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Stojak J, Rocha D, Mörke C, Kühn C, Blanquet V, Taniguchi H. Establishment of a cloning-free CRISPR/Cas9 protocol to generate large deletions in the bovine MDBK cell line. J Appl Genet 2024; 65:399-402. [PMID: 38418802 PMCID: PMC11003909 DOI: 10.1007/s13353-024-00846-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/11/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
The CRISPR/Cas9 technique applied to modify the cattle genome has value in increasing animal health and welfare. Here, we established a simple, fast, and efficient cloning-free CRISPR/Cas9 protocol for large deletions of genomic loci in the frequently used model bovine MDBK cell line. The main advantages of our protocol are as follows: (i) pre-screening of the sgRNA efficiency with a fast and simple cleavage assay, (ii) reliable detection of genomic edits primarily by PCR and confirmed by DNA sequencing, and (iii) single cell sorting with FACS providing specific genetic information from modified cells of interest. Therefore, our method could be successfully applied in different studies, including functional validation of any genetic or regulatory elements.
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Affiliation(s)
- Joanna Stojak
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, Poland.
| | - Dominique Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Caroline Mörke
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Christa Kühn
- Research Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
- Agricultural and Environmental Faculty, University Rostock, 18059, Rostock, Germany
- Friedrich-Loeffler-Institut (FLI), 17493, Greifswald, Insel Riems, Germany
| | - Veronique Blanquet
- Faculté Des Sciences Et Techniques, University of Limoges, 123 Avenue Albert Thomas, 87060, Limoges, France
| | - Hiroaki Taniguchi
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, Poland.
- African Genome Center, University Mohammed VI Polytechnic (UM6P), Lot 660, Hay Moulay Rachid, 43150, Ben Guerir, Morocco.
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2
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Teng J, Gao Y, Yin H, Bai Z, Liu S, Zeng H, Bai L, Cai Z, Zhao B, Li X, Xu Z, Lin Q, Pan Z, Yang W, Yu X, Guan D, Hou Y, Keel BN, Rohrer GA, Lindholm-Perry AK, Oliver WT, Ballester M, Crespo-Piazuelo D, Quintanilla R, Canela-Xandri O, Rawlik K, Xia C, Yao Y, Zhao Q, Yao W, Yang L, Li H, Zhang H, Liao W, Chen T, Karlskov-Mortensen P, Fredholm M, Amills M, Clop A, Giuffra E, Wu J, Cai X, Diao S, Pan X, Wei C, Li J, Cheng H, Wang S, Su G, Sahana G, Lund MS, Dekkers JCM, Kramer L, Tuggle CK, Corbett R, Groenen MAM, Madsen O, Gòdia M, Rocha D, Charles M, Li CJ, Pausch H, Hu X, Frantz L, Luo Y, Lin L, Zhou Z, Zhang Z, Chen Z, Cui L, Xiang R, Shen X, Li P, Huang R, Tang G, Li M, Zhao Y, Yi G, Tang Z, Jiang J, Zhao F, Yuan X, Liu X, Chen Y, Xu X, Zhao S, Zhao P, Haley C, Zhou H, Wang Q, Pan Y, Ding X, Ma L, Li J, Navarro P, Zhang Q, Li B, Tenesa A, Li K, Liu GE, Zhang Z, Fang L. A compendium of genetic regulatory effects across pig tissues. Nat Genet 2024; 56:112-123. [PMID: 38177344 PMCID: PMC10786720 DOI: 10.1038/s41588-023-01585-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 10/13/2023] [Indexed: 01/06/2024]
Abstract
The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biological discovery and exploitation in animal breeding and human biomedicine. Here we show results from the pilot phase of PigGTEx by processing 5,457 RNA-sequencing and 1,602 whole-genome sequencing samples passing quality control from pigs. We build a pig genotype imputation panel and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We evaluate tissue specificity of regulatory effects and elucidate molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying 207 pig complex phenotypes and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, supporting the importance of pigs as a human biomedical model.
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Affiliation(s)
- Jinyan Teng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Yahui Gao
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Hongwei Yin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhonghao Bai
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Haonan Zeng
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Lijing Bai
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Bingru Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiujin Li
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Zhiting Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Qing Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis, CA, USA
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenjing Yang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Xiaoshan Yu
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Dailu Guan
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Brittney N Keel
- ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Gary A Rohrer
- ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | - William T Oliver
- ARS, USDA, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Maria Ballester
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Daniel Crespo-Piazuelo
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Programme, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Oriol Canela-Xandri
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- Baillie Gifford Pandemic Science Hub, University of Edinburgh, Edinburgh, UK
| | - Charley Xia
- Lothian Birth Cohort studies, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Yuelin Yao
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- School of Informatics, The University of Edinburgh, Edinburgh, UK
| | - Qianyi Zhao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wenye Yao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Liu Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Houcheng Li
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Huicong Zhang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Wang Liao
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Tianshuo Chen
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Peter Karlskov-Mortensen
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Merete Fredholm
- Animal Genetics, Bioinformatics and Breeding, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alex Clop
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Elisabetta Giuffra
- Paris-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Jun Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Xiaodian Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Shuqi Diao
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Xiangchun Pan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Chen Wei
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Jinghui Li
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Hao Cheng
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Ryan Corbett
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marta Gòdia
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Dominique Rocha
- Paris-Saclay University, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Mathieu Charles
- Paris-Saclay University, INRAE, AgroParisTech, GABI, SIGENAE, Jouy-en-Josas, France
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich, Switzerland
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Research, Qingdao, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Zhongyin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zhe Zhang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Zitao Chen
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Leilei Cui
- School of Life Sciences, Nanchang University, Nanchang, China
- Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Jiangxi, China
- UCL Genetics Institute, University College London, London, UK
| | - Ruidong Xiang
- Faculty of Veterinary and Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - Xia Shen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine, Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yunxiang Zhao
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jicai Jiang
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Fuping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolong Yuan
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Chris Haley
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Qishan Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yuchun Pan
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xiangdong Ding
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Jiaqi Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China
| | - Pau Navarro
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Qin Zhang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Bingjie Li
- Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
| | - Albert Tenesa
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Beltsville, MD, USA.
| | - Zhe Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University (SCAU), Guangzhou, China.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.
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3
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Gaiani N, Bourgeois-Brunel L, Rocha D, Boulling A. Analysis of the impact of DGAT1 p.M435L and p.K232A variants on pre-mRNA splicing in a full-length gene assay. Sci Rep 2023; 13:8999. [PMID: 37268760 DOI: 10.1038/s41598-023-36142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023] Open
Abstract
DGAT1 is playing a major role in fat metabolism and triacylglyceride synthesis. Only two DGAT1 loss-of-function variants altering milk production traits in cattle have been reported to date, namely p.M435L and p.K232A. The p.M435L variant is a rare alteration and has been associated with skipping of exon 16 which results in a non-functional truncated protein, and the p.K232A-containing haplotype has been associated with modifications of the splicing rate of several DGAT1 introns. In particular, the direct causality of the p.K232A variant in decreasing the splicing rate of the intron 7 junction was validated using a minigene assay in MAC-T cells. As both these DGAT1 variants were shown to be spliceogenic, we developed a full-length gene assay (FLGA) to re-analyse p.M435L and p.K232A variants in HEK293T and MAC-T cells. Qualitative RT-PCR analysis of cells transfected with the full-length DGAT1 expression construct carrying the p.M435L variant highlighted complete skipping of exon 16. The same analysis performed using the construct carrying the p.K232A variant showed moderate differences compared to the wild-type construct, suggesting a possible effect of this variant on the splicing of intron 7. Finally, quantitative RT-PCR analyses of cells transfected with the p.K232A-carrying construct did not show any significant modification on the splicing rate of introns 1, 2 and 7. In conclusion, the DGAT1 FLGA confirmed the p.M435L impact previously observed in vivo, but invalidated the hypothesis whereby the p.K232A variant strongly decreased the splicing rate of intron 7.
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Affiliation(s)
- Nicolas Gaiani
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Dominique Rocha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Arnaud Boulling
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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4
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Sousa D, Afonso M, Rocha D, Craveiro A, Martins S, Barata J, Valente M. EP08.02-036 Selpercatinib Striking Response in a Case of Cerebral and Auditory Canal Metastasis of RET Fusion-Positive Non-Small-Cell Lung Cancer. J Thorac Oncol 2022. [DOI: 10.1016/j.jtho.2022.07.718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Liu S, Gao Y, Canela-Xandri O, Wang S, Yu Y, Cai W, Li B, Xiang R, Chamberlain AJ, Pairo-Castineira E, D'Mellow K, Rawlik K, Xia C, Yao Y, Navarro P, Rocha D, Li X, Yan Z, Li C, Rosen BD, Van Tassell CP, Vanraden PM, Zhang S, Ma L, Cole JB, Liu GE, Tenesa A, Fang L. A multi-tissue atlas of regulatory variants in cattle. Nat Genet 2022; 54:1438-1447. [PMID: 35953587 PMCID: PMC7613894 DOI: 10.1038/s41588-022-01153-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/07/2022] [Indexed: 12/12/2022]
Abstract
Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of the Farm animal GTEx (FarmGTEx) project for the research community based on 7,180 publicly available RNA-sequencing (RNA-seq) samples. We describe the transcriptomic landscape of more than 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.
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Affiliation(s)
- Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.,National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,School of Life Sciences, Westlake University, Hangzhou, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - Oriol Canela-Xandri
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ying Yu
- National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Bingjie Li
- Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, UK
| | - Ruidong Xiang
- Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, Victoria, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Victoria, Australia
| | - Erola Pairo-Castineira
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK.,The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Kenton D'Mellow
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Charley Xia
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Yuelin Yao
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Pau Navarro
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Dominique Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, France
| | - Xiujin Li
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Ze Yan
- National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congjun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Paul M Vanraden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Shengli Zhang
- National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA.
| | - Albert Tenesa
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK. .,The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
| | - Lingzhao Fang
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA. .,MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK. .,Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
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6
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Lopes-Rocha L, Rocha D, Pinho T. A Multidisciplinary Approach to Maxillary Lateral Incisor Agenesis (MLIA): A Case Report. Oper Dent 2022; 47:367b-374. [PMID: 36001812 DOI: 10.2341/21-069-s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2021] [Indexed: 11/23/2022]
Abstract
Maxillary lateral incisor agenesis (MLIA) is a condition that significantly compromises smile esthetics and is a particular concern in younger patients. The treatment options include orthodontics for space opening with rehabilitation or space closure with canine camouflage. Currently, there is some controversy regarding the most appropriate treatment. In this case report, we propose a multidisciplinary approach through the combination of orthodontic treatment, frenectomy, and a restorative finishing stage with composite resin and dental implants. More specifically, this treatment was planned to orthodontically close the anterior space by opening the premolar area for subsequent placement of implants and enameloplasty with a composite resin. The replacement of a missing lateral incisor by an implant is a predictable treatment approach, but it might best be deferred until dental maturity and then accurately placed in a well-developed site through a multidisciplinary approach. Precluding the closure of the anterior spaces and the opening of the posterior zone for implant placement, allows for a more stable and appealing esthetic and functional rehabilitation for young patients, in whom esthetic appearance and self-esteem play a primary role.
