1
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Chen N, Xia X, Hanif Q, Zhang F, Dang R, Huang B, Lyu Y, Luo X, Zhang H, Yan H, Wang S, Wang F, Chen J, Guan X, Liu Y, Li S, Jin L, Wang P, Sun L, Zhang J, Liu J, Qu K, Cao Y, Sun J, Liao Y, Xiao Z, Cai M, Mu L, Siddiki AZ, Asif M, Mansoor S, Babar ME, Hussain T, Silva GLLP, Gorkhali NA, Terefe E, Belay G, Tijjani A, Zegeye T, Gebre MG, Ma Y, Wang Y, Huang Y, Lan X, Chen H, Migliore NR, Colombo G, Semino O, Achilli A, Sinding MHS, Lenstra JA, Cheng H, Lu W, Hanotte O, Han J, Jiang Y, Lei C. Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing. Nat Commun 2023; 14:7803. [PMID: 38016956 PMCID: PMC10684552 DOI: 10.1038/s41467-023-43626-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.
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Affiliation(s)
- Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193, Beijing, China
| | - Fengwei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environment Science, Yunnan University, Kunming, 650500, China
| | - Huixuan Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shikang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jialei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiwen Guan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangkai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shuang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Liangliang Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Pengfei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, 675000, China
| | - Yanhong Cao
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Junli Sun
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Yuying Liao
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, 530001, China
| | - Zhengzhong Xiao
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Ming Cai
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Lan Mu
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, 650224, China
| | - Amam Zonaed Siddiki
- Genomics Research Group, Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, 4225, Bangladesh
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Masroor Ellahi Babar
- The University of Agriculture, Dera Ismail Khan, Khyber Pakhtunkhwa, 29050, Pakistan
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Islamabad, 44100, Pakistan
| | | | - Neena Amatya Gorkhali
- National Animal Breeding and Genetics Centre, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar, Lalitpur, 45200, Nepal
| | - Endashaw Terefe
- College of Agriculture and Environmental Science, Department of Animal Science, Arsi University, Asella, Ethiopia
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia
| | - Gurja Belay
- College of Natural and Computational Sciences, The School of Graduate Studies, Addis Ababa University, 1000, Addis Ababa, Ethiopia
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Tsadkan Zegeye
- Mekelle Agricultural Research Center, P.O. Box 258, 7000, Mekelle, Tigray, Ethiopia
| | - Mebrate Genet Gebre
- School of Animal and Rangeland Science, College of Agriculture, Haramaya University, 2040, Haramaya, Oromia, Ethiopia
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, 750000, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan, 250100, China
| | - Wenfa Lu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia.
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193, Beijing, China.
- Livestock Genetics Program, International Livestock Research Institute (ILRI), 00100, Nairobi, Kenya.
- Yazhouwan National Laboratory, Sanya, 572024, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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2
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Delsol N, Stucky BJ, Oswald JA, Cobb CR, Emery KF, Guralnick R. Ancient DNA confirms diverse origins of early post-Columbian cattle in the Americas. Sci Rep 2023; 13:12444. [PMID: 37528222 PMCID: PMC10394069 DOI: 10.1038/s41598-023-39518-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023] Open
Abstract
Before the arrival of Europeans, domestic cattle (Bos taurus) did not exist in the Americas, and most of our knowledge about how domestic bovines first arrived in the Western Hemisphere is based on historical documents. Sixteenth-century colonial accounts suggest that the first cattle were brought in small numbers from the southern Iberian Peninsula via the Canary archipelago to the Caribbean islands where they were bred locally and imported to other circum-Caribbean regions. Modern American heritage cattle genetics and limited ancient mtDNA data from archaeological colonial cattle suggest a more complex story of mixed ancestries from Europe and Africa. So far little information exists to understand the nature and timing of the arrival of these mixed-ancestry populations. In this study we combine ancient mitochondrial and nuclear DNA from a robust sample of some of the earliest archaeological specimens from Caribbean and Mesoamerican sites to clarify the origins and the dynamics of bovine introduction into the Americas. Our analyses support first arrival of cattle from diverse locales and potentially confirm the early arrival of African-sourced cattle in the Americas, followed by waves of later introductions from various sources over several centuries.
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Affiliation(s)
- Nicolas Delsol
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Brian J Stucky
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD, USA
| | - Jessica A Oswald
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biology Department, University of Nevada, Reno, Reno, NV, 89557, USA
- U.S. Fish and Wildlife Service, National Fish and Wildlife Forensic Laboratory, Ashland, OR, 97520, USA
| | - Charles R Cobb
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Kitty F Emery
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
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3
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Ginja C, Guimarães S, da Fonseca RR, Rasteiro R, Rodríguez-Varela R, Simões LG, Sarmento C, Belarte MC, Kallala N, Torres JR, Sanmartí J, Arruda AM, Detry C, Davis S, Matos J, Götherström A, Pires AE, Valenzuela-Lamas S. Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle. iScience 2023; 26:107196. [PMID: 37485357 PMCID: PMC10359934 DOI: 10.1016/j.isci.2023.107196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 12/22/2022] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.
