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Bioinformatics analysis of candidate genes for milk production traits in water buffalo (Bubalus bubalis)

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Abstract

Water buffalo (Bubalus bubalis) is an important livestock species in developing countries due to its contribution to meat, milk production, and a certain form of labor. However, the genetic potential of buffalo milk production traits has not been fully exploited. To date, 516 candidate genes associated with milk production traits of buffalo have been identified. The present study aimed to explore the possible molecular mechanisms underlying milk production traits of this species through functional genomics analysis of these candidate genes by using different bioinformatics tools. Gene ontology (GO) analysis indicated that these candidate genes were associated with complex biological processes, such as cell proliferation and mitotic nuclear division. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that these candidate genes were enriched in multiple signaling pathways, such as AMPK, ErbB, Toll-like receptor, and Jak-STAT. In addition, one function module consisting of 57 nodes and 139 edges were identified from the protein-protein interaction (PPI) network. GO analysis showed that the 57 candidate genes in this function module were enriched in three main biological processes, including homeostasis, metabolism, and cell response. These three distinct biological processes are well known for regulating mammary gland activities, which explained clearly the mechanism underlying milk production traits. This study provides a novel perspective for better understanding of the biological processes linked with milk production traits. This knowledge is conducive to the improvement of milk yield and composition of this species.

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Funding

This work was supported by the National Science Foundation of China (31872352), Fundamental Research Funds for the Central Universities (2662018PY091), Natural Science Foundation of Hubei Province (2017CFB549, 2018CFA015), Hubei Provincial Modern Agro-industry Technology Research System, and Modern Agro-industry Technology Research System (CARS-36).

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Authors and Affiliations

  1. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Wuhan, 430070, China

    C. Du, T. X. Deng, Y. Zhou & G. H. Hua

  2. College of Animal Science and Technology of Huazhong Agricultural University, Wuhan, 430070, China

    C. Du, T. X. Deng, Y. Zhou & G. H. Hua

  3. Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China

    T. X. Deng

  4. Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt

    N. Ghanem

  5. Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan, 430070, China

    G. H. Hua

Authors
  1. C. Du
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  2. T. X. Deng
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  3. Y. Zhou
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  4. N. Ghanem
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  5. G. H. Hua
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Contributions

Hua G.H. supervised Du C. for writing the manuscript. Deng T.X. and Zhou Y. provided software and technical support. Ghanem N. polished the language. All authors read and approved the final manuscript.

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Correspondence to G. H. Hua.

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Du, C., Deng, T.X., Zhou, Y. et al. Bioinformatics analysis of candidate genes for milk production traits in water buffalo (Bubalus bubalis) . Trop Anim Health Prod 52, 63–69 (2020). https://doi.org/10.1007/s11250-019-01984-1

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