Analyses of pig genomes provide insight into porcine demography and evolution

Martien A.M. Groenen, Alan L. Archibald, Hirohide Uenishi, Christopher K. Tuggle, Yasuhiro Takeuchi, Max F. Rothschild, Claire Rogel-Gaillard, Chankyu Park, Denis Milan, Hendrik Jan Megens, Shengting Li, Denis M. Larkin, Heebal Kim, Laurent A.F. Frantz, Mario Caccamo, Hyeonju Ahn, Bronwen L. Aken, Anna Anselmo, Christian Anthon, Loretta AuvilBouabid Badaoui, Craig W. Beattie, Christian Bendixen, Daniel Berman, Frank Blecha, Jonas Blomberg, Lars Bolund, Mirte Bosse, Sara Botti, Zhan Bujie, Megan Bystrom, Boris Capitanu, Denise Carvalho-Silva, Patrick Chardon, Celine Chen, Ryan Cheng, Sang Haeng Choi, William Chow, Richard C. Clark, Christopher Clee, Richard P.M.A. Crooijmans, Harry D. Dawson, Patrice Dehais, Fioravante De Sapio, Bert Dibbits, Nizar Drou, Zhi Qiang Du, Kellye Eversole, Joao Fadista, Susan Fairley, Thomas Faraut, Geoffrey J. Faulkner, Katie E. Fowler, Merete Fredholm, Eric Fritz, James G.R. Gilbert, Elisabetta Giuffra, Jan Gorodkin, Darren K. Griffin, Jennifer L. Harrow, Alexander Hayward, Kerstin Howe, Zhi Liang Hu, Sean J. Humphray, Toby Hunt, Henrik Hornshoøj, Jin Tae Jeon, Patric Jern, Matthew Jones, Jerzy Jurka, Hiroyuki Kanamori, Ronan Kapetanovic, Jaebum Kim, Jae Hwan Kim, Kyu Won Kim, Tae Hun Kim, Greger Larson, Kyooyeol Lee, Kyung Tai Lee, Richard Leggett, Harris A. Lewin, Yingrui Li, Wansheng Liu, Jane E. Loveland, Yao Lu, Joan K. Lunney, Jian Ma, Ole Madsen, Katherine Mann, Lucy Matthews, Stuart McLaren, Takeya Morozumi, Michael P. Murtaugh, Jitendra Narayan, Dinh Truong Nguyen, Peixiang Ni, Song Jung Oh, Suneel Onteru, Frank Panitz, Eung Woo Park, Hong Seog Park, Geraldine Pascal, Yogesh Paudel, Miguel Perez-Enciso, Ricardo Ramirez-Gonzalez, James M. Reecy, Sandra Rodriguez-Zas, Gary A. Rohrer, Lauretta Rund, Yongming Sang, Kyle Schachtschneider, Joshua G. Schraiber, John Schwartz, Linda Scobie, Carol Scott, Stephen Searle, Bertrand Servin, Bruce R. Southey, Goran Sperber, Peter Stadler, Jonathan V. Sweedler, Hakim Tafer, Bo Thomsen, Rashmi Wali, Jian Wang, Jun Wang, Simon White, Xun Xu, Martine Yerle, Guojie Zhang, Jianguo Zhang, Jie Zhang, Shuhong Zhao, Jane Rogers, Carol Churcher, Lawrence B. Schook

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Abstract

For 10,000a €‰years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Original languageEnglish (US)
Pages (from-to)393-398
Number of pages6
JournalNature
Volume491
Issue number7424
DOIs
StatePublished - Nov 15 2012

