Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity

Saeid Naderi, Hamid Reza Rezaei, Pierre Taberlet, Stéphanie Zundel, Seyed Abbas Rafat, Hamid Reza Naghash, Mohamed A.A. El-Barody, Okan Ertugrul, François Pompanon, Mahamoud Abo-Shehada, Paolo Marsan Ajmone, Jamil Al Tarrayrah, Antonella Angiolillo, Philip Baret, Roswitha Baumung, Albano Beja-Pereira, Marco Bertaglia, Salvatore Bordonaro, Mike Bruford, Régis CalozGabriele Canali, Javier Canon, Irene Cappuccio, Antonello Carta, Mario Cicogna, Paola Crepaldi, Stella Dalamitra, Daniela Krugmann, Petrit Dobi, Dominik Popielarczyk, Susana Dunner, Giuseppe D'Urso, M. A.A. El-Barody, Phillip England, Georg Erhardt, Okan Ertugrul, Eva Maria Prinzenberg, Eveline Ibeagha-Awemu, Ewa Strzelec, Fadlaoui Aziz, Francesca Fornarelli, David Garcia, Andreas Georgoudis, Lühken Gesine, Stefano Giovenzana, Katja Gutscher, Godfrey Hewitt, Anila Hoda, Brandt Horst, Anton Istvan, Gabriela Juma, Stéphane Joost, Sam Jones, Katerina Karetsou, Georgios Kliambas, Evren Koban, Olga Kutita, Fesus Lazlo, Johannes A. Lenstra, Christina Ligda, Shirin Lipsky, Gordon Luikart, Marie Louise Glowatzki, Marta Marilli, Donata Marletta, Elisabetta Milanesi, Riccardo Negrini, Isaäc J. Nijman, Gabriela Obexer-Ruff, Christos Papachristoforou, Lorraine Pariset, Marco Pellecchia, Christina Peter, Trinidad Perez, Emilio Pietrolà, Fabio Pilla, Roman Niznikowski, Jutta Roosen, Riccardo Scarpa, Tiziana Sechi, Pierre Taberlet, Martin Taylor, Inci Togan, Michel Trommetter, Alessio Valentini, Lisette M. Van Cann, Augustin Vlaic, Louise Wiskin, Stéphanie Zundel

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Abstract

Background. From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species. Methodolog/Principal Findings. The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogioups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals. Conclusions/Significance. We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.

Original languageEnglish
Article numbere1012
JournalPLoS ONE
Volume2
Issue number10
DOIs
StatePublished - Oct 10 2007

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