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Affiliation(s)
- Catarina Ginja
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Silvia Guimarães
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Rute R. da Fonseca
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Luciana G. Simões
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Cindy Sarmento
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Maria Carme Belarte
- ICREA, Institut Català de Recerca i Estudis Avançats, Barcelona, Spain
- ICAC, Institut Català d'Arqueologia Clàssica, Tarragona, Spain
| | - Nabil Kallala
- INP, Institut National du Patrimoine, Tunis, Tunisia
- Faculté des Sciences Humaines et Sociales, Université de Tunis, Tunis, Tunisia
| | | | - Joan Sanmartí
- In memoriam, Departament de Prehistòria, Història Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Ana Margarida Arruda
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Cleia Detry
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Simon Davis
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- LARC/DGPC, Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisboa, Portugal
| | - José Matos
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P, Oeiras, Portugal
- CE3C, Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
| | | | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- Faculdade de Medicina Veterinária, Universidade Lusófona, Lisboa, Portugal
| | - Silvia Valenzuela-Lamas
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
- Archaeology of Social Dynamics, Consejo Superior de Investigaciones Científicas-Institució Milà i Fontanals d'Humanitats (CSIC-IMF), Barcelona, Spain
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4
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Xia X, Qu K, Wang Y, Sinding MHS, Wang F, Hanif Q, Ahmed Z, Lenstra JA, Han J, Lei C, Chen N. Global dispersal and adaptive evolution of domestic cattle: a genomic perspective. STRESS BIOLOGY 2023; 3:8. [PMID: 37676580 PMCID: PMC10441868 DOI: 10.1007/s44154-023-00085-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/26/2023] [Indexed: 09/08/2023]
Abstract
Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations.
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Affiliation(s)
- Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, 675000, China
| | - Yan Wang
- Qingdao Municipal Bureau of Agriculture and Rural Affairs, Qingdao, 266000, China
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, 12350, Pakistan
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jianlin Han
- Livestock Genetic Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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5
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Dorji J, Vander Jagt CJ, Chamberlain AJ, Cocks BG, MacLeod IM, Daetwyler HD. Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle. Sci Rep 2022; 12:5582. [PMID: 35379858 PMCID: PMC8980051 DOI: 10.1038/s41598-022-09427-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Maternal diversity based on a sub-region of mitochondrial genome or variants were commonly used to understand past demographic events in livestock. Additionally, there is growing evidence of direct association of mitochondrial genetic variants with a range of phenotypes. Therefore, this study used complete bovine mitogenomes from a large sequence database to explore the full spectrum of maternal diversity. Mitogenome diversity was evaluated among 1883 animals representing 156 globally important cattle breeds. Overall, the mitogenomes were diverse: presenting 11 major haplogroups, expanding to 1309 unique haplotypes, with nucleotide diversity 0.011 and haplotype diversity 0.999. A small proportion of African taurine (3.5%) and indicine (1.3%) haplogroups were found among the European taurine breeds and composites. The haplogrouping was largely consistent with the population structure derived from alternate clustering methods (e.g. PCA and hierarchical clustering). Further, we present evidence confirming a new indicine subgroup (I1a, 64 animals) mainly consisting of breeds originating from China and characterised by two private mutations within the I1 haplogroup. The total genetic variation was attributed mainly to within-breed variance (96.9%). The accuracy of the imputation of missing genotypes was high (99.8%) except for the relatively rare heteroplasmic genotypes, suggesting the potential for trait association studies within a breed.
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Affiliation(s)
- Jigme Dorji
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Benjamin G Cocks
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Hans D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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6
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Petretto E, Dettori ML, Pazzola M, Manca F, Amills M, Vacca GM. Mitochondrial DNA diversity of the Sardinian local cattle stock. Sci Rep 2022; 12:2486. [PMID: 35169207 PMCID: PMC8847569 DOI: 10.1038/s41598-022-06420-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this research was to characterize the genetic diversity of the Sarda (Sa, n = 131), Sardo Bruna (SB, n = 44) and Sardo Modicana (SM, n = 26) cattle breeds, reared in the island of Sardinia (Italy). A portion of the mitochondrial DNA hypervariable region was sequenced, in order to identify a potential signature of African introgression. The FST coefficients among populations ranged between 0.056 for Sa vs SB and 0.167 for SB vs SM. AMOVA analysis indicated there was a significant differentiation of the three breeds, although most of diversity was gathered at the within-breed level. The Median Joining Network of the Sardinian sequences showed a potential founder effect signature. A MJ network including Sardinian cattle plus African, Italian, Iberian and Asian sequences, revealed the presence of haplogroup T3, already detected in Sa cattle, and the presence of Hg T1 and Hg T1′2′3, in Sa and SB. The presence of a private haplotype belonging to haplogroup T1, which is characteristic of African taurine breeds, may be due to the introgression of Sardinian breeds with African cattle, either directly (most probable source: North African cattle) or indirectly (through a Mediterranean intermediary already introgressed with African blood).
