DOI QR코드

DOI QR Code

Genetic Diversity of Myanmar and Indonesia Native Chickens Together with Two Jungle Fowl Species by Using 102 Indels Polymorphisms

  • Maw, Aye Aye (United Graduate School of Agricultural Science, Kagoshima University) ;
  • Shimogiri, Takeshi (Faculty of Agriculture, Kagoshima University) ;
  • Riztyan, Riztyan (United Graduate School of Agricultural Science, Kagoshima University) ;
  • Kawabe, Kotaro (Frontier Science Research Centre, Kagoshima University) ;
  • Kawamoto, Yasuhiro (Faculty of Agriculture, University of the Ryukyus) ;
  • Okamoto, Shin (Faculty of Agriculture, Kagoshima University)
  • Received : 2011.12.26
  • Accepted : 2012.04.03
  • Published : 2012.07.01

Abstract

The efficiency of insertion and/or deletion (indels) polymorphisms as genetic markers was evaluated by genotyping 102 indels loci in native chicken populations from Myanmar and Indonesia as well as Red jungle fowls and Green jungle fowls from Java Island. Out of the 102 indel markers, 97 were polymorphic. The average observed and expected heterozygosities were 0.206 to 0.268 and 0.229 to 0.284 in native chicken populations and 0.003 to 0.101 and 0.012 to 0.078 in jungle fowl populations. The coefficients of genetic differentiation (Gst) of the native chicken populations from Myanmar and Indonesia were 0.041 and 0.098 respectively. The genetic variability is higher among native chicken populations than jungle fowl populations. The high Gst value was found between native chicken populations and jungle fowl populations. Neighbor-joining tree using genetic distance revealed that the native chickens from two countries were genetically close to each other and remote from Red and Green jungle fowls of Java Island.