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Affiliation(s)
- L Lopes-Rocha
- Lígia Lopes-Rocha, DDS, UNIPRO, Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, Gandra Campus, Paredes, Portugal
| | - D Rocha
- Duarte Rocha, DDS, UNIPRO, Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, Gandra Campus, Paredes, Portugal
| | - T Pinho
- *Teresa Pinho, DDS, PhD, UNIPRO, Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, Gandra Campus, Paredes, Portugal. IBMC - Institute of Molecular and Cellular Biology, i3S - Institute of Innovation and Research in Health, Oporto University, Portugal
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7
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Mazzon E, Delfino C, Mirelis S, Arévalo M, Rojas D, Lara L, Carcamo D, Jurado F, Rocha D, Venturelli PM, Mansilla E. Breaking Down Barriers: Easter Island's First Telestroke Thrombolysis Experience and Case Report. J Stroke Cerebrovasc Dis 2022; 31:106412. [PMID: 35354109 DOI: 10.1016/j.jstrokecerebrovasdis.2022.106412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/19/2022] Open
Abstract
Easter Island (Rapa Nui), Chile, is remote, located in the Polynesian Triangle in Oceania. The closest continental point is Chile, 3,512 km east. It has a population of 7,750 inhabitants, who are Chilean citizens, and receives more than 60,000 tourists a year. For this entire population, there is a medium complexity hospital without a neurology specialist. In 2019, local professionals were trained in a Telestroke program with remote clinical support conducted by neurologists located on mainland Chile. We present a 50-year-old native male, with unknown medical history, who suddenly presented right-half-body weakness and aphasia. He was evaluated via Telestroke consultation, and thrombolysis with tenecteplase was indicated. The patient improved rapidly and 45 min later the NIHSS score was 0 points. To our knowledge, this is the first reported case of Telestroke treatment in such a remote area, highlighting the importance of telemedicine to overcome geographical and technological stroke care barriers and to improve patients' outcome, no matter where they live.
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Affiliation(s)
- E Mazzon
- Servicio de Salud Metropolitano Sur, Unidad de TeleACV, Santiago De Chile, Chile; Clínica Alemana, Unidad de Tratamiento del Ataque Cerebrovascular (UTAC), Universidad del Desarrollo, Santiago De Chile, Chile; Centro de Estudios Clínicos, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Chile.
| | - C Delfino
- Centro de Estudios Clínicos, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Chile
| | - S Mirelis
- Hospital San Martín de Quillota, Unidad de Emergencias, Quillota, Chile
| | - M Arévalo
- Servicio de Salud Metropolitano Sur, Unidad de TeleACV, Santiago De Chile, Chile
| | - D Rojas
- Servicio de Salud Metropolitano Sur, Unidad de TeleACV, Santiago De Chile, Chile
| | - L Lara
- Servicio de Salud Metropolitano Sur, Unidad de TeleACV, Santiago De Chile, Chile
| | - D Carcamo
- Servicio de Salud Metropolitano Sur, Unidad de TeleACV, Santiago De Chile, Chile; Clínica Alemana, Unidad de Tratamiento del Ataque Cerebrovascular (UTAC), Universidad del Desarrollo, Santiago De Chile, Chile
| | - F Jurado
- Servicio de Salud Metropolitano Sur, Unidad de TeleACV, Santiago De Chile, Chile; Facultad de Medicina, Universidad de Chile, Chile
| | - D Rocha
- Servicio de Salud Metropolitano Sur, Unidad de TeleACV, Santiago De Chile, Chile
| | - P Muñoz Venturelli
- Clínica Alemana, Unidad de Tratamiento del Ataque Cerebrovascular (UTAC), Universidad del Desarrollo, Santiago De Chile, Chile; Centro de Estudios Clínicos, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Chile; The George Institute for Global Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - E Mansilla
- Servicio de Salud Metropolitano Sur, Unidad de TeleACV, Santiago De Chile, Chile; Facultad de Medicina, Universidad de Chile, Chile
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8
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Oliveira A, Rocha D, De Martin A, Limoeiro A, Nascimento W, Fontana C, Pelegrine R, Martinez E, Bueno C. Evaluation of antimicrobial activity against Enterococcus faecalis of activated chelating agents in different final rinse protocols: An ex vivo study. J Clin Exp Dent 2022; 14:e646-e651. [PMID: 36046170 PMCID: PMC9422971 DOI: 10.4317/jced.59547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
Background To evaluate the antimicrobial activity of the following chelating agents against Enterococcus faecalis using quantitative polymerase chain reaction (qPCR) analysis: 1% peracetic acid (PA), 1% peracetic acid with 0.1% cetrimide (PAC), and 17% ethylenediaminetetraacetic acid (EDTA) activated by passive ultrasonic irrigation (PUI) or with Easy Clean (EC), all followed by 2.5% sodium hypochlorite (NaOCl).
Material and Methods A total of 80 permanent human mandibular premolars were randomly divided into eight experimental groups according to the chemical solution and agitation protocol used: Group PA + PUI; Group PA + EC; Group PAC + PUI; PAC + EC; group EDTA + PUI; EDTA + EC, all followed by 2.5% NaOCl; and two control groups with saline solution(NaCl): NaCl + PUI and NaCl + EC. Microbial samples were collected before (S1) and after the irrigation protocol (S2). Intracanal E. faecalis reduction analysis was performed by qPCR. Intragroup analysis was performed using the Wilcoxon signed-rank test for paired data, and intergroup analysis was performed using the Wilcoxon Mann-Whitney U test for independent samples. The significance level was set at p< 0.05.
Results A significant difference was found between S1 and S2 in all groups except NaCl+ EC (p = 0.1602). Comparison between groups showed that PAC + PUI was significantly different from PA +EC (p = 0.0448).
Conclusions The activated chelating agents were effective against E. faecalis, with significant results compared to the control groups. The peracetic acid with cetrimide activated by PUI showed better results than peracetic acid with EC. Key words:Easy clean, Final irrigation protocols, Passive ultrasonic irrigation, Peracetic acid.
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9
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El Hou A, Rocha D, Venot E, Blanquet V, Philippe R. Long-range linkage disequilibrium in French beef cattle breeds. Genet Sel Evol 2021; 53:63. [PMID: 34301193 PMCID: PMC8306006 DOI: 10.1186/s12711-021-00657-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The advent of new genotyping technologies has allowed whole-genome LD studies in most cattle populations. However, to date, long-range LD (LRLD) between distant variants on the genome has not been investigated in detail in cattle. Here, we present the first comprehensive study of LRLD in French beef cattle by analysing data on 672 Charolais (CHA), 462 Limousine (LIM) and 326 Blonde d'Aquitaine (BLA) individuals that were genotyped on the Illumina BovineHD Beadchip. Furthermore, whole-genome LD and haplotype block structure were analysed in these three breeds. RESULTS We computed linkage disequilibrium (r2) values for 5.9, 5.6 and 6.0 billion pairs of SNPs on the 29 autosomes of CHA, LIM and BLA, respectively. Mean r2 values drop to less than 0.1 for distances between SNPs greater than 120 kb. However, for the first time, we detected the existence of LRLD in the three main French beef breeds. In total, 598, 266, and 795 LRLD events (r2 ≥ 0.6) were detected in CHA, LIM and BLA, respectively. Each breed had predominantly population-specific LRLD interactions, although shared LRLD events occurred in a number of regions (55 LRLD events were shared between two breeds and nine between the three breeds). Examples of possible functional gene interactions and QTL co-location were observed with some of these LRLD events, which suggests epistatic selection. CONCLUSIONS We identified long-range linkage disequilibrium for the first time in French beef cattle populations. Epistatic selection may be the main source of the observed LRLD events, but other forces may also be involved. LRLD information should be accounted for in genome-wide association studies.
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Affiliation(s)
- Abdelmajid El Hou
- INRAE, PEIRENE EA7500, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France
| | - Dominique Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Eric Venot
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Véronique Blanquet
- INRAE, PEIRENE EA7500, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France
| | - Romain Philippe
- INRAE, PEIRENE EA7500, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France.
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10
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Féménia M, Charles M, Boulling A, Rocha D. Identification and characterisation of mitochondrial sequences integrated into the ovine nuclear genome. Anim Genet 2021; 52:556-559. [PMID: 34060107 DOI: 10.1111/age.13096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2021] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA sequences are frequently transferred into the nuclear genome, generating nuclear mitochondrial DNA sequences (NUMTs). Here, we analysed, for the first time, NUMTs in the ovine genome. We obtained 760 alignment matches covering 513.8 kbp of the sheep nuclear genome. After a merging step, we identified 390 NUMT regions with a total length of ~720 kbp, representing 0.02% of the nuclear genome. We discovered copies of all mitochondrial regions and found that most NUMT regions are intergenic or intronic. Ovine NUMTs are mostly not transcribed. However, we identified within some of the NUMTs, potential new genes encoding nuclear humanin isoforms. To rule out the possibility that the identified NUMTs could be artifacts of the Oar Rambouillet v1.0 genome assembly, we validated experimentally nine NUMT regions by PCR amplification. As we found several NUMT regions showing high similarity to the mitochondrial genome that potentially could pose a risk to ovine DNA mitochondrial studies, special care must be taken for the selection of primers for PCR amplification of mitochondrial DNA sequences.
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Affiliation(s)
- M Féménia
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France
| | - M Charles
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France.,SIGENAE, INRAE, Jouy-en-Josas, F-78350, France
| | - A Boulling
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France
| | - D Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France
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11
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Vinet A, Bouyer C, Forestier L, Oulmouden A, Blanquet V, Picard B, Cassar-Malek I, Bonnet M, Rocha D, Renand G. The Blonde d'Aquitaine T3811>G3811 mutation in the myostatin gene: association with growth, carcass, and muscle phenotypes in veal calves. J Anim Sci 2021; 99:6129922. [PMID: 33624102 DOI: 10.1093/jas/skab039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/02/2021] [Indexed: 11/12/2022] Open
Abstract
The mutation T3811 → G3811 (TG3811) discovered in the myostatin gene of the Blonde d'Aquitaine breed is suspected of contributing to the outstanding muscularity of this breed. An experiment was designed to estimate the effect of this mutation in an F2 and back-cross Blonde d'Aquitaine × Holstein population. By genotyping all known mutations in the myostatin gene, it was ensured that the TG3811 mutation was indeed the only known mutation segregating in this population. Fifty-six calves (43 F2, 13 back-cross) were intensively fattened and slaughtered at 24.0 ± 1.4 wk of age. The effects of the mutation were estimated by comparing the calves with the [T/T] (n = 18), [T/G] (n = 30), and [G/G] (n = 8) genotypes. Highly significant substitution effects (P < 0.001), above + 1.2 phenotypic SD, were shown on carcass yield and muscularity scores. Birth weight (P < 0.001) was positively affected by the mutation (+0.8 SD) but not growth rate (P = 0.97), while carcass length (P = 0.03), and fatness (P ≤ 0.03) were negatively affected (-0.5 to -0.7 SD). The characteristics of the Triceps brachii muscle were affected by the mutation (P < 0.001), with lower ICDH activity (oxidative) and a higher proportion of myosin type 2X muscle fibers (fast twitch). The effects of the TG3811 mutation were similar to those of other known myostatin mutations, although the Blonde d'Aquitaine animals, which are predominantly [G/G] homozygous, do not exhibit extreme double muscling.