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Affiliation(s)
- Elena Petretto
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Fabio Manca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Marcel Amills
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
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7
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The Sequence Analysis of Mitochondrial DNA Revealed Some Major Centers of Horse Domestications: The Archaeologist's Cut. J Equine Vet Sci 2021; 109:103830. [PMID: 34871751 DOI: 10.1016/j.jevs.2021.103830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 11/22/2022]
Abstract
The question about the time and the place of horse domestication, a process which had a profound impact on the progress of mankind, is disputable. According to the most widely accepted hypothesis, the earliest domestication of the horse happened in the western parts of the Eurasian steppes, between the Northern Black Sea region and present-day Kazakhstan and Turkmenistan. It seems that it occurred not earlier than the first half and most probably during the middle (even the last third) of the fourth millennium BC (from ∼ 5.5 kya). The next steps of large-scale horse breeding occurred almost simultaneously in Eurasia and North Africa due to the development of the social structure of human communities. On the other hand, the morphological differences between wild and domestic animals are rather vague and the genetic introgression between them is speculative. In this review, we have tried to gather all available scientific data on the existing possible hypotheses for the earliest domestication of the horse, as well as to highlight some data on the most plausible ones. This is due to the frequency of some significant data on the frequency of strictly defined mitotypes in different historical periods of human civilizations existing in the same periods.
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Wanjala G, Bagi Z, Kusza S. Meta-Analysis of Mitochondrial DNA Control Region Diversity to Shed Light on Phylogenetic Relationship and Demographic History of African Sheep ( Ovis aries) Breeds. BIOLOGY 2021; 10:762. [PMID: 34439994 PMCID: PMC8389696 DOI: 10.3390/biology10080762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022]
Abstract
To improve sheep breeding and conservation of genetic resources, the mitochondrial DNA control region (mtDNA CR) of 399 sequences of African indigenous sheep breeds from previously published research articles were meta-analyzed to elucidate their phylogenetic relationship, diversity, and demographic history. A total of 272 haplotypes were found, of which 207 were unique and a high level of mtDNA CR variability was observed. Generally, the number of polymorphic sites, nucleotide and haplotype diversity were high (284, 0.254 ± 0.012 and 0.993 ± 0.002, respectively). The median-joining (MJ) network of haplotypes produced three major haplogroups (A, B and C), with haplogroup B being dominant. A mixture of populations suggests a common matrilineal origin and lack of and/or a weak phylogeographic structure. Mismatch analysis showed recent expansion of North African breeds, whereas East African and continental populations exhibited selection pressures for adaptation. A slight historical genetic difference was also observed between the fat tail and thin tail sheep breeds. However, further investigations are required using more samples and long sequence segments to achieve deeper levels of conclusions on the African sheep phylogenetic relationship. The present meta-analysis results contribute to the general understanding of African native sheep populations for improved management of sheep genetic resources.
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Affiliation(s)
- George Wanjala
- Centre for Agricultural Genomics and Biotechnology, H-4032 Egyetem tér 1, 4032 Debrecen, Hungary; (G.W.); (Z.B.)
- Doctoral School of Animal Science, University of Debrecen, H-4032 Böszörményi út 138, 4032 Debrecen, Hungary
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, H-4032 Egyetem tér 1, 4032 Debrecen, Hungary; (G.W.); (Z.B.)
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, H-4032 Egyetem tér 1, 4032 Debrecen, Hungary; (G.W.); (Z.B.)
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9
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Zinovieva NA, Sheiko IP, Dotsev AV, Sheiko RI, Mikhailova ME, Sermyagin AA, Abdelmanova AS, Kharzinova VR, Reyer H, Wimmers K, Sölkner J, Pleshanov NV, Brem G. Genome-wide SNP analysis clearly distinguished the Belarusian Red cattle from other European cattle breeds. Anim Genet 2021; 52:720-724. [PMID: 34131930 DOI: 10.1111/age.13102] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 01/06/2023]
Abstract
Local breeds can serve as an important source of genetic variability in domestic animal species. This study aimed to assess the genetic diversity and population structure of Belarusian Red cattle and their differentiation from other European cattle populations based on genome-wide SNP genotypes. Twenty pedigree-recorded non-closely related cows of Belarusian Red cattle were genotyped using the Illumina BovineHD BeadChip. Genotypes of 22 other European cattle breeds were included in the study for comparison. A total of 28 562 SNPs passed through the quality control checks and were selected for analysis. The Belarusian Red cattle displayed a moderate level of genetic variability (U HE = 0.341, HO = 0.368), and the highest heterozygote excess (U FIS = -0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, FST -based Neighbor-Net tree and Admixture clustering, clearly distinguished the Belarusian Red cattle from the other European cattle breeds. Moreover, the presence of ancestral genomic components of Danish Red and Brown Swiss breeds were clearly visible, which agrees with the breed's history and its recent development. Our study highlights the importance of maintaining the specific genomic components, which makes a significant contribution to the global genetic diversity in the modern population of Belarusian Red cattle, allowing us to consider them a valuable national genetic resource. Our research results will be useful for the development of conservation programs for this local cattle breed.
