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Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

  • Liu, Jian-Bin (Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences) ;
  • Wang, Fan (Lanzhou Veterinary Research Institute of Chinese Academy of Agricultural Sciences, China Agricultural Veterinarian Biology Science and Technology Co. Ltd.) ;
  • Lang, Xia (Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences) ;
  • Zha, Xi (Institute of Livestock Research, Tibet Academy of Agriculture and Animal Science) ;
  • Sun, Xiao-Ping (Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences) ;
  • Yue, Yao-Jing (Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences) ;
  • Feng, Rui-Lin (Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences) ;
  • Yang, Bo-Hui (Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences) ;
  • Guo, Jian (Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences)
  • Received : 2012.09.13
  • Accepted : 2012.12.03
  • Published : 2013.03.01

Abstract

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright's F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.

Keywords

Cashmere Goat;Geographic Distance;Pairwise Distance;Genetic Diversity

References

  1. Araújo, A. M., S. E. F. Guimaraes, T. M. M. Machado, P. S. Lopes, C. S. Pereira, F. L. R. Silva, M. T. Rodrigues, V. S. Columbiano and C. G. Fonseca. 2006. Genetic diversity between herds of Alpine and Saanen dairy goats and naturalized Brazilian Moxotó breed. Genet. Mol. Biol. 29:67-74. https://doi.org/10.1590/S1415-47572006000100014
  2. Arranz, J., Y. Bayon and F. San Primitivo. 1998. Genetic relationships among Spanish sheep using microsatellites. Anim. Genet. 29:435-440. https://doi.org/10.1046/j.1365-2052.1998.296371.x
  3. Avise, J. C. 2000. The history and formation of species. Cambridge: Harvard University Press, USA. 439.
  4. Balloux, F. and N. Lugon-Moulin. 2002. The estimation of population differentiation with microsatellite markers. Mol. Ecol. 11:155-165. https://doi.org/10.1046/j.0962-1083.2001.01436.x
  5. Barker, J. S. F., S. G. Tan, S. S. Moore, T. K. Mukherjee, J. L. Matheson and O. S. Selvaraj. 2001. Genetic variation within and relationships among populations of Asian goats (Capra hircus). J. Anim. Breed. Genet. 118:213-233. https://doi.org/10.1046/j.1439-0388.2001.00296.x
  6. Botstein, D., R. L. White, M. Skolnick and R. W. Davis. 1980. Construction of a genetic linkage map in man using restriction fragment polymorphisms. Am. J. Hum. Genet. 32:314-331.
  7. Bowcock, A. M., A. Ruiz Linare, J. Tomfohrde, E. Minch, J. R. Kidd and L. L. Cavalli-Sforza. 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455-457. https://doi.org/10.1038/368455a0
  8. Bruford, M. W. and R. K. Wayne. 1993. Microsatellites and their application to population genetic studies. Curr. Opin. Genet. Dev. 3:939-943. https://doi.org/10.1016/0959-437X(93)90017-J
  9. Bruno-de-Sousa, C., A. M. Martinez, C. Ginja, F. Santos-Silva, M. I. Carolino, J. V. Delgado and L. T. Gama. 2011. Genetic diversity and population structure in Portuguese goat breeds. Livest. Sci. 135:131-139. https://doi.org/10.1016/j.livsci.2010.06.159
  10. Canon, J., D. Garcia, M. A. Garcia-Atance, G. Obexer-Ruff, J. A. Lenstra, P. Ajmone-Marsan and S. Dunner. 2006. Geographical partitioning of goat diversity in Europe and the Middle East. Anim. Genet. 37:327-334. https://doi.org/10.1111/j.1365-2052.2006.01461.x
  11. Chen, S. L., B. Fan, B. Liu, M. Yu, S. H. Zhao, M. J. Zhu, T. G. Xiong and K. Li. 2006. Genetic variations of 13 indigenous Chinese goat breeds based on cytochrome b gene sequences. Biochem. Genet. 44:89-99.
  12. Crawford, A. M., K. G. Dodds, A. J. Ede, C. A. Pierson, G. W. Montgomery, H. G. Garmonsway, A. E. Beattie, K. Davies, J. F. Maddox, S. W. Kappes, R. T. Stone, T. C. Nguyen, J. M. Penty, E. A. Lord, J. E. Broom, J. Buitkamp, W. Schwaiger, J. T. Epplen, P. Matthew, M. E. Matthews, D. J. Hulme, K. J. Beh, R. A. McGraw and C. W. Beattie. 1995. An autosomal genetic linkage map of the sheep genome. Genetics 140:703-724.