Keywords

Genetic Markers;Indels Polymorphism;Jungle Fowl;Native Chicken

References

  1. Akishinnonomiya, F., T. Miyake, S. Sumi, M. Takada, S. Ohno and N. Kondo. 1994. One subspecies of the Red jungle fowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds. Proc. Natl. Acad. Sci. USA. 91:12505-12509. https://doi.org/10.1073/pnas.91.26.12505
  2. Bambang, S. and A. Bustanul. 2009. Overview on poultry sector and HPAI situation for Indonesia with special emphasis on the Island of Java - Background Paper, Africa/Indonesia Region Report. 3:3-9.
  3. Brandström, M. and H. Ellegren. 2007. The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) genome: A high frequency of deletions in tandem duplicates. Genetics 176:1691-1701. https://doi.org/10.1534/genetics.107.070805
  4. Burgos, S., J. Otte and D. R. Holst. 2009. Poultry HPAI and livelihoods in Myanmar - A Review, Mekong Team Working Paper. 8:23.
  5. Kinoshita, K., T. Ichiki, Y. Yamamoto, K. Tsunoda, H. Okabayashi, H. Mannen, K. Tanaka, T. Yamagata, K. Nozawa, M. Nishibori, Y. Kurosawa, Maung Maung Nyunt, Than Daing, Than Hla, Nay Win and Y. Maeda. 2004. Gene constitution of egg white proteins of native chicken populations in Myanmar. Researches Report of the Society for Native Livestock. 21:225-235.
  6. Maeda, Y., Y. Yamamoto, T. Nishida, T. Hashiguchi, I. Okada and H. B. Rajubhandary. 1992. Protein polymorphism in native and Red jungle fowls in Nepal. Asian-Aust. J. Anim.Sci. 5:747-752. https://doi.org/10.5713/ajas.1992.747
  7. Mwacharo, J. M., H. Jianlin and T. Amano. 2006. Native African chicken: valuable genetic resources for future breeding improvement. J. Anim. Genet. Jpn. 34:63-69. https://doi.org/10.5924/abgri2000.34.2_63
  8. Niu, D., Y. Fu, J. Luo, H. Ruan, X .P. Yu, G. Chen and Y. P. Zhang. 2002. The origin and genetic diversity of Chinese native chicken breeds. Biochem.Genet. 40:163-174. https://doi.org/10.1023/A:1015832108669
  9. Nei, M. 1972. Genetic distance between populations. Am. Nat. 106: 283-292. https://doi.org/10.1086/282771
  10. Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proc. Nat. Acad. Sci. USA. 70:3321-3323. https://doi.org/10.1073/pnas.70.12.3321
  11. Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583-590.
  12. Natalle, S. C. F., R. L. Resque, E. M. Ribeiro-Rodrigues, J. F. Guerreiro, N. P. C. Santos, A. R. Santos and S. Santos. 2010. X-linked insertion/deletion polymorphisms: Forensic applications of a 33-markers panel. Int. J. Legal Med. 124: 589-593. https://doi.org/10.1007/s00414-010-0441-9
  13. Okamoto, S., K. Kinoshita, Y. Yamamoto, K. Tsunoda, H. Okabayashi, H. Mannen, K. Tanaka, T. Yamagata, K. Nozawa, M. Nishibori, Y. Kurosawa, Maung Maung Nyunt, Than Daing, Than Hla, Nay Win and Y. Maeda. 2004. Blood protein variations of native fowls in Myanmar. Researches Report of the Society for Native Livestock. 21:237-242.
  14. Okamoto, S., I. Keiichiro, T. Zhu , Y. Maeda, H. Dexing, F. T. Yang, H. Y. Zhang, X. U. Wenbo, S. Liming and H. Tsutomu. 2003. Blood protein ploymorphisms in native chicken breeds in Yunnan Province of China. Anim. Sci. 74:471-476. https://doi.org/10.1046/j.1344-3941.2003.00140.x
  15. Okumura, F., T. Shimogiri, K. Kawabe, S. Okamoto, M. Nishibori, Y. Yamamoto and Y. Maeda. 2006. Gene constitution of South-East Asian native chickens, commercial chickens and jungle fowl using polymorphisms of four Calpain genes. Anim. Sci. J. 77:188-195. https://doi.org/10.1111/j.1740-0929.2006.00336.x
  16. Sambrook, J., E. F. Fritsch and T. Maniatis. 1989. Molecular cloning: A laboratory manual, 2 2nd edition, Cold Spring Laboratory Press, Cold Spring Harbor, New York, USA.
  17. Saitou, U. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406.
  18. Tamura, K., J. Dudley, M. Nei and S. Kumar. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Bio. Evol. 24:1596-1599. https://doi.org/10.1093/molbev/msm092
  19. Theresa, M. C., E. W. Lisa, M. G. Karla and J. C. Daniel. 2002. A comparison of two methods of calculating Gst, A genetic measure of population differentiation. Am. J. Bot. 89:460-465. https://doi.org/10.3732/ajb.89.3.460
  20. Vali, U., M. Brandstrom, M. Johansson and H. Ellegren. 2008. Insertion-deletion polymorphisms (indels) as genetic markers in natural populations. BMC Genet. 9:1-8.
  21. Weir, B. S. 1996. Genetic data analysis II. Sinauer. Sunder land, MA.
  22. Wong, G. K. S., L. Hillier, M. Brandstrom, R. Croojmans, I. Ovcharenko, L. Gordon, L. Stubbs, S. Lucas, T. Glavina, P. Kaiser,U. Gunnarsson, C. Webber and I. Overton. 2004. A genetic variation map for chicken with 2.8 million single nucleotide polymorphisms. Nature 432:717-722. https://doi.org/10.1038/nature03156
  23. Yamamoto, Y., A. Ali, R. A. Mohammad, R. M. Mohammad, S. H. Syed, O. F. Mohammad and T. Amano. 2010. Composition of genes controlling blood groups and morpho-genetic traits of Bangladesh native chikens and its phylogenetic study. Researches Report of the Society for Native Livestock. 25: 131-146.
  24. Yamashita, H., S. Okamoto, Y. Maeda and H. Tsutomu. 1994. Genetic relationships among domestic and jungle fowls revealed by DNA fingerprinting analysis. Jpn. Poult. Sci. 31: 335-344. https://doi.org/10.2141/jpsa.31.335

Cited by

  1. The Genetic Diversity of Eight Chicken Populations Assessed by 102 Indels Markers vol.50, pp.2, 2013, https://doi.org/10.2141/jpsa.0120088
  2. Genome-Wide Characterization of Insertion and Deletion Variation in Chicken Using Next Generation Sequencing vol.9, pp.8, 2014, https://doi.org/10.1371/journal.pone.0104652