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4 results on '"Faculty of Life Sciences, Division of Genetics and Bioinformatics"'

1. Analyses of pig genomes provide insight to porcine demography and evolution

Author

Ronan Kapetanovic, Patrice Dehais, Zhi-Qiang Du, Loretta Auvil, Ricardo H. Ramirez-Gonzalez, Kyung-Tai Lee, Patrick Chardon, Hiroyuki Kanamori, Gary A. Rohrer, Jianguo Zhang, Celine Chen, Simon D. M. White, Guojie Zhang, Jian Wang, Hyeonju Ahn, Ole Madsen, Miguel Pérez-Enciso, Richard Clark, Bruce R. Southey, Yasuhiro Takeuchi, Bronwen Aken, Bo Thomsen, Frank Panitz, Katie E. Fowler, Peter F. Stadler, Jennifer Harrow, Takeya Morozumi, Ryan Cheng, Christian Bendixen, Laurent A. F. Frantz, Yogesh Paudel, Sara Botti, Kellye Eversole, Jaebum Kim, Jian Ma, Matthew Jones, Jan Gorodkin, Zhi-Liang Hu, John C. Schwartz, Suneel Kumar Onteru, Tae-Hun Kim, Fioravante De Sapio, Nizar Drou, Stephen M. J. Searle, Wan Sheng Liu, Yingrui Li, Yao Lu, Thomas Faraut, Richard P. M. A. Crooijmans, Joan K. Lunney, Göran O. Sperber, Bert Dibbits, Denis Milan, Richard M. Leggett, Boris Capitanu, Xun Xu, Bertrand Servin, Megan Bystrom, Carol Scott, Kyle M. Schachtschneider, Bouabid Badaoui, Harris A. Lewin, Mirte Bosse, Sang-Haeng Choi, Yongming Sang, Jane Rogers, Patric Jern, Kerstin Howe, Sean Humphray, Henrik Hornshøj, Martien A. M. Groenen, Jerzy Jurka, James M. Reecy, Frank Blecha, Darren K. Griffin, Susan Fairley, Jonas Blomberg, Claire Rogel-Gaillard, Eung-Woo Park, Jonathan V. Sweedler, Hong-Seog Park, Stuart McLaren, Denise Carvalho-Silva, Christopher K. Tuggle, Géraldine Pascal, Rashmi Wali, Mario Caccamo, Katherine M. Mann, Lawrence B. Schook, C M Clee, James G. R. Gilbert, Christian Anthon, Merete Fredholm, Chankyu Park, Harry D. Dawson, Craig W. Beattie, Elisabetta Giuffra, Zhan Bujie, Kyu-Won Kim, Toby Hunt, Jae-Hwan Kim, Daniel Berman, Shuhong Zhao, Hakim Tafer, Jin-Tae Jeon, Sandra L. Rodriguez-Zas, Hendrik-Jan Megens, Linda Scobie, Jie Zhang, Alan Archibald, Joshua G. Schraiber, Jitendra Narayan, Alexander Hayward, Lucy Matthews, Lauretta A. Rund, Jane E. Loveland, Peixiang Ni, Denis M. Larkin, Song-Jung Oh, Dinh Truong Nguyen, Kyooyeol Lee, Lars Bolund, João Fadista, William Chow, Jun Wang, Hirohide Uenishi, Shengting Li, Eric Fritz, Heebal Kim, Geoffrey J. Faulkner, Martine Yerle, Michael P. Murtaugh, Max F. Rothschild, Carol Churcher, Greger Larson, Anna Anselmo, Laboratoire de radiobiologie et d'étude du génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), The Genome Analysis Centre (TGAC), Parco Tecnologico Padano, CERSA, Department of Clinical Genetics, Odense University Hospital, The Wellcome Trust Sanger Institute [Cambridge], Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de la Recherche Agronomique (INRA), Faculty of Life Sciences, Division of Genetics and Bioinformatics, Faculty of Life Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory [Hong Kong], The University of Hong Kong (HKU), Beijing Genomics Institute [Shenzhen] (BGI), Department of Biochemistry, University of Nijmegen, The Netherlands, University of Nijmegen, Molecular Carcinogenesis [Sutton], Institute of cancer research, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Tours (UT), Canadian Light Source Inc., University of Saskatchewan [Saskatoon] (U of S), Department of Mechanical Engineering, University of Auckland, University of Auckland [Auckland], ANR-07-GANI-0001,DELISUS,An integrated study of the haplotypic variability at the whole genome level on animals finely phenotyped from French porcine populations(2007), European Project: LSHB-CT-2006-037377, European Project: 249894,EC:FP7:ERC,ERC-2009-AdG,SELSWEEP(2010), European Project: 38710,SABRE, European Project: 222664,EC:FP7:KBBE,FP7-KBBE-2007-2A,QUANTOMICS(2009), European Commission, European Research Council, Biotechnology and Biological Sciences Research Council (UK), Wellcome Trust, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Université de Tours, Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Sainsbury Laboratory Cambridge, Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
pig, Evolution, receptor, Molecular Sequence Data, Population Dynamics, Sus scrofa, sus-scrofa, Locus (genetics), Genomics, Biology, Animal Breeding and Genomics, Genome, Article, genomic, taste, 03 medical and health sciences, Phylogenetics, evolution, Genetics, Animals, animal, Fokkerij en Genomica, Domestication, gene, Gene, Phylogeny, Demography, 030304 developmental biology, 0303 health sciences, locus, variants, Multidisciplinary, Phylogenetic tree, [SDV.BA]Life Sciences [q-bio]/Animal biology, 0402 animal and dairy science, 04 agricultural and veterinary sciences, sequence, 040201 dairy & animal science, Models, Animal, WIAS, genetic, Selective sweep, complex
Abstract

