The Experts below are selected from a list of 2442 Experts worldwide ranked by ideXlab platform
Alessandro Achilli - One of the best experts on this subject based on the ideXlab platform.
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mitochondrial genomes from modern and ancient turano mongolian Cattle reveal an ancient diversity of Taurine maternal lineages in east asia
Heredity, 2021Co-Authors: Xiaoting Xia, Johannes A. Lenstra, Alessandro Achilli, Bin Tong, Yongzhen Huang, Jianlin Han, Zhouyong Sun, Hong Chen, Chuzhao Lei, Ningbo ChenAbstract:Turano-Mongolian Cattle are a group of Taurine Cattle from Northern and Eastern Asia with distinct morphological traits, which are known for their ability to tolerate harsh environments, such as the Asian steppe and the Tibetan plateau. Through the analysis of 170 mitogenomes from ten modern breeds, two sub-lineages within T3 (T3119 and T3055) were identified as specific of Turano-Mongolian Cattle. These two T3 sub-lineages, together with the previously identified T4, were also present in six Neolithic samples, dated to ~3900 years BP, which might represent the earliest domestic Taurine stocks from Southwest Asia. The rare haplogroup Q, found in three Tibetan Cattle, testifies for the legacy of ancient migrations from Southwest Asia and suggests that the isolated Tibetan Plateau preserved unique prehistoric genetic resources. These findings confirm the geographic substructure of Turano-Mongolian Cattle breeds, which have been shaped by ancient migrations and geographic barriers.
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mitogenomes from egyptian Cattle breeds new clues on the origin of haplogroup q and the early spread of bos taurus from the near east
PLOS ONE, 2015Co-Authors: Anna Olivieri, Alessandro Achilli, Silvia Bonfiglio, Francesca Gandini, Alessandro Fichera, Ermanno Rizzi, Vincenza Battaglia, Stefania Brandini, Anna De Gaetano, Ahmed ElbeltagiAbstract:Background Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of Taurine Cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous Taurine breeds from the Nile Delta region might provide new insights on the early spread of Cattle rearing outside the Near East. Methodology Using Illumina high-throughput sequencing we characterized the mitogenomes from two Cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed. Conclusions Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African Cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.
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the enigmatic origin of bovine mtdna haplogroup r sporadic interbreeding or an independent event of bos primigenius domestication in italy
PLOS ONE, 2010Co-Authors: Silvia Bonfiglio, Alessandro Achilli, Anna Olivieri, Paolo Ajmonemarsan, Licia Colli, R Negrini, Luigi Liotta, Antonio Torroni, L FerrettiAbstract:Background When domestic Taurine Cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced Cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern Taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of Cattle domestication occurred. Methodology The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. These mtDNAs were then integrated in a phylogenetic tree encompassing all available P, Q and R complete mtDNA sequences. Conclusions Phylogenetic analyses of 28 mitochondrial genomes belonging to haplogroups P (N = 2), Q (N = 16) and R (N = 10) together with an extensive survey of all previously published mtDNA datasets revealed major similarities between haplogroups Q and T. Therefore, Q most likely represents an additional minor lineage domesticated in the Near East together with the founders of the T subhaplogroups. Whereas, haplogroup R is found, at least for the moment, only in Italy and nowhere else, either in modern or ancient samples, thus supporting an origin from European aurochsen. Haplogroup R could have been acquired through sporadic interbreeding of wild and domestic animals, but our data do not rule out the possibility of a local and secondary event of B. primigenius domestication in Italy.
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the multifaceted origin of Taurine Cattle reflected by the mitochondrial genome
PLOS ONE, 2009Co-Authors: Alessandro Achilli, Silvia Bonfiglio, Anna Olivieri, Arianna Malusa, Maria Pala, Baharak Hooshair Kashani, Ugo A Perego, Paolo AjmonemarsanAbstract:A Neolithic domestication of Taurine Cattle in the Fertile Crescent from local aurochsen (Bos primigenius) is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of Taurine Cattle mitochondrial DNA (mtDNA) control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3) of Near Eastern ancestry, but also identifying eight mtDNAs (1.3%) that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R) which, after the deep bifurcation that gave rise to the Taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare) Taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.
