Genetic diversity of three indigenous pig breeds in Colombia

Zungo (ZU), San Pedreno (SP) and Casco de Mula (CM) are Colombian indigenous pig breeds originated from European populations that are well adapted to tropical conditions. These breeds have a great potential to be used in pure and crossbred schemes due to their high reproductive performance and resistance to tropical diseases. We investigated the genetic diversity and genetic structure of these pig breeds using microsatellite molecular markers. Fifty-five ZU, SP and CM animals were genotyped for 10 microsatellites using capillary electrophoresis. The average number of alleles per marker ranged from 5.56 +/- 1.88 in ZU to 6.70 +/- 1.64 in SP. Observed heterozygosity ranged from 0.68 +/- 0.05 in ZU to 0.74 +/- 0.03 in SP. Polymorphic information content was high for most of the microsatellites in all breeds. Inbreeding coefficient (F-IS) values were low for all microsatellites, with an average of 0.035 +/- 0.037. Higher average values closer to and above 0.1 were observed for the fixation index of the global population (F-IT) (0.131 +/- 0.041) and the coefficient of relatedness between individuals from different populations (F-ST) (0.099 +/- 0.013). Principal components and structure analyses showed a high level of clustering per breed and very low admixture levels between them. The panel of markers used in this study proved to be useful to investigate genetic diversity and pedigree relationships in pig populations. The Colombian pig breeds that we evaluated had a high genetic variability and a well-differentiated genetic structure, which are key for decision making in conservation programs and for the implementation of future animal breeding plans in these populations.