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Affiliation(s)
- Aurélie Vinet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Claire Bouyer
- INRAE, Université de Limoges, UMR Génomique Animale, Amélioration, Adaptation, Limoges, France
| | - Lionel Forestier
- INRAE, Université de Limoges, UMR Génomique Animale, Amélioration, Adaptation, Limoges, France
| | - Ahmad Oulmouden
- INRAE, Université de Limoges, UMR Génomique Animale, Amélioration, Adaptation, Limoges, France
| | - Véronique Blanquet
- INRAE, Université de Limoges, UMR Génomique Animale, Amélioration, Adaptation, Limoges, France
| | - Brigitte Picard
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Isabelle Cassar-Malek
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Muriel Bonnet
- INRAE, Université Clermont Auvergne, Vetagro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Dominique Rocha
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Gilles Renand
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
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12
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Ramírez-Ayala LC, Rocha D, Ramos-Onsins SE, Leno-Colorado J, Charles M, Bouchez O, Rodríguez-Valera Y, Pérez-Enciso M, Ramayo-Caldas Y. Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions. Genet Sel Evol 2021; 53:3. [PMID: 33397281 PMCID: PMC7784321 DOI: 10.1186/s12711-020-00597-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/11/2020] [Indexed: 02/01/2023] Open
Abstract
Background In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine cattle have difficulty coping with. Results In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 whole-genome sequences from six additional taurine, indicus and crossed breeds to estimate the genetic diversity, structure and accurate ancestral origin of the CHCU animals. Although CHCU animals are assumed to form a closed population, the results of our admixture analysis indicate a limited introgression of Bos indicus. We used the extended haplotype homozygosity (EHH) approach to identify regions in the genome that may have had an important role in the adaptation of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of Bos indicus, but they were not sufficient to explain adaptation of CHCU to tropical conditions by Bos indicus introgression only. EHH suggested signals of potential adaptation in genomic windows that include genes of taurine origin involved in thermogenesis (ATP9A, GABBR1, PGR, PTPN1 and UCP1) and hair development (CCHCR1 and CDSN). Within these genes, we identified single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute to some of the observed phenotypic differences between CHCU and CHFR animals. Conclusions Whole-genome data confirm that CHCU cattle are closely related to Charolais from France (CHFR) and Canada, but also reveal a limited introgression of Bos indicus genes in CHCU. We observed possible signals of recent adaptation to tropical conditions between CHCU and CHFR founder populations, which were largely independent of the Bos indicus introgression. Finally, we report candidate genes and variants that may have a functional impact and explain some of the phenotypic differences observed between CHCU and CHFR cattle.
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Affiliation(s)
- Lino C Ramírez-Ayala
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Dominique Rocha
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France
| | - Sebas E Ramos-Onsins
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Jordi Leno-Colorado
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain
| | - Mathieu Charles
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France.,INRAE, SIGENAE, Jouy-En-Josas, 78350, France
| | - Olivier Bouchez
- INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, US, 1426, France
| | | | - Miguel Pérez-Enciso
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Spain.,Institut Català de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Université Paris-Saclay, INRAE, Jouy-En-Josas, AgroParisTech, GABI, 78350, France. .,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes De Montbui, 08140, Spain.
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13
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Rodríguez-Valera Y, Rocha D, Naves M, Renand G, Pérez-Pineda E, Ramayo-Caldas Y, Ramos-Onsins SE. The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the "Charolais de Cuba" Cattle. Animals (Basel) 2020; 10:ani10122233. [PMID: 33261195 PMCID: PMC7760288 DOI: 10.3390/ani10122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The Charolais de Cuba cattle is a tropical adapted breed founded in Cuba around 120 years ago from Charolais French specimens. Nowadays, it is still a closed breed and remains as a small population. In this work, we analyzed the inbreeding and diversity patterns, as well as the population size, of this recent adapted breed via a run of homozygosity (ROH) analysis. We found that the genomic inbreeding levels are higher in the Charolais de Cuba breed compared to French and British Charolais populations. Nevertheless, we detected that the effective population size experienced a very similar decline during the last century in the three Charolais populations studied. Finally, a number of regions with exceptional patterns of long homozygosity were identified in this breed, and these could be related to processes of adaptation to tropical conditions. Abstract Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.
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Affiliation(s)
- Yoel Rodríguez-Valera
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Dominique Rocha
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Michel Naves
- INRAE, URZ, 97170 Petit Bourg, Guadeloupe, France;
| | - Gilles Renand
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
| | - Eliecer Pérez-Pineda
- Faculty of Agricultural Sciences, University of Granma, Bayamo 95100, Cuba; (Y.R.-V.); (E.P.-P.)
| | - Yuliaxis Ramayo-Caldas
- GABI, INRAE, AgroParisTech, University Paris-Saclay, F-78350 Jouy-en-Josas, France; (D.R.); (G.R.)
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
| | - Sebastian E. Ramos-Onsins
- Plant and Animal Genomics, Centre of Research in Agricultural Genomics (CRAG) Consortium CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Spain
- Correspondence: (Y.R.-C.); (S.E.R.-O.)
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14
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Mazzon E, Rocha D, Brunser AM, De la Barra C, Stecher X, Bernstein T, Zúñiga P, Díaz V, Martínez G, Muñoz Venturelli P. Cervical Artery Dissections with and without stroke, risk factors and prognosis: a Chilean prospective cohort. J Stroke Cerebrovasc Dis 2020; 29:104992. [PMID: 32689597 DOI: 10.1016/j.jstrokecerebrovasdis.2020.104992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/16/2022] Open
Abstract
We aimed to characterize spontaneous cervical artery dissection (CeAD) patients with and without stroke and describe risk factors for cerebrovascular complications in a Chilean prospective cohort. METHODS Consecutive CeAD patients admitted to a Chilean center confirmed by neuroimaging. Logistic regression was used. RESULTS 168 patients were included, median follow-up time was 157 days. Stroke occurred in 49 (29.2%) cases, 4 (2%) patients died, all of whom had a stroke, and 10 (6%) presented CeAD recurrence. In univariate analyses, men (odds ratio [OR] 3.97, 95% confidence interval [CI] 1.97-8.00, P < 0.001), internal carotid artery CeAD (OR 2.82, 95% CI 1.38-5.78, P = 0.005) and vessel occlusion (OR 4.45, 95% CI 1.38-14.38, P = 0.035) increased stroke risk. Conversely, vertebral artery dissection (OR 0.35, 95% CI 0.16-0.74, P = 0.006) and longer symptom onset to admission (O-A) time (OR 0.79, 95% CI 0.70-0.90, P < 0.001) were associated to decreased stroke risk. After multivariate analysis, men (OR 2.88, 95% CI 1.32-6.27, P = 0.008) and O-A time (OR 0.80, 95% CI 0.69-0.92, P = 0.002) remained independently associated with stroke. CONCLUSION CeAD presented commonly as a non-stroke entity, with favorable prognosis. Albeit to a higher frequency of CeAD in women, stroke occurred predominantly in men, who were admitted earlier.
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Affiliation(s)
- E Mazzon
- Servicio de Neurología, Departmento de Neurología y Psiquiatría, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - D Rocha
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - A M Brunser
- Servicio de Neurología, Departmento de Neurología y Psiquiatría, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - C De la Barra
- Departmento de Imagenología, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - X Stecher
- Departmento de Imagenología, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - T Bernstein
- Departmento de Imagenología, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - P Zúñiga
- Departmento de Imagenología, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - V Díaz
- Servicio de Neurología, Departmento de Neurología y Psiquiatría, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - G Martínez
- División de Enfermedades Cardiovasculares, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - P Muñoz Venturelli
- Servicio de Neurología, Departmento de Neurología y Psiquiatría, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile; Centro de Estudios Clínicos, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile; The George Institute for Global Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
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15
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Mariadassou M, Ramayo-Caldas Y, Charles M, Féménia M, Renand G, Rocha D. Detection of selection signatures in Limousin cattle using whole-genome resequencing. Anim Genet 2020; 51:815-819. [PMID: 32686174 DOI: 10.1111/age.12982] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2020] [Indexed: 12/27/2022]
Abstract
Limousin, a renowned beef breed originating from central France, has been selectively bred over the last 100 years to improve economically important traits. We used whole-genome sequencing data from 10 unrelated Limousin bull calves to detect polymorphisms and identify regions under selection. A total of 13 943 766 variants were identified. Moreover, 311 852 bi-allelic SNPs and 92 229 indels located on autosomes were fixed for the alternative allele in all sequenced animals, including the previously reported missense deleterious F94L mutation in MSTN. We performed a whole-genome screen to discover genomic regions with excess homozygosity, using the pooled heterozygosity score and identified 171 different candidate selective sweeps. In total, 68 candidate genes were found in only 57 of these regions, indicating that a large fraction of the genome under selection might lie in non-coding regions and suggesting that a majority of adaptive mutations might be regulatory in nature. Many QTL were found within candidate selective sweep regions, including QTL associated with shear force or carcass weight. Among the putative selective sweeps, we located genes (MSTN, NCKAP5, RUNX2) that potentially contribute to important phenotypes in Limousin. Several candidate regions and genes under selection were also found in previous genome-wide selection scans performed in Limousin. In addition, we were able to pinpoint candidate causative regulatory polymorphisms in GRIK3 and RUNX2 that might have been under selection. Our results will contribute to improved understanding of the mechanisms and targets of artificial selection and will facilitate the interpretation of GWASs performed in Limousin.
