Porcine colonization of the Americas: a 60k SNP story

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.WBP is funded by COLCIENCIAS (Francisco José de Caldas fellowship 497/2009, Colombia), CAS thanks grants from CAPES and EMBRAPA (Brazil), YRC is recipient of a PhD studentship from MICINN (Spain, ref. AP2008-01450), AEC is recipient of a PhD studentship from MICINN (Spain). Work funded by Consolider CSD2007-00036 ‘Center for Research in Agrigenomics’ and AGL2010-14822 grants (Spain) to MPE, EU SABRE project FOOD-CT-2006-01625, USDA project 2007-04315 (USA), Facultad de Ciencias Agrarias, San Pedro (UNA), Unión de Gremios de la Producción (UGP) and Empresa San Rafael Agricola y Ganadera SRL (Paraguay), Universidad Técnica de Oruro (Bolivia), Programa de Conservación de los Bancos de Germoplasma, Instituto Colombiano Agropecuario (grant 048-2011) and Ministerio de Agricultura y Desarrollo Rural (Colombia), and Centro de Validación de Tecnologías Agropecuarias (CEDEVA, Formosa, Argentina).Peer reviewe

Selection in the Making: A Worldwide Survey of Haplotypic Diversity Around a Causative Mutation in Porcine IGF2

Domestic species allow us to study dramatic evolutionary changes at an accelerated rate due to the effectiveness of modern breeding techniques and the availability of breeds that have undergone distinct selection pressures. We present a worldwide survey of haplotype variability around a known causative mutation in porcine gene IGF2, which increases lean content. We genotyped 34 SNPs spanning 27 kb in 237 domestic pigs and 162 wild boars. Although the selective process had wiped out variability for at least 27 kb in the haplotypes carrying the mutation, there was no indication of an overall reduction in genetic variability of international vs. European local breeds; there was also no evidence of a reduction in variability caused by domestication. The haplotype structure and a plot of Tajima's D against the frequency of the causative mutation across breeds suggested a temporal pattern, where each breed corresponded to a different selective stage. This was observed comparing the haplotype neighbor-joining (NJ) trees of breeds that have undergone increasing selection pressures for leanness, e.g., European local breeds vs. Pietrain. These results anticipate that comparing current domestic breeds will decisively help to recover the genetic history of domestication and contemporary selective processes

Data from: Porcine colonization of the Americas: a 60k SNP story

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 harbours, 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 analysing 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

FinalData_HDY-12-OR0223

Dataset corresponds to the article: "Porcine colonization of the Americas: A 60k SNP story." W. Burgos, C.A. Souza et al. For any correspondence, please address M. Perez-Enciso ([email protected]) Complete dataset contains 46259 SNP genotypes for 389 individuals. Info_sample.txt file contains information about location (Origin) and population (POPname) for each sample. MPE_378.* files contains genotypes for samples included for all analyses in the paper (PLINK format). MPE_389.* files also contains samples with high missing values that were used only in principal component analysis (PLINK format). The SNP_LD_pruned.dat file is a list of SNPs included after LD pruning. ADMIXTURE and PCA analyses were carried out using only those SNPs

Porcine colonization of the Americas: a 60k SNP story

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.WBP is funded by COLCIENCIAS (Francisco José de Caldas fellowship 497/2009, Colombia), CAS thanks grants from CAPES and EMBRAPA (Brazil), YRC is recipient of a PhD studentship from MICINN (Spain, ref. AP2008-01450), AEC is recipient of a PhD studentship from MICINN (Spain). Work funded by Consolider CSD2007-00036 ‘Center for Research in Agrigenomics’ and AGL2010-14822 grants (Spain) to MPE, EU SABRE project FOOD-CT-2006-01625, USDA project 2007-04315 (USA), Facultad de Ciencias Agrarias, San Pedro (UNA), Unión de Gremios de la Producción (UGP) and Empresa San Rafael Agricola y Ganadera SRL (Paraguay), Universidad Técnica de Oruro (Bolivia), Programa de Conservación de los Bancos de Germoplasma, Instituto Colombiano Agropecuario (grant 048-2011) and Ministerio de Agricultura y Desarrollo Rural (Colombia), and Centro de Validación de Tecnologías Agropecuarias (CEDEVA, Formosa, Argentina).Peer reviewe