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Hubert Leveziel - One of the best experts on this subject based on the ideXlab platform.
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Pheomelanin coat colour dilution in French Cattle Breeds is not correlated with the TYR, TYRP1 and DCT transcription levels.
Pigment Cell Research, 2004Co-Authors: Sylvain Guibert, Hubert Leveziel, Raymond Julien, Michael Girardot, Ahmad OulmoudenAbstract:In this study we report the isolation of full-length cDNAs and the expression patterns of TYR, TYRP1 and DCT in four e/e Cattle Breeds exhibiting different pheomelanic coat colours ranging from reddish brown to creamy white phenotypes. Predicted proteins encoded by bovine TYR, TYRP1 and DCT display high levels of homology and contain all characteristic domains shared between their mouse and human counterparts. The full expression of these three genes is observed in melanocytes of black areas of E D /E D Prim'Holstein's animals. On the other hand, e/e melanocytes of animals belonging to the Blonde d'Aquitaine (blond), Limousine (red) and Salers (reddish brown) Breeds present different levels of down-regulated TYR and DCT expression and a complete repression of TYRP1. Surprisingly, e/e melanocytes of animals belonging to the Charolais breed (creamy white) present an inverse relationship between TYR, TYRPI and DCT expression and its lower melanogenic activity. The sum of these results shows that the dilution of the coat colour in French Cattle Breeds is not correlated with a transcription level of TYR family genes. Other possible modifier loci are suggested.
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detection of genes influencing economic traits in three french dairy Cattle Breeds
Genetics Selection Evolution, 2003Co-Authors: Didier Boichard, Yves Amigues, Cecile Grohs, F Bourgeois, Frederique Cerqueira, Remi Faugeras, Andre Neau, Rachel Rupp, Marieyvonne Boscher, Hubert LevezielAbstract:A project of QTL detection was carried out in the French Holstein, Normande, and Montbeliarde dairy Cattle Breeds. This granddaughter design included 1 548 artificial insemination bulls distributed in 14 sire families and evaluated after a progeny-test for 24 traits (production, milk composition, persistency, type, fertility, mastitis resistance, and milking ease). These bulls were also genotyped for 169 genetic markers, mostly microsatellites. The QTL were analysed by within-sire linear regression of daughter yield deviations or deregressed proofs on the probability that the son receives one or the other paternal QTL allele, given the marker information. QTL were detected for all traits, including those with a low heritability. One hundred and twenty QTL with a chromosome-wise significance lower than 3% were tabulated. This threshold corresponded to a 15% false discovery rate. Amongst them, 32 were genome-wise significant. Estimates of their contribution to genetic variance ranged from 6 to 40%. Most substitution effects ranged from 0.6 to 1.0 genetic standard deviation. For a given QTL, only 1 to 5 families out of 14 were informative. The confidence intervals of the QTL locations were large and always greater than 20 cM. This experiment confirmed several already published QTL but most of them were original, particularly for non-production traits.
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a first genotyping assay of french Cattle Breeds based on a new allele of the extension gene encoding the melanocortin 1 receptor mc1r
Genetics Selection Evolution, 2000Co-Authors: Francois Rouzaud, Juliette Martin, Paul Francois Gallet, Didier Delourme, Valerie Goulemotleger, Yves Amigues, François Ménissier, Hubert Leveziel, Raymond JulienAbstract:The seven transmembrane domain melanocortin-1 receptor (Mc1r) encoded by the coat color extension gene (E) plays a key role in the signaling pathway of melanin synthesis. Upon the binding of agonist (melanocortin hormone, α-MSH) or antagonist (Agouti protein) ligands, the melanosomal synthesis of eumelanin and/or phaeomelanin pigments is stimulated or inhibited, respectively. Different alleles of the extension gene were cloned from unrelated animals belonging to French Cattle Breeds and sequenced. The wild type E allele was mainly present in Normande Cattle, the dominant ED allele in animals with black color (i.e. Holstein), whereas the recessive e allele was identified in homozygous animals exhibiting a more or less strong red coat color (Blonde d'Aquitaine, Charolaise, Limousine and Salers). A new allele, named E1, was found in either homozygous (E1/E1) or heterozygous (E1/E) individuals in Aubrac and Gasconne Breeds. This allele displayed a 4 amino acid duplication (12 nucleotides) located within the third cytoplasmic loop of the receptor, a region known to interact with G proteins. A first genotyping assay of the main French Cattle Breeds is described based on these four extension alleles.
