Please wait a minute...
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
Download: 
Export:  BibTeX | EndNote (RIS)      
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:
Fund: 

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: chenyan0204@163.com; Shen Hong-xue, E-mail: 1263080725@qq.com   
About author:  Xu Ling, E-mail: jiujiuyake@sina.com; Zhang Wen-gang, E-mail: zhangwengang_19@sina.com;

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.

Acosta A C, Uffo O, Sanz A, Ronda R, Osta R, Rodellar C, Martin-Burriel I, Zaragoza P. 2013. Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci. Journal of Animal Breeding and Genetics, 130, 79–86.

Abdel-Nour M, Tsalikis J, Kleinman D, Girardin S E. 2014. The emerging role of mTOR signalling in antibacterial immunity. Immunology and Cell Biology, 92, 346–353.

Al-Mamun H A, Clark S A, Kwan P, Gondro C. 2015. Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genetics Selection Evolution, 47, doi: 10.1186/s12711-015-0169-6

Bahbahani H, Clifford H, Wragg D, Mbole-Kariuki M N, Van Tassell C, Sonstegard T, Woolhouse M, Hanotte O. 2015. Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis. Scientific Reports, 5, doi: 10.1038/srep11729

Berntson G G, Zipf W B, O’Dorisio T M, Hoffman J A, Chance R E. 1993. Pancreatic polypeptide infusions reduce food intake in Prader-Willi syndrome. Peptides, 14, 497–503.

Boyles A L, Scott W K, Martin E R, Schmidt S, Li Y J, Ashley-Koch A, Bass M P, Schmidt M, Margaret A, Pericak-Vance M A, Speer M C, Hauser E R. 2005. Linkage disequilibrium inflates type I error rates in multipoint linkage analysis when parental genotypes are missing. Human Heredity, 59, 220–227.

Cong J L, Liu R, Wang Y, Jiang H, Zhang Y Z. 2016. MiR-634 decreases cell proliferation and induces apoptosis by targeting mTOR signaling pathway in cervical cancer cells. Artificial Cells, Nanomedicine, and Biotechnology, 44, 1694–1701.

Decker J E, McKay S D, Rolf M M, Kim J, Molina A A, Sonstegard T S, Hanotte O, Gotherstrom A, Seabury C M, Praharani L, Babar M E, Correia de Almeida Regitano L, Yildiz M A, Heaton M P, Liu W S, Lei C Z, Reecy J M, Saif-Ur-Rehman M, Schnabel R D, Taylor J F. 2014. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics, 10, e1004254.

Denbow D M, Duke G E, Chaplin S B. 1988. Food intake, gastric secretion, and motility as affected by avian pancreatic polypeptide administered centrally in chickens. Peptides, 9, 449–454.

Dray S, Dufour A B. 2007. The ade4 package: Implementing the duality diagram for ecologists. Journal of Statistical Software, 22, 1–20.

Druet T, Perez-Pardal L, Charlie C, Gautier M. 2013. Identification of large selective sweeps associated with major genes in cattle. Animal Genetics, 44, 758–762.

Flury C, Tapio M, Sonstegard T, Drogemuller C, Leeb T, Simianer H, Hanotte O, Rieder S. 2010. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. Journal of Animal Breeding Genetics, 127, 339–347.

Huang D W, Sherman B T, Lempicki R A. 2009a. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4, 44–57.

Huang D W, Sherman B T, Lempicki R A. 2009b. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 37, 1–13.

Huson D H, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23, 254–267.

Kim E S, Rothschild M F. 2014. Genomic adaptation of admixed dairy cattle in East Africa. Frontiers in Genetics, 5, 443.

Liu C H, Nu X Q. 2007. Conservation and utilization of Enshi cattle. China Herbivores, 27, 57–59. (in Chinese)

Li X F, Zhang Y S, Zhang J, Li H B, Chen M X, Suo X J, Xiong Q. 2014. Survey of number distribution and growth of Enshi yellow cattle. The Chinese Livestock and Poultry Breeding, 10, 49–51. (in Chinese)

Makina S O, Muchadeyi F C, van Marle-Koster E, MacNeil M D, Maiwashe A. 2014. Genetic diversity and population structure among six cattle breeds in South Africa using a whole genome SNP panel. Frontiers in Genetics, 5, 333.

Nei M. 1972. Genetic distance between populations. American Naturalist, 106, 283–292.

O’Brie A M P, Mészáros G, Utsunomiya Y T, Sonstegard T S, Garcia J F, Van T, Curtis P, Carvalheiro R, da Silva M V B, Sölkner J. 2014. Linkage disequilibrium levels in Bos indicus and Bos taurus cattle using medium and high density SNP chip data and different minor allele frequency distributions. Livestock Science, 166, 121–132.

Plotree D, Plotgram D. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics, 5, 163–166.

Porto-Neto L R, Kijas J W, Reverter A. 2014. The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes. Genetics Selection Evolution, 46, 22.

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A, Bender D, Maller J, Sklar P, de Bakker P I, Daly M J, Sham P C. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81, 559–575.

Qanbari S, Pausch H, S, Jansen, Somel M, Strom T M, Fries R, Nielsen R, Simianer H. 2014. Classic selective sweeps revealed by massive sequencing in cattle. PLoS Genetics, 10, e1004148.

Randhawa I A, Khatkar M S, Thomson P C, Raadsma H W. 2016. A Meta-assembly of selection signatures in cattle. PLoS ONE, 11, e0153013.

Raymond M, Rousset F. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248–249

Rousset F. 2008. Genepop’007: A complete reimplementation of the Genepop software for Windows and Linux. Molecular Ecology Resources, 8, 103–106.

Shen H X, Zhu D J, Tian Z M, Xiong X, Ma Y. 2016a. Investigation report of breeding and industrialization development of Yiling yellow cattle. China Cattle Science, 42, 78–80. (in Chinese)

Shen H X, Zhu D J, Tian Z M, Xiong X, Ma Y. 2016b. Investigation report of origin and distribution of Yiling yellow cattle. China Cattle Science, 42, 76–77. (in Chinese)

Shen H X, Zhu D J, Tian Z M, Xiong X, Ma Y. 2016c. Investigation report of textual research on the formation process of Yiling yellow cattle. China Cattle Science, 42, 76–79. (in Chinese)

Weir B S, Cockerham C C. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358–1370.

Xue D X, Wang H Y, Zhang T, Liu J X. 2014. Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers. PLoS ONE, 9, e95436.

Xu L Y, Hou Y, Bickhart D M, Zhou Y, Hay El H, Song J Z, Sonstegard T S, Van T, Curtis P, Liu G E. 2016. Population-genetic properties of differentiated copy number variations in cattle. Scientific Reports, 6, 23161.

Yin D Z, Song H Y. 2011. Regulation of Wnt signaling: Mechanisms and biological significance. Chinese Journal of Cell Biology, 33, 103–111. (in Chinese)

Zhang L, Jia S, Plath M, Huang Y, Li C, Lei C, Zhao X, Chen H. 2015. Impact of parental Bos taurus and Bos indicus origins on copy number variation in traditional Chinese cattle breeds. Genome Biology and Evolution, 7, 2352–2361.
No related articles found!
No Suggested Reading articles found!