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Affiliation(s)
- M Mariadassou
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, F-78350, France
| | - Y Ramayo-Caldas
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France.,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture, Torre Marimon, Caldes de Montbui, 08140, Spain
| | - M Charles
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France.,INRAE, SIGENAE, Université Paris-Saclay, Jouy-en-Josas, F-78350, France
| | - M Féménia
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France
| | - G Renand
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France
| | - D Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France
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16
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Baptista M, Craveiro A, Rocha D, Barata J, Martins S, Valente M, Valente M. DIAGNOSTIC APPROACH OF A YOUNG MALE WITH PLEUROPARENCHYMAL FIBROELASTOSIS. Chest 2020. [DOI: 10.1016/j.chest.2020.05.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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17
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Colombo J, Rocha D, Limoeiro AS, Nascimento W, Fontana C, Pelegrine R, Bueno CS, De Martin A. Micro- CT evaluation of sealers removal by reciprocal instrumentation followed by continuous ultrasonic irrigation in teeth with oval root canals. J Clin Exp Dent 2020; 15:e233-e238. [PMID: 37008240 PMCID: PMC10062467 DOI: 10.4317/jced.60013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/27/2023] [Indexed: 02/20/2023] Open
Abstract
Background The ability of the Reciproc system (R40) followed by continuous ultrasonic irrigation (CUI) to remove filling material from oval root canals of mandibular premolars filled with gutta-percha and AH Plus or Bio-C Sealer was evaluated by microtomography (micro-CT). Material and Methods The straight and oval root canals of 42 mandibular premolars were prepared with the ProDesign R 35.05 reciprocal file and randomly divided into two groups according to the material used to fill the canals (n=21): Group AH - Master Cone and AH Plus; Group BC - Master Cone and Bio-C Sealer. After filling and provisional sealing, the teeth were stored at 100% relative humidity and a temperature of 37°C for 30 days. The filling material was then removed with an R40 file. The material was considered completely removed when the R40 file reached the working length (WL), and no remaining filling material was visible on the canal walls. CUI was then performed. The teeth were scanned by micro- CT before and after removal of the filling material. The remaining filling material was measured in mm in the last apical 5 mm. The data were analyzed with the nonparametric Friedman test and subsequently with the Dunn test. The Mann-Whitney U test was also performed. Statistical significance was accepted at the 5% level. Results After instrumentation with the Reciproc R40, the volume of residual filling material was significantly greater in the BC group than in the AH group (P = 0.035). After CUI, there was no difference in the volume of residual material between the two groups (P = 0.705). Conclusions Bio-C sealer was more difficult to remove with the Reciproc file than AH Plus. CUI improved the removal of residual filling material regardless of sealer type. However, no technique was able to completely clear the canals of filling material. Key words:Bioceramic cement, CUI, micro-CT, reciproc, retreatment.
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18
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Guillocheau GM, El Hou A, Meersseman C, Esquerré D, Rebours E, Letaief R, Simao M, Hypolite N, Bourneuf E, Bruneau N, Vaiman A, Vander Jagt CJ, Chamberlain AJ, Rocha D. Survey of allele specific expression in bovine muscle. Sci Rep 2019; 9:4297. [PMID: 30862965 PMCID: PMC6414783 DOI: 10.1038/s41598-019-40781-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 02/22/2019] [Indexed: 02/04/2023] Open
Abstract
Allelic imbalance is a common phenomenon in mammals that plays an important role in gene regulation. An Allele Specific Expression (ASE) approach can be used to detect variants with a cis-regulatory effect on gene expression. In cattle, this type of study has only been done once in Holstein. In our study we performed a genome-wide analysis of ASE in 19 Limousine muscle samples. We identified 5,658 ASE SNPs (Single Nucleotide Polymorphisms showing allele specific expression) in 13% of genes with detectable expression in the Longissimus thoraci muscle. Interestingly we found allelic imbalance in AOX1, PALLD and CAST genes. We also found 2,107 ASE SNPs located within genomic regions associated with meat or carcass traits. In order to identify causative cis-regulatory variants explaining ASE we searched for SNPs altering binding sites of transcription factors or microRNAs. We identified one SNP in the 3’UTR region of PRNP that could be a causal regulatory variant modifying binding sites of several miRNAs. We showed that ASE is frequent within our muscle samples. Our data could be used to elucidate the molecular mechanisms underlying gene expression imbalance.
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Affiliation(s)
| | - Abdelmajid El Hou
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Cédric Meersseman
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,GMA, INRA, Université de Limoges, 87060, Limoges, France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Emmanuelle Rebours
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Morgane Simao
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Nicolas Hypolite
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Emmanuelle Bourneuf
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,CEA, DRF/iRCM/SREIT/LREG, Jouy-en-Josas, France
| | - Nicolas Bruneau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Anne Vaiman
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Amanda J Chamberlain
- Agriculture Victoria Research, AgriBiociences Centre, Bundoora, Victoria, Australia
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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19
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Jemaa SB, Thamri N, Mnara S, Rebours E, Rocha D, Boussaha M. Linkage disequilibrium and past effective population size in native Tunisian cattle. Genet Mol Biol 2019; 42:52-61. [PMID: 30776288 PMCID: PMC6428135 DOI: 10.1590/1678-4685-gmb-2017-0342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/14/2018] [Indexed: 12/30/2022] Open
Abstract
To carry out effective genome-wide association studies, information about linkage disequilibrium (LD) is essential. Here, we used medium-density SNP chips to provide estimates of LD in native Tunisian cattle. The two measures of LD that were used, mean r2 and D', decreased from 0.26 to 0.05 and from 0.73 to 0.40, respectively, when the distance between markers increased from less than 20 Kb to 200 Kb. The decay in LD over physical distance occurred at a faster rate than that reported for European and other indigenous breeds, and reached background levels at less than 500 Kb distance. This is consistent with the absence of strong selective pressure within the Tunisian population and suggests that, in order to be effective, any potential genome-wide association mapping studies will need to use chips with higher marker density. An analysis of effective population size (Ne) based on LD data showed a decline in past Ne, with a sudden drop starting about eight generations ago. This finding, combined with the high levels of recent inbreeding revealed by runs of homozygosity (ROH) analysis, indicate that this population is endangered and may be in urgent need of a conservation plan that includes a well-designed genetic management program.
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Affiliation(s)
- Slim Ben Jemaa
- National Institute of Agronomic Research of Tunisia, Laboratoire des Productions Animales et Fourragères, Ariana, Tunisia
| | - Nejia Thamri
- Livestock and Pasture Office, Tunis Belvedere, Tunisia
| | | | - Emmanuelle Rebours
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
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20
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Florim S, Almeida A, Rocha D, Portugal P. Acute mesenteric ischaemia: a pictorial review. Insights Imaging 2018; 9:673-682. [PMID: 30120722 PMCID: PMC6206376 DOI: 10.1007/s13244-018-0641-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/30/2018] [Accepted: 06/18/2018] [Indexed: 12/15/2022] Open
Abstract
Abstract Acute mesenteric ischaemia (AMI) is an uncommon cause of acute hospital admission with high mortality rates (50–90%) that requires early diagnosis and treatment. With the increase in average life expectancy, AMI represents one of the most threatening abdominal conditions in elderly patients. Untreated, AMI will cause mesenteric infarction, intestinal necrosis, an overwhelming inflammatory response and death. Early intervention can reverse this process leading to a full recovery, but the diagnosis of AMI is difficult. The failure to recognise AMI before intestinal necrosis has developed is responsible for the high mortality of the disease. Unfortunately, common CT findings in bowel ischaemia are not specific. Therefore, it is often a combination of nonspecific clinical, laboratory and radiological findings that helps most in the correct interpretation of CT findings. The purpose of this article is to provide an overview of the anatomy, physiology of mesenteric perfusion and discussions of causes, pathogenesis and CT findings in various types of acute bowel ischaemia. Familiarity with various imaging features of mesenteric injury is essential to make a timely diagnosis that will lead to improved patient outcomes. Teaching Points • AMI is a potentially life-threatening disorder whose prognosis depends on early recognition, accurate diagnosis and timely intervention. • Arterial inflow occlusion due to thrombosis or embolisation is the most common cause of AMI. • Four aetiological types of AMI have been associated with different characteristics and risk factors (EAMI, TAMI, VAMI and NOMI). • Physical examination and laboratory findings are not sensitive or specific for diagnosing AMI; therefore, MDCT is still the first-line imaging method in suspected AMI. • Although a number of scoring systems for prognosis have been proposed, these have not been validated in large-scale studies.
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Affiliation(s)
- S Florim
- Department of Radiology, Centro Hospitalar Vila Nova de Gaia/Espinho, Rua Conceição Fernandes, 4434-502, Vila Nova de Gaia, Portugal.
| | - A Almeida
- Department of Radiology, Centro Hospitalar Vila Nova de Gaia/Espinho, Rua Conceição Fernandes, 4434-502, Vila Nova de Gaia, Portugal
| | - D Rocha
- Department of Radiology, Centro Hospitalar Vila Nova de Gaia/Espinho, Rua Conceição Fernandes, 4434-502, Vila Nova de Gaia, Portugal
| | - P Portugal
- Department of Radiology, Centro Hospitalar Vila Nova de Gaia/Espinho, Rua Conceição Fernandes, 4434-502, Vila Nova de Gaia, Portugal
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21
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Rodriguez-Valera Y, Renand G, Naves M, Fonseca-Jiménez Y, Moreno-Probance TI, Ramos-Onsins S, Rocha D, Ramayo-Caldas Y. Genetic diversity and selection signatures of the beef 'Charolais de Cuba' breed. Sci Rep 2018; 8:11005. [PMID: 30030481 PMCID: PMC6054659 DOI: 10.1038/s41598-018-29453-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/12/2018] [Indexed: 01/19/2023] Open
Abstract
In this study, we used BovineSNP50 Genotyping BeadChip data to estimate the structure, putative ancestral origin as well as to identify regions with selective sweeps that may have had an important role in the adaptation to tropical conditions of the 'Charolais de Cuba' (CHCU) breed. According to a principal component analysis, CHCU samples cluster together with taurine breeds with an estimated 93% of taurus ancestral alleles. Despite the short period since importation, we detected differentiation (Fst = 0.049) between the French Charolaise (CHA) and CHCU. However, CHA breed was the closest breed to CHCU followed by other hybrids breed with a clear CHA origin. Linkage disequilibrium (r2) decay tends to be lower in CHCU compared to CHA probably due to a less intense artificial selection programs of CHCU. Signals of recent adaptation to tropical conditions between CHCU and CHA were identified. Genes mapping within those regions reflect different functions related to immunity, metabolic changes and heat tolerance (CHCU) and muscle development and meat quality (CHA) that may have had an important role in the phenotypic differentiation of these breeds. Further studies will expand our knowledge on the molecular basis of adaptation of cattle to tropical conditions and molecular process associated with meat quality traits.