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Affiliation(s)
- N A Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - I P Sheiko
- Scientific and Practical Center of the National Academy of Sciences of Belarus for Animal Husbandry, Zhodino, 222160, Belarus
| | - A V Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - R I Sheiko
- Institute of Genetics and Cytology of the National Academy of Science of Belarus, Minsk, 220072, Belarus
| | - M E Mikhailova
- Institute of Genetics and Cytology of the National Academy of Science of Belarus, Minsk, 220072, Belarus
| | - A A Sermyagin
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - A S Abdelmanova
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - V R Kharzinova
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - H Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, 18196, Germany
| | - K Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, 18196, Germany
| | - J Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, 1180, Austria
| | - N V Pleshanov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, St. Petersburg - Pushkin, 196601, Russia
| | - G Brem
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, 1210, Austria
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Mitochondrial genomes from modern and ancient Turano-Mongolian cattle reveal an ancient diversity of taurine maternal lineages in East Asia. Heredity (Edinb) 2021; 126:1000-1008. [PMID: 33782560 PMCID: PMC8178343 DOI: 10.1038/s41437-021-00428-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Turano-Mongolian cattle are a group of taurine cattle from Northern and Eastern Asia with distinct morphological traits, which are known for their ability to tolerate harsh environments, such as the Asian steppe and the Tibetan plateau. Through the analysis of 170 mitogenomes from ten modern breeds, two sub-lineages within T3 (T3119 and T3055) were identified as specific of Turano-Mongolian cattle. These two T3 sub-lineages, together with the previously identified T4, were also present in six Neolithic samples, dated to ~3900 years BP, which might represent the earliest domestic taurine stocks from Southwest Asia. The rare haplogroup Q, found in three Tibetan cattle, testifies for the legacy of ancient migrations from Southwest Asia and suggests that the isolated Tibetan Plateau preserved unique prehistoric genetic resources. These findings confirm the geographic substructure of Turano-Mongolian cattle breeds, which have been shaped by ancient migrations and geographic barriers.
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11
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Sudrajad P, Subiharta S, Adinata Y, Lathifah A, Lee JH, Lenstra JA, Lee SH. An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis. PLoS One 2020; 15:e0241038. [PMID: 33170846 PMCID: PMC7654832 DOI: 10.1371/journal.pone.0241038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 10/07/2020] [Indexed: 12/01/2022] Open
Abstract
The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity.
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Affiliation(s)
- Pita Sudrajad
- Assessment Institute for Agricultural Technology–Central Java, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Kabupaten Semarang, Indonesia
- * E-mail:
| | - Subiharta Subiharta
- Assessment Institute for Agricultural Technology–Central Java, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Kabupaten Semarang, Indonesia
| | - Yudi Adinata
- Beef Cattle Research Station, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Kabupaten Semarang, Indonesia
| | | | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | | | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
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12
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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13
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Mkize LS, Zishiri OT. Population genetic structure and maternal lineage of South African crossbred Nguni cattle using the cytochrome b gene in mtDNA. Trop Anim Health Prod 2020; 52:2079-2089. [PMID: 32048149 DOI: 10.1007/s11250-020-02231-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The Nguni cattle breed predominates South Africa and is endowed with traits favourable against environmental stressors such as heat stress and resistance to diseases. Interventions to improve production have led to the erosion of the genetic integrity of local breeds and the introduction of exotic breeds has proved ineffective as they fail to perform well due to different climatic conditions and production systems. In this study, the genetic structure and genetic lineage of Nguni crossbreds from 6 populations were assessed using the mitochondrial cytochrome b gene. Twelve polymorphic sites were detected resulting in 11 haplotypes with haplotype and nucleotide diversities of 0.550 ± 0.135 and 0.0019 ± 0.0011, respectively. Only 2 of the 6 populations displayed recent population expansion events, whereas the majority adhered to neutral evolution. The basal haplotype contained approximately 60% of the studied populations and there were four unique haplotypes that were revealed. A possible Nguni descript haplotype was uncovered, and this haplotype was found in all populations but was however devoid of individuals from around the world. The genetic structure of the populations was rather low (average pairwise FST = 0.066 and Slatkins FST = 0.094), and approximately 96% of the total genetic variation was accounted for by differences within populations. Phylogenetic analyses supported the clustering of all the samples within the Bos taurus clade and no Bos indicus haplotype was detected. Furthermore, no intermediate haplotype of taurine and indicine was detected. Overall, the maternal lineage of the crossbreds points to a taurine origin and the low genetic diversity depicts the retention of the Nguni genetic pool and possibly its superior adaptive traits.
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Affiliation(s)
| | - Oliver Tendayi Zishiri
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
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14
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Yankova I, Marinov M, Neov B, Petrova M, Spassov N, Hristov P, Radoslavov G. Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages. Genes (Basel) 2019; 10:genes10100757. [PMID: 31561553 PMCID: PMC6826387 DOI: 10.3390/genes10100757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 01/03/2023] Open
Abstract
The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs’ populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire.