Roberta Ciampolini - One of the best experts on this subject based on the ideXlab platform.
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A genomic map of climate adaptation in Mediterranean Cattle Breeds
Molecular Ecology, 2019Co-Authors: Laurence Flori, Sara Casu, Roberta Ciampolini, Katayoun Moazami-goudarzi, Véronique Alary, Abdelillah Araba, Ismaïl Boujenane, Nadjet Boushaba, François Casabianca, Armelle Coeur D'acierAbstract:Domestic species such as Cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous Cattle Breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate sub-types. This provided insights into both the demographic and adaptive histories of Mediterranean Cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g. NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting Cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied, on standing genomic variation of taurine origin or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean Cattle Breeds and strongly support conservation of these populations
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BOVITA: a first overview on genomewide genetic diversity of Italian autochthonous Cattle Breeds
'Informa UK Limited', 2017Co-Authors: Salvatore Mastrangelo, Alessandro Bagnato, Luca Battaglini, Riccardo Bozzi, Antonello Carta, Gennaro Catillo, Martino Cassandro, Sara Casu, Paolo Ajmone-marsan, Roberta CiampoliniAbstract:Analysis of genomic data is increasingly becoming part of the livestock industry and is an invaluable resource for effective management of breeding programs in small populations. The recent availability of genome-wide SNP panels allows providing background information concerning genome structure in domestic animals, opening new perspectives to livestock genetics. BOVITA was established to join local efforts and resources for the genomic characterization of Italian local Cattle Breeds. Despite the growing diffusion of some cosmopolite specialized Breeds, several autochthonous Breeds are still bred in Italy. The main aim of the BOVITA is to investigate the genomic structure of Italian local Cattle Breeds, to provide information on their genetic status that will be useful for the management of the genetic variability, as a contribution to biodiversity conservation and prioritization actions. A total of about 800 animals (20-32 per breed) belonging to thirty Italian Cattle Breeds (Agerolese, Bara-Pustertaler, Burlina, Cabannina, Calvana, Chianina, Cinisara, Garfagnina, Italian Brown, Italian Holstein, Italian Simmental, Marchigiana, Maremmana, Modenese, Modicana, Mucca Pisana, Pezzata Rossa d’Oropa, Piedmontese, Pinzgau, Podolica, Pontremolese, Pustertaler, Reggiana, Rendena, Romagnola, Rossa Siciliana, Sarda, Sardo-Bruna, SardoModicana and Ottonese-Varzese) and two cosmopolitan Breeds (Charolaise and Limousine) genotyped with the Illumina BovineSNP50 v2 BeadChip array were collected for the analysis. The genotypes of several Breeds were detected in the frame of the project, whereas for some Breeds these data are derived by previous studies. The dataset will be analyzed to: study several aspects of population genetic diversity, multidimensional scaling plot, population structure, linkage disequilibrium, and runs of homozygosity. In addition, comparative analysis of conserved haplotypes will be conducted to identify genomic segments under selection pressure. Such information also provides important insights into the mechanisms of evolution and is useful for the annotation of significant functional genomics regions. Data analysis will also be useful to select SNPs suitable for parentage test and breed genetic traceability. The analysis of the data will pinpoint the genetic distinctiveness of Italian Breeds. Moreover, the obtained results contribute to a better characterization of history and genetic structure of Italian Cattle Breeds
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BOVITA: a first overview on genome-wide genetic diversity of Italian autochthonous Cattle Breeds
Taylor & Francis, 2017Co-Authors: S. Mastrangelo, Alessandro Bagnato, Luca Battaglini, Riccardo Bozzi, Gennaro Catillo, Martino Cassandro, P. Ajmone-marsan, A. Carta, S. Casu, Roberta CiampoliniAbstract:Analysis of genomic data is increasingly becoming part of the livestock industry and is an invaluable resource for effective management of breeding programs in small populations. The recent availability of genome-wide SNP panels allows providing background information concerning genome structure in domestic animals, opening new perspectives to livestock genetics. BOVITA was established to join local efforts and resources for the genomic characterization of Italian local Cattle Breeds. Despite the growing diffusion of some cosmopolite specialized Breeds, several autochthonous Breeds are still bred in Italy. The main aim of the BOVITA is to investigate the genomic structure of Italian local Cattle Breeds, to