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Journal of Applied Genetics

, Volume 56, Issue 4, pp 481–491 | Cite as

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

  • Huayu Wu
  • Uma Gaur
  • Supamit Mekchay
  • Xianwen Peng
  • Lianghua Li
  • Hua Sun
  • Zhongxu Song
  • Binke Dong
  • Mingbo Li
  • Klaus Wimmers
  • Siriluck Ponsuksili
  • Kui Li
  • Shuqi Mei
  • Guisheng Liu
Animal Genetics • Original Paper

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.

Keywords

Allele specific expression Disease resistance Pig SNP Streptococcus suis 

Notes

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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Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2015

Authors and Affiliations

  • Huayu Wu
    • 1
    • 2
  • Uma Gaur
    • 1
    • 2
  • Supamit Mekchay
    • 3
  • Xianwen Peng
    • 1
    • 2
  • Lianghua Li
    • 1
    • 2
  • Hua Sun
    • 1
    • 2
  • Zhongxu Song
    • 1
  • Binke Dong
    • 1
    • 2
  • Mingbo Li
    • 1
  • Klaus Wimmers
    • 4
  • Siriluck Ponsuksili
    • 5
  • Kui Li
    • 6
  • Shuqi Mei
    • 1
    • 2
  • Guisheng Liu
    • 1
    • 2
  1. 1.Institute of Animal Science and Veterinary MedicineHubei Academy of Agricultural SciencesWuhanChina
  2. 2.Hubei Key Laboratory of Animal Embryo Engineering and Molecular BreedingWuhanChina
  3. 3.Department of Animal ScienceFaculty of Agriculture Chiang Mai UniversityChiang MaiThailand
  4. 4.Leibniz Institute for Farm Animals Biology (FBN)Research Unit ‘Molecular Biology’DummerstorfGermany
  5. 5.Leibniz Institute for Farm Animals Biology (FBN)Research Group ‘Functional Genome Analysis’DummerstorfGermany
  6. 6.Beijing Institute of Animal Science and Veterinary MedicineChinese Academy of Agricultural SciencesBeijingChina

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