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model., The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 249894 (SelSweep)

Published
2012
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2. LUPA: a European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs

Author

Michel Georges, Christophe Hitte, Anne-Sophie Lequarré, Merete Fredholm, Tosso Leeb, Catherine André, Hannes Lohi, Leif Andersson, Kerstin Lindblad-Toh, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-Research), Université de Liège, Science for Life Laboratory, Uppsala University-Department of Medical Biochemistry and Microbiology, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Faculty of Life Sciences, Division of Genetics and Bioinformatics, Faculty of Life Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Institute of Genetics, Vetsuisse Faculty-University of Bern, Folkhälsan Institute of Genetics, HMNC Brain Health-Department of Veterinary Biosciences-Program in Molecular Medicine-Biomedicum Helsinki, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], European Project: 201370,EC:FP7:HEALTH,FP7-HEALTH-2007-A,LUPA(2008), Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), De Villemeur, Hervé, Unravelling the molecular basis of common complex human disorders using the dog as a model system - LUPA - - EC:FP7:HEALTH2008-01-01 - 2012-06-30 - 201370 - VALID, Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)

Subjects
International Cooperation, ved/biology.organism_classification_rank.species, [SDV.GEN] Life Sciences [q-bio]/Genetics, Disease, Canine, 0403 veterinary science, MESH: Dogs, Human health, Single nucleotide polymorphism arrays, MESH: Animals, Dog Diseases, Genetics, 0303 health sciences, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, MESH: Polymorphism, Single Nucleotide, MESH: DNA, Chromosome Mapping, 04 agricultural and veterinary sciences, Pedigree, Europe, LUPA, Canine genome, 040301 veterinary sciences, MESH: Pedigree, MESH: Dog Diseases, High density, Single-nucleotide polymorphism, Computational biology, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Dogs, Animals, Humans, SNP, Inherited disorders, Model organism, 030304 developmental biology, Genetic association, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, General Veterinary, ved/biology, DNA, Disease Models, Animal, MESH: International Cooperation, MESH: Genome-Wide Association Study, Animal Science and Zoology, MESH: Europe, MESH: Disease Models, Animal, MESH: Chromosome Mapping, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Genome-Wide Association Study
Abstract

International audience; The domestic dog offers a unique opportunity to explore the genetic basis of disease, morphology and behaviour. Humans share many diseases with our canine companions, making dogs an ideal model organism for comparative disease genetics. Using newly developed resources, genome-wide association studies in dog breeds are proving to be exceptionally powerful. Towards this aim, veterinarians and geneticists from 12 European countries are collaborating to collect and analyse the DNA from large cohorts of dogs suffering from a range of carefully defined diseases of relevance to human health. This project, named LUPA, has already delivered considerable results. The consortium has collaborated to develop a new high density single nucleotide polymorphism (SNP) array. Mutations for four monogenic diseases have been identified and the information has been utilised to find mutations in human patients. Several complex diseases have been mapped and fine mapping is underway. These findings should ultimately lead to a better understanding of the molecular mechanisms underlying complex diseases in both humans and their best friend.

Published
2011
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3. Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping

