Asian-Australasian Journal of Animal Sciences

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

DOI QR Code

Evaluation of the genetic diversity of six Chinese indigenous chickens

  • Sha, Yuzhu (College of Animal Science and Technology, Gansu Agricultural University) ;
  • Gao, Caixia (State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences) ;
  • Liu, Meimei (College of Animal Science and Technology, Gansu Agricultural University) ;
  • Zhao, Shengguo (College of Animal Science and Technology, Gansu Agricultural University)
  • Received : 2019.07.28
  • Accepted : 2019.10.30
  • Published : 2020.10.01
Download PDF
⟨ Previous Next ⟩

Abstract

Objective: The extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China. Methods: In the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds. Results: Twenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious. Conclusion: The genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.

Keywords

References

  1. Rubin CJ, Zody MC, Eriksson J, et al. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 2010;25:587-91. https://doi.org/10.1038/nature08832
  2. Cabarles Jr JC. Production potentials of native chickens (Gallus gallus domesticus L.) of Western Visayas, Philippines. Trop Anim Health Prod 2013;45:405-10. https://doi.org/10.1007/s11250-012-0230-1
  3. Notter DR. The importance of genetic diversity in livestock populations of the future. J Anim Sci 1999;77:61-9. https://doi.org/10.2527/1999.77161x
  4. Miao YW, Peng MS, Wu GS, et al. Chicken domestication: an updated perspective based on mitochondrial genomes. Heredity 2013;110:277-82. https://doi.org/10.1038/hdy.2012.83
  5. Liu YP, Wu GS, Yao YG, et al. Multiple maternal origins of chickens: out of the Asian jungles. Mol Phylogenet Evol 2006; 38:12-9. https://doi.org/10.1016/j.ympev.2005.09.014
  6. Niu D, Fu Y, Luo J, et al. The origin and genetic diversity of Chinese native chicken breeds. Biochem Genet 2002;40:163-74. https://doi.org/10.1023/A:1015832108669
  7. Desjardins P, Morais R. Sequence and gene organization of the chicken mitochondrial genome: a novel gene order in higher vertebrates. J Mol Biol 1990;212:599-634. https://doi.org/10.1016/0022-2836(90)90225-B
  8. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. Dnasp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003;19:2496-7. https://doi.org/10.1093/bioinformatics/btg359
  9. Jolliffe IT. Principal component analysis. New York, USA: Springer-Verlag; 2005.
  10. Zhang J, Yang B, Wen X, Sun G. Genetic variation and relationships in the mitochondrial DNA D-loop region of Qinghai indigenous and commercial pig breeds. Cell Mol Biol Lett 2018;23:31. https://doi.org/10.1186/s11658-018-0097-x
  11. Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999;16:37-48. https://doi.org/10.1093/oxfordjournals.molbev.a026036
  12. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870-4. https://doi.org/10.1093/molbev/msw054
  13. Silva P, Guan X, Ho-Shing O, et al. Mitochondrial DNA-based analysis of genetic variation and relatedness among Sri Lankan indigenous chickens and the Ceylon junglefowl (Gallus lafayetti). Anim Genet 2009;40:1-9. https://doi.org/10.1111/j.1365-2052.2008.01783.x
  14. West B, Zhou BX. Did chicken go North? New evidence for domestication. J Archaeol Sci 1989;15:515-33. https://doi.org/10.1016/0305-4403(88)90080-5
  15. Fumihito A, Miyak T, Takada M, et al. Monophyletic origin and unique dispersal patterns of domestic fowls. Proc Natl Acad Sci USA 1996;93:6792-5. https://doi.org/10.1073/pnas.93.13.6792
  16. Oka T, Ino Y, Nomura K, et al. Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Anim Genet 2007;38:287-93. https://doi.org/10.1111/j.1365-2052.2007.01604.x
  17. Chen X, Lu H, Sheng L, Li Y. Identifying populations for priority conservation of important species. Chinese Biodiversity 2002;10:332-8.
  18. Muir WM, Wong GK, Zhang Y, et al. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci USA 2008;105:17312-7. https://doi.org/10.1073/pnas.0806569105
  19. Ohno S. The one ancestor per generation rule and three other rules of mitochondrial inheritance. Proc Natl Acad Sci USA 1997;94:8033-5. https://doi.org/10.1073/pnas.94.15.8033
  20. Fumihito A, Miyake T, Sumi S, Takada M, Ohno S, Kondo N. One subspecies of the red junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds. Proc Natl Acad Sci USA 1994;91:12505-9. https://doi.org/10.1073/pnas.91.26.12505
  21. Kanginakudru S, Metta M, Jakati RD, Nagaraju J. Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC Evol Biol 2008; 8:174. https://doi.org/10.1186/1471-2148-8-174
  22. Song C, Chen H, Ma Y, et al. Maternal origins of six indigenous chicken breeds in China. Acta Vet Zootec Sinica 2007;38:735-40. http://doi.org/10.3321/j.issn:0366-6964.2007.07.019
  23. Gong P, Liu L, Li D, et al. The investigation of genetic diversity of Piao chicken based on mitochondrial DNA D-loop region sequence. J Yunnan Agric Univ 2011;26:211-4.