Monitoring conservation effects on a Chinese indigenous chicken breed using major histocompatibility complex B-G gene and DNA Barcodes

  • Tu, Yunjie (Poultry Institute, Chinese Academy of Agricultural Sciences) ;
  • Shu, Jingting (Poultry Institute, Chinese Academy of Agricultural Sciences) ;
  • Ji, Gaige (Poultry Institute, Chinese Academy of Agricultural Sciences) ;
  • Zhang, Ming (Poultry Institute, Chinese Academy of Agricultural Sciences) ;
  • Zou, Jianmin (Poultry Institute, Chinese Academy of Agricultural Sciences)
  • Received : 2017.08.23
  • Accepted : 2018.03.13
  • Published : 2018.10.01


Objective: We report monitoring conservation effect for a Chinese indigenous chicken (Langshan) breed using major histocompatibility complex (MHC) and DNA barcords. Methods: The full length of MHC B-G gene and mitochondrial cytochrome oxidase I (COI) gene in generations 0, 5, 10, 15, 16, and 17 was measured using re-sequencing and sequencing procedures, respectively. Results: There were 292 single nucleotide polymorphisms of MHC B-G gene identified in six generations. Heterozygosity (He) and polymorphic information content (PIC) of MHC B-G gene in generations 10, 15, 16, and 17 remained stable. He and PIC of MHC B-G gene were different in six generations, with G10, G15, G16, G17 >G5>G0 (p<0.05). For the COI gene, there were five haplotypes in generations 0, 5, 10, 15, 16, and 17. Where Hap2 and Hap4 were the shared haplotypes, 164 individuals shared Hap2 haplotypes, while Hap1 and Hap3 were the shared haplotypes in generations 0 and 5 and Hap5 was a shared haplotype in generations 10, 15, 16, and 17. The sequence of COI gene in 6 generations was tested by Tajima's and D value, and the results were not significant, which were consistent with neutral mutation. There were no differences in generations 10, 15, 16, and 17for measured phenotypic traits. In other generations, for annual egg production, with G5, G10, G15, G16, G17>G0 (p<0.05). For age at the first egg and age at sexual maturity, with G10, G15, G16, G17>G5>G0 (p<0.05). Conclusion: Combined with the results of COI gene DNA barcodes, MHC B-G gene, and phenotypic traits we can see that genetic diversity remained stable from generations 10 to 17 and the equimultiple random matching pedigrees conservation population conservation effect of Langshan chicken was effective as measured by these criteria.


Supported by : National Natural Science Foundation of China, Jiangsu Natural Science Foundation


  1. APA. The American standard of perfection. Davenport, IA, USA: Am Poult Assoc Inc; 1947. 187 p.
  2. Frankham R. Genetics and conservation biology. C R Biol 2003;326(Suppl 1):S22-9.
  3. Snook RR, Brustle L, Slate JA. Test and review of the role of effective population size on experimental sexual selection patterns. Evolution 2009;63:1923-33.
  4. Keller LF, Waller M. Inbreeding effects in wild populations. Trends Ecol Evol 2002;17:230-41.
  5. Lacy RC. Loss of genetic diversity from managed populations: interacting effects of drift, mutation, immigration, selection, and population subdivision. Conserv Biol 1987;1:143-58.
  6. Plesnar-Bielak A, Skrzynecka AM, Prokop ZM, Radwan J. Mating system affects population performance and extinction risk under environmental challenge. Proc R Soc B 2012;279:4661-7.
  7. Mendelsohn R. The challenge of conserving indigenous domesticated animals. Ecol Econ 2003;45:501-10.
  8. Huang FM, Zhou QX, Cheng GC, Su YJ. Small group of conservation method: Langshan (N Series) blood group analysis of the genetic population structure. China Poult 1990;4:22-4.
  9. Chen KW. China's poultry resource distribution characteristics and protection methods. Guide to Chinese Poult 2002;4:7-8.
  10. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual, 2nd edition. New York, USA: Cold Spring Harbor Laboratory; 1989.
  11. Rozas J, Sdnchez-DelBarrio JC, Messeguer X. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003;19:2496-7.
  12. Tu YJ, Chen KW, Zhang SJ, et al. Genetic diversity of 14 indigenous grey goose breeds in China based on microsatellite markers. Asian-Australas J Anim Sci 2006;19:1-6.
  13. Zanetti E, De Marchi M, Dalvit C, Cassandro M. Variation of genetic diversity over time in local Italian chicken breeds undergoing in situ conservation. Poult Sci 2011;90:2195-201.
  14. Hajibabaei M, Janzen DH, Burns JM. DNA barcodes distinguish species of tropical Lepidoptera. Proc Natl Acad Sci USA 2006;103:968-71.
  15. Yoo HS, Eah JY, Kim JS, et al. DNA barcoding Korean birds. Mol Cells 2006;22:323-7.
  16. Tu YJ, Gao YS, Zhou XM, et al. The genetic diversity analysis of mtDNA CO I genes in six indigenous chicken breeds in China. J Yangzhou Univ (Agricultural and Life Science Edition) 2007;28:31-3.
  17. Tu YJ, Gao YS, Su YJ, Wang KH, Tong HB. Genetic diversity and phylogenetic analysis of CO I gene in some indigenous chicken breeds. J Anhui Agric Univ 2011;38:39-42.
  18. Ouborg NJ. Integrating population genetics and conservation biology in the era of genomics. Biol Lett 2010;6:3-6.
  19. Noel F, Machon N, Porcher E. No genetic diversity at molecular markers and strong phenotypic plasticity in populations of Ranunculus nodiflorus, an endangered plant species in France. Ann Bot 2007;99:1203-12.
  20. Lamont SJ. Immunogenetics and the major histocompatihility complex. Vet Immunol Immunopathol 1991;30:121-7.
  21. Miller MM, Goto R, Bernot A. Two Mhc class I and two Mhc class II genes map to the chicken Rfp-Y system outside the B complex. Proc Natl Acad Sci USA 1994;91:4397-401.
  22. Yang G, Chen XY, Ren WH, Yan J. MHC and its application in the population and conservation genetics. Yi Chuan 2002;24:712-4.
  23. Bacon LD, Zajchowski L, Clark ME, Etches RJ. Identification and evaluation of major histocompatibility complex antigens in chicken chimeras and their relationship to germline transmission. Poult Sci 2002;81:1427-38.
  24. Zeng QQ. Isolation of MHC class I loci and adaptive evolutionary studies of MHC for the golden pheasant [doctoral thesis]. Zhejiang University; 2013.
  25. Barber LD, Parham P. Peptide binding to major histocompatibility complex molecules. Ann Rev Cell Boil 1993;9:163-206.
  26. Eshel I, HamiltonParent W. Parent-offspring correlation in fitness under fluctuating selection. Proc R Soc Lond B-Biol Sci 1984;222:1-14.
  27. Reche PA, Reinherz EL. Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms. J Mol Biol 2003;331:623-41.
  28. Lively CM, Jokelaf J. Temporal and spatial distributions of parasites and sex in a freshwater snail. Evol Ecol Res 2002;4:219-26.
  29. Bonneaud C, Perez-Tris J, Federici P. Major histocompatibility alleles associated with local resistance to realaria in a passerine. Evolution 2006;60:383-9.
  30. Schaal BA, Leverich WJ, Rogstad SH. Comparison of methods for assessing genetic variation in plant conservation biology. In: Falk DA, Holsinger KE, editors. Genetics and conservation of rare plants. New York, USA: Oxford University Press; 1991. pp. 123-34.