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Affiliation(s)
- Iskra Yankova
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Miroslav Marinov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Boyko Neov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Maria Petrova
- Department of Structure and Function of Chromatin, Institute of Molecular Biology, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Nikolai Spassov
- Palaeontology and Mineralogy Department, National Museum of Natural History, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Peter Hristov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Georgi Radoslavov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
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15
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Ginja C, Gama LT, Cortés O, Burriel IM, Vega-Pla JL, Penedo C, Sponenberg P, Cañón J, Sanz A, do Egito AA, Alvarez LA, Giovambattista G, Agha S, Rogberg-Muñoz A, Lara MAC, Delgado JV, Martinez A. The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers. Sci Rep 2019; 9:11486. [PMID: 31391486 PMCID: PMC6685949 DOI: 10.1038/s41598-019-47636-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/16/2019] [Indexed: 12/31/2022] Open
Abstract
Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.
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Affiliation(s)
- Catarina Ginja
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
| | - Luis Telo Gama
- CIISA.Faculdade de Medicina Veterinaria, Universidade de Lisboa, Lisbon, Portugal
| | - Oscar Cortés
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.
| | - Inmaculada Martin Burriel
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Jose Luis Vega-Pla
- Laboratorio de Investigación Aplicada, Servicio de Cría Caballar de las Fuerzas Armadas, Córdoba, Spain
| | - Cecilia Penedo
- Veterinary Genetics Laboratory, University of California, Davis, California, USA
| | - Phil Sponenberg
- Virginia-Maryland Regional College of Veterinary Medicine. Virginia Tech, Virginia, USA
| | - Javier Cañón
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Arianne Sanz
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | | | | | | | - Saif Agha
- Animal Production Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | | | | | | | - Juan Vicente Delgado
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Amparo Martinez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.,Animal Beeding Consulting S.L. Universidad de Córdoba, Córdoba, Spain
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16
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da Fonseca RR, Ureña I, Afonso S, Pires AE, Jørsboe E, Chikhi L, Ginja C. Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle. BMC Genomics 2019; 20:334. [PMID: 31053061 PMCID: PMC6500009 DOI: 10.1186/s12864-019-5685-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns. RESULTS We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow. CONCLUSIONS Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.
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Affiliation(s)
- Rute R. da Fonseca
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Irene Ureña
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Ana Elisabete Pires
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- LARC, Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisbon, Portugal
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lounès Chikhi
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande n°6, P-2780-156 Oeiras, Portugal
| | - Catarina Ginja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
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Siripan S, Wonnapinij P, Auetrakulvit P, Wangthongchaicharoen N, Surat W. Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:609-617. [PMID: 30957607 DOI: 10.1080/24701394.2019.1597072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B. taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.
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Affiliation(s)
- Sirianong Siripan
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand
| | - Passorn Wonnapinij
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand.,b Centre for Advanced Studies in Tropical Natural Resources , National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU) , Bangkok , Thailand
| | - Prasit Auetrakulvit
- c Department of Archaeology, Faculty of Archaeology , Silpakorn University , Bangkok , Thailand
| | | | - Wunrada Surat
- a Department of Genetics, Faculty of Science, Evolutionary Genetics and Computational Biology Research Unit , Kasetsart University , Bangkok , Thailand.,b Centre for Advanced Studies in Tropical Natural Resources , National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU) , Bangkok , Thailand
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18
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Elayadeth‐Meethal M, Thazhathu Veettil A, Maloney SK, Hawkins N, Misselbrook TH, Sejian V, Rivero MJ, Lee MRF. Size does matter: Parallel evolution of adaptive thermal tolerance and body size facilitates adaptation to climate change in domestic cattle. Ecol Evol 2018; 8:10608-10620. [PMID: 30464832 PMCID: PMC6238145 DOI: 10.1002/ece3.4550] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/01/2018] [Accepted: 08/04/2018] [Indexed: 01/18/2023] Open
Abstract
The adaptive potential of livestock under a warming climate is increasingly relevant in relation to the growing pressure of global food security. Studies on heat tolerance demonstrate the interplay of adaptation and acclimatization in functional traits, for example, a reduction in body size and enhanced tolerance in response to a warming climate. However, current lack of understanding of functional traits and phylogenetic history among phenotypically distinct populations constrains predictions of climate change impact. Here, we demonstrate evidence of parallel evolution in adaptive tolerance to heat stress in dwarf cattle breeds (DCB, Bos taurus indicus) and compare their thermoregulatory responses with those in standard size cattle breeds (SCB, crossbred, Bos taurus indicus × Bos taurus taurus). We measured vital physiological, hematological, biochemical, and gene expression changes in DCB and SCB and compared the molecular phylogeny using mitochondrial genome (mitogenome) analysis. Our results show that SCB can acclimatize in the short term to higher temperatures but reach their tolerance limit under prevailing tropical conditions, while DCB is adapted to the warmer climate. Increased hemoglobin concentration, reduced cellular size, and smaller body size enhance thermal tolerance. Mitogenome analysis revealed that different lineages of DCB have evolved reduced size independently, as a parallel adaptation to heat stress. The results illustrate mechanistic ways of dwarfing, body size-dependent tolerance, and differential fitness in a large mammal species under harsh field conditions, providing a background for comparing similar populations during global climate change. These demonstrate the value of studies combining functional, physiological, and evolutionary approaches to delineate adaptive potential and plasticity in domestic species. We thus highlight the value of locally adapted breeds as a reservoir of genetic variation contributing to the global domestic genetic resource pool that will become increasingly important for livestock production systems under a warming climate.
