Abstract
BackgroundInbreeding 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.ResultsThe 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.ConclusionsHigh-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.
Highlights
Inbreeding is among the major concerns in management of local livestock populations
A total of 97 pigs from domestic and wild autochthonous populations from the Iberian Peninsula were genotyped with the Porcine SNP60 Beadchip [9]
The SNPs located on the sex chromosomes and those with more than 5% missing genotypes were excluded from the analysis, resulting in a total of 47,594 SNPs used for the analysis
Summary
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. Progressive population decline has called the attention of the conservation management and scientific communities Both for wild and domesticated populations alike there is a fear that inbreeding may lead to loss of allelic variation and adverse phenotypic consequences [1]. Variation conserved in local breeds is often related to important traits that classically are attributed to traditional populations, such as adaptation to the environment and greater resistance to local pathogens. In addition to these concerns, local populations are often considered to be part of the local culture and history. Wild boar is an important reservoir of infectious diseases as relevant as tuberculosis in the Iberian Peninsula [4], and of concern for public and animal health
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