Author

Vaysse, A., Ratnakumar, A., Derrien, T., Axelsson, E., Rosengren Pielberg, G., Sigurdsson, S., Fall, T., Seppälä, E.H., Hansen, M.S., Lawley, C.T., Karlsson, E.K., Bannasch, D.L., Vilà, C., Lohi, H., Galibert, F., Fredholm, M., Häggström, O., Hedhammar, A., André, C., Lindblad-Toh, K., Hitte, C., van Steenbeek, F.G., Fieten, H., Leegwater, P.A.J., LUPA Consortium, x, Webster, M.T., Advances in Veterinary Medicine, Tissue Repair, Geneeskunde van gezelschapsdieren, Research Programs Unit, Department of Medical and Clinical Genetics, Research Programme of Molecular Medicine, Veterinary Biosciences, Departments of Faculty of Veterinary Medicine, Broad Institute of MIT and Harvard, Sigurdsson, Snaever, Sigurdsson, Snaevar, Karlsson, Elinor K., Lindblad-Toh, Kerstin, Webster, Matthew T., Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Science for Life Laboratory, Uppsala University-Department of Medical Biochemistry and Microbiology, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet [Stockholm], Department of Basic Veterinary Biosciences, HMNC Brain Health-Biomedicum Helsinki-Folkhälsan Institute of Genetics, Illumina, Inc., FAS Center for Systems Biology, Harvard University [Cambridge], Department of Population Health and Reproduction, University of California [Davis] (UC Davis), University of California-University of California, Department of Integrative Ecology (CSIC), Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Faculty of Life Sciences, Division of Genetics and Bioinformatics, Faculty of Life Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Swedish University of Agricultural Sciences (SLU), This research was mainly supported by The LUPA Consortium, which is a Collaborative Research Project funded by the European Commission under the 7th Research Framework Programme (www.eurolupa.org)., The LUPA Consortium, European Project: 201370,EC:FP7:HEALTH,FP7-HEALTH-2007-A,LUPA(2008), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Harvard University, University of California (UC)-University of California (UC), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), De Villemeur, Hervé, and Unravelling the molecular basis of common complex human disorders using the dog as a model system - LUPA - - EC:FP7:HEALTH2008-01-01 - 2012-06-30 - 201370 - VALID

Subjects
POSITIVE SELECTION, Genotyping Techniques, Genome-wide association study, Breeding, 413 Veterinary science, MESH: Dogs, 0302 clinical medicine, MESH: Behavior, Animal, MESH: Animals, Genome Sequencing, MESH: Genetic Variation, mapping, MESH: Phylogeny, Genome Evolution, Phylogeny, 0303 health sciences, education.field_of_study, Behavior, Animal, MESH: Polymorphism, Single Nucleotide, 1184 Genetics, developmental biology, physiology, Genomics, Genome Scans, selection, dog, identification, genomic, Fixation (population genetics), COAT COLOR, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], PERSONALITY-TRAITS, Gene Flow, Genetics and Breeding, education, Single-nucleotide polymorphism, MESH: Breeding, MESH: Phenotype, 03 medical and health sciences, CANIS-FAMILIARIS, Effective Population Size, MESH: Genotyping Techniques, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genome-Wide Association Studies, Genetics, Genetik, Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genetic Drift, MESH: Ear, Computational Biology, Genetic Variation, MESH: Haplotypes, Phenotypic trait, HAPLOTYPE STRUCTURE, variation phénotypique, Mutation, MESH: Genome-Wide Association Study, marqueur de sélection, Population Genetics, 030217 neurology & neurosurgery, Evolutionary Genetics, Cancer Research, cartographie génomique, LINKAGE DISEQUILIBRIUM, MESH: Selection, Genetic, [SDV.GEN] Life Sciences [q-bio]/Genetics, Natural Selection, Body Size, WIDE ASSOCIATION, Genetics (clinical), DOMESTIC DOG, MESH: Heterozygote, Gene Ontologies, Homozygote, race canine, 402 Animal and Dairy Science, Ear, Gene Pool, Phenotype, Research Article, MESH: Homozygote, Heterozygote, 403 Veterinary Science, lcsh:QH426-470, Population, Polymorphism, Single Nucleotide, Dogs, Genetic drift, Genome Analysis Tools, DNA-SEQUENCE, Evolutionary Modeling, Genetic variation, Animals, Selection, Genetic, Selection (genetic algorithm), 030304 developmental biology, Evolutionary Biology, MESH: Body Size, Genetic Maps, Comparative Genomics, GENE, lcsh:Genetics, Haplotypes, Neutral Theory, Genetic Polymorphism, Animal Genetics, Genome-Wide Association Study
Abstract

The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of .170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.

Published
2011
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4. Investigation of tissue-specific human orthologous alternative splice events in pig.

Author

Nygard AB, Jørgensen CB, Cirera S, and Fredholm M

Subjects
Animals, Computer Simulation, Expressed Sequence Tags, Humans, Organ Specificity, Polymerase Chain Reaction, Protein Isoforms biosynthesis, Reproducibility of Results, Sequence Analysis, DNA, Species Specificity, Alternative Splicing, Protein Isoforms genetics, Swine genetics
Abstract

Alternative splicing of pre-mRNA can contribute to differences between tissues or cells either by regulating gene expression or creating proteins with various functions encoded by one gene. The number of investigated alternative splice events in pig has so far been limited. In this study we have investigated alternative splice events detected in humans, in orthologous pig genes. A total of 17 genes with predicted exon skipping events were selected for further studies. The splice events for the selected genes were experimentally verified using real-time quantitative PCR analysis (qPCR) with splice-specific primers in 19 different tissues. The same splice variants as reported in humans were detected in 15 orthologous pig genes, however, the expression pattern predicted in the in silico analyses was only experimentally verified in a few cases. The results support the findings that splice events resulting in preservation of open reading frame are indicative of a functional significance of the splice variants of the gene.

Published
2010
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