Porcine colonization of the Americas: a 60k SNP story

Abstract

The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbors, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analyzing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level.

Mining the pig genome to investigate the domestication process

“…Population structures determined in wild boars and domestic pigs using the high-density genotyping panel (for example, Ai et al, 2013, Burgos-Paz et al, 2013, Wilkinson et al, 2013 confirm previous findings primarily based on mitochondrial (Figure 2) and microsatellite markers, evidencing a strong differentiation between Asian and European individuals. Moreover, the presence of admixture from Asian breeds into commercial European breeds and vice versa was also obvious.…”

“…This is the case for the 60K SNP panel (Ramos et al, 2009), which was built on the basis of sequence variation found in a pool of six populations (Duroc, Landrace, Pietrain and Large White breeds and a wild boar pool containing mainly European and a few Japanese samples). Ascertainment bias has been observed in the 60K SNP panel, especially in nonEuropean pig populations Burgos-Paz et al, 2013). Population structure analyses based on this panel are restricted to the detection of differences exclusively targeting ascertained SNPs.…”

Exploración Inicial de la Estructura Genética del Cerdo Doméstico (Sus scrofa domestica) en Sampués, Sucre, Colombia, utilizando Microsatélites

“…Inicialmente llegaron a las Antillas y desde allí emigraron al resto del continente. Colón trajo cerdos en su segundo viaje (Burgos et al, 2013). Años después, y por exigencia de Carlos V, la excursión de Rodrigo Bastidas que salió de la Española y fundó Santa Marta en 1525, trajo 300 cerdos (Peña y Mora, 1977 El ADN se extrajo de las muestras mediante una modificación al protocolo descrito por Sambrook y Russell (2001), a partir del bulbo piloso, mediante digestión de proteínas con la enzima Proteinasa K y una purificación con fenol-cloroformo.…”

Genetic characterization of the domestic pig (Sus scrofa domestica) in Cerete-Colombia, using microsatellite markers

“…Los cerdos domésticos del continente americano tienen su origen en los cerdos ibéricos traídos por Colón en su segundo viaje (1). Años más tarde por imposición de Carlos V, la expedición de Rodrigo Bastidas que partió de la española y fundó a Santa Marta en 1525, trajo 300 cerdos (2).…”

“…The snout is cylindrical in shape with a bulky edge; hairless and smooth; the nostrils are small and its eyes have round pupils. Domestic pigs in the Americas have their origin in the Iberian pigs brought by Columbus on his second voyage (1). Years later by imposition of Carlos V, the expedition of Rodrigo Bastidas who left La Española and founded Santa Marta in 1525, brought 300 pigs (2).…”