ORIGINAL ARTICLE Mitochondrial D-loop analysis reveals low diversity in Mangalica pigs and their relationship to historical specimens J. Molna ´r 1 , G. To ´ th 2 , V. Ste ´ ger 2 , A. Zsolnai 3 , A. Ja ´ nosi 4 , A. Mohr 1 , R. Sza ´ nto ´ -Ege ´ sz 1 , P. To ´ th 5 , A. Micsinai 1 , J. Ra ´ tky 3 & F. Marincs 2 1 Biomi Ltd., Go ¨ do ¨ ll} o, Hungary 2 Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Center, Go ¨ do ¨ ll} o, Hungary 3 Research Institute for Animal Breeding and Nutrition, Herceghalom, Hungary 4 Central Food Research Institute, Budapest, Hungary 5 Olmos and To ´ th Ltd., Debrecen, Hungary Keywords Ancestor DNA; genetic distances; phylogenetic tree; pig breeds; SNP. Correspondence F. Marincs, Agricultural Genomics and Bioinformatics Group, Agricultural Biotechnology Center, H-2100 Go ¨ do ¨ ll} o, Szent- Gyo ¨ rgyi Albert u. 4., Hungary. Tel: +36 28 526 225; Fax: +36 28 526 198; E-mail: marincsf@abc.hu Received: 23 February 2012; accepted: 4 June 2012 Summary The genetic relationship between 195 Mangalica and 79 non-Mangalica pigs was studied using mitochondrial D-loop SNP genotyping. Altogether, 35 polymorphic sites and 27 haplotypes were identified. Of the haplo- types, eight and 16 are Mangalica and non-Mangalica specific, respec- tively, while three contain both Mangalica and non-Mangalica individuals. Genetic distance values and phylogenetic analysis indicate that Mangalica individuals are very closely related, and five haplotypes represent approximately 92% of the Mangalica pigs involved in the study, thus determining the major maternal lineages. In contrast to previous microsatellite studies, individuals of Mangalica could not be distinguished as three separate breeds using mtDNA genotyping. Comparing modern and archaeological mtDNA sequences revealed that present day Mangalica is related to pigs that lived in the Carpathian basin where postulated ancestors of Mangalica also lived. This is the first DNA-based genetic evidence to support the described breeding history of Mangalica. Introduction Breeds are defined as distinct groups of domesticated animal species that can be distinguished by both qual- itative and/or quantitative characters. However, using the traditional definition, it is not easy to attribute individual animals to a specific breed. Members of a breed may share a common ancestry, but they do not necessarily represent a closed and geographically sep- arated population. On the other hand, in geographi- cally and/or ecologically isolated populations of a breed, unique physiological characteristics may arise due to different selection criteria set during the breed- ing process. Therefore, isolated populations may become genetically distinct from other populations of the same breed with similar phenotype and could be considered as different breeds. Furthermore, animals of the same species, which might belong to potentially different breeds, are often similar physiologically and cover the same region, and there is little reproductive isolation between their populations. Therefore, in addition to or even replacing the traditional character- ization of breeds based on phenotypical, physiological and adaptive characters, molecular approaches are spreading quickly as an alternative. For the genetic studies of breeds, microsatellite, AFLP, mtDNA and chromosomal SNP markers are widely employed (Toro et al. 2009). Pig (Sus scrofa) is a domesticated animal, which has a large number of breeds. For example, the website of the International Livestock Research Institute (ILRI) claims that domesticated pig has 350 breeds (http:// agtr.ilri.cgiar.org; Module: “Improving knowl- edge”, Table 1). The genetic diversity, phylogenetics © 2012 Blackwell Verlag GmbH • J. Anim. Breed. Genet. 130 (2013) 312–320 doi:10.1111/j.1439-0388.2012.01014.x J. Anim. Breed. Genet. ISSN 0931-2668