Genetic diversity of Brazilian pig breeds evidenced by microsatellite markers B.P. Sollero a , S.R. Paiva b , D.A. Faria b , S.E.F. Guimarães c , S.T.R. Castro b , A.A. Egito b , M.S.M. Albuquerque b , U. Piovezan d , G.R. Bertani e , A. da S. Mariante b, ⁎ a University of Brasília, Faculty of Agronomy and Veterinarian, Brasília/DF, Brazil b Embrapa Genetic Resources and Biotechnology, Laboratory of Animal Genetics, Brasília/DF, 02372, Brazil c Federal University of Viçosa, Department of Animal Sciences, Viçosa/MG, 36570-000, Brazil d Embrapa Pantanal, Corumbá/MS, 79320-900, Brazil e Federal University of Pernambuco, Department of Biochemistry, Recife/PE, 50.670-901, Brazil article info abstract Article history: Received 21 May 2008 Received in revised form 22 September 2008 Accepted 25 September 2008 The genetic diversity within and between five genetic groups of pigs in Brazil, (n = 182) represented by three naturalized breeds (Moura, Piau and Monteiro), one commercial breed (Landrace) and one commercial composite (MS60) was estimated using 28 microsatellite markers. The genetic structure within these groups was also tested. The results showed that 14% of the total variation (p b 0.001) observed was due to differences between breeds. Based on the UPGMA dendrogram obtained from Nei's D A genetic distance it was possible to differentiate three groups. The first was formed by the commercial breed, Landrace, and the composite MS60, the second by two of the naturalized breeds (Piau and Monteiro) and the third by the Moura naturalized breed. Within breed variability indicated that the Piau breed had the highest value of expected heterozygosity among the naturalized breeds, whereas Landrace had the highest value between the commercial breeds. Using a Bayesian analysis, a population substructure was identified in Monteiro and Piau breeds. Furthermore, lower values for breed certification probability were observed for these two breeds as well as a significant genetic differentiation between the Moura and Landrace breeds and the composite MS60. The microsatellite marker panel possessed high precision (99.99%) when used in paternity exclusion in naturalized pig breeds and proved to be an effective tool for the management and conservation of naturalized pig breeds. © 2008 Elsevier B.V. All rights reserved. Keywords: Conservation genetics Farm animal genetic resources Molecular markers Sus scrofa 1. Introduction The Brazilian pig industry is based mainly on high technology and intensive production systems, using breeds with high genetic standards, specialized for meat production (Mariante et al., 2003). The pig breeds described as natur- alized are the ones that guaranteed the sustainability of many Brazilian families for centuries. Since the beginning of the 20th century these populations have been gradually substituted by commercial breeds marked by a massive importation and use of exotic breeds, mainly from Europe (Cavalcanti, 2000). Nowadays, remaining animals of the naturalized pig breeds are being raised only by smallholders and the demand of consumers has been focused on lean meat. The naturalized pig breeds of Brazil are characterized by their toughness, resistance to diseases, low management requirements and feeding as well as a high adaptability. Between these naturalized pig breeds, the Piau is the most notorious. This breed is used in some programs of genetic improvement since 1939 (Vianna, 1956), aiming dual fitness like meat and fat, and it has some morphological character- istics similar to commercial pig breeds. The Monteiro is another naturalized pig breed found especially in Pantanal Matogrossense with morphological, physiological and beha- vioral adjustments very different from others naturalized and commercial pig breeds (Herrera et al., 1996). The Moura breed is the one that was spread out in southern region from Brazil Livestock Science 123 (2009) 8–15 ⁎ Corresponding author. Tel.: +55 61 3448 4904; fax: +55 61 3340 3624. E-mail address: mariante@cenargen.embrapa.br (A.S. Mariante). 1871-1413/$ – see front matter © 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.livsci.2008.09.025 Contents lists available at ScienceDirect Livestock Science journal homepage: www.elsevier.com/locate/livsci