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Affiliation(s)
- Muhammed Elayadeth‐Meethal
- Kerala Veterinary and Animal Sciences UniversityWayanadIndia
- School of Human SciencesUniversity of Western AustraliaCrawleyAustralia
- Rothamsted ResearchNorth WykeUK
| | | | - Shane K. Maloney
- School of Human SciencesUniversity of Western AustraliaCrawleyAustralia
| | | | | | - Veerasamy Sejian
- ICAR‐National Institute of Animal Nutrition and PhysiologyBangaloreIndia
| | | | - Michael R. F. Lee
- Rothamsted ResearchNorth WykeUK
- Bristol Veterinary SchoolUniversity of BristolLangfordUK
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19
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Di Lorenzo P, Lancioni H, Ceccobelli S, Colli L, Cardinali I, Karsli T, Capodiferro MR, Sahin E, Ferretti L, Ajmone Marsan P, Sarti FM, Lasagna E, Panella F, Achilli A. Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin. PLoS One 2018; 13:e0192567. [PMID: 29462170 PMCID: PMC5819780 DOI: 10.1371/journal.pone.0192567] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin. METHODOLOGY The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison. CONCLUSION The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (Chianina, Marchigiana, Maremmana, Podolica Italiana and Romagnola) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.
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Affiliation(s)
- Piera Di Lorenzo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- * E-mail: (HL); (AA)
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, University of Akdeniz, Antalya, Turkey
| | | | - Emine Sahin
- Korkuteli Vocational School, University of Akdeniz, Antalya, Turkey
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Francesca Maria Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesco Panella
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
- * E-mail: (HL); (AA)
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20
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Abdoli R, Zamani P, Ghasemi M. Genetic similarities and phylogenetic analysis of human and farm animal species based on mitogenomic nucleotide sequences. Meta Gene 2018. [DOI: 10.1016/j.mgene.2017.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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21
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Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017; 7:16196. [PMID: 29170422 PMCID: PMC5700937 DOI: 10.1038/s41598-017-16438-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.
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22
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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23
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Zhang Y, Lu Y, Yindee M, Li K, Kuo H, Ju Y, Ye S, Faruque MO, Li Q, Wang Y, Cuong VC, Pham LD, Bouahom B, Yang B, Liang X, Cai Z, Vankan D, Manatchaiworakul W, Kowlim N, Duangchantrasiri S, Wajjwalku W, Colenbrander B, Zhang Y, Beerli P, Lenstra JA, Barker JSF. Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region. Mol Ecol 2016; 25:1530-50. [DOI: 10.1111/mec.13518] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 11/30/2015] [Accepted: 12/10/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Yi Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yongfang Lu
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Marnoch Yindee
- Department of Clinical Science and Public Health Faculty of Veterinary Science Mahidol University Kanchanaburi Campus Kanchanaburi 71150 Thailand
| | - Kuan‐Yi Li
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Hsiao‐Yun Kuo
- Livestock Research Institute Council of Agriculture Tainan 71246 Taiwan
| | - Yu‐Ten Ju
- Department of Animal Science and Technology National Taiwan University Taipei 10673 Taiwan
| | - Shaohui Ye
- College of Animal Science and Technology Yunnan Agricultural University Kunming 650201 China
| | - Md Omar Faruque
- Department of Animal Breeding and Genetics Bangladesh Agricultural University Mymensingh 2202 Bangladesh
| | - Qiang Li
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Vu Chi Cuong
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Lan Doan Pham
- Key Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 Vietnam
| | - Bounthong Bouahom
- National Agriculture and Forestry Research Institute P.O. Box 811 Vientiane Capital Lao P.D.R
| | - Bingzhuang Yang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Xianwei Liang
- Guangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 China
| | - Zhihua Cai
- College of Animal Science Anhui Science and Technology University Fengyang 233100 China
| | - Dianne Vankan
- The School of Veterinary Science University of Queensland, Gatton Campus Gatton Qld 4343 Australia
| | - Wallaya Manatchaiworakul
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Nonglid Kowlim
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Somphot Duangchantrasiri
- Khao‐Nang‐Ram Wildlife Research Station Department of National Parks Wildlife and Plant Conservation Bangkok 10900 Thailand
| | - Worawidh Wajjwalku
- Department of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 Thailand
| | - Ben Colenbrander
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - Yuan Zhang
- National Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 China
| | - Peter Beerli
- Department of Scientific Computing Florida State University Tallahassee FL 32306‐4120 USA
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The Netherlands
| | - J. Stuart F. Barker
- School of Environmental and Rural Science University of New England Armidale NSW 2351 Australia
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24
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Lancioni H, Di Lorenzo P, Cardinali I, Ceccobelli S, Capodiferro MR, Fichera A, Grugni V, Semino O, Ferretti L, Gruppetta A, Attard G, Achilli A, Lasagna E. Survey of uniparental genetic markers in the Maltese cattle breed reveals a significant founder effect but does not indicate local domestication. Anim Genet 2016; 47:267-9. [DOI: 10.1111/age.12408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie; Università degli Studi di Perugia; Perugia 06123 Italy
| | - Piera Di Lorenzo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali; Università degli Studi di Perugia; Perugia 06121 Italy
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie; Università degli Studi di Perugia; Perugia 06123 Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali; Università degli Studi di Perugia; Perugia 06121 Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Chimica, Biologia e Biotecnologie; Università degli Studi di Perugia; Perugia 06123 Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Alessandro Fichera
