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Genome-wide SNP data unveils the globalization of domesticated pigs

Authors: Yang, Bin; Cui, Leilei; Pérez-Enciso, M.; Traspov, Aleksei; Crooijmans, Richard P.M.A.; Zinovieva, Natalia; Schook, Lawrence B.; +15 Authors

Genome-wide SNP data unveils the globalization of domesticated pigs

Abstract

Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection.A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection.Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.

Countries
Spain, Finland, Netherlands, Germany, Denmark, Germany, Spain, Denmark, United Kingdom, Italy
Keywords

pig, EXPRESSION, Asia, Internationality, Swine, Sus scrofa, GENETIC-STRUCTURE, QH426-470, Breeding, SF1-1100, Polymorphism, Single Nucleotide, domestication, BREEDS, REVEALS, Journal Article, Genetics, Life Science, Animals, Selection, Genetic, ADAPTATION, POPULATION, POLYMORPHISMS, whole genome, INTROGRESSION, Australia, genetic diversity, ASSOCIATION, Animal science, dairy science, DOG DOMESTICATION, Animal culture, Europe, Genetics, developmental biology, physiology, Ecology, Evolution, Behavior and Systematics; Animal Science and Zoology; Genetics, Research Article, Genome-Wide Association Study

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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