Genetic diversity and population structure in Portuguese goat breeds C. Bruno-de-Sousa a,b , A.M. Martinez c , C. Ginja a,d , F. Santos-Silva a , M.I. Carolino a , J.V. Delgado c , L.T. Gama a,b, ⁎ a L-INIA, Instituto Nacional de Recursos Biológicos, 2005-048 Vale de Santarém, Portugal b Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, 1300-477 Lisboa, Portugal c Departamento de Genética, Universidad de Córdoba, Campus Rabanales C-5 14071, Córdoba, Spain d Veterinary Genetics Laboratory, University of California, One Shields Avenue, Davis, CA 95616, USA article info abstract Article history: Received 21 January 2010 Received in revised form 13 June 2010 Accepted 28 June 2010 Genetic diversity was assessed in the Portuguese native breeds of goats Algarvia (AL), Bravia (BR), Charnequeira (CH), Preta de Montesinho (PM), Serpentina (SP) and Serrana (SR), by analyzing 25 microsatellite markers in 193 animals. Genetic variability was high, with means for expected heterozygosity of 0.70 across loci, and nearly 7.0 and 4.4 for total and effective number of alleles per locus, respectively. The six breeds analyzed had similar levels of genetic variability, and the estimated F ST was 0.031, indicating that, with the neutral genetic markers used, the proportion of genetic variability accounted for by differences among breeds is small. Depending on the breed considered, between 0.16 and 0.28 of the loci presented significant departures from Hardy–Weinberg proportions, mostly because of a deficit in heterozygosity, with a significant positive F IS in most breeds, particularly in PM. The dendrogram based on Nei's standard genetic distance and the analysis by principal components indicate a separation of AL and BR from the remaining breeds, with some clustering of PM with SR, and of SP with CH, in agreement with their geographical distribution. Individual distances based on allele sharing indicate that only AL and BR animals tended to cluster together, while overlapping was common for the other breeds. The analysis with STRUCTURE confirmed the separation of AL and BR, which were more closely identified with independent clusters of potential ancestral populations. For the other breeds, there was clear evidence of admixture, with various ancestral populations contributing differently to the current breeds. Evidence was found of a geographical cline, with a given ancestral population contributing more to breeds located nearby, and with a declining contribution as the geographical distribution of breeds became more distant. Our results indicate that native breeds of goats in Portugal present high levels of genetic diversity, but the differentiation among closely located breeds is weak. Some of the breeds show signs of genetic erosion, which imply the need for urgent measures of conservation and sustainable management of their gene pool. © 2010 Elsevier B.V. All rights reserved. Keywords: Genetic diversity Goats Microsatellites Native breeds Population structure 1. Introduction As in most countries of the Mediterranean region, native goat breeds in Portugal play a major role in utilizing resources available under extensive production systems and marginal areas, thus contributing for environmental and socio-economic stability. Traditionally, local breeds of goats have been an integral part of local culture and are the basis of several high quality food products, but their major role is the productive use of shrub and forest areas which, if not used by goats, would be left abandoned (Gama, 2006). Breeds of goats in Portugal have evolved over time to fit the diversity of local environmental conditions, and five native breeds were recognized until recently, specifically Algarvia, Bravia, Charnequeira, Serpentina and Serrana (Direcção Geral Livestock Science 135 (2011) 131–139 ⁎ Corresponding author. Tel.: + 351 243767382; fax: + 351 243767307. E-mail address: luis.gama@inrb.pt (L.T. Gama). 1871-1413/$ – see front matter © 2010 Elsevier B.V. All rights reserved. doi:10.1016/j.livsci.2010.06.159 Contents lists available at ScienceDirect Livestock Science journal homepage: www.elsevier.com/locate/livsci