The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

Abstract

A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by (δμ)² and DA distances, and the divergence times between populations were estimated by (δμ)². Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles (10), whereas, Bohai black and Buffalo had the smallest number of private alleles (2). Chinese Holstein showed the highest genetic variability. Its observed number of alleles (Na), mean effective number of alleles (MNA), and mean heterozygosity (He) were 7.7500, 4.9722, and 0.7719, respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first, followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations. Luxi and Bohai were estimated to have diverged 0.039–0.105 million years ago (MYA), however, buffalo and Holstein diverged 0.501–1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136–0.363, 0.273–0.729, and 0.326–0.600 MYA, respectively.
- genetic diversity,
- genetic differentiation,
- microsatellite,
- bovine subfamily

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References(35)

References

[1]	Barker, J.S.F., Moore, S.S., Hetzel, D.J.S. et al. Anim. Genet., 28 (1997),pp. 103-115
[2]	Chen, Y.C., Wang, Y.Y., Chang, H. et al.
[3]	Crawford, A.M., Cuthbertson, R.P Mutations in sheep microsatellite Genome Res., 6 (1996),pp. 876-879
[4]	Editorial section of the “Bovine breeds in China”
[5]	Felsenstein, J. Confidence limits on phylogenies: An approach using the bootstrap Evolution, 39 (1985),pp. 783-791
[6]	Francis, C.Y., Yang, R.C., Tim, B.
[7]	Goldstein, D.B., Ruiz-Linares, A., Feldmann, M. et al. Genetic absolute dating based on microsatellite and origin of modern humans Proc. Natl. Acad. Sci. USA, 92 (1995),pp. 6723-6727
[8]	Hartl, G.B., Goltenboth, R., Grillitsch, M. et al. On the biochemical systematics of Bovini Biochem. Syst. Ecol., 16 (1988),pp. 575-579
[9]	Ibeagha-Awemu, E.M., Erhardt, G. Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms J. Anim. Breed. Genet., 122 (2005),pp. 12-20
[10]	Kantanen, J., Olsaker, I., Holm, L.E. et al. Genetic diversity and population structure of 20 North European cattle breeds J. Hered., 91 (2000),pp. 446-457
[11]	Kikkawa, Y., Amano, T., Suzuki, H. Analysis of genetic diversity of domestic cattle in east and southeast Asia in terms of variations in restriction sites and sequences of mitochondrial DNA Biochem. Genet., 33 (1995),pp. 51-60
[12]	Kim, K.S., Yeo, J.S., Choi, C.B. Genetic diversity of north-east Asian cattle based on microsatellite data Anim. Genet., 33 (2001),pp. 201-204
[13]	Kimura, M., Crow, J.F. The number of alleles that can be maintained in a finite population Genetics, 49 (1964),pp. 725-738
[14]	Li, M.H., Sternbauer, K., Haahr, P.T. et al. Genetic components in contemporary Faroe Islands cattle as revealed by microsatellite analysis J. Anim. Breed. Genet., 122 (2005),pp. 309-317
[15]	Loftus, R.T., MacHugh, D.E., Bradley, D.G. et al. Evidence for two independent domestications of cattle Proc. Natl. Acad. Sci. USA., 91 (1994),pp. 2757-2761
[16]	Luo, Y.F., Wang, Z.G., Li, J.Q. et al. Genetic variation and genetic relationship among 13 Chinese and introduced cattle breeds using microsatellite DNA markers Biodiversity Science, 14 (2006),pp. 498-507
[17]	Ma, Y.H., Xu, G.G., Wang, D.Y. et al. Study on dynamic information of animal genetic resources in China Sci. Agr. Sin., 35 (2002),pp. 552-555
[18]	MacHugh, D.E., Loftus, R.T., Cunningham, P. et al. Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers Anim. Genet., 29 (1998),pp. 333-340
[19]	MacHugh, D.E., Shriver, M.D., Loftus, R.T. et al. Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus) Genetics, 146 (1997),pp. 1071-1086
[20]	Marlin-Burriel, I., Garcia-Muro, E., Zaragoza, P. Genetic diversity analysis of six Spanish native Cattle breeds using microsatellites Anim. Genet., 30 (1999),pp. 177-182
[21]	Mateus, J.C., Penedo, M.C.T., Alves, V.C. et al. Genetic diversity and differentiation in Portuguese cattle breeds using microsatellite Anim. Genet., 35 (2003),pp. 106-113
[22]	Ohta, T., Kimura, M. The model of mutation appropriate to estimate the number of the electrophoretically detectable alleles in a genetic population Genet. Res., 22 (1973),pp. 201-204
[23]	Olivier, L.
[24]	Page, R.D.M. TREEVIEW: An application to display phylogenetic trees on personal computers Comp. Appl. Biosc., 12 (1996),pp. 357-358
[25]	Qie, X.B., Han, J.L., Lkhagva, B. et al. Genetic diversity and differentiation of Mongolian and Russian yak populations J. Anim. Breed. Genet., 122 (2005),pp. 117-126
[26]	Ritz, L.R., Glowatzki, M.L., MacHugh, D.E. et al. Phylogenetic analysis of the tribe Bovini using microsatellite Anim. Genet., 31 (2000),pp. 178-185
[27]	Saitou, N., Nei, M. The neighbour-joining method: a new method for reconstructing phylogenetic trees Mol. Bio. Evol., 4 (1987),pp. 406-425
[28]	Sambrook, J., Fritch, E.F., Maniartis, T.
[29]	Sun, W.B., Chen, H., Lei, C.Z. et al. Study on population genetic characteristics of Qinchuan cows using microsatellite markers J. Genet. Genomics., 34 (2007),pp. 17-25
[30]	Takezaki, N., Nei, M. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA Genetics, 144 (1996),pp. 389-399
[31]	Tu, Z.C., Zhang, Y.P., Qiu, H. Mitochondrial DNA polymorphism and genetic diversity in Chinese yaks Acta. Genet. Sin, 25 (1998),pp. 205-212
[32]	Tu, Z.C., Zhang, Y.P., Qiu, H. Genetic diversity and divergence in chinese yak (Bos grunniens) populations inferred from blood protein electrophoresis Biochem. Genet., 35 (1997),pp. 13-14
[33]	Wang, M.Q., Weigend, S., Barre-Dirie, A. et al. Analysis of two Chinese yak (Bos grunniens) populations using bovine microsatellite primers J. Anim. Breed. Genet., 120 (2003),pp. 237-244
[34]	Yang, Z.P., Chang, H., Li, X.Y. et al. A study of ecological and morphological characters of Tibet zebu as a new genetic resource. Sci. Agric. Sin., 35 (2002),pp. 1396-1400
[35]	Zhou, G.L., Jin, H.G., Zhu, Q. et al. Genetic diversity analysis of five cattle breeds native to China using microsatellite J. Genet., 84 (2005),pp. 77-80

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