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Affiliation(s)
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Michel Naves
- UR143, Unité de Recherches Zootechniques, Institut National de la Recherche Agronomique, Guadeloupe, France
| | | | | | - Sebastian Ramos-Onsins
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), Campus UAB, Bellaterra, 08193, Spain
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Yuliaxis Ramayo-Caldas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, 08140, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
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22
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Bouwman AC, Daetwyler HD, Chamberlain AJ, Ponce CH, Sargolzaei M, Schenkel FS, Sahana G, Govignon-Gion A, Boitard S, Dolezal M, Pausch H, Brøndum RF, Bowman PJ, Thomsen B, Guldbrandtsen B, Lund MS, Servin B, Garrick DJ, Reecy J, Vilkki J, Bagnato A, Wang M, Hoff JL, Schnabel RD, Taylor JF, Vinkhuyzen AAE, Panitz F, Bendixen C, Holm LE, Gredler B, Hozé C, Boussaha M, Sanchez MP, Rocha D, Capitan A, Tribout T, Barbat A, Croiseau P, Drögemüller C, Jagannathan V, Vander Jagt C, Crowley JJ, Bieber A, Purfield DC, Berry DP, Emmerling R, Götz KU, Frischknecht M, Russ I, Sölkner J, Van Tassell CP, Fries R, Stothard P, Veerkamp RF, Boichard D, Goddard ME, Hayes BJ. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nat Genet 2018; 50:362-367. [PMID: 29459679 DOI: 10.1038/s41588-018-0056-5] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/03/2018] [Indexed: 11/09/2022]
Abstract
Stature is affected by many polymorphisms of small effect in humans 1 . In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10-8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP-seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals.
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Affiliation(s)
- Aniek C Bouwman
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Wageningen, the Netherlands
| | - Hans D Daetwyler
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Amanda J Chamberlain
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | - Carla Hurtado Ponce
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Simon Boitard
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Marlies Dolezal
- Platform of Bioinformatics and Statistics, University of Veterinary Medicine, Vienna, Austria
| | - Hubert Pausch
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan, Germany.,Animal Genomics, ETH Zurich, Zurich, Switzerland
| | - Rasmus F Brøndum
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Phil J Bowman
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | - Bo Thomsen
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mogens S Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet-Tolosan, France
| | - Dorian J Garrick
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Johanna Vilkki
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | - Min Wang
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Anna A E Vinkhuyzen
- University of Queensland, Institute for Molecular Bioscience, St Lucia, Queensland, Australia.,University of Queensland, Queensland Brain Institute, St Lucia, Queensland, Australia
| | - Frank Panitz
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Christian Bendixen
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Lars-Erik Holm
- Section for Molecular Genetics and Systems Biology. Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | | | - Chris Hozé
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France.,Allice, Paris, France
| | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | | | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Aurelien Capitan
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France.,Allice, Paris, France
| | - Thierry Tribout
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Anne Barbat
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Pascal Croiseau
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | | | | | - Christy Vander Jagt
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | | | - Anna Bieber
- Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Deirdre C Purfield
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Ireland
| | - Reiner Emmerling
- Institute of Animal Breeding, Bavarian State Research Centre for Agriculture, Poing, Germany
| | - Kay-Uwe Götz
- Institute of Animal Breeding, Bavarian State Research Centre for Agriculture, Poing, Germany
| | | | | | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, USA
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan, Germany
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science/Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
| | - Roel F Veerkamp
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Wageningen, the Netherlands
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Mike E Goddard
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia.,Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria, Australia
| | - Ben J Hayes
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia. .,Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Queensland, Australia.
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23
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Ferreira A, Vale A, Matos E, Rocha D, Ferradosa I, Calvo T, Mendes A, Fernandes A. Polysomnography versus level III sleep study in women. Sleep Med 2017. [DOI: 10.1016/j.sleep.2017.11.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Alves F, Towers JR, Baird RW, Bearzi G, Bonizzoni S, Ferreira R, Halicka Z, Alessandrini A, Kopelman AH, Yzoard C, Rasmussen MH, Bertulli CG, Jourdain E, Gullan A, Rocha D, Hupman K, Mrusczok MT, Samarra FIP, Magalhães S, Weir CR, Ford JKB, Dinis A. The incidence of bent dorsal fins in free-ranging cetaceans. J Anat 2017; 232:263-269. [PMID: 29148044 DOI: 10.1111/joa.12729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2017] [Indexed: 11/30/2022] Open
Abstract
Laterally bent dorsal fins are rarely observed in free-ranging populations of cetaceans, contrary to captivity, where most killer whale Orcinus orca adult males have laterally collapsed fins. This topic has been poorly explored, and data/information on its occurrence and possible causes are limited. The present study: (i) undertakes a review of the available information on bent dorsal fins in free-ranging cetaceans, and updates it with new records, (ii) reports on the proportion of bent fins in different study populations, and (iii) discusses possible causes. An empirical approach based on bibliographic research and compilation of 52 new records collected worldwide resulted in a total of 17 species of cetaceans displaying bent dorsal fins. The species with the highest number of records (64%) and from most locations was O. orca. On average, individuals with bent dorsal fins represent < 1% of their populations, with the exception of false killer whales Pseudorca crassidens and O. orca. While line injuries associated with fisheries interactions may be the main cause for P. crassidens, and the vulnerability to health issues caused by the evolutionary enlargement of the fin may be the cause for O. orca adult males, factors contributing to this abnormality for other species are still unclear. The occurrence of bent dorsals could be influenced by a set of variables rather than by a single factor but, irrespective of the cause, it is suggested that it does not directly affect the animals' survivorship. While still rare in nature, this incident is more common (at least 101 known cases) and widespread (geographically and in species diversity) than hypothesized, and is not confined only to animals in captive environments. Investigation into the occurrence of bent fins may be an interesting avenue of research.
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Affiliation(s)
- F Alves
- CIIMAR/CIIMAR-Madeira, Interdisciplinary Centre of Marine and Environmental Research of Madeira, Funchal, Portugal.,Oceanic Observatory of Madeira, Funchal, Portugal.,Ventura, Marina do Funchal, Madeira, Portugal
| | - J R Towers
- Fisheries and Oceans Canada, Pacific Biological Station, Cetacean Research Program, Nanaimo, BC, Canada.,World Cetacean Alliance, Brighton, UK
| | - R W Baird
- Cascadia Research Collective, Olympia, WA, USA
| | - G Bearzi
- Dolphin Biology and Conservation, Cordenons, PN, Italy
| | - S Bonizzoni
- Dolphin Biology and Conservation, Cordenons, PN, Italy
| | - R Ferreira
- Oceanic Observatory of Madeira, Funchal, Portugal
| | - Z Halicka
- Ventura, Marina do Funchal, Madeira, Portugal.,University of Algarve, Faro, Portugal
| | - A Alessandrini
- CIIMAR/CIIMAR-Madeira, Interdisciplinary Centre of Marine and Environmental Research of Madeira, Funchal, Portugal.,University of Algarve, Faro, Portugal
| | - A H Kopelman
- Coastal Research and Education Society of Long Island, West Sayville, NY, USA
| | - C Yzoard
- University of La Laguna, Tenerife, Spain
| | - M H Rasmussen
- Húsavík Research Center, University of Iceland, Húsavík, Iceland.,Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - C G Bertulli
- Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - E Jourdain
- Norwegian Orca Survey, Andøya, Vesterålen, Norway
| | - A Gullan
- Dolphin Encountours Research Center and DolphinCare-Africa, Ponta do Ouro, Mozambique
| | - D Rocha
- Dolphin Encountours Research Center and DolphinCare-Africa, Ponta do Ouro, Mozambique
| | - K Hupman
- Coastal-Marine Research Group, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | | | - F I P Samarra
- Marine and Freshwater Research Institute, Reykjavík, Iceland
| | | | - C R Weir
- Falklands Conservation, Stanley, Falkland Islands
| | - J K B Ford
- Fisheries and Oceans Canada, Pacific Biological Station, Cetacean Research Program, Nanaimo, BC, Canada
| | - A Dinis
- CIIMAR/CIIMAR-Madeira, Interdisciplinary Centre of Marine and Environmental Research of Madeira, Funchal, Portugal.,Oceanic Observatory of Madeira, Funchal, Portugal
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25
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Letaief R, Rebours E, Grohs C, Meersseman C, Fritz S, Trouilh L, Esquerré D, Barbieri J, Klopp C, Philippe R, Blanquet V, Boichard D, Rocha D, Boussaha M. Identification of copy number variation in French dairy and beef breeds using next-generation sequencing. Genet Sel Evol 2017; 49:77. [PMID: 29065859 PMCID: PMC5655909 DOI: 10.1186/s12711-017-0352-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/17/2017] [Indexed: 11/15/2022] Open
Abstract
Background Copy number variations (CNV) are known to play a major role in genetic variability and disease pathogenesis in several species including cattle. In this study, we report the identification and characterization of CNV in eight French beef and dairy breeds using whole-genome sequence data from 200 animals. Bioinformatics analyses to search for CNV were carried out using four different but complementary tools and we validated a subset of the CNV by both in silico and experimental approaches.
Results We report the identification and localization of 4178 putative deletion-only, duplication-only and CNV regions, which cover 6% of the bovine autosomal genome; they were validated by two in silico approaches and/or experimentally validated using array-based comparative genomic hybridization and single nucleotide polymorphism genotyping arrays. The size of these variants ranged from 334 bp to 7.7 Mb, with an average size of ~ 54 kb. Of these 4178 variants, 3940 were deletions, 67 were duplications and 171 corresponded to both deletions and duplications, which were defined as potential CNV regions. Gene content analysis revealed that, among these variants, 1100 deletions and duplications encompassed 1803 known genes, which affect a wide spectrum of molecular functions, and 1095 overlapped with known QTL regions. Conclusions Our study is a large-scale survey of CNV in eight French dairy and beef breeds. These CNV will be useful to study the link between genetic variability and economically important traits, and to improve our knowledge on the genomic architecture of cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0352-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France.