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Viola Grugni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Anthony Gruppetta
- Department of Rural Sciences and Food Systems; Institute of Earth Systems; University of Malta; Msida MSD 2080 Malta
| | - George Attard
- Department of Rural Sciences and Food Systems; Institute of Earth Systems; University of Malta; Msida MSD 2080 Malta
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie; Università degli Studi di Perugia; Perugia 06123 Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali; Università degli Studi di Perugia; Perugia 06121 Italy
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25
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Olivieri A, Gandini F, Achilli A, Fichera A, Rizzi E, Bonfiglio S, Battaglia V, Brandini S, De Gaetano A, El-Beltagi A, Lancioni H, Agha S, Semino O, Ferretti L, Torroni A. Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East. PLoS One 2015; 10:e0141170. [PMID: 26513361 PMCID: PMC4626031 DOI: 10.1371/journal.pone.0141170] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/04/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East. METHODOLOGY Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed. CONCLUSIONS Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.
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Affiliation(s)
- Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
- * E-mail:
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Alessandro Fichera
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (Milano), Italy
- Fondazione Telethon, Milano, Italy
| | - Silvia Bonfiglio
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Anna De Gaetano
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Ahmed El-Beltagi
- Animal Production Research Institute (APRI), Ministry of Agriculture, Cairo, Egypt
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Saif Agha
- Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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26
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Park SDE, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol 2015; 16:234. [PMID: 26498365 PMCID: PMC4620651 DOI: 10.1186/s13059-015-0790-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/25/2015] [Indexed: 11/10/2022] Open
Abstract
Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0790-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephen D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland.
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,Department of Animal Science, University of Connecticut, Storrs, CT, 06029, USA.
| | - Paul A McGettigan
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Ceiridwen J Edwards
- Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Rd, Oxford, OX1 3QY, UK.
| | - Amanda J Lohan
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Alison Murphy
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Martin Braud
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Mark T Donoghue
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Yuan Liu
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Andrew T Chamberlain
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Steven Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA.
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Shuaishuai Tai
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland.
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA. .,Recombinetics Inc., St. Paul, MN, 55104, USA.
| | - Brendan J Loftus
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. .,UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
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27
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Scheu A, Powell A, Bollongino R, Vigne JD, Tresset A, Çakırlar C, Benecke N, Burger J. The genetic prehistory of domesticated cattle from their origin to the spread across Europe. BMC Genet 2015; 16:54. [PMID: 26018295 PMCID: PMC4445560 DOI: 10.1186/s12863-015-0203-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/20/2015] [Indexed: 11/25/2022] Open
Abstract
Background Cattle domestication started in the 9th millennium BC in Southwest Asia. Domesticated cattle were then introduced into Europe during the Neolithic transition. However, the scarcity of palaeogenetic data from the first European domesticated cattle still inhibits the accurate reconstruction of their early demography. In this study, mitochondrial DNA from 193 ancient and 597 modern domesticated cattle (Bos taurus) from sites across Europe, Western Anatolia and Iran were analysed to provide insight into the Neolithic dispersal process and the role of the local European aurochs population during cattle domestication. Results Using descriptive summary statistics and serial coalescent simulations paired with approximate Bayesian computation we find: (i) decreasing genetic diversity in a southeast to northwest direction, (ii) strong correlation of genetic and geographical distances, iii) an estimated effective size of the Near Eastern female founder population of 81, iv) that the expansion of cattle from the Near East and Anatolia into Europe does not appear to constitute a significant bottleneck, and that v) there is evidence for gene-flow between the Near Eastern/Anatolian and European cattle populations in the early phases of the European Neolithic, but that it is restricted after 5,000 BCE. Conclusions The most plausible scenario to explain these results is a single and regionally restricted domestication process of cattle in the Near East with subsequent migration into Europe during the Neolithic transition without significant maternal interbreeding with the endogenous wild stock. Evidence for gene-flow between cattle populations from Southwestern Asia and Europe during the earlier phases of the European Neolithic points towards intercontinental trade connections between Neolithic farmers. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0203-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amelie Scheu
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany. .,German Archaeological Institute, Scientific Department, Im Dol 2-6, Haus 2, 14195, Berlin, Germany.
| | - Adam Powell
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany.
| | - Ruth Bollongino
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany. .,Muséum National d'Histoire Naturelle, UMR7209, "Archéozoologie, archéobotanique: sociétés, pratiques et environnements", InEE, Département d'Ecologie et Gestion de la Biodiversité, CP 56, 55 rue Buffon, 75005, Paris, Cedex 05, France.