Daniel G Bradley - One of the best experts on this subject based on the ideXlab platform.
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genetic and expression analysis of Cattle identifies candidate genes in pathways responding to trypanosoma congolense infection
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Harry Noyes, Daniel G Bradley, Andy Brass, Isaiah Obara, Susan Anderson, Alan Archibald, Paul R Fisher, Abigail R Freeman, J P Gibson, Michael M GicheruAbstract:African bovine trypanosomiasis caused by Trypanosoma sp., is a major constraint on Cattle productivity in sub-Saharan Africa. Some African Bos taurus breeds are highly tolerant of infection, but the potentially more productive Bos indicus zebu breeds are much more susceptible. Zebu Cattle are well adapted for plowing and haulage, and increasing their tolerance of trypanosomiasis could have a major impact on crop cultivation as well as dairy and beef production. We used three strategies to obtain short lists of candidate genes within QTL that were previously shown to regulate response to infection. We analyzed the transcriptomes of trypanotolerant N'Dama and susceptible Boran Cattle after infection with Trypanosoma congolense. We sequenced EST libraries from these two breeds to identify polymorphisms that might underlie previously identified quantitative trait loci (QTL), and we assessed QTL regions and candidate loci for evidence of selective sweeps. The scan of the EST sequences identified a previously undescribed polymorphism in ARHGAP15 in the Bta2 trypanotolerance QTL. The polymorphism affects gene function in vitro and could contribute to the observed differences in expression of the MAPK pathway in vivo. The expression data showed that TLR and MAPK pathways responded to infection, and the former contained TICAM1, which is within a QTL on Bta7. Genetic analyses showed that selective sweeps had occurred at TICAM1 and ARHGAP15 loci in African Taurine Cattle, making them strong candidates for the genes underlying the QTL. Candidate QTL genes were identified in other QTL by their expression profile and the pathways in which they participate.
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maternal and paternal genealogy of eurasian Taurine Cattle bos taurus
Heredity, 2009Co-Authors: Juha Kantanen, Ruslan Popov, Zoya Ivanova, Ceiridwen J Edwards, Daniel G Bradley, H Viinalass, S Thessler, Tatyana Kiselyova, Mirjana Cinkulov, S StojanovicAbstract:Maternally inherited mitochondrial DNA (mtDNA) has been used extensively to determine origin and diversity of Taurine Cattle (Bos taurus) but global surveys of paternally inherited Y-chromosome diversity are lacking. Here, we provide mtDNA information on previously uncharacterised Eurasian breeds and present the most comprehensive Y-chromosomal microsatellite data on domestic Cattle to date. The mitochondrial haplogroup T3 was the most frequent, whereas T4 was detected only in the Yakutian Cattle from Siberia. The mtDNA data indicates that the Ukrainian and Central Asian regions are zones where hybrids between Taurine and zebu (B. indicus) Cattle have existed. This zebu influence appears to have subsequently spread into southern and southeastern European breeds. The most common Y-chromosomal microsatellite haplotype, termed here as H11, showed an elevated frequency in the Eurasian sample set compared with that detected in Near Eastern and Anatolian breeds. The Taurine Y-chromosomal microsatellite haplotypes were found to be structured in a network according to the Y-haplogroups Y1 and Y2. These data do not support the recent hypothesis on the origin of Y1 from the local European hybridization of Cattle with male aurochsen. Compared with mtDNA, the intensive culling of breeding males and male-mediated crossbreeding of locally raised native breeds has accelerated loss of Y-chromosomal variation in domestic Cattle, and affected the contribution of genetic drift to diversity. In conclusion, to maintain diversity, breeds showing rare Y-haplotypes should be prioritised in the conservation of Cattle genetic resources.