  13. Davis, M. B. and R. G. Shaw. 2001. Range shifts and adaptive responses to quaternary climate change. Science 292:673-679. https://doi.org/10.1126/science.292.5517.673
  14. Di, R., S. M. Farhad Vahidi, Y. H. Ma, X. H. He, Q. J. Zhao, J. L. Han, W. J. Guan, M. X. Chu, W. Sun and Y. P. Pu. 2011. Microsatellite analysis revealed genetic diversity and population structure among Chinese cashmere goats. Anim. Genet. 42:428-431. https://doi.org/10.1111/j.1365-2052.2010.02072.x
  15. Evanno, G., S. Regnaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  16. Falush, D., M. Stephens and K. J. Pritchard. 2003. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164:1567-1587.
  17. Fatima, S., C. D. Bhonga, D. N. Ranka and C. G. Joshi. 2008. Genetic variability and bottleneck studies in Zalawadi, Gohilwadi and Surti goat breeds of Gujarat (India) using microsatellites. Small Rumin. Res. 77:58-64. https://doi.org/10.1016/j.smallrumres.2008.01.009
  18. Fernandez, H., S. Hughes, J. D. Vigne, D. Helmer, G. Hodgins, C. Miquel, C. Hanni, G. Luikart and P. Taberlet. 2006. Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas. Proc. Natl. Acad. Sci. USA. 103:15375-15379. https://doi.org/10.1073/pnas.0602753103
  19. Gamaa, L. T. and M. C. Bressan. 2011. Biotechnology applications for the sustainable management of goat genetic resources. Small Rumin. Res. 98:133-146. https://doi.org/10.1016/j.smallrumres.2011.03.031
  20. Ganai, N. A. and B. T. Yadav. 2001. Genetic variation within and among three Indian breeds of goat using heterologous microsatellite markers. Anim. Biotechnol. 12:121-136. https://doi.org/10.1081/ABIO-100108338
  21. Glowatzki-Mullis, M. L., J. Muntwyler, E. Baumle and C. Gaillard. 2008. Genetic diversity measures of Swiss goat breeds as decision making support for conservation policy. Small Rumin. Res. 74:202-211. https://doi.org/10.1016/j.smallrumres.2007.07.002
  22. Goudet, J. 2002. Fstat: a program to estimate and test gene diversities and fixation indices. Version 2.9.3.2. Available at http://www.unil.ch/izea/softwares/fstat.html.
  23. Gour, D. S., G. Malik, S. P. S. Ahlawat, A. K. Pandey, R. Sharma, N. Gupta, S. C. Gupta, P. S. Bisen and D. Kumar. 2006. Analysis of genetic structure of Jamunapari goats by microsatellite markers. Small Rumin. Res. 66:140-149. https://doi.org/10.1016/j.smallrumres.2005.07.053
  24. Groeneveld, L. F., J. A. Lenstra, H. Eding, M. A. Toro, B. Scherf, D. Pilling, R. Negrini, E. K .Finlay, H. Jianlin, E. Groeneveld and S. Weigend. The GLOBALDIV Consortium. 2010. Genetic diversity in farm animals-a review. Anim. Genet. 41:6-31. https://doi.org/10.1111/j.1365-2052.2010.02038.x
  25. Guo, X. and R. C. Elston. 1999. Linkage informative content of polymorphic genetic markers. Hum. Hered. 49:112-118. https://doi.org/10.1159/000022855
  26. Gutierrez-Espeleta, G. A., S. T. Kalinowski, W. M. Boyce and P. W. Hedrick. 2000. Genetic variation and population structure in desert bighorn sheep: implications for conservation. Conserv. Genet. 1:3-15. https://doi.org/10.1023/A:1010125519304
  27. Hedrick, P. W. 1999. Highly variable loci and their interpretation in evolution and conservation. Evolution 53:313-318. https://doi.org/10.2307/2640768
  28. Hedrick, P. W. and P. S. Miller. 1992. Conservation genetics: techniques and fundamentals. Ecol. Appl. 2:30-46. https://doi.org/10.2307/1941887
  29. Hochberg, Y. 1988. A sharper Bonferroni procedure for multiple test of significance. Biometrika. 75.:800-802. https://doi.org/10.1093/biomet/75.4.800
  30. Iamartino, D., A. Bruzzone, A. Lanza, M. Blasi and F. Pilla. 2005. Genetic diversity of Southern Italian goat populations assessed by microsatellite markers. Small Rumin. Res. 57:249-255. https://doi.org/10.1016/j.smallrumres.2004.08.003
  31. Kang, J. F., X. L. Li, R. Y. Zhou, L. H. Li, G. R Zheng and H. Y. Zhao. 2011. Genetic diversity and differentiation of four goat lineages based on analysis of complete mtDNA d-loop. Front. Agric. In China 5:87-93. https://doi.org/10.1007/s11703-010-1061-3