provide information on their genetic status that will be useful for the management of the genetic variability, as a contribution to biodiversity conservation and prioritization actions. A total of about 800 animals (20-32 per breed) belonging to thirty Italian Cattle Breeds (Agerolese, Bara-Pustertaler, Burlina, Cabannina, Calvana, Chianina, Cinisara, Garfagnina, Italian Brown, Italian Holstein, Italian Simmental, Marchigiana, Maremmana, Modenese, Modicana, Mucca Pisana, Pezzata Rossa d\u2019Oropa, Piedmontese, Pinzgau, Podolica, Pontremolese, Pustertaler, Reggiana, Rendena, Romagnola, Rossa Siciliana, Sarda, Sardo-Bruna, SardoModicana and Ottonese-Varzese) and two cosmopolitan Breeds (Charolaise and Limousine) genotyped with the Illumina BovineSNP50 v2 BeadChip array were collected for the analysis. The genotypes of several Breeds were detected in the frame of the project, whereas for some Breeds these data are derived by previous studies. The dataset will be analyzed to: study several aspects of population genetic diversity, multidimensional scaling plot, population structure, linkage disequilibrium, and runs of homozygosity. In addition, comparative analysis of conserved haplotypes will be conducted to identify genomic segments under selection pressure. Such information also provides important insights into the mechanisms of evolution and is useful for the annotation of significant functional genomics regions. Data analysis will also be useful to select SNPs suitable for parentage test and breed genetic traceability. The analysis of the data will pinpoint the genetic distinctiveness of Italian Breeds. Moreover, the obtained results contribute to a better characterization of history and genetic structure of Italian Cattle Breeds
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statistical analysis of individual assignment tests among four Cattle Breeds using fifteen str loci
Journal of Animal Science, 2006Co-Authors: Roberta Ciampolini, Elena Ciani, V Cetica, E Mazzanti, Xenia Fosella, Fabio Marroni, M Biagetti, C Sebastiani, P Papa, G FilippiniAbstract:Assignment tests based on multilocus genotypes are becoming increasingly important to cer- tify quality and origin of livestock products and assure food safety and authenticity. The purpose of this study was to determine the potential of microsatellites (STR) for determining the breed origin of beef products among Cattle Breeds present in the market. We typed 19 STR in 269 animals from 4 Cattle Breeds. Based on Wright's F-statistics, 4 loci were discarded, and the remaining 15 loci (FIT = 0.101, FST = 0.089, and FIS = 0.013) were used to compute the likelihood that each multilocus genotype of the total sample was drawn from its true breed instead of another breed. To avoid occurrence of zero likelihood when one or more alleles were missing from a tested breed, sample allele frequencies were esti-
Ivica Medugorac - One of the best experts on this subject based on the ideXlab platform.
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Summary statistics—neutral genetic diversity of 15 Cattle Breeds.
2015Co-Authors: Mojca Simčič, Johann Sölkner, Anamarija Smetko, Doris Seichter, Gregor Gorjanc, Dragomir Kompan, Ivica MedugoracAbstract:The sample size (N), total number of observed alleles (nA), mean number of alleles per haplotype block (mA = nA/ 4817), number of private alleles (npA), number of rare alleles defined as alleles observed in only two subpopulations (nrA), average observed heterozygosity (HO), HO estimated from SNP genotypes (HO[SNP]), average expected heterozygosity (HE) and allelic richness (AR[21]). RHF, Red Holstein; FGV, Franken Gelbvieh; DFV, German Fleckvieh; MWF, Murnau—Werdenfelser; BBV, Braunvieh; OBV, Original Braunvieh; API, Pinzgauer; SIC, Cika; HRI, Istrian Cattle; HRP, Slavonian—Syrmian Podolic; PMT, Piedmontese; RMG—Romagnola; HRB, Croatian Buša; IMB, Illyrian Mountain Buša; NDA, N’Dama.Summary statistics—neutral genetic diversity of 15 Cattle Breeds.
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a genome wide scan for signatures of differential artificial selection in ten Cattle Breeds
BMC Genomics, 2013Co-Authors: Sophie Rothammer, Doris Seichter, M Forster, Ivica MedugoracAbstract:Background Since the times of domestication, Cattle have been continually shaped by the influence of humans. Relatively recent history, including breed formation and the still enduring enormous improvement of economically important traits, is expected to have left distinctive footprints of selection within the genome. The purpose of this study was to map genome-wide selection signatures in ten Cattle Breeds and thus improve the understanding of the genome response to strong artificial selection and support the identification of the underlying genetic variants of favoured phenotypes. We analysed 47,651 single nucleotide polymorphisms (SNP) using Cross Population Extended Haplotype Homozygosity (XP-EHH).
