NordGen Nordic Genetic Resource Center

Nordic, Norway

NordGen Nordic Genetic Resource Center

Nordic, Norway
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Pertoldi C.,University of Aarhus | Pertoldi C.,University of Aalborg | Pellegrino I.,University of Piemonte Orientale | Cucco M.,University of Piemonte Orientale | And 7 more authors.
Evolutionary Ecology Research | Year: 2012

Background: Danish populations of the little owl (Athene noctua) have experienced dramatic declines in size over the past century. Before 1960 the little owl population was abundant in Denmark (estimated N>2000), but between 1960 and 1980 the population declined rapidly, and since 1980 the little owl population has survived only in small and fragmented areas. Question: Is the decline in population size associated with reduced genetic variation in these Danish populations of the little owl? Are the populations genetically fragmented? Field site: Samples were collected from birds in Denmark (from 57°45′7″N to 54°33′35″N). Methods: We extracted DNA from the feathers of museum specimens of Danish little owls collected between 1918 and 1980. We also extracted DNA from feathers collected between 1984 and 2010. We performed a genetic analysis of 15 microsatellites on these samples. Conclusions: Older samples showed relatively little genetic variability, with more recent ones showing even less. In addition, pairwise FST values showed evidence for genetic substructuring with small but significant genetic differences between the extant population and the extinct owl populations on the Danish isle of Funen. The modest loss of genetic variability observed since the 1960s and 1970s may be associated with a diminished distributional range and population bottlenecks. © 2012 Volker Loeschcke.


Kantanen J.,Natural Resources Institute Finland | Kantanen J.,University of Eastern Finland | Lovendahl P.,University of Aarhus | Strandberg E.,Swedish University of Agricultural Sciences | And 6 more authors.
Frontiers in Genetics | Year: 2015

Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production's effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is t he reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programmes for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species. © 2015 Kantanen, Løvendahl, Strandberg, Eythorsdottir, Li, Kettunen-praebel, Berg and Meuwissen.


Pertoldi C.,University of Aalborg | Purfield D.C.,Trinity College Dublin | Berg P.,NordGen Nordic Genetic Resource Center | Jensen T.H.,University of Aalborg | And 3 more authors.
Journal of Animal Science | Year: 2014

In this paper we present results from a genetic characterization of a herd of the Danish Jutland cattle breed named the Kortegaard herd (n = 135; 57 males and 78 females). The herd is genotyped on the Bovine HD BeadChip microarray with 697,548 evenly spaced SNP across the bovine genome. The aim of the study was to characterize the genetic profile of the Kortegaard herd, which has been closed for several generations, by quantifying the degree of genetic homogeneity within the herd and to compare its genetic profile to that of other cattle breeds. A total of 868 animals from the Angus, Belgian Blue, Charolais, Friesian, Hereford, Holstein, Holstein-Friesian crosses, Limousin, and Simmental breeds was used for genetic profile comparisons. The level of genetic variation within the breeds were quantified by the expected heterozygosity (HE), observed heterozygosity (HO), average minor allele frequency (MAF), the degree of polymorphism, and runs of homozygosity (ROH), which are contiguous lengths of homozygous genotypes of varying length. Interestingly, the Kortegaard herd had the lowest within-breed genetic variation (lowest HE, HO, and MAF), showed moderate levels of short ROH (<5 Mb), and had the highest mean long ROH (>5 Mb) compared to all the other breeds. This is possibly due to recent consanguineous matings, a strong founder effect, and a lack of gene flow from other herds and breeds. We further examined whether the observed genetic patterns in the Kortegaard herd can be used to design breeding strategies for the preservation of the genetic pool by focusing on a subset of SNP outside homozygote regions. By calculating the pairwise identical-by-state between all possible matings, we designed a breeding plan that maximized heterozygosity in the short term. The benefits and limitations of such a breeding strategy are discussed. © 2014 American Society of Animal Science. All rights reserved.


PubMed | University of Aarhus, Norwegian University of Life Sciences, Swedish University of Agricultural Sciences, University of Eastern Finland and 3 more.
Type: | Journal: Frontiers in genetics | Year: 2015

Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal productions effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species.


