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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.18.0605    [Accepted] Published online January 2, 2019.
Genomic diversity and admixture patterns among six Chinese indigenous cattle breeds in Yunnan
Rong Li1, Chunqing Li1,2, Hongyu Chen1, Xuehong Liu3, Heng Xiao1, Shanyuan Chen1,2,* 
1School of Life Sciences, Yunnan University, Kunming 650091, China
2National Demonstration Center for Experimental Life Sciences Education (Yunnan University), Yunnan University, Kunming 650500, China
3Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650221, China
Correspondence:  Shanyuan Chen, Tel: +8618687122260, Fax: +8687165031412, Email: chensy@ynu.edu.cn
Received: 12 August 2018   • Revised: 7 November 2018   • Accepted: 8 December 2018
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.


All 120 individuals were genotyped using Illumina BovineHD BeadChip (777 962 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.


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.
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.
Keywords: Bos taurus; Bos indicus; Heterozygosity; Population Structure; Single Nucleotide Polymorphisms
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