Abstract
BackgroundPigs 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.ResultsA 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.ConclusionsKey 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.
Highlights
Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural rev‐ olution, and have since been transported and traded across the globe
In the late eighteenth century, Chinese pigs may have been imported to America, and crossed with local pigs of European ancestry there [8], most likely the Asian influence in American village pigs was through crosses with international breeds [9]
The wild boars were from widespread regions around the world and the five out-group populations are Babyrousa babyrussa, Sus barbatus, Sus celebensis and Sus verrucosus from the islands of Southeast Asia and Phacochoerus africanus from Africa
Summary
Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural rev‐ olution, and have since been transported and traded across the globe. Sus scrofa is native to Eurasia and North Africa, but was introduced into other parts of the world, i.e. into the Americas, primarily in its domesticated form, during the time of the European colonization in the sixteenth century, and later in Australia and New Zealand [6] Both demographic processes, and natural as well as artificial selection, have led to the formation of a multitude of pig breeds around the world that vary in coat color, ear shape, body size, snout bluntness, behavior, growth rate, fatness, and prolificacy and other economically important traits. At least since the 1840s, modern breeds such as Berkshire, Hampshire, Russian local pigs, Duroc, Large White and Landrace were introduced into China [10] Such domestic animals were traded, loaded onto ships and released elsewhere. Asian haplotypes predominate in East Africa, whereas European haplotypes predominate in West Africa [12]
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