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Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study

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Abstract

Cattle and water buffalo belong to the same subfamily Bovinae and share chromosome banding and gene order homology. In this study, we used genome-wide Illumina BovineSNP50 BeadChip to analyze 91 DNA samples from three breeds of water buffalo (Nili-Ravi, Murrah and their crossbred with local GuangXi buffalos in China), to demonstrate the genetic divergence between cattle and water buffalo through a large single nucleotide polymorphism (SNP) transferability study at the whole genome level, and performed association analysis of functional traits in water buffalo as well. A total of 40,766 (75.5 %) bovine SNPs were found in the water buffalo genome, but 49,936 (92.5 %) were with only one allele, and finally 935 were identified to be polymorphic and useful for association analysis in water buffalo. Therefore, the genome sequences of water buffalo and cattle shared a high level of homology but the polymorphic status of the bovine SNPs varied between these two species. The different patterns of mutations between species may associate with their phenotypic divergence due to genome evolution. Among 935 bovine SNPs, we identified a total of 9 and 7 SNPs significantly associated to fertility and milk production traits in water buffalo, respectively. However, more works in larger sample size are needed in future to verify these candidate SNPs for water buffalo.

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Acknowledgments

We thank the farm staff for helping to collect blood samples. Financial assistance from Chinese Projects from the Chinese government (201303118, 2011ZX08007-003, 31272427, 2011DFA32250, 2010-Z16, 2011-G26, YJH0044, 201070934339, 201171034317, 20110146110005), Innovation China UK (ICUK PoC-RVC-003), the National Modern Agro-industry Technology Research System of China (nycytx-10), and the earmarked fund for Modern Agro-industry Technology Research System (No. CARS-37-04B) are greatly appreciated.

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Authors and Affiliations

  1. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    Jun Jing Wu, Li Jun Song, Fang Jie Wu, Li Guo Yang & Shu Jun Zhang

  2. Guangxi Key Laboratory of Buffalo Genetics, Reproduction and Breeding, Guangxi Buffalo Research Institute, Nanning, 530001, People’s Republic of China

    Xian Wei Liang & Bing Zhuang Yang

  3. Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Herts, AL9 7TA, UK

    D. Claire Wathes, Geoff E. Pollott & Zhangrui Cheng

  4. Department of Animal Science, Guangxi University, 100 Daxue Road, Nanning, 530005, People’s Republic of China

    De Shun Shi & Qing You Liu

  5. Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, People’s Republic of China

    Jun Jing Wu

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  1. Jun Jing Wu
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  2. Li Jun Song
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Corresponding author

Correspondence to Shu Jun Zhang.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Table S1 Summary of the 935 polymorphic bovine SNPs found in water buffalo (PDF 171 kb)

Supplementary Table S2 Summary of the original P values for top 25 SNPs in second step for each trait (DOC 38 kb)

11033_2012_1932_MOESM3_ESM.doc

Supplementary Figure S1 The triangle plot of the three clusters using STRUCTURE 2.2 (CR: Crossbred; ML: Murrah; and NL: Nili-Ravi) (DOC 93 kb)

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Wu, J.J., Song, L.J., Wu, F.J. et al. Investigation of transferability of BovineSNP50 BeadChip from cattle to water buffalo for genome wide association study. Mol Biol Rep 40, 743–750 (2013). https://doi.org/10.1007/s11033-012-1932-1

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  • DOI: https://doi.org/10.1007/s11033-012-1932-1

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