Asian-Australasian Journal of Animal Sciences

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
권호 표지
DOI QR코드

DOI QR Code

Chinese Holstein Cattle Shows a Genetic Contribution from Native Asian Cattle Breeds: A Study of Shared Haplotypes and Demographic History

  • Ferreri, Miro (College of Veterinary Medicine, China Agricultural University) ;
  • Gao, Jian (College of Veterinary Medicine, China Agricultural University) ;
  • Wang, Zhi (College of Veterinary Medicine, China Agricultural University) ;
  • Chen, Liben (College of Veterinary Medicine, China Agricultural University) ;
  • Su, Jingliang (College of Veterinary Medicine, China Agricultural University) ;
  • Han, Bo (College of Veterinary Medicine, China Agricultural University)
  • Received : 2010.12.25
  • Accepted : 2011.04.08
  • Published : 2011.08.01
Download PDF
⟨ Previous Next ⟩

Abstract

The Chinese Holstein cattle breed, an introduced breed in China, has been crossbred with native cattle breeds. We hypothesised that the Chinese Holstein local population in Beijing share haplotypes with native Asian cattle breeds, the result of a sudden population expansion in the recent past. We also hypothesised that crossbreeding and population expansion left traces that shaped the genetic makeup of the breed. Evaluation of this was performed by mitochondrial DNA (mtDNA) sequence analysis of Chinese Holstein cattle from Beijing (n = 41) and a comparison of them with the published mtDNA sequences (n = 293) of 14 Asian breeds with an emphasis on Chinese native cattle breeds. Three shared common haplotypes between Chinese Holstein cattle and native Asian cattle were found. Moreover, a high level of haplotype diversity in Chinese Holstein cattle (h = 0.9557) and low nucleotide diversity (${\pi}$ = 0.0052) was found, indicating a past population bottleneck followed by rapid population growth. These findings are supported by the significantly negative deviation of Tajima's D (-1.82085), the star-like pattern of dominant haplotypes and the pairwise mismatch distribution analysis, which showed a unimodal pattern.