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independent mitochondrial origin and historical genetic differentiation in north eastern asian Cattle
Molecular Phylogenetics and Evolution, 2004Co-Authors: Hideyuki Mannen, Daniel G Bradley, M Kohno, Y Nagata, Soichi Tsuji, J S Yeo, D Nyamsamba, Y Zagdsuren, Michinari Yokohama, Koh NomuraAbstract:In order to clarify the origin and genetic diversity of Cattle in North Eastern Asia, this study examined mitochondrial displacement loop sequence variation and frequencies of Bos taurus and Bos indicus Y chromosome haplotypes in Japanese, Mongolian, and Korean native Cattle. In mitochondrial analyses, 20% of Mongolian Cattle carried B. indicus mitochondrial haplotypes, but Japanese and Korean Cattle carried only B. taurus haplotypes. In contrast, all samples revealed B. taurus Y chromosome haplotypes. This may be due to the import of zebu and other Cattle during the Mongol Empire era with subsequent crossing with native Taurine Cattle. B. taurus mtDNA sequences fall into several geographically distributed haplogroups and one of these, termed here T4, is described in each of the test samples, but has not been observed in Near Eastern, European or African Cattle. This may have been locally domesticated from an East Eurasian strain of Bos primigenius.
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microsatellite dna variation and the evolution domestication and phylogeography of Taurine and zebu Cattle bos taurus and bos indicus
Genetics, 1997Co-Authors: David E Machugh, Mark D Shriver, R T Loftus, Patrick Cunningham, Daniel G BradleyAbstract:Genetic variation at 20 microsatellite loci was surveyed to determine the evolutionary relationships and molecular biogeography of 20 different Cattle populations from Africa, Europe and Asia. Phylogenetic reconstruction and multivariate analysis highlighted a marked distinction between humpless (Taurine) and humped (zebu) Cattle, providing strong support for a separate origin for domesticated zebu Cattle. A molecular clock calculation using bison (Bison sp.) as an outgroup gave an estimated divergence time between the two subspecies of 610,000-850,000 years. Substantial differences in the distribution of alleles at 10 of these loci were observed between zebu and Taurine Cattle. These markers subsequently proved very useful for investigations of gene flow and admixture in African populations. When these data were considered in conjunction with previous mitochondrial and Y chromosomal studies, a distinctive male-mediated pattern of zebu genetic introgression was revealed. The introgression of zebu-specific alleles in African Cattle afforded a high resolution perspective on the hybrid nature of African Cattle populations and also suggested that certain West African populations of valuable disease-tolerant Taurine Cattle are under threat of genetic absorption by migrating zebu herds.
Anna Olivieri - One of the best experts on this subject based on the ideXlab platform.
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mitogenomes from egyptian Cattle breeds new clues on the origin of haplogroup q and the early spread of bos taurus from the near east
PLOS ONE, 2015Co-Authors: Anna Olivieri, Alessandro Achilli, Silvia Bonfiglio, Francesca Gandini, Alessandro Fichera, Ermanno Rizzi, Vincenza Battaglia, Stefania Brandini, Anna De Gaetano, Ahmed ElbeltagiAbstract:Background Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of Taurine Cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous Taurine breeds from the Nile Delta region might provide new insights on the early spread of Cattle rearing outside the Near East. Methodology Using Illumina high-throughput sequencing we characterized the mitogenomes from two Cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed. Conclusions Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African Cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.
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the enigmatic origin of bovine mtdna haplogroup r sporadic interbreeding or an independent event of bos primigenius domestication in italy
PLOS ONE, 2010Co-Authors: Silvia Bonfiglio, Alessandro Achilli, Anna Olivieri, Paolo Ajmonemarsan, Licia Colli, R Negrini, Luigi Liotta, Antonio Torroni, L FerrettiAbstract:Background When domestic Taurine Cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced Cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern Taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of Cattle domestication occurred. Methodology The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. These mtDNAs were then integrated in a phylogenetic tree encompassing all available P, Q and R complete mtDNA sequences. Conclusions Phylogenetic analyses of 28 mitochondrial genomes belonging to haplogroups P (N = 2), Q (N = 16) and R (N = 10) together with an extensive survey of all previously published mtDNA datasets revealed major similarities between haplogroups Q and T. Therefore, Q most likely represents an additional minor lineage domesticated in the Near East together with the founders of the T subhaplogroups. Whereas, haplogroup R is found, at least for the moment, only in Italy and nowhere else, either in modern or ancient samples, thus supporting an origin from European aurochsen. Haplogroup R could have been acquired through sporadic interbreeding of wild and domestic animals, but our data do not rule out the possibility of a local and secondary event of B. primigenius domestication in Italy.
