Li Rong, Li Chunqing, Chen Hongyu, Liu Xuehong, Xiao Heng, Chen Shanyuan
School of Life Sciences, Yunnan University, Kunming, Yunnan 650500, China.
National Demonstration Center for Experimental Life Sciences Education, Yunnan University, Kunming Yunnan 650500, China.
Asian-Australas J Anim Sci. 2019 Aug;32(8):1069-1076. doi: 10.5713/ajas.18.0605. Epub 2019 Jan 2.
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 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.
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.
云南不仅是连接中国与南亚和东南亚的边境地区，也是普通牛（Bos taurus）和瘤牛（Bos indicus）的混合区域。本研究的目的是了解云南本地各牛品种的基因组多样性水平和混合程度。
使用Illumina BovineHD BeadChip（777,962个单核苷酸多态性[SNPs]）对所有120个个体进行基因分型。使用PLINK软件计算质量控制和基因组多样性指标。使用EIGENSOFT软件中实现的SMARTPCA程序进行主成分分析（PCA）。使用ADMIXTURE软件揭示品种间的混合模式。
经过质量控制程序后，共获得604,630个SNPs。在六个品种中，滇东北的昭通牛平均杂合度最高，而滇西的德宏驼峰牛杂合度最低。基于233,788个SNPs的精简数据集进行的PCA清楚地将德宏驼峰牛（被认为是纯种瘤牛品种）与其他五个品种区分开来。混合分析进一步揭示了两个聚类（K = 2，交叉验证误差最低），分别对应普通牛和瘤牛谱系。除德宏驼峰牛外，所有六个品种均显示出普通牛和瘤牛之间不同程度的混合。正如预期的那样，德宏驼峰牛未显示出普通牛影响的迹象。
总体而言，除滇西的德宏驼峰牛外，云南的六个本地牛品种具有相当大的基因组多样性。德宏驼峰牛是纯种瘤牛品种，而其他五个品种具有混合起源，普通牛和瘤牛之间有不同程度的混合。瘤牛和普通牛之间的这种杂交混合促进了瘤牛从热带和亚热带地区向云南其他高地地区的传播。
