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Journal of Integrative Agriculture  2017, Vol. 16 Issue (10): 2246-2256    DOI: 10.1016/S2095-3119(17)61679-4
Animal Science · Veterinary Medicine Advanced Online Publication | Current Issue | Archive | Adv Search |
Genetic background analysis and breed evaluation of Yiling yellow cattle
Xu Ling1*, Zhang Wen-gang1*, Li Jun-ya1, Zhu De-jiang2, Xu Xiao-cheng3, Tian Yan-zi3,XIONG Xiong2, Guo Ai-zhen4, Cao Bing-hai5, Niu Hong1, Zhu Bo1, Wang Ze-zhao1, Liang Yong-hu1, Shen Hong-xue3, Chen Yan1
1 Cattle Genetics and Breeding Innovation Team, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
2 Animal husbandry Technical Extension Station of Yiling, Yichang 443000, P.R.China
3 Animal Husbandry and Veterinary Bureau of Yiling, Yichang 443000, P.R.China
4 The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P.R.China
5 Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R.China
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Abstract  Traditionally, Chinese indigenous cattle is geographically widespread.  The present study analyzed based on genome-wide variants to evaluate the genetic background among 157 individuals from four representative indigenous cattle breeds of Hubei Province of China: Yiling yellow cattle (YL), Bashan cattle (BS), Wuling cattle (WL), Zaobei cattle (ZB), and 21 individuals of Qinchuan cattle (QC) from the nearby Shanxi Province of China.  Linkage disequilibrium (LD) analysis showed the LD of YL was the lowest (r2=0.32) when the distance between markers was approximately 2 kb.  Principle component analysis (PCA), and neighbor-joining (NJ)-tree revealed a separation of Yiling yellow cattle from other geographic nearby local cattle breeds.  In PCA plot, the YL and QC groups were segregated as expected; moreover, YL individuals clustered  together more obviously.  In the NJ-tree, the YL group formed an independent branch and BS, WL, ZB groups were mixed.  We then used the FST statistic approach to reveal long-term selection sweep of YL and other 4 cattle breeds.  According to the selective sweep, we identified the unique pathways of YL, associated with production traits.  Based on the results, it can be proposed that YL has its unique genetic characteristics of excellence resource, and it is an indispensable cattle breed in China.   
Keywords:  Yiling yellow cattle        breed evaluation        principle component analysis        neighbor-joining tree  
Received: 22 December 2016   Accepted: 30 September 2017

This work was funded in part by the National Natural Science Foundation of China (31402039, 31472079, 31372294), the Beijing Natural Science Foundation (6154032), the Species and Breed Resources Conservation of the Ministry of Agriculture of China (2017-2019), the Cattle Breeding Innovative Research Team of Chinese Academy of Agricultural Sciences (cxgc-ias-03), and the National Beef Cattle Industrial Technology System (CARS-37).

Corresponding Authors:  Correspondence Chen Yan, Tel: +86-10-62816065; E-mail:; Shen Hong-xue, E-mail:   
About author:  Xu Ling, E-mail:; Zhang Wen-gang, E-mail:;

Cite this article: 

Xu Ling, Zhang Wen-gang, Li Jun-ya, Zhu De-jiang, Xu Xiao-cheng, Tian Yan-zi, Xiong Xiong, Guo Ai-zhen, Cao Bing-hai, Niu Hong, Zhu Bo, Wang Ze-zhao, Liang Yong-hu, Shen Hong-xue, Chen Yan. 2017. Genetic background analysis and breed evaluation of Yiling yellow cattle. Journal of Integrative Agriculture, 16(10): 2246-2256.

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