Keywords

References

  1. Avise, J. C. 2000. Phylogeography. Harvard University Press, London: p. 447.
  2. Avise, J. C., D. Walker and G. C. Johns. 1998. Speciation durations and Pleistocene effects on vertebrate phylogeography. Proc. Biol. Sci. 265(1407):1707-1712. https://doi.org/10.1098/rspb.1998.0492
  3. Bertorelle, G. and M. Slatkin. 1995. The number of segregating sites in expanding human populations, with implications for estimates of demographic parameters. Mol. Biol. Evol. 12(5):887-892.
  4. Cai, X., H. Chen and C. Lei. 2010. Matrilineal genetic inter-introgression of Bos taurus and Bos indicus in China. Livest. Sci. 128:12-19. https://doi.org/10.1016/j.livsci.2009.06.017
  5. Chen, S. Y., Z. Y. Duan, T. Sha, J. Xiangyu, S. F. Wu and Y. P. Zhang. 2006. Origin, genetic diversity, and population structure of Chinese domestic sheep. Gene 376:216-223. https://doi.org/10.1016/j.gene.2006.03.009
  6. Clement, M., D. Posada and K. A. Crandall. 2000. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9(10):1657-1659. https://doi.org/10.1046/j.1365-294x.2000.01020.x
  7. Dong, F. 2006. The outlook for Asian dairy markets: The role of demographics, income, and prices. Food Policy 31:260-270. https://doi.org/10.1016/j.foodpol.2006.02.007
  8. Excoffier, L and S. Schneider. 1999. Why hunter-gatherer populations do not show signs of pleistocene demographic expansions. Proc. Natl. Acad. Sci. USA 96(19):10597-10602. https://doi.org/10.1073/pnas.96.19.10597
  9. Excoffier, L., P. E. Smouse and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131(2):479-491.
  10. Fu, Y. X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147(2):915-925.
  11. Fuller, F., J. Huang, H. Ma and S. Rozelle 2006. Got milk? The rapid rise of China's dairy sector and its future prospects. Food Policy 31(4):201-215. https://doi.org/10.1016/j.foodpol.2006.03.002
  12. Jia, S., H. Chen, G. Zhang, Z. Wang, C. Lei, R. Yao and X. Han. 2007. Genetic variation of mitochondrial D-loop region and evolution analysis in some Chinese cattle breeds. J. Genet. Genomics 34(6):510-518. https://doi.org/10.1016/S1673-8527(07)60056-3
  13. Lai, S. J., Y. P. Liu, Y. X. Liu, X. W. Li and Y. G. Yao. 2006. Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation. Mol. Phylogenet. Evol. 38(1):146-154. https://doi.org/10.1016/j.ympev.2005.06.013
  14. Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson and D. G. Higgins. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947-2948. https://doi.org/10.1093/bioinformatics/btm404
  15. Lei, C. Z., H. Chen, H. C. Zhang, X. Cai, R. Y. Liu, L. Y. Luo, C. F. Wang, W. Zhang, Q. L. Ge, R. F. Zhang, X. Y. Lan and W. B. Sun. 2006. Origin and phylogeographical structure of Chinese cattle. Anim. Genet. 37(6):579-582. https://doi.org/10.1111/j.1365-2052.2006.01524.x
  16. Librado, P. and J. Rozas. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451-1452. https://doi.org/10.1093/bioinformatics/btp187
  17. Liu, Y. P., G. S. Wu, Y. G. Yao, Y. W. Miao, G. Luikart, M. Baig, A. Beja-Pereira, Z. L. Ding, M. G. Palanichamy and Y. P. Zhang. 2006. Multiple maternal origins of chickens: Out of the Asian jungles. Mol. Phylogenet. Evol. 38:12-19. https://doi.org/10.1016/j.ympev.2005.09.014
  18. Liu, J. X., Y. M. Wu and Z. E. Zhou. 2002. Current situation and prospect for dairy production in China. In: Smallholder dairy production and marketing (Ed. D. Rangnekar and W. Thorpe). Opportunities and constraints. Proceedings of a South-South workshop held at NDDB, Anand, India, 2001. NDDB (National Dairy Development Board), Anand, India, and ILRI (International Livestock Research Institute), Nairobi, Kenya. p. 538.
  19. Mannen, H., M. Kohno, Y. Nagata, S. Tsuji, D. G. Bradley, J. S. Yeo, D. Nyamsamba, Y. Zagdsuren, M. Yokohama, K. Nomura and T. Amano. 2004. Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle. Mol. Phylogenet. Evol. 32(2):539-544. https://doi.org/10.1016/j.ympev.2004.01.010
  20. Marjoram, P. and P. Donnelly. 1994. Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics 136(2):673- 683.
  21. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
  22. Nei, M. and F. Tajima. 1981. DNA polymorphism detectable by restriction endonucleases. Genetics 97(1):145-163.
  23. Posada, D. and K. A. Crandall. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol. Evol. 16:3745.
  24. Qiu, H., Z. R. Qing, Y. C. Chen and A. D. Wang. 1988. Bovine breeds in China. Shanghai Scientific and Technical Publishers, Shanghai.
  25. Ray, N., M. Currat and L. Excoffier. 2003. Intra-deme molecular diversity in spatially expanding populations. Mol. Biol. Evol. 20(1):76-86. https://doi.org/10.1093/molbev/msg009
  26. Richards, M. B., V. A. Macaulay, H. J. Bandelt and B. C. Sykes. 1998. Phylogeography of mitochondrial DNA in western Europe. Ann. Hum. Genet. 62(Pt 3):241-260. https://doi.org/10.1046/j.1469-1809.1998.6230241.x
  27. Rogers, A. R., A. E. Fraley, M. J. Bamshad, W. S. Watkins and L. B. Jorde. 1996. Mitochondrial mismatch analysis is insensitive to the mutational process. Mol. Biol. Evol. 13(7):895-902. https://doi.org/10.1093/molbev/13.7.895
  28. Rogers, A. R. and H. Harpending. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9(3):552-569.
  29. Singh, V. K., A. K. Mangalam, S. Dwivedi and S. Naik. 1998. Primer premier: program for design of degenerate primers from a protein sequence. Biotechniques 24(2):318-319.
  30. Slatkin, M. 1991. Inbreeding coefficients and coalescence times. Genet. Res. 58(2):167-175. https://doi.org/10.1017/S0016672300029827
  31. Slatkin, M. and C. A. Muirhead. 1999. Overdominant alleles in a population of variable size. Genetics 152(2):775-781.
  32. Stepien, C. A. 1999. Phylogeographical structure of the Dover sole Microstomus pacificus: the larval retention hypothesis and genetic divergence along the deep continental slope of the northeastern Pacific Ocean. Mol. Ecol. 8(6):923-939. https://doi.org/10.1046/j.1365-294x.1999.00643.x
  33. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3):585-595.
  34. Templeton, A. R., K. A. Crandall and C. F. Sing. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132(2):619-633.
  35. Tsuji, S., H. Mannen, F. Mukai, M. Shojo, K. Oyama, T. Kojima, C. Kano, Y. Kinoshita and E. Yamaguchi. 2004. Trace of native cattle in Japanese Holstein assessed by mitochondrial DNA sequence polymorphism. J. Dairy Sci. 87(9):3071-3075. https://doi.org/10.3168/jds.S0022-0302(04)73440-2

Cited by

  1. Mitochondrial DNA diversity of mud crab Scylla olivacea (Portunidae) in Peninsular Malaysia: a preliminary assessment vol.40, pp.11, 2013, https://doi.org/10.1007/s11033-013-2755-4