| | - Emmanuelle Rebours
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Cédric Meersseman
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France.,GMA, INRA, Université de Limoges, UMR1061, Unité Génétique Moléculaire Animale, 123 avenue Albert Thomas, 87060, Limoges Cedex, France
| | - Sébastien Fritz
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Lidwine Trouilh
- LISBP, CNRS, INRA, INSA, Université de Toulouse, Toulouse, France
| | - Diane Esquerré
- GenPhySE, INRA, Université de Toulouse INPT ENSAT, Université de Toulouse INPT ENVT, 52627, Castanet-Tolosan, France
| | - Johanna Barbieri
- GenPhySE, INRA, Université de Toulouse INPT ENSAT, Université de Toulouse INPT ENVT, 52627, Castanet-Tolosan, France
| | | | - Romain Philippe
- GMA, INRA, Université de Limoges, UMR1061, Unité Génétique Moléculaire Animale, 123 avenue Albert Thomas, 87060, Limoges Cedex, France
| | - Véronique Blanquet
- GMA, INRA, Université de Limoges, UMR1061, Unité Génétique Moléculaire Animale, 123 avenue Albert Thomas, 87060, Limoges Cedex, France
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
| | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
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26
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Sanchez MP, Govignon-Gion A, Croiseau P, Fritz S, Hozé C, Miranda G, Martin P, Barbat-Leterrier A, Letaïef R, Rocha D, Brochard M, Boussaha M, Boichard D. Within-breed and multi-breed GWAS on imputed whole-genome sequence variants reveal candidate mutations affecting milk protein composition in dairy cattle. Genet Sel Evol 2017; 49:68. [PMID: 28923017 PMCID: PMC5604355 DOI: 10.1186/s12711-017-0344-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/30/2017] [Indexed: 01/06/2023] Open
Abstract
Background Genome-wide association studies (GWAS) were performed at the sequence level to identify candidate mutations that affect the expression of six major milk proteins in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) dairy cattle. Whey protein (α-lactalbumin and β-lactoglobulin) and casein (αs1, αs2, β, and κ) contents were estimated by mid-infrared (MIR) spectrometry, with medium to high accuracy (0.59 ≤ R2 ≤ 0.92), for 848,068 test-day milk samples from 156,660 cows in the first three lactations. Milk composition was evaluated as average test-day measurements adjusted for environmental effects. Next, we genotyped a subset of 8080 cows (2967 MON, 2737 NOR, and 2306 HOL) with the BovineSNP50 Beadchip. For each breed, genotypes were first imputed to high-density (HD) using HD single nucleotide polymorphisms (SNPs) genotypes of 522 MON, 546 NOR, and 776 HOL bulls. The resulting HD SNP genotypes were subsequently imputed to the sequence level using 27 million high-quality sequence variants selected from Run4 of the 1000 Bull Genomes consortium (1147 bulls). Within-breed, multi-breed, and conditional GWAS were performed. Results Thirty-four distinct genomic regions were identified. Three regions on chromosomes 6, 11, and 20 had very significant effects on milk composition and were shared across the three breeds. Other significant effects, which partially overlapped across breeds, were found on almost all the autosomes. Multi-breed analyses provided a larger number of significant genomic regions with smaller confidence intervals than within-breed analyses. Combinations of within-breed, multi-breed, and conditional analyses led to the identification of putative causative variants in several candidate genes that presented significant protein–protein interactions enrichment, including those with previously described effects on milk composition (SLC37A1, MGST1, ABCG2, CSN1S1, CSN2, CSN1S2, CSN3, PAEP, DGAT1, AGPAT6) and those with effects reported for the first time here (ALPL, ANKH, PICALM). Conclusions GWAS applied to fine-scale phenotypes, multiple breeds, and whole-genome sequences seems to be effective to identify candidate gene variants. However, although we identified functional links between some candidate genes and milk phenotypes, the causality between candidate variants and milk protein composition remains to be demonstrated. Nevertheless, the identification of potential causative mutations that underlie milk protein composition may have immediate applications for improvements in cheese-making. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0344-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie-Pierre Sanchez
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France.
| | - Armelle Govignon-Gion
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France.,Institut de l'Elevage, 75012, Paris, France
| | - Pascal Croiseau
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France
| | - Sébastien Fritz
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France.,Allice, 75012, Paris, France
| | - Chris Hozé
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France.,Allice, 75012, Paris, France
| | - Guy Miranda
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France
| | - Patrice Martin
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France
| | | | - Rabia Letaïef
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France
| | | | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris Saclay, 78350, Jouy-en-Josas, France
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27
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Rocha D, Ashokan PK, Santhoshkumar AV, Anoop EV, Sureshkumar P. Anatomy and Functional Status of Haustoria in Field Grown Sandalwood Tree (<i>Santalum album</i> L.). CURR SCI INDIA 2017. [DOI: 10.18520/cs/v113/i01/130-133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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28
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Meersseman C, Letaief R, Léjard V, Rebours E, Guillocheau G, Esquerré D, Djari A, Chamberlain A, Vander Jagt C, Klopp C, Boussaha M, Renand G, Maftah A, Petit D, Rocha D. Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle. DNA Res 2017; 24:221-233. [PMID: 28338730 PMCID: PMC5499805 DOI: 10.1093/dnares/dsx004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters. Combining bovine gene information and expression data obtained using RNA-Seq, we identified 120 putative bidirectional promoters active in bovine muscle. We experimentally validated in vitro 16 of these bidirectional promoters. Finally, using gene expression and whole-genome genotyping data, we explored the variability of the activity in muscle of the identified bidirectional promoters and discovered genetic variants affecting their activity. We found that the expression level of 77 genes is correlated with the activity of 12 bidirectional promoters. We also identified 57 single nucleotide polymorphisms associated with the activity of 5 bidirectional promoters. To our knowledge, our study is the first analysis in any species of the genetic variability of the activity of bidirectional promoters.
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Affiliation(s)
- Cédric Meersseman
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.,GMA, INRA, Université de Limoges, 87060 Limoges, France
| | - Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Véronique Léjard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuelle Rebours
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gabriel Guillocheau
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet Tolosan, France
| | - Anis Djari
- SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan, France
| | - Amanda Chamberlain
- Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.,AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia
| | - Christy Vander Jagt
- Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.,AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia
| | | | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | - Daniel Petit
- GMA, INRA, Université de Limoges, 87060 Limoges, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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29
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Boussaha M, Michot P, Letaief R, Hozé C, Fritz S, Grohs C, Esquerré D, Duchesne A, Philippe R, Blanquet V, Phocas F, Floriot S, Rocha D, Klopp C, Capitan A, Boichard D. Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences. Genet Sel Evol 2016; 48:87. [PMID: 27846802 PMCID: PMC5111192 DOI: 10.1186/s12711-016-0268-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/04/2016] [Indexed: 12/22/2022] Open
Abstract
Background In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability. Results In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data. Conclusions To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0268-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Pauline Michot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Rabia Letaief
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Chris Hozé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Sébastien Fritz
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Diane Esquerré
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, Castanet Tolosan, France
| | - Amandine Duchesne
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Romain Philippe
- GMA, INRA, Université de Limoges, 87060, Limoges Cedex, France
| | | | - Florence Phocas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Sandrine Floriot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Aurélien Capitan
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Allice, Maison Nationale des Eleveurs, 75012, Paris, France
| | - Didier Boichard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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30
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Sanchez M, Govignon-Gion A, Ferrand M, Gelé M, Pourchet D, Amigues Y, Fritz S, Boussaha M, Capitan A, Rocha D, Miranda G, Martin P, Brochard M, Boichard D. Whole-genome scan to detect quantitative trait loci associated with milk protein composition in 3 French dairy cattle breeds. J Dairy Sci 2016; 99:8203-8215. [DOI: 10.3168/jds.2016-11437] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/16/2016] [Indexed: 11/19/2022]
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31
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Letaief R, Grohs C, Fritz S, Rocha D, Boussaha M, Esquerré D, Barbieri J, Fritz S, Klopp C, Philippe R, Blanquet V, Boichard D. P8006 Identification and characterization of copy number variations in cattle. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4183a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ramayo-Caldas Y, Renand G, Ballester M, Saintilan R, Rocha D. P5007 Systems biology approach provides novel insights into gene networks controlling tenderness and meat quality traits across French beef breeds. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4118a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Guillocheau G, Rocha D. P1020 Identification of polymorphisms modifying gene expression regulation in cattle. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement424x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ramayo-Caldas Y, Renand G, Ballester M, Saintilan R, Rocha D. Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds. Genet Sel Evol 2016; 48:37. [PMID: 27107817 PMCID: PMC4842279 DOI: 10.1186/s12711-016-0216-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/13/2016] [Indexed: 01/19/2023] Open
Abstract
Background Studies to identify markers associated with beef tenderness have focused on Warner–Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d’Aquitaine beef cattle breeds. Results Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle. Conclusions Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one-dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi-breed beef cattle context. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0216-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Maria Ballester
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Genètica i Millora Animal, IRTA, 08140, Torre Marimon, Caldes de Montbui, Spain
| | | | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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Boussaha M, Esquerré D, Barbieri J, Djari A, Pinton A, Letaief R, Salin G, Escudié F, Roulet A, Fritz S, Samson F, Grohs C, Bernard M, Klopp C, Boichard D, Rocha D. Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds. PLoS One 2015; 10:e0135931. [PMID: 26317361 PMCID: PMC4552564 DOI: 10.1371/journal.pone.0135931] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/28/2015] [Indexed: 11/26/2022] Open
Abstract
High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest.
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Affiliation(s)
- Mekki Boussaha
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- * E-mail:
| | - Diane Esquerré
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Johanna Barbieri
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Anis Djari
- INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France
| | - Alain Pinton
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Rabia Letaief
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Gérald Salin
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Frédéric Escudié
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Alain Roulet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Sébastien Fritz
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- Union Nationale des Coopératives Agricoles d’Elevage et d’Insémination Animale, Paris, France
| | - Franck Samson
- INRA, UR1077, Mathématique Informatique et Génome, Domaine de Vilvert, Jouy-en-Josas, France
| | - Cécile Grohs
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Maria Bernard
- INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France
| | - Christophe Klopp
- INRA, SIGENAE, UR 875, INRA Auzeville, BP 52627, Castanet-Tolosan, France
| | - Didier Boichard
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
| | - Dominique Rocha
- INRA, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR1313, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josas, France
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Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brøndum RF, Liao X, Djari A, Rodriguez SC, Grohs C, Esquerré D, Bouchez O, Rossignol MN, Klopp C, Rocha D, Fritz S, Eggen A, Bowman PJ, Coote D, Chamberlain AJ, Anderson C, VanTassell CP, Hulsegge I, Goddard ME, Guldbrandtsen B, Lund MS, Veerkamp RF, Boichard DA, Fries R, Hayes BJ. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet 2014; 46:858-65. [DOI: 10.1038/ng.3034] [Citation(s) in RCA: 564] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 06/20/2014] [Indexed: 12/14/2022]
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Billerey C, Boussaha M, Esquerré D, Rebours E, Djari A, Meersseman C, Klopp C, Gautheret D, Rocha D. Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics 2014; 15:499. [PMID: 24948191 PMCID: PMC4073507 DOI: 10.1186/1471-2164-15-499] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/13/2014] [Indexed: 01/24/2023] Open
Abstract
Background The advent of large-scale gene expression technologies has helped to reveal in eukaryotic cells, the existence of thousands of non-coding transcripts, whose function and significance remain mostly poorly understood. Among these non-coding transcripts, long non-coding RNAs (lncRNAs) are the least well-studied but are emerging as key regulators of diverse cellular processes. In the present study, we performed a survey in bovine Longissimus thoraci of lincRNAs (long intergenic non-coding RNAs not overlapping protein-coding transcripts). To our knowledge, this represents the first such study in bovine muscle. Results To identify lincRNAs, we used paired-end RNA sequencing (RNA-Seq) to explore the transcriptomes of Longissimus thoraci from nine Limousin bull calves. Approximately 14–45 million paired-end reads were obtained per library. A total of 30,548 different transcripts were identified. Using a computational pipeline, we defined a stringent set of 584 different lincRNAs with 418 lincRNAs found in all nine muscle samples. Bovine lincRNAs share characteristics seen in their mammalian counterparts: relatively short transcript and gene lengths, low exon number and significantly lower expression, compared to protein-encoding genes. As for the first time, our study identified lincRNAs from nine different samples from the same tissue, it is possible to analyse the inter-individual variability of the gene expression level of the identified lincRNAs. Interestingly, there was a significant difference when we compared the expression variation of the 418 lincRNAs with the 10,775 known selected protein-encoding genes found in all muscle samples. In addition, we found 2,083 pairs of lincRNA/protein-encoding genes showing a highly significant correlated expression. Fourteen lincRNAs were selected and 13 were validated by RT-PCR. Some of the lincRNAs expressed in muscle are located within quantitative trait loci for meat quality traits. Conclusions Our study provides a glimpse into the lincRNA content of bovine muscle and will facilitate future experimental studies to unravel the function of these molecules. It may prove useful to elucidate their effect on mechanisms underlying the genetic variability of meat quality traits. This catalog will complement the list of lincRNAs already discovered in cattle and therefore will help to better annotate the bovine genome. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-499) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Dominique Rocha
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France.
