Domestication and Genome Evolution
International Journal of Genetics and Genomics
Volume 2, Issue 4, August 2014, Pages: 47-56
Received: Jul. 18, 2014; Accepted: Jul. 30, 2014; Published: Aug. 10, 2014
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Glazko, Valeriy, Department of Zoo engineering, Russian State Agrarian University, Moscow agricultural Academy named after K.A. Timiryazev, Moscow, Russia
Zybaylov, Boris, Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
Glazko, Tatiana, Department of Zoo engineering, Russian State Agrarian University, Moscow agricultural Academy named after K.A. Timiryazev, Moscow, Russia
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Background. Pressure on modern agriculture to increase production is rising with the increase in human population. To meet this demand it is important to effectively manage domesticated species. However, genetic mechanisms and genomic targets of domestication are still poorly understood. It is well known that phenotypic variability in domesticated animals is higher compared to the variability in the closest wild relatives. Indeed, there are many breeds clearly distinguishable from each other by their morphological and physiological traits. In this report we review some of available literature and present original data to define genomic targets of domestication. Results. Using both publically available data and results of our own research we demonstrate the existence of a well-defined genomic signature (also called “sub-genome”), which consists of the molecular targets of artificial selection. The genetic signatures of domestication are revealed by comparison of different mammalian species and breeds. As a result, we found that a wide repertoire of genes is involved in the domestication process. The vast majority of these genes either plays a role in the neuroendocrine regulation, immune response, or encodes the milk proteins. Comparison of cattle genome to wild relatives reveals higher degree of polymorphism within retrotransposons, enzymes of the exogenous substrate metabolism, and in the genetic elements associated with the immune system. Conclusions. Our data for first time challenges the current explanation of phenotypic variation in domesticated species as a consequence of inbreeding and concomitant increase in homozygosity. Instead, we clearly show that there is no difference in the bulk genetic variability, and other explanation for difference in phenotypic variability is needed. We discover different targets of natural and artificial selection: in the case of domesticated species systems that are responsible for exogenous substrate metabolism are the targets, while in the case of wild species, genetic systems that are responsible for energy metabolism are targeted. We further speculate that the hyperactivity of mobile genetic elements – as evident from the higher polymorphisms within retro transposons – could be the source of increased genetic variability in domesticated species.
Allele Distribution, Genetic Variability, Inverted Repeats, PCR Amplification Spectra, Mobile Genetic Elements
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Glazko, Valeriy, Zybaylov, Boris, Glazko, Tatiana, Domestication and Genome Evolution, International Journal of Genetics and Genomics. Vol. 2, No. 4, 2014, pp. 47-56. doi: 10.11648/j.ijgg.20140204.11
Bailey E, Lear TL. 1994. Comparison of thoroughbred and Arabian horses using RAPD markers. Anim. Genet. Suppl 1, p.105-108.
Barendse, W., Harrison, B.E., Bunch R.J., Thomas, M.B., Turner, L.B., 2009. Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits. BMC Genomics. 10, 178.
Beck, J., Sieber A., 2010. Is the spatial distribution of mankind’s most basic economic traits determined by climate and soil alone? PLoS ONE. 5(5), e10416.
Bogolyubskiy, S.N., 1959. Origin and Transformation of Domestic Animals. Soviet Science, Мoscow.
Chena, S.Y., Duan, Z.Y., Shaa, T., Xiangyub, J., Wub, S.F., Zhanga, Y.P., 2006. Origin, genetic diversity, and population structure of Chinese domestic sheep. Gene. 376(2), 216–223.
Coop, G., Pickrell, J.K., Novembre, J., Kudaravalli, S., Li, J., Absher, D., Myers, R.M., Cavalli-Sforza, L.L., Feldman, M.W., Pritchard, J.K., 2009. The role of geography in human adaptation. PLoS Genet. 5(6), e1000500.
Diamond, J., 2002. Evolution, consequences and future of plant and animal domestication. Nature. 418(6898), 700–707.
Feeney, K.M., Parish, J.L., 2009.Targeting mitotic chromosomes: a conserved mechanism to ensure viral genome persistence. Proceedings of the Royal Society: B. 276(1662):1535–1544.
Flori, L., Fritz, S., Jaffrezic, F., Boussaha M. et al., 2009. The Genome response to artificial selection: a case study in dairy cattle. PLoS ONE. 4(8), e6595.
Glazko, V.I., 1999. The polymorphism of proteins, RAPD-PCR and ISSR-PCR markers in European and American bison and cattle. Cytology and Genetics. (Tsitol. Genet. Russian). 33(6), 30–38.
Glazko, V.I., 2000. Genetically determined enzyme polymorphism in soy varieties (Glycine max) and in wild soy (Glycine soja). Cytology and Genetics. (Tsitol. Genet. Russian). 34(2), 77–84.
Glazko, V.I., 2003. An attempt at understanding the genetic basis of domestication. Animal Science Papers and Reports. 21(2), 109–120.