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the multifaceted origin of Taurine Cattle reflected by the mitochondrial genome
PLOS ONE, 2009Co-Authors: Alessandro Achilli, Silvia Bonfiglio, Anna Olivieri, Arianna Malusa, Maria Pala, Baharak Hooshair Kashani, Ugo A Perego, Paolo AjmonemarsanAbstract:A Neolithic domestication of Taurine Cattle in the Fertile Crescent from local aurochsen (Bos primigenius) is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of Taurine Cattle mitochondrial DNA (mtDNA) control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3) of Near Eastern ancestry, but also identifying eight mtDNAs (1.3%) that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R) which, after the deep bifurcation that gave rise to the Taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare) Taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.
Silvia Bonfiglio - One of the best experts on this subject based on the ideXlab platform.
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mitogenomes from egyptian Cattle breeds new clues on the origin of haplogroup q and the early spread of bos taurus from the near east
PLOS ONE, 2015Co-Authors: Anna Olivieri, Alessandro Achilli, Silvia Bonfiglio, Francesca Gandini, Alessandro Fichera, Ermanno Rizzi, Vincenza Battaglia, Stefania Brandini, Anna De Gaetano, Ahmed ElbeltagiAbstract:Background Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of Taurine Cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous Taurine breeds from the Nile Delta region might provide new insights on the early spread of Cattle rearing outside the Near East. Methodology Using Illumina high-throughput sequencing we characterized the mitogenomes from two Cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed. Conclusions Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African Cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.
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the enigmatic origin of bovine mtdna haplogroup r sporadic interbreeding or an independent event of bos primigenius domestication in italy
PLOS ONE, 2010Co-Authors: Silvia Bonfiglio, Alessandro Achilli, Anna Olivieri, Paolo Ajmonemarsan, Licia Colli, R Negrini, Luigi Liotta, Antonio Torroni, L FerrettiAbstract:Background When domestic Taurine Cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced Cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern Taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of Cattle domestication occurred. Methodology The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. These mtDNAs were then integrated in a phylogenetic tree encompassing all available P, Q and R complete mtDNA sequences. Conclusions Phylogenetic analyses of 28 mitochondrial genomes belonging to haplogroups P (N = 2), Q (N = 16) and R (N = 10) together with an extensive survey of all previously published mtDNA datasets revealed major similarities between haplogroups Q and T. Therefore, Q most likely represents an additional minor lineage domesticated in the Near East together with the founders of the T subhaplogroups. Whereas, haplogroup R is found, at least for the moment, only in Italy and nowhere else, either in modern or ancient samples, thus supporting an origin from European aurochsen. Haplogroup R could have been acquired through sporadic interbreeding of wild and domestic animals, but our data do not rule out the possibility of a local and secondary event of B. primigenius domestication in Italy.
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the multifaceted origin of Taurine Cattle reflected by the mitochondrial genome
PLOS ONE, 2009Co-Authors: Alessandro Achilli, Silvia Bonfiglio, Anna Olivieri, Arianna Malusa, Maria Pala, Baharak Hooshair Kashani, Ugo A Perego, Paolo AjmonemarsanAbstract:A Neolithic domestication of Taurine Cattle in the Fertile Crescent from local aurochsen (Bos primigenius) is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of Taurine Cattle mitochondrial DNA (mtDNA) control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3) of Near Eastern ancestry, but also identifying eight mtDNAs (1.3%) that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R) which, after the deep bifurcation that gave rise to the Taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare) Taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.
Juha Kantanen - One of the best experts on this subject based on the ideXlab platform.
