Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

Abstract

BackgroundNative pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies.MethodsA panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results.ResultsGenetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and within-breed components of genetic diversity.ConclusionsNative pig breeds in Iberia reveal high levels of genetic diversity, a solid breed structure and a clear organization in well-defined clusters.

Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information

“…Individual genotypes have been previously reported by Gama et al (2013) for Iberian Peninsula breeds and by Revidatti et al (2014) for Criollo pig breeds for a panel of 24 microsatellites recommended for genetic diversity studies by the International Society for Animal Genetics/Food and Agriculture Organization of the United Nations. In addition, wild boar samples from four different European geographic locations (Spain, Portugal, Italy and Poland) that covered the two major mitochondrial DNA haplogroups observed in the continental European wild boars (E1a and E1c) (Scandura et al, 2011) were included in the analysis.…”

“…Among those studies, specific results have been published based on the same set of breeds and microsatellites assessed here, reporting the genetic relationships among Iberian Peninsula pig breeds and Criollo pig breeds (Revidatti et al, 2014). In addition, Gama et al (2013) briefly evaluated conservation priorities among Iberian pig breeds considering the current levels of within-and between-breed genetic diversity. However, a comprehensive analysis in terms of conservation priorities of Criollo breeds is lacking, in spite of their importance in the social economy, where they play a major role as a source of food and income.…”

Genetic diversity of domestic pigs in Tierralta (Colombia) using microsatellites

“…Mean observed heterozygosity (51.20%) and mean expected heterozygosity (52.59%; Table 3) show a high degree of variability. These values are similar to those reported in Denmark and the Netherlands and are outweighed by those reported in China, Brazil and Thailand (Sancristobal et al ., 2006;Fang et al ., 2009;Gama et al, 2013). The mean number of alleles per locus and the allelic richness (Table 3) indicate that this population exhibits some degree of variability.…”

Variación genética en cerdo doméstico (Sus scrofa domestica) de Córdoba-Colombia basada en marcadores microsatélites

“…El número de alelo por locus varió de 2 (SW2019) a 15 (IFNG), con un promedio en 10.3 alelos (A). Otros estudios de diversidad genética en cerdos reportan valores mayores y menores así: entre 13.31 y 24.8 alelos (16,17) y entre 2.0 y 3.9 alelos (18) .…”

“…El PIC obtenido (Cuadro 2) varió entre 0.17 (SW1067) y 0.83 (IFNG), correspondiendo estos valores con los marcadores que presentaron el alleles (16,17) and 2.0 to 3.9 alleles (18) . The total number of identified alleles was 207, with the highest variation observed in IFNG (A=11.3, H= 0.917) and SW957 (A= 10.6; H= 0.838).…”