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Rocha D, Billerey C, Samson F, Boichard D, Boussaha M. Identification of the putative ancestral allele of bovine single-nucleotide polymorphisms. J Anim Breed Genet 2014; 131:483-6. [PMID: 24862839 DOI: 10.1111/jbg.12095] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 04/26/2014] [Indexed: 11/29/2022]
Abstract
Identifying the action of natural selection from patterns of standing genetic variation has long been of interest to the population genetic community. Thanks to the availability of large single-nucleotide polymorphism (SNP) data sets for many species and of high-throughput SNP genotyping methods, whole-genomic surveys to detect selective sweeps are now possible. Knowing the ancestral allele increases the power to detect selection. We present here a comparative genomic approach to determine the putative ancestral allele of bovine SNPs deposited in public databases. We analysed 19,551,488 SNPs and identified the putative ancestral allele for 14,339,107 SNPs. Our predicted ancestral alleles were in agreement with ancestral alleles detected by genotyping outgroup species for 97% SNPs from the BovineSNP50 BeadChip. This comparison indicates that our comparative genomic-based approach to identify putative ancestral alleles is reliable.
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Affiliation(s)
- D Rocha
- Unité Génétique Animale et Biologie Intégrative, INRA, UMR1313, Jouy-en-Josas, France; Unité Génétique Animale et Biologie Intégrative, AgroParisTech, UMR1313, Jouy-en-Josas, France
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Léjard V, Rebours E, Meersseman C, Rocha D. Construction and validation of a novel dual reporter vector for studying mammalian bidirectional promoters. Plasmid 2014; 74:1-8. [PMID: 24857937 DOI: 10.1016/j.plasmid.2014.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 10/25/2022]
Abstract
Regulation of gene expression plays important role in cellular functions. With the development of sequencing techniques, more and more genomes are available and genome-wide analyses of genomic structures that may affect gene expression regulation are now possible. Analyses of several genomes have found a class of regulatory regions that contain elements that initiate transcription of two different genes positioned with a head-to-head arrangement in two opposite directions. These regulatory regions are known as bidirectional promoters. Although bidirectional promoters have been known for years, recent genome-scale studies have shown that the regulation of the expression of up to 10% of the genes are controlled by bidirectional promoters. These findings are based mostly on computational work and only a limited number of putative bidirectional promoters have been experimentally validated. Developing methods to study bidirectional promoters will allow researchers to understand how these regions are regulated and the roles that divergent transcription plays in the expression of genes. Here, we have developed a novel dual-fluorescence reporter gene vector to study the transcriptional output of mammalian bidirectional promoters. We demonstrate that this vector is capable of expressing reporter genes under the control of bidirectional promoters, using the known human OSGEP/APEX bidirectional promoter.
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Affiliation(s)
- Véronique Léjard
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Emmanuelle Rebours
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Cédric Meersseman
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Dominique Rocha
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France.
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van den Berg I, Fritz S, Rodriguez S, Rocha D, Boussaha M, Lund MS, Boichard D. Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology. Genet Sel Evol 2014; 46:31. [PMID: 24884971 PMCID: PMC4046048 DOI: 10.1186/1297-9686-46-31] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 04/29/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causative mutations in a QTL region. For this, a concordance analysis was applied for a leg conformation trait in dairy cattle. Several QTL were detected for which the QTL status (homozygous or heterozygous for the QTL) was inferred for each individual. Subsequently, the inferred QTL status was used in a concordance analysis to reduce the number of candidate mutations. METHODS Twenty QTL for rear leg set side view were mapped using Bayes C. Marker effects estimated during QTL mapping were used to infer the QTL status for each individual. Subsequently, polymorphisms present in the QTL regions were extracted from the whole-genome sequences of 71 Holstein bulls. Only polymorphisms for which the status was concordant with the QTL status were kept as candidate causative mutations. RESULTS QTL status could be inferred for 15 of the 20 QTL. The number of concordant polymorphisms differed between QTL and depended on the number of QTL statuses that could be inferred and the linkage disequilibrium in the QTL region. For some QTL, the concordance analysis was efficient and narrowed down to a limited number of candidate mutations located in one or two genes, while for other QTL a large number of genes contained concordant polymorphisms. CONCLUSIONS For regions for which the concordance analysis could be performed, we were able to reduce the number of candidate mutations. For part of the QTL, the concordant analyses narrowed QTL regions down to a limited number of genes, of which some are known for their role in limb or skeletal development in humans and mice. Mutations in these genes are good candidates for QTN (quantitative trait nucleotides) influencing rear leg set side view.
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Affiliation(s)
- Irene van den Berg
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France.
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Meersseman C, Léjard V, Rebours E, Boussaha M, Maftah A, Petit D, Rocha D. Bovine TWINKLE and mitochondrial ribosomal protein L43 genes are regulated by an evolutionary conserved bidirectional promoter. Gene 2013; 537:154-63. [PMID: 24361965 DOI: 10.1016/j.gene.2013.11.088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 11/30/2013] [Indexed: 11/16/2022]
Abstract
TWINKLE is a mitochondrial DNA helicase playing an important role in mitochondrial DNA replication. In human, mutations in this gene cause progressive external ophtalmoplegia and mitochondrial DNA depletion syndrome-7. TWINKLE is well conserved among multicellular eukaryotes and is believed to be a key regulator of mitochondrial DNA copy number in mammals. Despite its involvement in several diseases and its important function in mitochondrial DNA metabolism, nothing is known about the regulation of the expression of TWINKLE. We have analysed the 5'-flanking genomic region of the bovine TWINKLE gene and found it was localised adjacent to the MRPL43 gene in a head-to-head orientation, suggesting that both genes are regulated by a shared bidirectional promoter. The bovine 75-bp long intergenic region shows substantial homology across different species and contains several conserved putative transcription factor binding sites. A TATA box, however, was lacking. Using a dual fluorescent reporter system and transient transfection assays, we have analysed the bovine intergenic region between TWINKLE and MRPL43. This small genomic fragment showed a bidirectional promoter activity. As the TWINKLE/MRPL43 bidirectional promoter tested was highly conserved, it is likely that the results we obtained here in cattle may be extended to the other species.
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Affiliation(s)
- Cédric Meersseman
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; INRA, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France; Université de Limoges, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France
| | - Véronique Léjard
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Emmanuelle Rebours
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Mekki Boussaha
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France
| | - Abderrahman Maftah
- INRA, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France; Université de Limoges, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France
| | - Daniel Petit
- INRA, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France; Université de Limoges, UMR1061 Génétique Moléculaire Animale, F-87060 Limoges, France
| | - Dominique Rocha
- INRA, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France; AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352 Jouy-en-Josas, France.
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Ferreira A, Vale A, Rocha D, Matos E, Calvo T. Positional sleep apnea therapy – Our experience. Sleep Med 2013. [DOI: 10.1016/j.sleep.2013.11.274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Rocha D, Matos E, Ferreira A, Calvo M. Comparison of the clinical and polysomnographic findings in OSA patients vs REM SDB. Sleep Med 2013. [DOI: 10.1016/j.sleep.2013.11.588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Beghain J, Boitard S, Weiss B, Boussaha M, Gut I, Rocha D. Genome-wide linkage disequilibrium in the Blonde d'Aquitaine cattle breed. J Anim Breed Genet 2013; 130:294-302. [PMID: 23855631 DOI: 10.1111/j.1439-0388.2012.01020.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 07/16/2012] [Indexed: 12/18/2022]
Abstract
We present here the first genome-wide characterization of linkage disequilibrium (LD) in the French Blonde d'Aquitaine (BLA) breed, a well-muscled breed renowned for producing high-yielding beef carcasses. To assess the pattern and extent of LD, we used a sample of 30 unrelated bulls and 36 923 single nucleotide polymorphisms (SNPs) covering all cattle autosomes. The squared correlation of the alleles at two loci (r(2) ) was used as a measure of LD. The analysis of adjacent marker pairs revealed that the level of LD decreases rapidly with physical distance between SNPs. Overall mean r(2) was 0.205 (±0.262). Strong LD (r(2) > 0.8) and useful LD (measured as r(2 ) > 0.2) were observed within genomic regions of up to 720 and 724 kb, respectively. We analysed the genetic structure of the BLA population and found stratification. The observed genetic sub-structuring is consistent with the known recent demographic history that occurred during BLA breed formation. Our results indicate that LD mapping of phenotypic traits in the BLA population is feasible; however, because of this sub-structuring, special care is needed to reduce the likelihood of false-positive associations between marker loci and traits of interest.
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Affiliation(s)
- J Beghain
- Undergraduate Programme in Bioinformatics, Institut Universitaire Technologique d'Aurillac/Université d'Auvergne, Jouy-en-Josa, France; INRA/AgroParisTech, UMR1313, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, Jouy-en-Josa, France
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Fritz S, Capitan A, Djari A, Rodriguez SC, Barbat A, Baur A, Grohs C, Weiss B, Boussaha M, Esquerré D, Klopp C, Rocha D, Boichard D. Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2. PLoS One 2013; 8:e65550. [PMID: 23762392 PMCID: PMC3676330 DOI: 10.1371/journal.pone.0065550] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/25/2013] [Indexed: 11/23/2022] Open
Abstract
The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10(-4)) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle.
