265-277 ◽  
Author(s):  
Barbara A. Stewart
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Morphological Variation ◽  
Protein Electrophoresis ◽  
Species Boundaries ◽  
Allopatric Populations ◽  
A Value ◽  
Electrophoretic Data

AbstractThe use of protein electrophoretic data for determining species boundaries in amphipods is addressed. Analysis of published literature on genetic differentiation in amphipods showed that pairs of allopatric populations which have genetic identities (I) above a value of 0.85 probably represent intraspecific populations, whereas pairs of populations which have genetic identities below about 0.45 probably represent different species. It was recommended that if I values fall between 0.45 and 0.85, additional factors such as evidence of a lack of gene flow between the populations, and concordant morphological variation should be considered.

Genetic differentiation and gene flow among six sheep breeds of Mongolian group in China

2008 ◽  
Vol 2 (3) ◽  
pp. 338-342 ◽  
Author(s):  
Yan Geng ◽  
Zhangping Yang ◽  
Hong Chang ◽  
Yongjiang Mao ◽  
Wei Sun ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Sheep Breeds

scholarly journals Dispersal and Differentiation of Deep-Sea Mussels of the GenusBathymodiolus(Mytilidae, Bathymodiolinae)

2009 ◽  
Vol 2009 ◽  
pp. 1-15 ◽  
Author(s):  
Akiko Kyuno ◽  
Mifue Shintaku ◽  
Yuko Fujita ◽  
Hiroto Matsumoto ◽  
Motoo Utsumi ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Shallow Water ◽  
Deep Sea ◽  
Dispersal Ability ◽  
Evolutionary Transition ◽  
Significant Genetic Differentiation ◽  
Evolutionary Processes ◽  
High Dispersal ◽  
High Gene

We sequenced the mitochondrial ND4 gene to elucidate the evolutionary processes ofBathymodiolusmussels and mytilid relatives. Mussels of the subfamily Bathymodiolinae from vents and seeps belonged to 3 groups and mytilid relatives from sunken wood and whale carcasses assumed the outgroup positions to bathymodioline mussels. Shallow water mytilid mussels were positioned more distantly relative to the vent/seep mussels, indicating an evolutionary transition from shallow to deep sea via sunken wood and whale carcasses.Bathymodiolus platifronsis distributed in the seeps and vents, which are approximately 1500 km away. There was no significant genetic differentiation between the populations. There existed high gene flow betweenB. septemdierumandB. breviorand low but not negligible gene flow betweenB. marisindicusandB. septemdierumorB. brevior, although their habitats are 5000–10 000 km away. These indicate a high adaptability to the abyssal environments and a high dispersal ability ofBathymodiolusmussels.

Sign in / Sign up

Export Citation Format

Share Document