Glazko, V.I., 2004. Polymorphism of proteins, RAPD-PCR and ISSR-PCR markers in Ungulata species and domestication problems. Proceeding of the Russian Academy of Agricultural Sciences. 4, 40–46.
Glazko, V.I., Tsvetkov, I.L., Ivanov, A.N., 2006. Genetic differentiation of rice cultivars by IRAP markers. Izvestiya of Timiryazev Academy. 4, 155–159.
Glazko, V.I., Tsvetkov, I.L., Sozinova, L.F., Glazko, T.T., 2009. Molecular and genetic markers of DNA polymorphism and their genome positioning. Proceeding of the Russian Academy of Agricultural Sciences (Russian). 3, 11–14.
Glazko, V.I., 2011. Nano- and microscales in genetic material organization: On the issue of Lima-de-Faria "chromosome fields". Dokl. Biochem. Biophys. 436, 5–7.
Glazko, V.I., Bardukov, N. V., Pheophilov, A.V., Sipko, T.P, Elkina, M.A., Glazko, T.T., 2012a. Polymorphism of ISSR and IRAP markers in genomes of musk-oxen (Ovibos moschatus) and horse (Equus caballus) of Altai breed. Izvestia of Timiryazev Agricultural Academy. Special Issue, 16–26.
Glazko, V.I., Pheophilov, A.V., Bardukov, N.V., Glazko, T.T., 2012b. Species-specific ISSR-PCR markers and the ways of their appearing. Izvestia of Timiryazev Agricultural Academy. (1), 118–125.
Glazov, E.A., Kongsuwan, K., Assavalapsakul, W., 2009. Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PLoS ONE. 4(7), e6349.
Khaldi, N., Shields, D.C., 2011. Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species. Biology Direct. 6(1), 40–49.
Kharchenko, P.N., Glazko, V.I., 2006. DNA Technologies in Agrobiology Development. Voskresenie, Мoscow.
Lewin, H.A., 2009. It’s a bull’s market. Science. 324, 478–479.
MacEachern, S., McEwan, J., Goddard, M., 2009a. Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae). BMC Genomics. 10, 177.
MacEachern, S., McEwan, J., McCulloch, A. et al., 2009b. Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there evidence of rapid evolution or reduced selective constraint in domestic cattle? BMC Genomics. 10, 179–193.
Nagornyk, T.A., Lopatina, N.V., Glazko, V. I., 2005. Genetic interrelation between varieties of cultural soja and wild species of Glycine. Proceedings of the National Academy of Science of Ukraine. 8, 163–172.
Nosil, P., Funk, D.J., Ortiz-Barrientos, D., 2009. Divergent selection and heterogeneous genomic divergence. Mol. Ecol. 18, 375–402.
Rebollo, R., Horard B., Hubert, B., Vieira C., 2010. Jumping genes and epigenetics: Towards new species. Gene. 454(1–2), 1–7.
Strömqvist, M., Falk, P., Bergström, S. et al., 1995. Human milk kappa-casein and inhibition of Helicobacter pylori adhesion to human gastric mucosa. J. Pediatr. Gastroenterol. Nutr. 21(3), 288-296.
Tang, H., Sezen, U., Paterson, А.H., 2010. Domestication and plant genomes. Curr. Opin. Plant Biol. 13(2), 160–166.
Tellam, R.L., Worley, K.C., 2009. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science. 324, 522–528.
The bovine HapMap consortium genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. 2009. Science. 324, 528–532.
Trut, L.N., 2007. Domestication in historical process and experiment. VOGiS Herald. 11(2), 273–289.
Van der Kuyl, A.C., 2011. Characterization of a full-length endogenous beta-retrovirus, EqERV-Beta1, in the genome of the horse (Equus caballus). Viruses. 3, 620–628.
Venner, S., Cédric Feschotte, C., Biémont, C., 2009. Transposable elements dynamics: toward a community ecology of the genome. Trends Genet. 25(7), 317–323.
Wade, C.M., Giulotto, E., Sigurdsson, S. et al., 2009. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science. 326(5954), 865-867.
Wilkins A. S., Wrangham R. W., Fitch W. T. The “Domestication Syndrome” in Mammals: A Unified Explanation Based on Neural Crest Cell Behavior and Genetics // Genetics – 2014. - V. 197. – P. 795–808
Zeder, M.A., 2008. Domestication and early agriculture in the Mediterranean basin: Origins, diffusion, and impact. PNAS. 105: (33), 11597–11604.
Zwierzchowski, L., Oprzadek, J., Dymnicki, E., Dzierzbicki, P., 2001. An association of growth hormone, K-casein, β-lactoglobulin. leptin and Pit-1 loci polymorphism with growth rate and carcass traits in beef cattle. Animal Science Papers and Reports. 19, 65–78.
Zietkiewicz E., Rafalski A., Labuda D. 1994. Genome fingerprinting by seguence repeat (SSR) anchored polymerase chain reaction amplification. Genomics. 20, 176–183.
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