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Affiliation(s)
- Sébastien Fritz
- UNCEIA, Genetics Team, Paris, France
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Aurelien Capitan
- UNCEIA, Genetics Team, Paris, France
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Anis Djari
- INRA, Sigenae, UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Sabrina C. Rodriguez
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
- INRA, Sigenae, UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Anne Barbat
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Aurélia Baur
- UNCEIA, Genetics Team, Paris, France
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Cécile Grohs
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Bernard Weiss
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Mekki Boussaha
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Diane Esquerré
- INRA, GeT Genomics Facility, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Christophe Klopp
- INRA, Sigenae, UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Dominique Rocha
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
| | - Didier Boichard
- INRA, UMR1313 Animal Genetics and Integrative Biology, Jouy-en-Josas, France
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Allais-Bonnet A, Grohs C, Medugorac I, Krebs S, Djari A, Graf A, Fritz S, Seichter D, Baur A, Russ I, Bouet S, Rothammer S, Wahlberg P, Esquerré D, Hoze C, Boussaha M, Weiss B, Thépot D, Fouilloux MN, Rossignol MN, van Marle-Köster E, Hreiðarsdóttir GE, Barbey S, Dozias D, Cobo E, Reversé P, Catros O, Marchand JL, Soulas P, Roy P, Marquant-Leguienne B, Le Bourhis D, Clément L, Salas-Cortes L, Venot E, Pannetier M, Phocas F, Klopp C, Rocha D, Fouchet M, Journaux L, Bernard-Capel C, Ponsart C, Eggen A, Blum H, Gallard Y, Boichard D, Pailhoux E, Capitan A. Novel insights into the bovine polled phenotype and horn ontogenesis in Bovidae. PLoS One 2013; 8:e63512. [PMID: 23717440 PMCID: PMC3661542 DOI: 10.1371/journal.pone.0063512] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/02/2013] [Indexed: 11/25/2022] Open
Abstract
Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae.
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Affiliation(s)
- Aurélie Allais-Bonnet
- Institut National de la Recherche Agronomique, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
| | - Cécile Grohs
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Ivica Medugorac
- Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Anis Djari
- Institut National de la Recherche Agronomique, Plateforme bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sébastien Fritz
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
- National Association of Livestock & Artificial Insemination Cooperatives, Paris, France
| | | | - Aurélia Baur
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
- National Association of Livestock & Artificial Insemination Cooperatives, Paris, France
| | - Ingolf Russ
- Tierzuchtforschung e.V. München, Grub, Germany
| | - Stéphan Bouet
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Sophie Rothammer
- Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Per Wahlberg
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Diane Esquerré
- GeT-PlaGe, Genotoul, Castanet-Tolosan, France
- Institut National de la Recherche Agronomique, UMR444 Génétique Cellulaire, Castanet-Tolosan, France
| | - Chris Hoze
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
- National Association of Livestock & Artificial Insemination Cooperatives, Paris, France
| | - Mekki Boussaha
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Bernard Weiss
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Dominique Thépot
- Institut National de la Recherche Agronomique, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
| | | | | | - Este van Marle-Köster
- Department of Animal & Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Sarah Barbey
- Institut National de la Recherche Agronomique, UE0326 Domaine expérimental du Pin-au-Haras, Exmes, France
| | - Dominique Dozias
- Institut National de la Recherche Agronomique, UE0326 Domaine expérimental du Pin-au-Haras, Exmes, France
| | - Emilie Cobo
- Institut National de la Recherche Agronomique, UE0326 Domaine expérimental du Pin-au-Haras, Exmes, France
| | | | | | | | | | | | | | - Daniel Le Bourhis
- Institut National de la Recherche Agronomique, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- National Association of Livestock & Artificial Insemination Cooperatives, Paris, France
| | - Laetitia Clément
- National Association of Livestock & Artificial Insemination Cooperatives, Paris, France
| | - Laura Salas-Cortes
- National Association of Livestock & Artificial Insemination Cooperatives, Paris, France
| | - Eric Venot
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Maëlle Pannetier
- Institut National de la Recherche Agronomique, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
| | - Florence Phocas
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Christophe Klopp
- Institut National de la Recherche Agronomique, Plateforme bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, Castanet-Tolosan, France
| | - Dominique Rocha
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | | | - Laurent Journaux
- National Association of Livestock & Artificial Insemination Cooperatives, Paris, France
| | | | - Claire Ponsart
- National Association of Livestock & Artificial Insemination Cooperatives, Paris, France
| | - André Eggen
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Yves Gallard
- Institut National de la Recherche Agronomique, UE0326 Domaine expérimental du Pin-au-Haras, Exmes, France
| | - Didier Boichard
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Eric Pailhoux
- Institut National de la Recherche Agronomique, UMR 1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
| | - Aurélien Capitan
- Institut National de la Recherche Agronomique, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
- National Association of Livestock & Artificial Insemination Cooperatives, Paris, France
- * E-mail:
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Djari A, Esquerré D, Weiss B, Martins F, Meersseman C, Boussaha M, Klopp C, Rocha D. Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics 2013; 14:307. [PMID: 23651547 PMCID: PMC3751807 DOI: 10.1186/1471-2164-14-307] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 05/01/2013] [Indexed: 01/28/2023] Open
Abstract
Background Genetic information based on molecular markers has increasingly being used in cattle breeding improvement programmes, as a mean to improve conventionally phenotypic selection. Advances in molecular genetics have led to the identification of several genetic markers associated with genes affecting economic traits. Until recently, the identification of the causative genetic variants involved in the phenotypes of interest has remained a difficult task. The advent of novel sequencing technologies now offers a new opportunity for the identification of such variants. Despite sequencing costs plummeting, sequencing whole-genomes or large targeted regions is still too expensive for most laboratories. A transcriptomic-based sequencing approach offers a cheaper alternative to identify a large number of polymorphisms and possibly to discover causative variants. In the present study, we performed a gene-based single nucleotide polymorphism (SNP) discovery analysis in bovine Longissimus thoraci, using RNA-Seq. To our knowledge, this represents the first study done in bovine muscle. Results Messenger RNAs from Longissimus thoraci from three Limousin bull calves were subjected to high-throughput sequencing. Approximately 36–46 million paired-end reads were obtained per library. A total of 19,752 transcripts were identified and 34,376 different SNPs were detected. Fifty-five percent of the SNPs were found in coding regions and ~22% resulted in an amino acid change. Applying a very stringent SNP quality threshold, we detected 8,407 different high-confidence SNPs, 18% of which are non synonymous coding SNPs. To analyse the accuracy of RNA-Seq technology for SNP detection, 48 SNPs were selected for validation by genotyping. No discrepancies were observed when using the highest SNP probability threshold. To test the usefulness of the identified SNPs, the 48 selected SNPs were assessed by genotyping 93 bovine samples, representing mostly the nine major breeds used in France. Principal component analysis indicates a clear separation between the nine populations. Conclusions The RNA-Seq data and the collection of newly discovered coding SNPs improve the genomic resources available for cattle, especially for beef breeds. The large amount of variation present in genes expressed in Limousin Longissimus thoracis, especially the large number of non synonymous coding SNPs, may prove useful to study the mechanisms underlying the genetic variability of meat quality traits.
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Affiliation(s)
- Anis Djari
- INRA, UMR 1313 GABI, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas, France
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Abstract
Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection and therefore could help in identifying mutations responsible for improved traits. We used genotyping data generated using Illumina's BovineSNP50 Genotyping BeadChips to identify selection signatures in the Blonde d'Aquitaine breed, a well-muscled French beef breed. For this purpose, we employed a hidden Markov model-based test, which detects selection by studying local variations in the allele frequency spectrum along the genome, within a single population. Three regions containing selective sweeps were identified. Annotation of genes located within these regions revealed interesting candidate genes. For example, myostatin (also known as GDF8), a known muscle growth factor inhibitor, is located within the selection signature region found on chromosome 2. In addition, we have identified chromosomal regions that show some evidence of selection within QTL regions for economically important traits. The results of this study could help to better understand the mechanisms related to the selection of the Blonde d'Aquitaine breed.
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Affiliation(s)
- S Boitard
- Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique/ENVT, UMR444, Castanet Tolosan, France
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Laporte B, Petit D, Rocha D, Boussaha M, Grohs C, Maftah A, Petit JM. Characterization of bovine FUT7 furthers understanding of FUT7 evolution in mammals. BMC Genet 2012; 13:74. [PMID: 22909383 PMCID: PMC3479001 DOI: 10.1186/1471-2156-13-74] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 08/02/2012] [Indexed: 11/10/2022] Open
Abstract
Background The Sialyl-Lewis X (Slex) is a well-known glycan structure involved in leukocyte homing and recruitment to inflammatory sites. SLex is well conserved among species and is mainly synthesized by FucT-VII in vertebrates. The enzyme responsible for its biosynthesis in cattle was not known. Results We cloned a cDNA sequence encoding bovine α3-fucosyltransferase VII that shares 83% identity with its human counterpart. Located at the BTA 11 telomeric region, the 1029 bp open reading frame is spread over two different exons, E1 which also contains the unique 5’-untranslated region and E2 which includes the entire 3’-untranslated region. The bfut7 expression pattern is restricted to thymus and spleen. A single transcript leading to the synthesis of a 342 aa protein was identified. The encoded fucosyltransferase, produced as a recombinant enzyme in COS-1 cells, was shown to be specifically responsible for SLex synthesis in cattle. In addition, we showed that the gene promoter evolved from fish to mammals towards a complex system related to the immune system. But beyond the fact that the gene regulation seems to be conserved among mammals, we also identified 7 SNPs including 3 missense mutations in the coding region in a small panel of animals. Conclusions The FUT7 sequence was highly conserved as well as the specific activity of the encoded protein FucT-VII. In addition, our in silico promoter analysis and the high rate of polymorphism suggested that its function is evolving toward a complex system related to the immune system. Furthermore, comparing bovine to human and mouse sequences, it appeared that a decrease in gene regulation was correlated with an increase in mutation rate and wider tissue expression.
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Affiliation(s)
- Benoît Laporte
- INRA UMR 1061, Unité de Génétique Moléculaire Animale, Université de Limoges, Faculté des Sciences et Techniques, 123 Avenue A, Thomas, Limoges 87060, France
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Amigues Y, Boitard S, Bertrand C, SanCristobal M, Rocha D. Genetic characterization of the Blonde d’Aquitaine cattle breed using microsatellite markers and relationship with three other French cattle populations. J Anim Breed Genet 2011; 128:201-8. [DOI: 10.1111/j.1439-0388.2010.00890.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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