The analysis of Y-chromosome variation has provided valuable clues about the paternal history of domestic animal populations. The main goal of the current work was to characterize Y-chromosome diversity in 31 goat populations from Central Eastern (Switzerland and Romania) and Southern Europe (Spain and Italy) as well as in reference populations from Africa and the Near East. Towards this end, we have genotyped seven single nucleotide polymorphisms (SNPs), mapping to the SRY, ZFY, AMELY and DDX3Y Y-linked loci, in 275 bucks from 31 populations. We have observed a low level of variability in the goat Y-chromosome, with just five haplotypes segregating in the whole set of populations. We have also found that Swiss bucks carry exclusively Y1 haplotypes (Y1A: 24%, Y1B1: 15%, Y1B2: 43% and Y1C: 18%), while in Italian and Spanish bucks Y2A is the most abundant haplotype (77%). Interestingly, in Carpathian goats from Romania the Y2A haplotype is also frequent (42%). The high Y-chromosome differentiation between Swiss and Italian/Spanish breeds might be due to the post-domestication spread of two different Near Eastern genetic stocks through the Danubian and Mediterranean corridors. Historical gene flow between Southern European and Northern African goats might have also contributed to generate such pattern of genetic differentiation.

Área de Genética y Reproducción Animal SERIDA Deva Camino de Rioseco 1225 Gijón 33394 Spain

Departament de Biologia Universitat de Girona 17003 Girona Spain

Departament de Ciència Animal i dels Aliments Facultat de Veterinària Universitat Autònoma de Barcelona 08193 Bellaterra Spain

Departamento de Genética Universidad de Córdoba 14071 Córdoba Spain

Department of Animal Genetics Center for Research in Agricultural Genomics CSIC IRTA UAB UB Campus Universitat Autònoma de Barcelona Bellaterra 08193 Spain

Department of Veterinary Medicine University of Sassari 07100 Sassari Italy

Dipartimento Agricoltura Ambiente e Alimenti Università Degli Studi Del Molise Campobasso Italy

Genetic Department Faculty of Agriculture Ain Shams University Cairo 11241 Egypt

Institut de l'Environnement et Recherches Agricoles 04 BP 8645 Ouagadougou 04 Burkina Faso

Institute of Genetics University of Bern Bern 3001 Switzerland

Institute of Life Sciences Faculty of Animal Science and Biotechnologies University of Agricultural Sciences and Veterinary Medicine 400372 Cluj Napoca Romania

Institute of Parasitology Biology Centre Czech Academy of Sciences 37005 České Budějovice Czechia

Instituto Canario de Investigaciones Agrarias Canary Islands Tenerife La Laguna 38108 Spain

Transgenesis Center of Excellence Isfahan Branch Islamic Azad University Isfahan Iran

Unitat de Races Autòctones Servei de Millora Agrària Son Ferriol 07198 Spain

University Mohammed 5 Agdal Faculty of Sciences 4 Av Ibn Battota Rabat Morocco

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