Kellermann V.,University of Aarhus | Kellermann V.,Monash University | Overgaard J.,University of Aarhus | Loeschcke V.,University of Aarhus | And 3 more authors.
PLoS ONE | Year: 2013

Traits do not evolve independently. To understand how trait changes under selection might constrain adaptive changes, phenotypic and genetic correlations are typically considered within species, but these capture constraints across a few generations rather than evolutionary time. For longer-term constraints, comparisons are needed across species but associations may arise because of correlated selection pressures rather than genetic interactions. Implementing a unique approach, we use known patterns of selection to separate likely trait correlations arising due to correlated selection from those reflecting genetic constraints. We examined the evolution of stress resistance in >90 Drosophila species adapted to a range of environments, while controlling for phylogeny. Initially we examined the role of climate and phylogeny in shaping the evolution of starvation and body size, two traits previously not examined in this context. Following correction for phylogeny only a weak relationship between climate and starvation resistance was detected, while all of the variation in the relationship between body size and climate could be attributed to phylogeny. Species were divided into three environmental groups (hot and dry, hot and wet, cold) with the expectation that, if genetic correlations underpin trait correlations, these would persist irrespective of the environment, whereas selection-driven evolution should produce correlations dependent on the environment. We found positive associations between most traits in hot and dry environments coupled with high trait means. In contrast few trait correlations were observed in hot/wet and cold environments. These results suggest trait associations are primarily driven by correlated selection rather than genetic interactions, highlighting that such interactions are unlikely to limit evolution of stress resistance. © 2013 Kellermann et al.


Bechsgaard J.S.,University of Aarhus | Hoffmann A.A.,University of Melbourne | Sgro C.,Monash University | Loeschcke V.,University of Aarhus | And 3 more authors.
PLoS ONE | Year: 2013

The evolutionary history of widespread and specialized species is likely to cause a different genetic architecture of key ecological traits in the two species groups. This may affect how these two groups respond to inbreeding. Here we investigate inbreeding effects in traits related to performance in 5 widespread and 5 tropical restricted species of Drosophila with the aim of testing whether the two species groups suffered differently from inbreeding depression. The traits investigated were egg-to-adult viability, developmental time and resistance to heat, cold and desiccation. Our results showed that levels of inbreeding depression were species and trait specific and did not differ between the species groups for stress resistance traits. However, for the life history traits developmental time and egg-to adult viability, more inbreeding depression was observed in the tropical species. The results reported suggest that for life history traits tropical species of Drosophila will suffer more from inbreeding depression than widespread species in case of increases in the rate of inbreeding e.g. due to declines in population sizes. © 2013 Bechsgaard et al.


Bubliy O.A.,University of Aarhus | Kristensen T.N.,University of Aarhus | Kristensen T.N.,NordGen Nordic Genetic Resource Center | Loeschcke V.,University of Aarhus
Journal of Experimental Biology | Year: 2013

Plastic responses to heat and desiccation stress in insects have been studied in many laboratory experiments on Drosophila. However, in these studies the possible interaction between the corresponding stress factors in natural environments has not been taken into consideration. We investigated changes in heat and desiccation resistance of adult Drosophila simulans after shortterm exposures to different temperatures (35, 31 and 18C) in combination with high and low relative humidity (ca. 90 and 20%, respectively). Hardening under extreme conditions (35 or 31C and low relative humidity) commonly resulted in higher resistance to heat and desiccation as compared with other less stressful combinations of temperature and humidity levels. The concentration of the heat-shock protein Hsp70 in the experimental flies increased following almost all applied treatments. Life span of the hardened flies under non-stressful conditions was reduced irrespective of the stress dose, indicating a fitness cost for the plastic responses. The results of the study show that hardening using combined heat and desiccation stress can be very efficient with regard to induction of plastic responses improving tolerance to both types of stress. This may favour adaptation to hot and dry climatic conditions, though the negative effects on fitness are likely to constrain evolution of such plastic responses. © 2013. Published by The Company of Biologists Ltd.


Kopp G.H.,Leibniz Institute for Primate Research | Roos C.,Leibniz Institute for Primate Research | Butynski T.M.,King Khalid Wildlife Research Center | Butynski T.M.,Sustainability Center | And 4 more authors.
Journal of Human Evolution | Year: 2014

Many species of Arabian mammals are considered to be of Afrotropical origin and for most of them the Red Sea has constituted an obstacle for dispersal since the Miocene-Pliocene transition. There are two possible routes, the 'northern' and the 'southern', for terrestrial mammals (including humans) to move between Africa and Arabia. The 'northern route', crossing the Sinai Peninsula, is confirmed for several taxa by an extensive fossil record, especially from northern Egypt and the Levant, whereas the 'southern route', across the Bab-el-Mandab Strait, which links the Red Sea with the Gulf of Aden, is more controversial, although post-Pliocene terrestrial crossings of the Red Sea might have been possible during glacial maxima when sea levels were low.Hamadryas baboons (. Papio hamadryas) are the only baboon taxon to disperse out of Africa and still inhabit Arabia. In this study, we investigate the origin of Arabian hamadryas baboons using mitochondrial sequence data from 294 samples collected in Arabia and Northeast Africa. Through the analysis of the geographic distribution of genetic diversity, the timing of population expansions, and divergence time estimates combined with palaeoecological data, we test: (i) if Arabian and African hamadryas baboons are genetically distinct; (ii) if Arabian baboons exhibit population substructure; and (iii) when, and via which route, baboons colonized Arabia.Our results suggest that hamadryas baboons colonized Arabia during the Late Pleistocene (130-12 kya [thousands of years ago]) and also moved back to Africa. We reject the hypothesis that hamadryas baboons were introduced to Arabia by humans, because the initial colonization considerably predates the earliest records of human seafaring in this region. Our results strongly suggest that the 'southern route' from Africa to Arabia could have been used by hamadryas baboons during the same time period as proposed for modern humans. © 2014 The Authors.


