Differentiation of wild boar and domestic pig populations based on the frequency of chromosomes carrying endogenous retroviruses

Sergey V. Nikitin, Nikolay S. Yudin, Sergey P. Knyazev, Ruslan B. Aitnazarov, Vitaliy A. Bekenev, Valentina S. Deeva, Galina M. Goncharenko, Victor F. Kobzev, Margarita A. Savina, Viktor I. Ermolaev

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DOI: 10.4236/ns.2010.26066                

Abstract

Analysis of the frequencies of chromosomes carrying various classes of porcine endogenous retroviruses (PERVs) and combinations of these classes was performed in the swine species Sus scrofa L. by using maps constructed in two principal component coordinates. Four population clusters can be recognized in the maps. Cluster 1 is formed by wild boars,cluster 2 by domestic meat breeds, cluster 3 by meat-and-lard (universal) breeds, and cluster 4 by miniature pigs. The maps indicate that modern domesticated swine meat breeds are the closest to the wild type. Meat-and-lard domestic swine breeds are more distant from wild boars, and miniature pigs are diverged the most. The maps showed that microevolution processes associated with PERV carriership frequency had two basic dimensions, or vectors: the vector of fat deposition variation and the “minus” selection vector (determination of commercial traits). Thus, PERVs may cause variation in pig physiology.

Keywords

Sus Scrofa; Endogenous Retroviruses; Pig Genetics; Microevolution; Genetic Distance De-termination

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Niebert, M. and Tonjes, R.R. (2005) Evolutionary spread and recombination of porcine endogenous retroviruses in suiformes. Journal of Virology, 79(1), 649-654.
[2]	Akiyoshi, D.E., Denaro, M., Zhu, H., et al. (1998) Identification of a full-length cDNA for an endogenous retrovirus of miniature swine. Journal of Virology, 72(5), 45034507.
[3]	Le Tissier, P., Stoye, J. P., Takeuchi, Y., et al. (1997) Two sets of human-tropic pig retrovirus. Nature, 389(6652), 681-682.
[4]	Takeuchi, Y., Patience, C., Magre, S., et al. (1998) Host range and interference studies of three classes of pig endogenous retrovirus. Journal of Virology, 72(12), 99869991.
[5]	Bosch, S., Arnauld, C. and Jestin, A. (2000) Study of full-length porcine endogenous retrovirus genomes with envelope gene polymorphism in a specific-pathogen-free Large White swine herd. Journal of Virology, 74(18), 8575-8581.
[6]	Herring, C., Quinn, G., Bower, R., Parsons, N., Logan, N. A., Brawley, A., Elsome, K., Whittam, A., FernandezSuarez, X.M., Cunningham, D., Onions, D., Langford, G. and Scobie, L. (2001) Mapping full-length porcine endogenous retroviruses in a large white pig. Journal of Virology. 75(24), 12252-12265.
[7]	Rogel-Gaillard, C., Bourgeaux, N., Billault, A., Vaiman, M. and Chardon, P. (1999) Construction of a swine BAC library: application to the characterization and mapping of porcine type C endoviral elements. Cytogenetics and Cell Genetics, 85(3-4), 205-211.
[8]	Lee, J.H., Webb, G.C., Allen, R.D. and Moran, C. (2002) Characterizing and mapping porcine endogenous retroviruses in Westran pigs. Journal of Virology, 76(11), 55485556.
[9]	Niebert, M. and Tönjes, R.R. (2003) Analyses of prevalence and polymorphisms of six replication-competent and chromosomally assigned porcine endogenous retroviruses in individual pigs and pig subspecies. Virology, 313(2), 427-434.
[10]	Edamura, K., Nasu, K., Iwami, Y., Nishimura, R., Ogawa, H., Sasaki, N. and Ohgawara, H. (2004) Prevalence of porcine endogenous retrovirus in domestic pigs in Japan and its potential infection in dogs xenotransplanted with porcine pancreatic islet cells. Journal of Veterinary Medical Science, 66(2), 129-135.
[11]	Jin, H., Inoshima, Y., Wu, D., et al. (2000) Expression of porcine endogenous retrovirus in peripheral blood leucocytes ten different breeds. Transplant Infectious Disease, 2(1), 11-14.
[12]	Li, Z., Ping, Y., Shengfu, L., Hong, B., Youping, L., Yangzhi, Z. and Jingqiu, C. (2004) Phylogenetic relationship of porcine endogenous retrovirus (PERV) in Chinese pigs with some type C retrovirus. Virus Research, 105(2), 167-173.
[13]	Aitnazarov, R.B., Ermolaev, V.I., Nikitin, S.V., et al. (2006) Associations between various endogenous virus types and genetic markers in domestic and wild pig populations. Russian Agricultural Sciences (Doklady Rossiiskoi Akademii Sel’skokhozyaistvennykh Nauk), 4, 39-43.
[14]	Nikitin, S.V., Yudin, N.S., Knyazev, S.P., et al. (2008) Frequency of chromosomes carrying endogenous retroviruses in the populations of domestic pig and wild boar. Russian Journal of Genetics, 44(6), 686-693.
[15]	Zhivotovskii, L.A. (1991) Populational biometry. in Russian, Nauka, Moscow.
[16]	Weir, B.S. (1995) Genetic data analysis. in Russian, MIR, Moscow.
[17]	Harpending, H.C. and Jenkins, T. (1973) Genetic distances among Southern African Populations. In: Methods and Theories of Anthropological Genetics. University of New Mexico Press, Albuquerque, 177-199.
[18]	Porter, V. (1993) Pigs: A handbook to the breeds of the world. Comstoc Publishing Associates, Ithaca–New York.
[19]	Gorelov, I.G. (1999) Siberian minipig, a new biomodel. Science in Siberia, 35(2221), 4-10.
[20]	Knyazev, S.P., Tikhonov, V.N., Suzuki, S., et al. (1985) Genetic peculiarities of domestic and wild pigs of Eurasia by serum polymorhic systems. Zoologichesky Zhournal, 61(10), 1563-1568.
[21]	Ovsyannikov, A.I. (1951) Raise of the Kemerovo pig breed. in Russian, Novosibirskoe Oblastnoe Gosudarstvennoe Izdatel’stvo, Novosibirsk.
[22]	Gudilin, I.I., Dement’ev, V.N., et al. (2003) The Kemerovo pig breed. Siberian Branch of the Russian Academy of Agricultural Sciences, Novosibirsk.
[23]	Knyazev, S.P., Nikitin, S.V., Kirichenko, A.V., et al. (2005) Differentiation of wild and domestic pig populations according to serum allotypes. Sel’skokhozyaistvennaya Biologiya. Biologiya Zhivotnykh, 6, 100-105.
[24]	Nikitin, S.V., Knyazev, S.P., Nikolaev, A.G., et al. (2006) Diversity of wild and domestic pig populations estimated by a set of serum allotypes. Russian Journal of Genetics, 42(3), 317-326.
[25]	Vila, C., Seddon, J. and Ellegren, H. (2005) Genes of domestic mammals augmented by backcrossing with wild ancestors. Trend in Genetics, 21(4), 214-218.
[26]	Larson, G., Albarella, U., Dobney, K., Rowley-Conwy, P., et al. (2007) Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proceedings of the National Academy of Science, USA, 104(39), 15276-15281.