| | - Jean-Denis Vigne
- Muséum National d'Histoire Naturelle, UMR7209, "Archéozoologie, archéobotanique: sociétés, pratiques et environnements", InEE, Département d'Ecologie et Gestion de la Biodiversité, CP 56, 55 rue Buffon, 75005, Paris, Cedex 05, France.
| | - Anne Tresset
- Muséum National d'Histoire Naturelle, UMR7209, "Archéozoologie, archéobotanique: sociétés, pratiques et environnements", InEE, Département d'Ecologie et Gestion de la Biodiversité, CP 56, 55 rue Buffon, 75005, Paris, Cedex 05, France.
| | - Canan Çakırlar
- University of Groningen, Institute of Archaeology, Poststraat 6, NL-9712 ER, Groningen, Netherlands.
| | - Norbert Benecke
- German Archaeological Institute, Scientific Department, Im Dol 2-6, Haus 2, 14195, Berlin, Germany.
| | - Joachim Burger
- Johannes Gutenberg-University Mainz, Institute of Anthropology, Palaeogenetics Group, 55099, Mainz, Germany.
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28
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Gargani M, Pariset L, Lenstra JA, De Minicis E, Valentini A. Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle. Front Genet 2015; 6:68. [PMID: 25788902 PMCID: PMC4349168 DOI: 10.3389/fgene.2015.00068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/10/2015] [Indexed: 12/02/2022] Open
Abstract
Analysis of DNA from archeological remains is a valuable tool to interpret the history of ancient animal populations. So far most studies of ancient DNA target mitochondrial DNA (mtDNA), which reveals maternal lineages, but only partially the relationships of current breeds and ancient populations. In this study we explore the feasibility of nuclear DNA analysis. DNA was extracted from 1000-years old cattle bone collected from Ferento, an archeological site in central Italy. Amplification of 15 microsatellite FAO-recommended markers with PCR products yielded genotypes for four markers. Expected heterozygosity was comparable with values of modern breeds, but observed heterozygosity was underestimated due to allelic loss. Genetic distances suggested a position intermediate between (1) Anatolian, Balkan, Sicilian and South-Italian cattle and (2) the Iberian, North-European and Central-European cattle, but also a clear relationship with two central-Italian breeds, Chianina and Romagnola. This suggests that these breeds are derived from medieval cattle living in the same area. Our results illustrate the potential of ancient DNA for reconstructing the history of local cattle husbandry.
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Affiliation(s)
- Maria Gargani
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia Viterbo, Italy
| | - Lorraine Pariset
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia Viterbo, Italy
| | | | - Elisabetta De Minicis
- Department of Sciences of Cultural Heritage (DISBEC), University of Tuscia Viterbo, Italy
| | | | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest systems, University of Tuscia Viterbo, Italy
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Hristov P, Teofanova D, Neov B, Radoslavov G. Haplotype diversity in autochthonous Balkan cattle breeds. Anim Genet 2014; 46:92-4. [DOI: 10.1111/age.12253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2014] [Indexed: 11/29/2022]
Affiliation(s)
- P. Hristov
- Department of Animal Diversity and Resources; Institute of Biodiversity and Ecosystem Research; Bulgarian Academy of Sciences; Sofia 1113 Bulgaria
| | - D. Teofanova
- Department of Animal Diversity and Resources; Institute of Biodiversity and Ecosystem Research; Bulgarian Academy of Sciences; Sofia 1113 Bulgaria
| | - B. Neov
- Department of Animal Diversity and Resources; Institute of Biodiversity and Ecosystem Research; Bulgarian Academy of Sciences; Sofia 1113 Bulgaria
| | - G. Radoslavov
- Department of Animal Diversity and Resources; Institute of Biodiversity and Ecosystem Research; Bulgarian Academy of Sciences; Sofia 1113 Bulgaria
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30
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Abstract
Cattle are our most important livestock species because of their production and role in human culture. Many breeds that differ in appearance, performance and environmental adaptation are kept on all inhabited continents, but the historic origin of the diverse phenotypes is not always clear. We give an account of the history of cattle by integrating archaeological record and pictorial or written sources, scarce until 300 years ago, with the recent contributions of DNA analysis. We describe the domestication of their wild ancestor, migrations to eventually all inhabited continents, the developments during prehistory, the antiquity and the Middle Ages, the relatively recent breed formation, the industrial cattle husbandry in the Old and New World and the current efforts to preserve the cattle genetic resources. Surveying the available information, we propose three main and overlapping phases during the development of the present genetic diversity: (i) domestication and subsequent wild introgression; (ii) natural adaptation to a diverse agricultural habitat; and (iii) breed development.
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31
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Magee DA, MacHugh DE, Edwards CJ. Interrogation of modern and ancient genomes reveals the complex domestic history of cattle. Anim Front 2014. [DOI: 10.2527/af.2014-0017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- David A. Magee
- Animal Genomics Laboratory, School of Agriculture and Food Science, College of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, School of Agriculture and Food Science, College of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
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