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Genome-wide identification of allele-specific expression in response to Streptococcus suis 2 infection in two differentially susceptible pig breeds

  • Animal Genetics • Original Paper
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Abstract

Although allele expression imbalance has been recognized in many species, and strongly linked to diseases, no whole transcriptome allele imbalance has been detected in pigs during pathogen infections. The pathogen Streptococcus suis 2 (SS2) causes serious zoonotic disease. Different pig breeds show differential susceptibility/resistance to pathogen infection, but the biological insight is little known. Here we analyzed allele-specific expression (ASE) using the spleen transcriptome of four pigs belonging to two phenotypically different breeds after SS2 infection. The comparative analysis of allele specific SNPs between control and infected animals revealed 882 and 1096 statistically significant differentially expressed allele SNPs (criteria: ratio≧2 or ≦0.5) in Landrace and Enshi black pig, respectively. Twenty nine allelically imbalanced SNPs were further verified by Sanger sequencing, and later six SNPs were quantified by pyrosequencing assay. The pyrosequencing results are in agreement with the RNA-seq results, except two SNPs. Looking at the role of ASE in predisposition to diseases, the discovery of causative variants by ASE analysis might help the pig industry in long term to design breeding programs for improving SS2 resistance.

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Acknowledgments

This work was supported by national post-doctor foundation (2012 M511596) and innovation system of agricultural science and technology in Hubei Province (2011-620-001-003) and open project from Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding (2012ZD145).

Conflict of interest

The authors declare that they have no conflict of interest.

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    Authors and Affiliations

    1. Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China

      Huayu Wu, Uma Gaur, Xianwen Peng, Lianghua Li, Hua Sun, Zhongxu Song, Binke Dong, Mingbo Li, Shuqi Mei & Guisheng Liu

    2. Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China

      Huayu Wu, Uma Gaur, Xianwen Peng, Lianghua Li, Hua Sun, Binke Dong, Shuqi Mei & Guisheng Liu

    3. Department of Animal Science, Faculty of Agriculture Chiang Mai University, Chiang Mai, 50200, Thailand

      Supamit Mekchay

    4. Leibniz Institute for Farm Animals Biology (FBN), Research Unit ‘Molecular Biology’, Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany

      Klaus Wimmers

    5. Leibniz Institute for Farm Animals Biology (FBN), Research Group ‘Functional Genome Analysis’, Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany

      Siriluck Ponsuksili

    6. Beijing Institute of Animal Science and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Malianwa, Haidian District, Beijing, 100193, China

      Kui Li

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    1. Huayu Wu
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    2. Uma Gaur
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    Correspondence to Guisheng Liu.

    Additional information

    Communicated by: Maciej Szydlowski

    Huayu Wu and Uma Gaur contributed equally to this work.

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    Wu, H., Gaur, U., Mekchay, S. et al. Genome-wide identification of allele-specific expression in response to Streptococcus suis 2 infection in two differentially susceptible pig breeds. J Appl Genetics 56, 481–491 (2015). https://doi.org/10.1007/s13353-015-0275-8

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    • DOI: https://doi.org/10.1007/s13353-015-0275-8

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