Genetic characterization of local Criollo pig breeds from the Americas using microsatellite markers1

Abstract

Little is known about local Criollo pig genetic resources and relationships among the various populations. In this paper, genetic diversity and relationships among 17 Criollo pig populations from 11 American countries were assessed with 24 microsatellite markers. Heterozygosities, F-statistics, and genetic distances were estimated, and multivariate, genetic structure and admixture analyses were performed. The overall means for genetic variability parameters based on the 24 microsatellite markers were the following: mean number of alleles per locus of 6.25 ± 2.3; effective number of alleles per locus of 3.33 ± 1.56; allelic richness per locus of 4.61 ± 1.37; expected and observed heterozygosity of 0.62 ± 0.04 and 0.57 ± 0.02, respectively; within-population inbreeding coefficient of 0.089; and proportion of genetic variability accounted for by differences among breeds of 0.11 ± 0.01. Genetic differences were not significantly associated with the geographical location to which breeds were assigned or their country of origin. Still, the NeighborNet dendrogram depicted the clustering by geographic origin of several South American breeds (Criollo Boliviano, Criollo of northeastern Argentina wet, and Criollo of northeastern Argentina dry), but some unexpected results were also observed, such as the grouping of breeds from countries as distant as El Salvador, Mexico, Ecuador, and Cuba. The results of genetic structure and admixture analyses indicated that the most likely number of ancestral populations was 11, and most breeds clustered separately when this was the number of predefined populations, with the exception of some closely related breeds that shared the same cluster and others that were admixed. These results indicate that Criollo pigs represent important reservoirs of pig genetic diversity useful for local development as well as for the pig industry.

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

“…Several studies have estimated the genetic diversity of pig breeds worldwide (Faubel et al, 2004; Ramírez et al, 2014;Revidatti et al, 2014). 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).…”

“…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.…”

“…Commercial (Duroc, Pietrain, Large White and Landrace) and the remaining European local pig breeds (Berkshire, Tamworth and Large Black) were genotyped for the same panel of 24 microsatellites used in Gama et al (2013) and Revidatti et al (2014): IGF1, S0002, S0005, S0026, S0068, S0090, S0101, S0155, S0178, S0215, S0225, S0226, S0227, S0228, S0355, S0386, SW024, SW072, SW240, SW632, SW857, SW911, SW936 and SW951. Laboratory protocols have been described in detail in Gama et al (2013) and Revidatti et al (2014) and allele nomenclature was standardized according to the ISAG (International Society for Animal Genetics) Pig Comparison Test.…”

“…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.…”

Evidence of balancing selection in multiple indigenous chicken populations

“…In particular, the Food and Agriculture Organization, FAO (2011) recommend the use of microsatellite systems to identify diversity in domestic animals, and a large number of studies have been performed in multiple species including chickens (Tadano et al, 2014;Abebe et al, 2015), cattle (Pelayo et al, 2015;Sharma et al, 2015), pigs (Choi et al, 2014;Revidatti et al, 2014), sheep (Agaviezor et al, 2012;Yilmaz et al, 2014;Ćurković et al, 2016), and goats (Nomura et al, 2012;Wei et al, 2014). Most previous studies have shown that the breeds cluster according to their geographic location, and vary in the degree of diversity depending on the breeding and management histories of the breeds using these types of marker systems, which were typically co-dominant and assumed to be drifting (Granevitze et al, 2009).…”