  32. Kantanen, J., I. Olsaker, L. E. Holm, S. Lien, J. Vilkki and K. Brusgaard. 2000. Genetic diversity and population structure of 20 North European cattle breeds. J. Hered. 91:446-457. https://doi.org/10.1093/jhered/91.6.446
  33. Kimura, M. and J. F. Crow. 1964. The number of alleles that can be maintained in a finite population. Genetics 49:725-738.
  34. Li, M. H., S. H. Zhao, C. Bian, H. S. Wang, H. Wei, B. Liu, M. Yu, B. Fan, S. L. Chen, M. J. Zhu, S. J. Li, T. A. Xiong and K. Li. 2002. Genetic relationships among twelve Chinese indigenous goat populations based on microsatellite analysis. Genet. Sel. Evol. 34:729-744. https://doi.org/10.1186/1297-9686-34-6-729
  35. Li, X. L. and A. Valentini. 2004. Genetic diversity of Chinese indigenous goat breeds based on microsatellite markers. J. Anim. Breed. Genet. 121:350-355. https://doi.org/10.1111/j.1439-0388.2004.00465.x
  36. Luikart, G., L. Gielly, L. Excoffier, J. D. Vigne, J. Bouvet and P. Taberlet. 2001. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc. Natl. Acad. Sci. USA. 98:5927-5932. https://doi.org/10.1073/pnas.091591198
  37. MacHugh, D. E., M. D. Shiriver, R. T. Loftus, P. Cunningham and D. G. Bradley. 1997. Microsatellite DNA variation and the evolution, domestication and phylogeography of Taurine and Zebu cattle (Bos taurus and Bos indicus). Genetics 146:1071-1086.
  38. Martínez, A. M., J. Acosta, J. L. Vega-Pla and J. V. Delgado. 2006. Analysis of the genetic structure of the canary goat populations using microsatellites. Livest. Sci. 102:140-145. https://doi.org/10.1016/j.livsci.2005.12.002
  39. Martinez-Martinez, A., J. L. Vega-Pla, M. N. Ribeiro, M. E. Camacho, M. A. Revidatti, A. Galarza, A. Stemmer, P. Sponenberg, B. Seguí, M. Gómez, D. Martín, L. L. Rocha, E. Chacón, E. Pimenta, J. Capote, M. Amills, A. Cabello, L. T. Gama, J. V. Delgado and M. P. C. Menezes. 2008. Genetic relationships between native goat populations from Spain, Portugal and America. In: Proceedings of the XXXI Conference of the International Society for Animal Genetics, Amsterdam, The Netherlands.
  40. Muema, E. K., J. W. Wakhungu, O. Hanotte and H. Jianlin. 2009. Genetic diversity and relationship of indigenous goats of Sub-saharan Africa using microsatellite DNA markers. Livest. Res. Rural Dev. 21.
  41. Nei, M. 1972. Genetic distance between populations. Am. Nat. 106:283-291. https://doi.org/10.1086/282771
  42. Nei, M. 1991. Relative efficiencies of different tree-making methods for molecular data. In: Phylogenetic Analysis of DNA Sequence, edited by M. M. Miyamoto and J. Cracrsft. New York: Oxford University Press 90-128.
  43. Nei, M., F. Tajima and Y. Tateno 1983. Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 19:153-170. https://doi.org/10.1007/BF02300753
  44. Nei, M.1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590.
  45. Oliveira, J. C. V., M. N. Ribeiro, L. L. Rocha, M. A. Gomes-Filho, J. V. Delgado, A. M. Martinez, M. P. C. Menezes, C. M. Bettencourt and L. T. Gama. 2010. Genetic relationships between two homologous goat breeds from Portugal and Brazil assessed by microsatellite markers. Small Rumin. Res. 93:79-87. https://doi.org/10.1016/j.smallrumres.2010.05.002
  46. Oliveira, J. D., M. L. Igarashi, T. M. Machado, M. M. Miretti, J. A. Ferro and E. P. Contel. 2007. Structure and genetic relationships between Brazilian naturalized and exotic purebred goat domestic goat (Capra hircus) breeds based on microsatellites. Genet. Mol. Biol. 30:356-363.
  47. Ozgecan, K. A. and E. Okan. 2012. Assessment of genetic diversity, genetic relationship and bottleneck using microsatellites in some native Turkish goat breeds. Small Rumin. Res. 105:53-60. https://doi.org/10.1016/j.smallrumres.2011.12.005
  48. Peter, C., M. Bruford, T. Perez, S. Dalamitra, G. Hewitt, G. Erhardt. 2007. Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds. Anim. Genet. 38:37-44. https://doi.org/10.1111/j.1365-2052.2007.01561.x
  49. Pritchard, K J., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
