Analyses of pig genomes provide insight into porcine demography and evolution

Journal article


Groenen, M., Archibald, A., Uenishi, H., Tuggle, C., Takeuchi, Y., Rothschild, M., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H., Li, S., Larkin, D., Kim, H., Frantz, L., Caccamo, M., Ahn, H., Aken, B., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Bujie, Z., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S., Chow, W., Clark, R., Clee, C., Crooijmans, R., Dawson, H., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G., Fowler, K., Fredholm, M., Fritz, E., Gilbert, J., Giuffra, E., Gorodkin, J., Griffin, D., Harrow, J., Hayward, A., Howe, K., Hu, Z., Humphray, S., Hunt, T., Hornshøj, H., Jeon, J., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J., Kim, K., Kim, T., Larson, G., Lee, K., Lee, K., Leggett, R., Lewin, H., Li, Y., Liu, W., Loveland, J., Lu, Y., Lunney, J., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M., Narayan, J., Truong Nguyen, D., Ni, P., Oh, S., Onteru, S., Panitz, F., Park, E., Park, H., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J., Rodriguez-Zas, S., Rohrer, G., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B., Sperber, G., Stadler, P., Sweedler, J., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C. and Schook, L. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 491 (7424), pp. 393-398. https://doi.org/10.1038/nature11622
AuthorsGroenen, M., Archibald, A., Uenishi, H., Tuggle, C., Takeuchi, Y., Rothschild, M., Rogel-Gaillard, C., Park, C., Milan, D., Megens, H., Li, S., Larkin, D., Kim, H., Frantz, L., Caccamo, M., Ahn, H., Aken, B., Anselmo, A., Anthon, C., Auvil, L., Badaoui, B., Beattie, C., Bendixen, C., Berman, D., Blecha, F., Blomberg, J., Bolund, L., Bosse, M., Botti, S., Bujie, Z., Bystrom, M., Capitanu, B., Carvalho-Silva, D., Chardon, P., Chen, C., Cheng, R., Choi, S., Chow, W., Clark, R., Clee, C., Crooijmans, R., Dawson, H., Dehais, P., De Sapio, F., Dibbits, B., Drou, N., Du, Z., Eversole, K., Fadista, J., Fairley, S., Faraut, T., Faulkner, G., Fowler, K., Fredholm, M., Fritz, E., Gilbert, J., Giuffra, E., Gorodkin, J., Griffin, D., Harrow, J., Hayward, A., Howe, K., Hu, Z., Humphray, S., Hunt, T., Hornshøj, H., Jeon, J., Jern, P., Jones, M., Jurka, J., Kanamori, H., Kapetanovic, R., Kim, J., Kim, J., Kim, K., Kim, T., Larson, G., Lee, K., Lee, K., Leggett, R., Lewin, H., Li, Y., Liu, W., Loveland, J., Lu, Y., Lunney, J., Ma, J., Madsen, O., Mann, K., Matthews, L., McLaren, S., Morozumi, T., Murtaugh, M., Narayan, J., Truong Nguyen, D., Ni, P., Oh, S., Onteru, S., Panitz, F., Park, E., Park, H., Pascal, G., Paudel, Y., Perez-Enciso, M., Ramirez-Gonzalez, R., Reecy, J., Rodriguez-Zas, S., Rohrer, G., Rund, L., Sang, Y., Schachtschneider, K., Schraiber, J., Schwartz, J., Scobie, L., Scott, C., Searle, S., Servin, B., Southey, B., Sperber, G., Stadler, P., Sweedler, J., Tafer, H., Thomsen, B., Wali, R., Wang, J., Wang, J., White, S., Xu, X., Yerle, M., Zhang, G., Zhang, J., Zhang, J., Zhao, S., Rogers, J., Churcher, C. and Schook, L.
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.

KeywordsGenomics Genetics Evolution
Year2012
JournalNature
Journal citation491 (7424), pp. 393-398
PublisherNature Publishing Group
ISSN0028-0836
Digital Object Identifier (DOI)https://doi.org/10.1038/nature11622
Publication dates
Print14 Nov 2012
Publication process dates
Deposited25 Nov 2014
Accepted27 Sep 2012
Output statusPublished
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https://repository.canterbury.ac.uk/item/872xx/analyses-of-pig-genomes-provide-insight-into-porcine-demography-and-evolution

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