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conservation priorities of genetic diversity in domesticated metapopulations a study in taurine Cattle Breeds
Ecology and Evolution, 2011Co-Authors: Ivica Medugorac, Claudia E Veitkensch, Jelena Ramljak, Muhamed Brka, Božidarka Markovic, Srđan Stojanovic, Hysen Bytyqi, Ljupche Kochoski, Kristaq Kume, Hanspeter GrunenfelderAbstract:We estimated neutral diversity of 21 European Cattle Breeds with 105 microsatellites. Nine of them resembled unselected Balkan Busa strains with diffuse breeding barriers and the 12 others were strongly differentiated, isolated Breeds. Because of the impact of neutral genetic diversity on long-term population adaptive capacity, we discuss the long-term outcome of different conservation priorities in a subdivided metapopulation of the investigated Cattle Breeds. The optimal contribution to a pool of total genetic diversity allocated more than 95% of long-term relevant neutral diversity to virtually unselected strains of the Balkan Busa, while the maximization of total variance preferred inbred Breeds. Current artificial selection methods, such as genomic selection sped up and a recovery of underestimated traits becomes quickly impossible. We emphasize that currently neutral and even deleterious alleles might be required for future genotypes in sustainable and efficient livestock breeding and production systems of a 21st century. We provide cumulative evidences that long-term survival relies on genetic complexity and complexity relies on allelic diversity. Our results suggest that virtually unselected, nonuniform strains harbor a crucial proportion of neutral diversity and should be conserved with high global priority. As one example, we suggest a cooperative maintenance of the nondifferentiated, highly fragmented, and fast vanishing metapopulation of Balkan Busa.
Yves Amigues - One of the best experts on this subject based on the ideXlab platform.
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detection of genes influencing economic traits in three french dairy Cattle Breeds
Genetics Selection Evolution, 2003Co-Authors: Didier Boichard, Yves Amigues, Cecile Grohs, F Bourgeois, Frederique Cerqueira, Remi Faugeras, Andre Neau, Rachel Rupp, Marieyvonne Boscher, Hubert LevezielAbstract:A project of QTL detection was carried out in the French Holstein, Normande, and Montbeliarde dairy Cattle Breeds. This granddaughter design included 1 548 artificial insemination bulls distributed in 14 sire families and evaluated after a progeny-test for 24 traits (production, milk composition, persistency, type, fertility, mastitis resistance, and milking ease). These bulls were also genotyped for 169 genetic markers, mostly microsatellites. The QTL were analysed by within-sire linear regression of daughter yield deviations or deregressed proofs on the probability that the son receives one or the other paternal QTL allele, given the marker information. QTL were detected for all traits, including those with a low heritability. One hundred and twenty QTL with a chromosome-wise significance lower than 3% were tabulated. This threshold corresponded to a 15% false discovery rate. Amongst them, 32 were genome-wise significant. Estimates of their contribution to genetic variance ranged from 6 to 40%. Most substitution effects ranged from 0.6 to 1.0 genetic standard deviation. For a given QTL, only 1 to 5 families out of 14 were informative. The confidence intervals of the QTL locations were large and always greater than 20 cM. This experiment confirmed several already published QTL but most of them were original, particularly for non-production traits.
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a first genotyping assay of french Cattle Breeds based on a new allele of the extension gene encoding the melanocortin 1 receptor mc1r
Genetics Selection Evolution, 2000Co-Authors: Francois Rouzaud, Juliette Martin, Paul Francois Gallet, Didier Delourme, Valerie Goulemotleger, Yves Amigues, François Ménissier, Hubert Leveziel, Raymond JulienAbstract:The seven transmembrane domain melanocortin-1 receptor (Mc1r) encoded by the coat color extension gene (E) plays a key role in the signaling pathway of melanin synthesis. Upon the binding of agonist (melanocortin hormone, α-MSH) or antagonist (Agouti protein) ligands, the melanosomal synthesis of eumelanin and/or phaeomelanin pigments is stimulated or inhibited, respectively. Different alleles of the extension gene were cloned from unrelated animals belonging to French Cattle Breeds and sequenced. The wild type E allele was mainly present in Normande Cattle, the dominant ED allele in animals with black color (i.e. Holstein), whereas the recessive e allele was identified in homozygous animals exhibiting a more or less strong red coat color (Blonde d'Aquitaine, Charolaise, Limousine and Salers). A new allele, named E1, was found in either homozygous (E1/E1) or heterozygous (E1/E) individuals in Aubrac and Gasconne Breeds. This allele displayed a 4 amino acid duplication (12 nucleotides) located within the third cytoplasmic loop of the receptor, a region known to interact with G proteins. A first genotyping assay of the main French Cattle Breeds is described based on these four extension alleles.
