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Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

Juan Manuel Herrero-Medrano12*, Hendrik-Jan Megens2, Martien AM Groenen2, Guillermo Ramis1, Mirte Bosse2, Miguel Pérez-Enciso34 and Richard PMA Crooijmans2

Author Affiliations

1 Departamento de Producción Animal, Fac. de Veterinaria, Área de Genética, C.P.30100 Murcia, Spain

2 Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands

3 Centre for Research in Agricultural Genomics, Consortium CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autonoma Barcelona, 08193 Bellaterra, Spain

4 Institut Català de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain

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BMC Genetics 2013, 14:106  doi:10.1186/1471-2156-14-106

Published: 30 October 2013



Inbreeding is among the major concerns in management of local livestock populations. The effective population size of these populations tends to be small, which enhances the risk of fitness reduction and extinction. High-density SNP data make it possible to undertake novel approaches in conservation genetics of endangered breeds and wild populations.

A total of 97 representative samples of domestic and wild pig populations from the Iberian Peninsula, subjected to different levels of threat with extinction, were genotyped with a 60 K SNP panel. Data analyses based on: (i) allele frequency differences; (ii) linkage disequilibrium and (iii) runs of homozygosity were integrated to study population relationships, inbreeding and demographic history.


The domestic pigs analyzed belonged to local Spanish and Portuguese breeds: Iberian ─ including the variants Retinto Iberian, Negro Iberian and Manchado de Jabugo ─, Bisaro and Chato Murciano. The population structure and persistence of phase analysis suggested high genetic relations between Iberian variants, with recent crossbreeding of Manchado de Jabugo with other pig populations. Chato Murciano showed a high frequency of long runs of homozygosity indicating recent inbreeding and reflecting the recent bottleneck reported by historical records. The Chato Murciano and the Manchado de Jabugo breeds presented the lowest effective population sizes in accordance with their status of highly inbred breeds. The Iberian wild boar presented a high frequency of short runs of homozygosity indicating past small population size but no signs of recent inbreeding. The Iberian breed showed higher genetic similarities with Iberian wild boar than the other domestic breeds.


High-density SNP data provided a consistent overview of population structure, demographic history and inbreeding of minority breeds and wild pig populations from the Iberian Peninsula. Despite the very different background of the populations used, we found a good agreement between the different analyses. Our results are also in agreement with historical reports and provide insight in the events that shaped the current genetic variation of pig populations from the Iberian Peninsula. The results exposed will aid to design and implement strategies for the future management of endangered minority pig breeds and wild populations.

Local breeds; Population genetics; SNP; Genetic diversity; Effective population size; Pig; Iberian Peninsula