Genome-wide SNP data unveils the globalization of domesticated pigs

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. Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0345-y) contains supplementary material, which is available to authorized users.

Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine

“…Higher values of K generally delineated substructure within reference groups, which was beyond our interest in describing the ancestry of feral swine. Our selection of K 17 closely aligned with the conclusions of Yang et al (2017) in their delineation of global S. scrofa samples into 17 genetic populations based on independent analyses of a similar data set—genotypes from Yang et al (2017) were included in the assembly of our reference set.…”

“…We assembled our reference set by compiling domestic pig and native wild boar HD SNP genotypes from previously published data sets ( n = 2,450; Alexandri et al, 2017; Burgos‐Paz et al, 2013; Goedbloed, Megens, et al, 2013; Iacolina et al, 2016; Roberts & Lamberson, 2015; Yang et al, 2017), which we augmented with novel genotypes produced by our research group ( n = 566; produced with extraction methods described above and genotyped with the Genomic Profiler for Porcine HD [GeneSeek]). To align with feral swine genotypes, we restricted our reference set to data sets similarly produced with either the PorcineSNP60 (versions 1 and 2; Illumina) or Genomic Profiler for Porcine HD (GeneSeek) BeadChip microarrays (Ramos et al, 2009).…”

Deleterious alleles in the context of domestication, inbreeding, and selection

“…1 European Nucleotide Archive (ENA) https://www.ebi.ac.uk/ena/data/view/PRJEB1683; 2 (Bosse et al., ) 3 (Yang et al., ) 4 (Derks et al., ) 5 (Ngeno, ) 6 (Ngeno et al., ) 7 (Derks et al., ), 8 (Derks, Megens et al. (submitted)).…”

“…(under review) is not accessible yet, the relevant vcf files are deposited into https://www.animalgenome.org/repository/pub/WUR2018.0809/. Genotype data from the same individuals were obtained from (Yang et al., ) and (Derks et al., ) for pigs and from (Derks et al., ) for chicken. The data obtained from Derks et al.…”

The major histocompatibility complex homozygous inbred Babraham pig as a resource for veterinary and translational medicine

“…Domesticated pigs have maintained a significant level of genetic diversity, both within and between breeds, despite strong selection for production traits and inbreeding . Inevitably, this diversity correlates with significant variation at the polymorphic immune loci.…”