Gabriele Marras - One of the best experts on this subject based on the ideXlab platform.
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analysis of runs of homozygosity and their relationship with inbreeding in five Cattle Breeds farmed in italy
Animal Genetics, 2015Co-Authors: Silvia Sorbolini, Giustino Gaspa, Corrado Dimauro, Gabriele Marras, Alessio Valentini, Paolo Ajmonemarsan, J L Williams, Nicolo Pietro Paolo MacciottaAbstract:Increased inbreeding is an inevitable consequence of selection in livestock populations. The analysis of high-density single nucleotide polymorphisms (SNPs) facilitates the identification of long and uninterrupted runs of homozygosity (ROH) that can be used to identify chromosomal regions that are identical by descent. In this work, the distribution of ROH of different lengths in five Italian Cattle Breeds is described. A total of 4095 bulls from five Cattle Breeds (2093 Italian Holstein, 749 Italian Brown, 364 Piedmontese, 410 Marchigiana and 479 Italian Simmental) were genotyped at 54K SNP loci. ROH were identified and used to estimate molecular inbreeding coefficients (FROH ), which were compared with inbreeding coefficients estimated from pedigree information (FPED ) and using the genomic relationship matrix (FGRM ). The average number of ROH per animal ranged from 54 ± 7.2 in Piedmontese to 94.6 ± 11.6 in Italian Brown. The highest number of short ROH (related to ancient consanguinity) was found in Piedmontese, followed by Simmental. The Italian Brown and Holstein had a higher proportion of longer ROH distributed across the whole genome, revealing recent inbreeding. The FPED were moderately correlated with FROH > 1 Mb (0.662, 0.700 and 0.669 in Italian Brown, Italian Holstein and Italian Simmental respectively) but poorly correlated with FGRM (0.134, 0.128 and 0.448 for Italian Brown, Italian Holstein and Italian Simmental respectively). The inclusion of ROH > 8 Mb in the inbreeding calculation improved the correlation of FROH with FPED and FGRM . ROH are a direct measure of autozygosity at the DNA level and can overcome approximations and errors resulting from incomplete pedigree data. In populations with high linkage disequilibrium (LD) and recent inbreeding (e.g. Italian Holstein and Italian Brown), a medium-density marker panel, such as the one used here, may provide a good estimate of inbreeding. However, in populations with low LD and ancient inbreeding, marker density would have to be increased to identify short ROH that are identical by descent more precisely.
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Use of locally weighted scatterplot smoothing (LOWESS) regression to study selection signatures in Piedmontese and Italian Brown Cattle Breeds.
Animal genetics, 2013Co-Authors: Elia Pintus, Silvia Sorbolini, A. Albera, Giustino Gaspa, Corrado Dimauro, Roberto Steri, Gabriele Marras, Nicolò Pietro Paolo MacciottaAbstract:Summary Selection is the major force affecting local levels of genetic variation in species. The availability of dense marker maps offers new opportunities for a detailed understanding of genetic diversity distribution across the animal genome. Over the last 50 years, Cattle Breeds have been subjected to intense artificial selection. Consequently, regions controlling traits of economic importance are expected to exhibit selection signatures. The fixation index (Fst) is an estimate of population differentiation, based on genetic polymorphism data, and it is calculated using the relationship between inbreeding and heterozygosity. In the present study, locally weighted scatterplot smoothing (LOWESS) regression and a control chart approach were used to investigate selection signatures in two Cattle Breeds with different production aptitudes (dairy and beef). Fst was calculated for 42 514 SNP marker loci distributed across the genome in 749 Italian Brown and 364 Piedmontese bulls. The statistical significance of Fst values was assessed using a control chart. The LOWESS technique was efficient in removing noise from the raw data and was able to highlight selection signatures in chromosomes known to harbour genes affecting dairy and beef traits. Examples include the peaks detected for BTA2 in the region where the myostatin gene is located and for BTA6 in the region harbouring the ABCG2 locus. Moreover, several loci not previously reported in Cattle studies were detected.