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Table_1_Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions.DOCX
2019Co-Authors: Melak Weldenegodguad, Ruslan Popov, Kisun Pokharel, Innokentyi Ammosov, Yao Ming, Zoya Ivanova, Juha KantanenAbstract:Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where Cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern FinnCattle, Western FinnCattle and Yakutian Cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian Taurine Cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian Cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European Taurine breeds. This result is in contrast to the results of marker-based Cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic Taurine Cattle may have been higher than that of the European Cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian Cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on Cattle genomes and on the value of the adapted breeds for the conservation of Cattle genetic resources.
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Data_Sheet_1_Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions.ZIP
2019Co-Authors: Melak Weldenegodguad, Ruslan Popov, Kisun Pokharel, Innokentyi Ammosov, Yao Ming, Zoya Ivanova, Juha KantanenAbstract:Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where Cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern FinnCattle, Western FinnCattle and Yakutian Cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian Taurine Cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian Cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European Taurine breeds. This result is in contrast to the results of marker-based Cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic Taurine Cattle may have been higher than that of the European Cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian Cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on Cattle genomes and on the value of the adapted breeds for the conservation of Cattle genetic resources.
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Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions
Frontiers Media S.A., 2019Co-Authors: Melak Weldenegodguad, Ruslan Popov, Kisun Pokharel, Innokentyi Ammosov, Yao Ming, Zoya Ivanova, Juha KantanenAbstract:Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where Cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern FinnCattle, Western FinnCattle and Yakutian Cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian Taurine Cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian Cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European Taurine breeds. This result is in contrast to the results of marker-based Cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic Taurine Cattle may have been higher than that of the European Cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian Cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on Cattle genomes and on the value of the adapted breeds for the conservation of Cattle genetic resources
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whole genome sequencing of three native Cattle breeds originating from the northernmost Cattle farming regions
bioRxiv, 2018Co-Authors: Melak Weldenegodguad, Ruslan Popov, Kisun Pokharel, Innokentyi Ammosov, Yao Ming, Zoya Ivanova, Juha KantanenAbstract:Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where Cattle farming has been traditionally practiced. In this study, we performed whole-genome resequencing to genetically characterize three rare native breeds namely, Eastern FinnCattle, Western FinnCattle and Yakutian Cattle, adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian Taurine Cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian Cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European Taurine breeds. This result is in contrast to the results of marker-based Cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic Taurine Cattle may have been higher than that of the European Cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian Cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on Cattle genomes and on the value of the adapted breeds for the conservation of Cattle genetic resources.
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maternal and paternal genealogy of eurasian Taurine Cattle bos taurus
Heredity, 2009Co-Authors: Juha Kantanen, Ruslan Popov, Zoya Ivanova, Ceiridwen J Edwards, Daniel G Bradley, H Viinalass, S Thessler, Tatyana Kiselyova, Mirjana Cinkulov, S StojanovicAbstract:Maternally inherited mitochondrial DNA (mtDNA) has been used extensively to determine origin and diversity of Taurine Cattle (Bos taurus) but global surveys of paternally inherited Y-chromosome diversity are lacking. Here, we provide mtDNA information on previously uncharacterised Eurasian breeds and present the most comprehensive Y-chromosomal microsatellite data on domestic Cattle to date. The mitochondrial haplogroup T3 was the most frequent, whereas T4 was detected only in the Yakutian Cattle from Siberia. The mtDNA data indicates that the Ukrainian and Central Asian regions are zones where hybrids between Taurine and zebu (B. indicus) Cattle have existed. This zebu influence appears to have subsequently spread into southern and southeastern European breeds. The most common Y-chromosomal microsatellite haplotype, termed here as H11, showed an elevated frequency in the Eurasian sample set compared with that detected in Near Eastern and Anatolian breeds. The Taurine Y-chromosomal microsatellite haplotypes were found to be structured in a network according to the Y-haplogroups Y1 and Y2. These data do not support the recent hypothesis on the origin of Y1 from the local European hybridization of Cattle with male aurochsen. Compared with mtDNA, the intensive culling of breeding males and male-mediated crossbreeding of locally raised native breeds has accelerated loss of Y-chromosomal variation in domestic Cattle, and affected the contribution of genetic drift to diversity. In conclusion, to maintain diversity, breeds showing rare Y-haplotypes should be prioritised in the conservation of Cattle genetic resources.