Bibliographical note

Funding Information:
Acknowledgements The authors recognize the contributions of the following individuals towards the establishment of the Swine Genome Sequencing Consortium and their leadership in realizing this effort: J. Jen, P. J. Burfening, D. Hamernik, R. A. Easter, N. Merchen, R. D. Green, J. Cassady, B. Harlizius, M. Boggess and M. Stratton. Also the authors acknowledge A. Hernandez, C. Wright at the University of Illinois Keck Center for Comparative and Functional Genomics; N. Bruneau and Prof. Ning Li for their contribution to PERV studies; D. Goodband and D. Berman for their efforts in genome annotation; D. Grafham of the Welcome Trust Sanger Institute for his efforts in the genome assembly and J. Hedegaard, M. Nielsen and R. O. Nielsen for their contribution on the miRNA analysis. We also recognize contributions from the National Institute of Agrobiological Sciences and the Institute of Japan Association for Techno-innovation in Agriculture, Forestry and Fisheries, Tsukuba, Japan, H. Shinkai, T. Eguchi-Ogawa, K. Suzuki, D. Toki, T. Matsumoto, N. Fujishima-Kanaya, A. Mikawa, N. Okumura, M. Tanaka-Matsuda, K. Kurita, H. Sasaki, K. Kamiya, A. Kikuta, T. Bito and N. Fujitsuka. We acknowledge support from the USDA CSREES/NIFA Swine Genome Coordination Program, College of Agricultural,Consumer andEnvironmental Sciences, University of Illinois; College of Agriculture and Life Sciences, Iowa State University; North Carolina Agricultural Research Service; USA National Pork Board; Iowa Pork Producers Association; North Carolina Pork Council; Danish government; TOPIGS Research Center IPG The Netherlands; INRA Genescope, France; Wellcome Trust Sanger Institute and BGI. We are grateful to the genome team at NCBI for their assistance in checking the Sscrofa10.2 assembly and for their independent annotation of the sequence. This project was also partially supported by grants: BBSRC grants (Ensembl): BB/E010520/1, BB/E010520/2, BB/I025328/1; EC FP6 ‘Cutting edge genomics for sustainable animal breeding (SABRE)’; EC FP7 ‘Quantomics’; C. J. Martin Overseas Based Biomedical Fellowship from the Australian NHMRC (575585); BBSRC (BB/H005935/1); Next-Generation BioGreen 21 Program (PJ009019, PJ0081162012), RDA, Republic of Korea; Consolider programme from Ministry of Research (Spain); NIH R13 RR020283A; NIH R13 RR032267A; ILLU 535-314; ILLU 538-379; ILLU-538-312; ILLU-538-34; CSREES, NIFA for funding genome coordination activities; NIH grant 5 P41LM006252; MAFF grants (IRPPIAUGT-AG 1101/1201); USDA-NRI-2009-35205-05192; USDA-NRSP8 Bioinformatics Coordination and Pig Genome Coordination funds; US-UK Fulbright Commission; Next-Generation BioGreen 21 (no. PJ0080892011) Program, RDA, Republic of Korea; USDA-ARS Project Plan 1235-51000-055-00D; USDA-ARS Project Plan 1265-32000-098-00D; USDA-NRI-2006-35204-17337 USDA AFRI NIFA/DHS 2010-39559-21860; NIH P20-RR017686; USDA ARS; USDA-NRSP8 Bioinformatics; USDA ARS Beltsville Area Summer Undergraduate Fellowships; BBSRC grant BB/ G004013/1; NSFC Outstanding Youth grant (31025026); The Swedish Research Council FORMAS; The Swedish Wenner-Gren Foundations; European Commission FP6 funded project LSHB-CT-2006-037377; BioGreen21, RDA grant PJ00622901; BioGreen21, RDA grant PJ00622902; BioGreen21, RDA grant PJ00622903; BioGreen21, RDA grant PJ00622903. The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 249894 (SelSweep); NIH P20-RR017686; NIH NIDA P30 DA018310; NIH NIDA R21 DA027548; NIAS, RDA grant PJ001758; BioGreen21, RDA grant PJ006229; NIAS, RDA grant 20040301034467; ANR grant ANR07-GANI-001 DeliSus; Danish funding agencies: FTP/DFF (09-066598); DSF/Strategic Growth Technologies (09-067036); the Lundbeck foundation (374/06); DCSC (Scientific Computing); The Funds for International Cooperation from the Ministry of Science and Technology of China 2002AA229061; PL-Grid project: POIG.02.03.00-00-007/08-00 ‘Genome Assembly’; USDA-NIFA-CREES AG 2006-35216-16668; AG 2002-34480-11828; AG 2003-34480-13172; AG 2004-34480-14417; AG 2005-34480-15939; AG 2006-34480-17150; AG 2008-34480-19328; AG 2009-34480-19875; AG 2002-35205-12712;somaticcellgenomics:Integrating QTL Discovery and Validation; AG 2008-35205-18769; AG 2009-65205-05642; AG 2004-3881-02193; AG 2011-67015-30229; AG 58-5438-2-313; AG 58-5438-7-317; and AG 58-0208-7-149; NIH grant 5 P41 LM006252.

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