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Breed-specific transcriptome response of spleen from six to eight week old piglet after infection with Streptococcus suis type 2

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Abstract

Different pig breeds have shown differential susceptibility to the pathogen infection; however, molecular mechanisms of the infection susceptibility are not fully understood. Streptococcus suis type 2 (SS2) is an important zoonotic pathogen. To identify the genes responsible for infection susceptibility, pigs from two different breeds (Enshi black and Landrace) were inoculated with SS2 and their spleen transcriptome profiles were investigated in the present study. The differentially expressed genes (DEGs) were analyzed from infected versus control pigs in each breed, and then compared between both pig breeds. Enshi black pig showed more DEGs than Landrace (830 vs. 611) and most of these were due to down-regulated genes (543 vs. 387). However some DEGs were uniquely expressed in one breed, some were expressed in opposite direction in both breeds. A number of candidate genes and pathways are identified which might be involved in susceptibility to SS2, for example, MMP9 and Resistin were only significantly expressed in Landrace. NPG3 and PMAP23 were up-regulated in Landrace whereas down-regulated in Enshi black. LENG8 in control Landrace have inherently higher expression than control Enshi black. IGKV6 is down-regulated in Landrace but up-regulated in Enshi black. Overall, the transcriptome profiles are consistent with the clinical signs, i.e. the Enshi black is more susceptible to SS2 infection than Landrace. This is the first study to identify differential gene expression between indigenous and modern commercial pigs after in vivo SS2 infection using RNA-seq. The significant DEGs in splenic profiles between two pig breeds suggested considerable involvement of genetic background in susceptibility to the SS2 infection in pigs.

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Acknowledgments

Thanks a lot to Dr. Nares Trakooljul (Leibniz Institute for Farm Animals Biology) in Germany for providing technical assistance to use the IPA software. This work was supported by National Key Project for Breeding of New Transgenic Varieties (2009ZX08009-141B) 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 (2011ZD102).

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The authors declare that no conflict of interest exists.

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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

    U. Gaur, QP. Luo, FY. Yuan, HY. Wu, M. Qiao, SQ. Mei & GS. Liu

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

    U. Gaur, QP. Luo, FY. Yuan, HY. Wu, M. Qiao, SQ. Mei & GS. Liu

  3. State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China

    YY. Xiong

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

    K. Wimmers

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

    K. Li

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  1. U. Gaur
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Correspondence to GS. Liu.

Additional information

U. Gaur, YY. Xiong and QP. Luo have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Clinical signs in Landrace and Enshi black piglets (DOCX 15 kb)

11033_2014_3680_MOESM2_ESM.doc

List of all DEGs: The list of all significant DEGs. There are 3 sheets: “Landrace” is DEGs in LI versus LC; “Enshi black” is DEGs in EI versus EC; “LC vs. EC” is DEGs in non-infected Landrace versus non-infected Enshi black. For each DEG is shown its Ensembl gene ID, fold-change, p value, adjusted q value (Benjamini-Hochberg correction), gene name and function description. Genes without names or descriptions are empty. (DOC 96 kb)

Selected DEGs according to functional classifications. (XLS 48 kb)

11033_2014_3680_MOESM4_ESM.tif

Canonical_Pathways: Significant canonical pathways based on DEGs identified by Fishers test using IPA. There are 3 sheets: “Landrace”, “Enshi black”, “LC vs. EC” which has the same meanings as S2. The ratio indicates the number of DEGs involved in each canonical pathway divided by the total number of genes/molecules within each pathway according to the IPA® Knowledge Base. (TIFF 1101 kb)

11033_2014_3680_MOESM5_ESM.tif

Significant GO_categories: GO categories identified according to p values using IPA. There are 3 sheets: the “Landrace”, “Enshi black”, “LC vs. EC” which has the same meanings as S2. (TIFF 19742 kb)

The expression of immunoglobulin genes in Landrace and Enshi black piglets (TIFF 3893 kb)

11033_2014_3680_MOESM7_ESM.tif

The top 20 up- & down-regulated DEGs in Landrace: The top 20 up- and down-regulated DEGs in Landrace piglet spleen following SS2 infection, meanwhile showed the expression status in Enshi black piglets. (TIFF 13820 kb)

11033_2014_3680_MOESM8_ESM.xls

The top 20 up- & down-regulated DEGs in Enshi: The top 20 up- and down-regulated DEGs in Enshi black piglet spleen following SS2 infection, meanwhile showed the expression status in Landrace piglets. (XLS 23 kb)

11033_2014_3680_MOESM9_ESM.xls

The top 20 up- & down-regulated DEGs in Landrace versus Enshi: The top 20 up DEGs in non-infected Landrace versus non-infected Enshi black piglet spleen. (XLS 370 kb)

11033_2014_3680_MOESM10_ESM.doc

The genes expressed in opposite directions in Landrace and Enshi black, Shows the DEG results of non-infected Landrace versus non-infected Enshi black. (DOC 31 kb)

Networks: This file contains 3 sheets for “Landrace”, “Enshi black” and “LC vs. EC”, respectively. (XLS 36 kb)

Network (s). (XLS 36 kb)

Network (s). (DOC 79 kb)

Network (s). (DOC 91 kb)

11033_2014_3680_MOESM15_ESM.doc

Chart for gene ACTA1-related networks: This is merged Networks 4 and 23 in Landrace, and network 5 in Enshi black of S11. (DOC 86 kb)

Primer sequences used for qPCR. (DOC 93 kb)

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Gaur, U., Xiong, Y., Luo, Q. et al. Breed-specific transcriptome response of spleen from six to eight week old piglet after infection with Streptococcus suis type 2. Mol Biol Rep 41, 7865–7873 (2014). https://doi.org/10.1007/s11033-014-3680-x

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