PubMed | Wayne State University, Wildlife Conservation Society, Leibniz Institute for Primate Research, NordGen Nordic Genetic Resource Center and King Saud University
Type: | Journal: Journal of human evolution | Year: 2014

Many species of Arabian mammals are considered to be of Afrotropical origin and for most of them the Red Sea has constituted an obstacle for dispersal since the Miocene-Pliocene transition. There are two possible routes, the northern and the southern, for terrestrial mammals (including humans) to move between Africa and Arabia. The northern route, crossing the Sinai Peninsula, is confirmed for several taxa by an extensive fossil record, especially from northern Egypt and the Levant, whereas the southern route, across the Bab-el-Mandab Strait, which links the Red Sea with the Gulf of Aden, is more controversial, although post-Pliocene terrestrial crossings of the Red Sea might have been possible during glacial maxima when sea levels were low. Hamadryas baboons (Papio hamadryas) are the only baboon taxon to disperse out of Africa and still inhabit Arabia. In this study, we investigate the origin of Arabian hamadryas baboons using mitochondrial sequence data from 294 samples collected in Arabia and Northeast Africa. Through the analysis of the geographic distribution of genetic diversity, the timing of population expansions, and divergence time estimates combined with palaeoecological data, we test: (i) if Arabian and African hamadryas baboons are genetically distinct; (ii) if Arabian baboons exhibit population substructure; and (iii) when, and via which route, baboons colonized Arabia. Our results suggest that hamadryas baboons colonized Arabia during the Late Pleistocene (130-12 kya [thousands of years ago]) and also moved back to Africa. We reject the hypothesis that hamadryas baboons were introduced to Arabia by humans, because the initial colonization considerably predates the earliest records of human seafaring in this region. Our results strongly suggest that the southern route from Africa to Arabia could have been used by hamadryas baboons during the same time period as proposed for modern humans.


Mueller A.H.,Carlsberg Laboratory | Mueller A.H.,Stanford University | Dockter C.,Carlsberg Laboratory | Gough S.P.,Carlsberg Laboratory | And 3 more authors.
Plant and Cell Physiology | Year: 2012

The barley (Hordeum vulgare L.) mutants fch2 and clo-f2 comprise an allelic group of 14 Chl b-deficient lines. The genetic map position of fch2 corresponds to the physical map position of the gene encoding chlorophyllide a oxygenase. This enzyme converts chlorophyllide a to chlorophyllide b and it is essential for Chl b biosynthesis. The fch2 and clo-f2 barley lines were shown to be mutated in the gene for chlorophyllide a oxygenase. A five-base insertion was found in fch2 and base deletions in clo-f2.101, clo-f2.105, clo-f2.2800 and clo-f2.3613. In clo-f2.105 and clo-f2.108, nonsense base exchanges were discovered. All of these mutations led to a premature stop of translation and none of the mutants formed Chl b. The mutant clo-f2.2807 was transcript deficient and formed no Chl b. Missense mutations in clo-f2.102 (leading to the amino acid exchange D495N) and clo-f2.103 (G280D) resulted in a total lack of Chl b, whereas in the missense mutants clo-f2.107 (P419L), clo-f2.109 (A94T), clo-f2.122 (C320Y), clo-f2.123 (A94T), clo-f2.133 (A376V) and clo-f2.181 (L373F) intermediate contents of Chl b were determined. The missense mutations affect conserved residues, and their effect on chlorophyllide a oxygenase is discussed. The mutations in clo-f2.102, clo-f2.103, clo-f2.133 and clo-f2.181 may influence electron transfer as illustrated in the active site of a structural model protein. The changes in clo-f2.107, clo-f2.109, clo-f2.122 and clo-f2.123 may lead to Chlb deficiency by interfering with the regulation of chlorophyllide a oxygenase. The correlation of mutations and phenotypes strongly supports that the barley locus fch2 encodes chlorophyllide a oxygenase. © 2012 The Author.

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