  50. Qi, J. F. 2004. Report on domestic animal genetic resources in China. China Agric. Press, Beijing.
  51. Qi, Y., J. Luo, X. F. Han, Y. Z. Zhu, C. Chen, J. X .Liu and H. J. Sheng. 2009. Genetic diversity and relationships of 10 Chinese goat breeds in the middle and Western China. Small Rumin. Res. 82:88-93. https://doi.org/10.1016/j.smallrumres.2009.01.015
  52. Reynolds, J, B. S Weir and C. C. Cockerham. 1983. Estimation of the coancestry coefficient: basis for a shortterm genetics distance. Genetics 105:767-769.
  53. Ruane, J. 1999. A critical review of the value of genetic distance studies in conservation of animal genetic resources. J. Anim. Breed. Genet. 116:317-323. https://doi.org/10.1046/j.1439-0388.1999.00205.x
  54. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
  55. Sechi, T., M. G. Usai, S. Casu and A. Carta 2005. Genetic diversity of Sardinian goat population based on microsatellites. Ital. J. Anim. Sci. 4:58-60.
  56. Slatkin, M. and N. H. Barton. 1989. A comparison of three indirect methods of estimating average levels of gene flow. Evolution 43:1349-1368. https://doi.org/10.2307/2409452
  57. Taberlet, P, A. Valentini, H. R. Rezaei, S. Naderi, F. Pompanon, R. Negrini and P. Ajmone-Marsan. 2008. Are cattle, sheep, and goats endangered species? Mol. Ecol. 17:275-284. https://doi.org/10.1111/j.1365-294X.2007.03475.x
  58. Tadlaoui-Ouafi, A., J. M. Babilliot, C. Leroux and P. Martin. 2002. Genetic diversity of the two main Moroccan goat breeds: phylogenetic relationships with four breeds reared in France. Small Rumin. Res. 45:225-233. https://doi.org/10.1016/S0921-4488(02)00111-6
  59. Takezaki, N. and M. Nei. 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144:389-399.
  60. Takezaki, N., M. Nei and K. Tamura. 2010. POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol. Biol. Evol. 27:747-752. https://doi.org/10.1093/molbev/msp312
  61. Toro, M. A., J. Fernández and A. Caballero. 2009. Molecular characterization of breeds and its use in conservation. Livest. Sci. 120:174-195. https://doi.org/10.1016/j.livsci.2008.07.003
  62. Traoré, A., I. álvarez, H. H. Tambourá, I. Fernández, A. Kaboré, L. J. Royo, J. P. Gutiérrez, M. Sangaré, G. Ouédraogo-Sanou, A. Toguyeni, L. Sawadogo and F. Goyache. 2009. Genetic characterisation of Burkina Faso goats using microsatellite polymorphism. Livest. Sci. 123:322-328. https://doi.org/10.1016/j.livsci.2008.11.005
  63. Tu, Y., Y. Jiang, Z. Y. Han and W. Q. Feng. 1989. Sheep and Goat Breeds in China. Shanghai Scientific & Technical Publishers. Shanghai, China.
  64. Visser, C., C. A. Hefer, E. van Marle-Koter and A. Kotze. 2004. Genetic variation of three commercial and three indigenous goat populations in South Africa. S. Afr. J. Anim. Sci. 34:24-27.
  65. Wang, J., Y. L. Chen, X. L. Wang and Z. X. Yang. 2008. The genetic diversity of seven indigenous Chinese goat breeds. Small Rumin. Res. 74:231-237. https://doi.org/10.1016/j.smallrumres.2007.03.007
  66. Wang, P. J., B. L. Shi, Y. C. Li, J. Y. Wang, H. W. Bai, S. Q. Jin and F. Q. Zhang. 2008. Study on improvement of Xinjiang goat using Liaoning cashmere goat. Chin. J. Anim. Sci. 27:8-11.
  67. Wilson, G. A. and B. Rannala. 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163:1177-1191.
  68. Wimmers, K., S. Ponsuksili, T. Hardgeg, A. Valle-Zarate, P. Mathur and P. Horst. 2000. Genetic distinctness of African, Asian and south American local chickens. Anim. Genet. 31:159-165. https://doi.org/10.1046/j.1365-2052.2000.00605.x
  69. Wright, S. 1969. Evolution and the genetics of populations: the theory of gene frequencies, Vol. 2. Univ. Chicago Press, Chicago.
  70. Wright, S. 1978. Evolution and the genetics of populations: variability within and among natural populations, vol 4. University of Chicago press, Chicago, IL, USA.
  71. Yeh, F., R. C. Yang and T. Boyle. 1997. Popgene, the user friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Center, University of Albert, Edmonton.

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