Porcine colonization of the Americas: a 60k SNP story
William Burgos-Paz,Carla A. Souza,Carla A. Souza,Hendrik-Jan Megens,Yuliaxis Ramayo-Caldas,M Melo,Clemente Lemus-Flores,E Caal,H. W. Soto,Remberto Martínez,Luz Angela Alvarez,L. Aguirre,V Iñiguez,M A Revidatti,O R Martínez-López,S Llambi,Anna Esteve-Codina,M. C. Rodríguez,Richard P. M. A. Crooijmans,Samuel Rezende Paiva,Lawrence B. Schook,Martien A. M. Groenen,Miguel Pérez-Enciso +22 more
TLDR
In this paper, the authors provided 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 American populations, including wild boar, Iberian, international and Chinese breeds.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.read more
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Population history and genomic signatures for high-altitude adaptation in Tibetan pigs
TL;DR: Tibetan pig populations have experienced substantial genetic differentiation during the long history of colonization in the Plateau and have developed a complex biological adaptation mechanism that could be different from that of Tibetans and other animals.
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Genome-wide SNP data unveils the globalization of domesticated pigs
Bin Yang,Leilei Cui,Miguel Pérez-Enciso,Aleksei Traspov,Richard P. M. A. Crooijmans,Natalia A Zinovieva,Lawrence B. Schook,Alan Archibald,Kesinee Gatphayak,Christophe Knorr,Alexander Triantafyllidis,Panoraia Alexandri,Gono Semiadi,Olivier Hanotte,Deodália Dias,Peter Dovč,Pekka Uimari,Laura Iacolina,Laura Iacolina,Massimo Scandura,Martien A. M. Groenen,Lusheng Huang,Hendrik-Jan Megens +22 more
TL;DR: In this paper, a worldwide survey on 60k genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa, was presented.
Journal ArticleDOI
The Evolution of Suidae
Laurent A. F. Frantz,Erik Meijaard,Erik Meijaard,Jaime Gongora,James Haile,Martien A. M. Groenen,Greger Larson +6 more
TL;DR: The current knowledge of this fascinating group of Cetartiodactyla is reviewed and a comprehensive evolutionary history from the Oligocene to the present day is provided.
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Conservation status and historical relatedness of Italian cattle breeds.
Salvatore Mastrangelo,Elena Ciani,Paolo Ajmone Marsan,Alessandro Bagnato,Luca Maria Battaglini,Riccardo Bozzi,Antonello Carta,Gennaro Catillo,Martino Cassandro,Sara Casu,Roberta Ciampolini,Paola Crepaldi,Mariasilvia D'Andrea,Rosalia Di Gerlando,Luca Fontanesi,Maria Longeri,Nicolò Pietro Paolo Macciotta,Roberto Mantovani,Donata Marletta,Donato Matassino,Marcello Mele,Giulio Pagnacco,Camillo Pieramati,Baldassare Portolano,Francesca Maria Sarti,Marco Tolone,Fabio Pilla +26 more
TL;DR: This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds using a medium-density single nucleotide polymorphism (SNP) array and the results will help design and implement conservation strategies.
Journal ArticleDOI
Comparative aspects of rodent and nonrodent animal models for mechanistic and translational diabetes research.
Simone Renner,Britta Dobenecker,Andreas Blutke,Susanne Zöls,Rüdiger Wanke,Mathias Ritzmann,Eckhard Wolf +6 more
TL;DR: In this review, anatomic, biochemical, physiological, and morphologic aspects relevant to diabetes research will be compared between different animal species, that is, mouse, rat, rabbit, pig, and non-human primates.
References
More filters
Journal ArticleDOI
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
Journal ArticleDOI
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Shaun Purcell,Shaun Purcell,Benjamin M. Neale,Benjamin M. Neale,Kathe Todd-Brown,Lori Thomas,Manuel A. R. Ferreira,David Bender,David Bender,Julian Maller,Julian Maller,Pamela Sklar,Pamela Sklar,Paul I.W. de Bakker,Paul I.W. de Bakker,Mark J. Daly,Mark J. Daly,Pak C. Sham +17 more
TL;DR: This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.
Journal ArticleDOI
Principal components analysis corrects for stratification in genome-wide association studies
Alkes L. Price,Alkes L. Price,Nick Patterson,Robert M. Plenge,Robert M. Plenge,Michael E. Weinblatt,Nancy A. Shadick,David Reich,David Reich +8 more
TL;DR: This work describes a method that enables explicit detection and correction of population stratification on a genome-wide scale and uses principal components analysis to explicitly model ancestry differences between cases and controls.
Journal ArticleDOI
Fast model-based estimation of ancestry in unrelated individuals
TL;DR: The results show that ADMIXTURE's computational speed opens up the possibility of using a much larger set of markers in model-based ancestry estimation and that its estimates are suitable for use in correcting for population stratification in association studies.
Journal ArticleDOI
adegenet: a R package for the multivariate analysis of genetic markers
TL;DR: The package adegenet for the R software is dedicated to the multivariate analysis of genetic markers by implementing formal classes and functions to manipulate and analyse genetic markers.
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