Genomic diversity and admixture patterns among six Chinese indigenous cattle breeds in Yunnan

  • Li, Rong (School of Life Sciences, Yunnan University) ;
  • Li, Chunqing (School of Life Sciences, Yunnan University) ;
  • Chen, Hongyu (School of Life Sciences, Yunnan University) ;
  • Liu, Xuehong (National Demonstration Center for Experimental Life Sciences Education, Yunnan University) ;
  • Xiao, Heng (School of Life Sciences, Yunnan University) ;
  • Chen, Shanyuan (School of Life Sciences, Yunnan University)
  • Received : 2018.08.12
  • Accepted : 2018.12.08
  • Published : 2019.08.01


Objective: Yunnan is not only a frontier zone that connects China with South and Southeast Asia, but also represents an admixture zone between taurine (Bos taurus) and zebu (Bos indicus) cattle. The purpose of this study is to understand the level of genomic diversity and the extent of admixture in each Yunnan native cattle breed. Methods: All 120 individuals were genotyped using Illumina BovineHD BeadChip (777,962 single nucleotide polymorphisms [SNPs]). Quality control and genomic diversity indexes were calculated using PLINK software. The principal component analysis (PCA) was assessed using SMARTPCA program implemented in EIGENSOFT software. The ADMIXTURE software was used to reveal admixture patterns among breeds. Results: A total of 604,630 SNPs was obtained after quality control procedures. Among six breeds, the highest level of mean heterozygosity was found in Zhaotong cattle from Northeastern Yunnan, whereas the lowest level of heterozygosity was detected in Dehong humped cattle from Western Yunnan. The PCA based on a pruned dataset of 233,788 SNPs clearly separated Dehong humped cattle (supposed to be a pure zebu breed) from other five breeds. The admixture analysis further revealed two clusters (K = 2 with the lowest cross validation error), corresponding to taurine and zebu cattle lineages. All six breeds except for Dehong humped cattle showed different degrees of admixture between taurine and zebu cattle. As expected, Dehong humped cattle showed no signature of taurine cattle influence. Conclusion: Overall, considerable genomic diversity was found in six Yunnan native cattle breeds except for Dehong humped cattle from Western Yunnan. Dehong humped cattle is a pure zebu breed, while other five breeds had admixed origins with different extents of admixture between taurine and zebu cattle. Such admixture by crossbreeding between zebu and taurine cattle facilitated the spread of zebu cattle from tropical and subtropical regions to other highland regions in Yunnan.


Bos taurus;Bos indicus;Heterozygosity;Population Structure;Single Nucleotide Polymorphisms


Supported by : National Science Foundation of China


  1. Loftus RT, Machugh DE, Bradley DG, Sharp PM, Cunningham P. Evidence for two independent domestications of cattle. Proc Natl Acad Sci USA 1994;91:2757-61.
  2. Loftus RT, Ertugrul O, Harba AH, et al. A microsatellite survey of cattle from a centre of origin: the Near East. Mol Ecol 1999;8:2015-22.
  3. Troy CS, Machugh DE, Bailey JF, et al. Genetic evidence for Near-Eastern origins of European cattle. Nature 2001;410:1088-91.
  4. Bruford MW, Bradley DG, Luikart G. DNA markers reveal the complexity of livestock domestication. Nat Rev Genet 2003;4:900-10.
  5. Mahgoub O, Babiker HA, Kadim IT, et al. Disclosing the origin and diversity of Omani cattle. Anim Genet 2013;44:336-9.
  6. Tanaka K, Takizawa T, Dorji T, et al. Polymorphisms in the bovine hemoglobin-beta gene provide evidence for gene-flow between wild species of Bos (Bibos) and domestic cattle in Southeast Asia. Anim Sci J 2011;82:36-45.
  7. Yu Y, Nie L, He ZQ, Wen JK, Jian CS, Zhang YP. Mitochondrial DNA variation in cattle of south China: origin and introgression. Anim Genet 1999;30:245-50.
  8. Gou X, Wang Y, Yang S, Deng W, Mao H. Genetic diversity and origin of Gayal and cattle in Yunnan revealed by mtDNA control region and SRY gene sequence variation. J Aaim Breed Genet 2010;127:154-60.
  9. China National Commission of Animal Genetic Resources. Animal Genetic Resources in China Bovines. Beijing,China: Chinese Agricultural Press; 2011.
  10. Yu Y, Lian LS, Wen JK, et al. Genetic diversity and relationship of Yunnan native cattle breeds and introduced beef cattle breeds. Biochem Genet 2004;42:1-9.
  11. Li R, Li C, Liu H, Zeng B, Xiao H, Chen S. Mitochondrial diversity and phylogeographic structure of native cattle breeds from Yunnan, Southwestern China. Livest Sci 2018;214:129-34.
  12. Rincon G, Weber KL, Eenennaam AL, Golden BL, Medrano JF. Hot topic: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys. J Dairy Sci 2011;94:6116-21.
  13. Canasalvarez JJ, Gonzalezrodriguez A, Munilla S, et al. Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip. J Anim Sci 2015;93:5164-74.
  14. Bahbahani H, Salim B, Almathen F, Al Enezi F, Mwacharo JM, Hanotte O. Signatures of positive selection in African Butana and Kenana dairy zebu cattle. Plos One 2018;13:e0190446.
  15. Kelleher MM, Berry DP, Kearney JF, Mcparland S, Buckley F, Purfield DC. Inference of population structure of purebred dairy and beef cattle using high-density genotype data. Animal 2017;11:15-23.
  16. Zimin AV, Delcher AL, Florea L, et al. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 2009;10:R42.
  17. Mastrangelo S, Saura M, Tolone M, et al. The genome-wide structure of two economically important indigenous Sicilian cattle breeds. J Anim Sci 2014;92:4833-42.
  18. Edea Z, Bhuiyan M, Dessie T, Rothschild M, Dadi H, Kim KS. Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds. Animal 2015;9:218-26.
  19. Purcell S, Neale B, Todd-Brown K, et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75.
  20. Nielsen R. Population genetic analysis of ascertained SNP data. Hum Genomics 2004;1:218-24.
  21. Lachance J, Tishkoff SA. SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it. Bioessays 2013;35:780-6.
  22. Lopez HD, Bauchet M, Tang K, et al. Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. Plos One 2009;4:e7888.
  23. Kijas JW, Lenstra JA, Hayes B, et al. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. Plos Biol 2012;10:e1001258.
  24. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006;38:904-9.
  25. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 2009;19:1655-64.
  26. R Development Core Team. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2011.
  27. Gao Y, Gautier M, Ding X, et al. Species composition and environmental adaptation of indigenous Chinese cattle. Sci Rep 2017;7:Article number: 16196.
  28. Gautier M, Laloe D, Moazamigoudarzi K. Correction: insights into the genetic history of french cattle from dense snp data on 47 worldwide breeds. Plos One 2010;5:260-5.
  29. Bradley DG, MacHugh DE, Cunningham P, Loftus RT. Mitochondrial diversity and the origins of African and European cattle. Proc Natl Acad Sci USA 1996;93:5131-5.
  30. Decker JE, Mckay SD, Rolf MM, et al. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. Plos Genetics 2014;10:e1004254.
  31. Chen N, Cai Y, Chen Q, et al. Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nat Commun 2018;9:2337.