Integrating Y-Chromosome, Mitochondrial and autosomal data to analyse the origin of pig breeds

We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populations. The analysis of nuclear markers evidenced the existence of a close genetic relationship between Near Eastern and European wild boars making difficult to infer their relative contributions to the gene pool of modern European breeds. Moreover, we have shown that European and Far Eastern pig populations have contributed maternal and paternal lineages to the foundation of African and South American breeds. While West African pigs from Nigeria and Benin exclusively harboured European alleles, Far Eastern and European genetic signatures of similar intensity were detected in swine breeds from Eastern Africa. This region seems to have been a major point of entry of livestock species in the African continent as a result of the Indian Ocean trade. Finally, South American creole breeds had essentially a European ancestry although Asian Y-chromosome and mitochondrial haplotypes were found in a few Nicaraguan pigs. The existence of Spanish and Portuguese commercial routes linking Asia with America might have favoured the introduction of Far Eastern breeds into this continent

Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds

We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite, and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populations. The analysis of nuclear markers evidenced the existence of a close genetic relationship between Near Eastern and European wild boars making it difficult to infer their relative contributions to the gene pool of modern European breeds. Moreover, we have shown that European and Far Eastern pig populations have contributed maternal and paternal lineages to the foundation of African and South American breeds. Although West African pigs from Nigeria and Benin exclusively harbored European alleles, Far Eastern and European genetic signatures of similar intensity were detected in swine breeds from Eastern Africa. This region seems to have been a major point of entry of livestock species in the African continent as a result of the Indian Ocean trade. Finally, South American creole breeds had essentially a European ancestry although Asian Y-chromosome and mitochondrial haplotypes were found in a few Nicaraguan pigs. The existence of Spanish and Portuguese commercial routes linking Asia with America might have favored the introduction of Far Eastern breeds into this continent. © The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.We are grateful to Carles Vila`, Carles Lalueza, and Ju- lio Rozas for critically reading the manuscript. We are also indebted to Maria San ̃ a for valuable comments about the process of pig domestication and to Francesc Calafell for helping in the statistical analyses. Many thanks to all of those contributing to sample collection: G. Aktan (Ay-FSafari), A.R. Jafari-Tabrizi (Iran Safari), S. Shushunov (Russian Hunting Agency), F. Pilla (University of Molise), J. Tibau (Institut de Recerca i Tecnologia Agroalimenta `- ries), J. Capote (Instituto Canario de Investigaciones Agrarias), A. Linden (University of Liege), J.L. Noguera (Institut de Recerca i Tecnologia Agroalimenta`ries), L. Silio ́ and M.C. Valdovinos (Instituto Nacional de Investi- gaciones Agrarias, Spain), E. Martı ́nez (Zoo of Madrid), N. Okumura (STAFF Institute Japan), G. Rohrer (United States Department of Agriculture), Z. Bosze (Agricultural Biotechnology Center, Hungary), M. Cumbreras (Diputa- cio ́ n de Huelva, Spain), E. von Eckardt (Sweden), M.T. Par- amio (Universitat Auto` noma de Barcelona, Spain), O. Vidal (Universitat de Girona, Spain), M. Kovac (Slovenia), D. Vidal and C. Gorta ́zar (Instituto de Investigacio ́ n en Re- cursos Cinege ́ticos, Spain), Instituto de Capacitacio ́ n del Oriente (Bolivia), Veterinarios Sin Fronteras (Spain). A.O. and D.G. were recipients of PhD grants from the Min- isterio de Educacio ́ n y Ciencia, (Spain) and Universitat Auto` noma de Barcelona. O.R. received funding from the Molecular Genetics Veterinary Service of the Universitat Auto ` noma of Barcelona (http://svgm.uab.es/svgm). This study was partially funded by projects AGL2002-04271- C03-03 and AGL2007-66707-C02-02 (Ministry of Educa- tion and Science, Spain) to M.A.; AGL2004-0103, AECI/ 5267/06, and BFU2004-02253 (Ministry of Education and Science, Spain) to M.P.E.; AGL2000-1229-C03-03 (Ministry of Education and Science, Spain) to A.S. and National Natural Science Foundation of China (grant 30425045) to L.S.H.Peer Reviewe