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Front. Genet. | doi: 10.3389/fgene.2018.00053

New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data

 Licia Colli1, 2*,  Marco Milanesi1, 3,  Elia Vajana1, Daniela Iamartino4, 5, Lorenzo Bomba1,  Francesco Puglisi6,  Marcello Del Corvo1,  Ezequiel L. Nicolazzi4,  Sahar Saad El-din Ahmed7,  Jesus R. Herrera8, Libertado Cruz8, Shuju Zhang9, 10, Aixin Liang10, Guohua Hua10, Liguo Yang9, 10, Xingjie Hao9, 10, Fuyuan Zuo11, Song-Jia Lai12, Shuilian Wang13, Ruyu Liu14, Yundeng Gong15,  Mahdi Mokhber16, Yongjiang Mao17, Feng Guan18, Augustin Vlaic19,  Bogdan Vlaic19, Luigi Ramunno20, Gianfranco Cosenza20, Ali Ahmad21,  Ihsan Soysal22, Emel Özkan Ünal22,  Mariena Ketudat-Cairns23,  Jose Fernando Garcia24, 25,  Yuri T. Utsunomiya25, Pietro S. Baruselli26, Maria Elisabete J. Amaral27, Rangsun Parnpai23, Marcela G. Drummond28, Peter Galbusera29, James Burton30, 31, Eileen Hoal32, Yulnawati Yusnizar33, 34, Cece Sumantri35, Bianca Moioli36, Alessio Valentini37, Alessandra Stella4,  John L. Williams38 and  Paolo Ajmone Marsan1, 2
  • 1Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Italy
  • 2Centro di Ricerca sulla Biodiversità e sul DNA Antico – BioDNA, Università Cattolica del Sacro Cuore, Italy
  • 3Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, UNESP, Brazil
  • 4PTP Science Park, Italy
  • 5LGS-AIA Associazione Italiana Allevatori, Italy
  • 6Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali, Università degli Studi di Parma, Italy
  • 7National Research Centre, Egypt
  • 8Philippine Carabao Centre, Philippines
  • 9Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, China
  • 10Hubei Province Engineering Research Center in Buffalo Breeding & Products, China
  • 11Southwest University, China
  • 12Institute of Animal Genetics and Breeding, Sichuan Agricultural University, China
  • 13Hunan Agricultural University, China
  • 14Guizhou University, China
  • 15Enshi Vocational and Technical College, China
  • 16Department of Animal Science, Faculty of Agricultural Science, Urmia University, Iran
  • 17Yangzhou University, China
  • 18China Jiliang University, China
  • 19University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Romania
  • 20Department of Agriculture, University of Naples “Federico II”, Italy
  • 21COMSATS Institute of Information Technology, Pakistan
  • 22Namik Kemal University, Turkey
  • 23Suranaree University of Technology, Thailand
  • 24School of Veterinary Medicine, Department of Support, Production and Animal Health, Universidade Estadual Paulista, UNESP, Brazil
  • 25School of Agricultural and Veterinarian Sciences, Department of Preventive Veterinary Medicine and Animal Reproduction, Universidade Estadual Paulista, UNESP, Brazil
  • 26Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo (USP), Brazil
  • 27Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista, UNESP, Brazil
  • 28Myleus Biotecnologia, Brazil
  • 29Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Belgium
  • 30Chester Zoo, United Kingdom
  • 31Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburg, United Kingdom
  • 32NRF/DST Centre of Excellence for Biomedical TB research, MRC Centre for TB research, and Division of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
  • 33Research Centre for Biotechnology, Indonesian Institute of Sciences, Indonesia
  • 34Indonesian Buffalo Conservation and Breeding Centre, Indonesia
  • 35Bogor Agricultural University, Indonesia
  • 36Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Italy
  • 37Dipartimento per l’Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, DIBAF, Università della Tuscia, Italy
  • 38The Davies Research Centre, School of Animal and Veterinary Science, University of Adelaide, Australia

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 behavioural 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 archaeological, 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 centres 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: river buffalo, Swamp buffalo, Bubalus bubalis, SNP, Genomic Diversity, Domestication, evolutionary history

Received: 10 Oct 2017; Accepted: 02 Feb 2018.

Edited by:

Martien Groenen, Wageningen University & Research, Netherlands

Reviewed by:

Jesús Fernández, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Spain
Evan K. Irving-Pease, University of Oxford, United Kingdom  

Copyright: © 2018 Colli, Milanesi, Vajana, Iamartino, Bomba, Puglisi, Del Corvo, Nicolazzi, Ahmed, Herrera, Cruz, Zhang, Liang, Hua, Yang, Hao, Zuo, Lai, Wang, Liu, Gong, Mokhber, Mao, Guan, Vlaic, Vlaic, Ramunno, Cosenza, Ahmad, Soysal, Ünal, Ketudat-Cairns, Garcia, Utsunomiya, Baruselli, Amaral, Parnpai, Drummond, Galbusera, Burton, Hoal, Yusnizar, Sumantri, Moioli, Valentini, Stella, Williams and Ajmone Marsan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Licia Colli, Università Cattolica del Sacro Cuore, Istituto di Zootecnica, Piacenza, Italy, licia.colli@unicatt.it