Frontiers in Genetics (Mar 2018)
New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data
- Licia Colli,
- Licia Colli,
- Marco Milanesi,
- Marco Milanesi,
- Marco Milanesi,
- Elia Vajana,
- Daniela Iamartino,
- Daniela Iamartino,
- Lorenzo Bomba,
- Francesco Puglisi,
- Marcello Del Corvo,
- Ezequiel L. Nicolazzi,
- Sahar S. E. Ahmed,
- Jesus R. V. Herrera,
- Libertado Cruz,
- Shujun Zhang,
- Aixin Liang,
- Guohua Hua,
- Liguo Yang,
- Xingjie Hao,
- Fuyuan Zuo,
- Song-Jia Lai,
- Shuilian Wang,
- Ruyu Liu,
- Yundeng Gong,
- Mahdi Mokhber,
- Yongjiang Mao,
- Feng Guan,
- Augustin Vlaic,
- Bogdan Vlaic,
- Luigi Ramunno,
- Gianfranco Cosenza,
- Ali Ahmad,
- Ihsan Soysal,
- Emel Ö. Ünal,
- Mariena Ketudat-Cairns,
- José F. Garcia,
- José F. Garcia,
- José F. Garcia,
- Yuri T. Utsunomiya,
- Yuri T. Utsunomiya,
- Pietro S. Baruselli,
- Maria E. J. Amaral,
- Rangsun Parnpai,
- Marcela G. Drummond,
- Peter Galbusera,
- James Burton,
- James Burton,
- Eileen Hoal,
- Yulnawati Yusnizar,
- Yulnawati Yusnizar,
- Cece Sumantri,
- Bianca Moioli,
- Alessio Valentini,
- Alessandra Stella,
- John L. Williams,
- Paolo Ajmone-Marsan,
- Paolo Ajmone-Marsan
Affiliations
- Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Licia Colli
- Centro di Ricerca sulla Biodiversità e sul DNA Antico (BioDNA), Piacenza, Italy
- Marco Milanesi
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Marco Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil
- Marco Milanesi
- International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
- Elia Vajana
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Daniela Iamartino
- PTP Science Park, Lodi, Italy
- Daniela Iamartino
- LGS-AIA Associazione Italiana Allevatori, Cremona, Italy
- Lorenzo Bomba
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Francesco Puglisi
- Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Università degli Studi di Parma, Parma, Italy
- Marcello Del Corvo
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Ezequiel L. Nicolazzi
- PTP Science Park, Lodi, Italy
- Sahar S. E. Ahmed
- Cell Biology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Giza, Egypt
- Jesus R. V. Herrera
- Philippine Carabao Centre, Nueva Ecija, Philippines
- Libertado Cruz
- Philippine Carabao Centre, Nueva Ecija, Philippines
- Shujun Zhang
- 0Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Aixin Liang
- 0Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Guohua Hua
- 0Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Liguo Yang
- 0Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Xingjie Hao
- 0Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Fuyuan Zuo
- 1Department of Animal Husbandry, Southwest University, Chongqing, China
- Song-Jia Lai
- 2Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
- Shuilian Wang
- 3College of Veterinary Medicine, Hunan Agricultural University, Changsha, China
- Ruyu Liu
- 4College of Animal Science, Guizhou University, Guiyang, China
- Yundeng Gong
- 5Enshi Technology College, Enshi, China
- Mahdi Mokhber
- 6Department of Animal Science, Faculty of Agricultural Science, Urmia University, Urmia, Iran
- Yongjiang Mao
- 7College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Feng Guan
- 8College of Life Science, China Jiliang University, Hangzhou, China
- Augustin Vlaic
- 9Department of Animal Genetics, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania
- Bogdan Vlaic
- 9Department of Animal Genetics, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania
- Luigi Ramunno
- 0Department of Agriculture, University of Naples Federico II, Portici, Italy
- Gianfranco Cosenza
- 0Department of Agriculture, University of Naples Federico II, Portici, Italy
- Ali Ahmad
- 1COMSATS Institute of Information Technology, Sahiwal, Pakistan
- Ihsan Soysal
- 2Department of Animal Science, Faculty of Agriculture, Namik Kemal University, Tekirdag, Turkey
- Emel Ö. Ünal
- 2Department of Animal Science, Faculty of Agriculture, Namik Kemal University, Tekirdag, Turkey
- Mariena Ketudat-Cairns
- 3School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
- José F. Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, Araçatuba, Brazil
- José F. Garcia
- International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
- José F. Garcia
- 4Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp.), São Paulo, Brazil
- Yuri T. Utsunomiya
- International Atomic Energy Agency (IAEA), Colaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
- Yuri T. Utsunomiya
- 4Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp.), São Paulo, Brazil
- Pietro S. Baruselli
- 5Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
- Maria E. J. Amaral
- 6Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, Brazil
- Rangsun Parnpai
- 3School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
- Marcela G. Drummond
- 7R&D Department, Myleus, Belo Horizonte, Brazil
- Peter Galbusera
- 8Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
- James Burton
- 9IUCN SSC Asian Wild Cattle Specialist Group and Chester Zoo, Upton by Chester, United Kingdom
- James Burton
- 0Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Roslin, United Kingdom
- Eileen Hoal
- 1NRF/DST Centre of Excellence for Biomedical TB Research, MRC Centre for TB Research, and Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
- Yulnawati Yusnizar
- 2Research Centre for Biotechnology, Indonesian Institute of Sciences, Jalan Raya, Indonesia
- Yulnawati Yusnizar
- 3Indonesian Buffalo Conservation and Breeding Centre, Ciapus-Bogor, Indonesia
- Cece Sumantri
- 4Department of Animal Production and Technology, Bogor Agricultural University (IPB), Bogor, Indonesia
- Bianca Moioli
- 5Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Monterotondo, Italy
- Alessio Valentini
- 6Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, DIBAF, Università della Tuscia, Viterbo, Italy
- Alessandra Stella
- PTP Science Park, Lodi, Italy
- John L. Williams
- 7The Davies Research Centre, School of Animal and Veterinary Science, University of Adelaide, Roseworthy, SA, Australia
- Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Paolo Ajmone-Marsan
- Centro di Ricerca sulla Biodiversità e sul DNA Antico (BioDNA), Piacenza, Italy
- DOI
- https://doi.org/10.3389/fgene.2018.00053
- Journal volume & issue
-
Vol. 9
Abstract
The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.
Keywords
