10.5061/DRYAD.30TK6
Yang, Bin
National Key Laboratory for Pig Genetic Improvement and Production
Technology, Nanchang, China
Cui, Leilei
National Key Laboratory for Pig Genetic Improvement and Production
Technology, Nanchang, China
Perez-Enciso, Miguel
Center for Research in Agricultural Genomics
Traspov, Aleksei
Federal Scientific Center for Animal Husbandry named after Academician
L.K. Ernst
Crooijmans, Richard P. M. A.
Wageningen University & Research
Zinovieva, Natalia
Federal Scientific Center for Animal Husbandry named after Academician
L.K. Ernst
Schook, Lawrence B.
University of Illinois at Urbana Champaign
Archibald, Alan
Roslin Institute
Gatphayak, Kesinee
Chiang Mai University
Knorr, Christophe
University of Göttingen
Triantafyllidis, Alex
Aristotle University of Thessaloniki
Alexandri, Panoraia
Aristotle University of Thessaloniki
Semiadi, Gono
Indonesian Institute of Sciences
Hanotte, Olivier
University of Nottingham
Dias, Deodália
University of Lisbon
Dovč, Peter
University of Ljubljana
Uimari, Pekka
University of Helsinki
Iacolina, Laura
Aalborg University
Scandura, Massimo
University of Sassari
Groenen, Martien A. M.
Wageningen University & Research
Huang, Lusheng
National Key Laboratory for Pig Genetic Improvement and Production
Technology, Nanchang, China
Megens, Hendrik-Jan
Wageningen University & Research
Data from: Genome-wide SNP data unveils the globalization of domesticated pigs
Dryad
dataset
2018
Holocene
Anthropocene
Sus scrofa
pig
2018-08-23T00:00:00Z
2018-08-23T00:00:00Z
en
https://doi.org/10.1186/s12711-017-0345-y
81112913 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Background: 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. Results: 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. Conclusions: 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.
Description_data_GSE_Global_pigsTable describing the samples. Note that
the submitted data includes a few animals that were removed from the paper
due to additional constraints applied in the review
process.GSE_global_pigs.mapPLINK MAP file, describing the SNPs
used.GSE_global_pigs.pedGenotype data used in PLINK PED file format.
Asia
Europe
Global