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. 2012 Nov 15;491(7424):393-8.
doi: 10.1038/nature11622.

Analyses of pig genomes provide insight into porcine demography and evolution

Martien A M Groenen  1 , 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 Auvil, Bouabid 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, João 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 Hornshøj, 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
Affiliations

Analyses of pig genomes provide insight into porcine demography and evolution

Martien A M Groenen et al. Nature. .

Abstract

For 10,000 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.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Phylogeny of the six mammals used in the dN/dS analysis.
KEGG pathways with genes that show accelerated evolution for each of the six mammals used in the dN/dS analysis. The bar charts show the individual dN/dS and dS values for each of the six mammals. The dN/dS and dS values refer to the time period of each of the six individual lineages. The number of proteins that show significantly accelerated dN/dS ratios in each lineage varies from 84 in the mouse to 311 in the pig lineage. Pathways significantly (P < 0.05) enriched within this group of genes are also shown with the number of genes shown in brackets. HPI, Helicobacter pylori infection. PowerPoint slide
Figure 2
Figure 2. Distribution of heterozygosity for individual pig genomes.
Shown is the distribution of the heterozygosity as the log2(SNPs) per 10k bin. a, Wild Sus scrofa: blue, south China; green, north China; orange, Italian; red, Dutch. b, Breeds: blue, Chinese breeds (Jiangquhai, Meishan, Xiang); red–yellow, European breeds (Hampshire, large white, landrace). Note that the Hampshire breed is a North American breed of European origin. PowerPoint slide
Figure 3
Figure 3. Demographic history of wild boars.
Demographic history was inferred using a hidden Markov model (HMM) approach as implemented in pairwise sequentially Markovian coalescence (PSMC). In the absence of known mutation rates for pig, we used the default mutation rate for human (μ) of 2.5 × 10−8. For the generation time (g) we used an estimate of 5 years. The Last Glacial Maximum (LGM) is highlighted in grey. WBnl, wild boar Netherlands; WBit, wild boar Italy; WBNch, wild boar north China; WBSch, wild boar south China. PowerPoint slide
Figure 4
Figure 4. Putative selective sweep region around the ERI2 gene on SSC3.
The y axis shows the log-transformed value of the ratio for the observed/expected derived allele frequency using a sliding window at a bin size of 50,000 bp. The x axis shows the position on SSC3 in base pairs. PowerPoint slide
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