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Elucidation of novel SNPs affecting immune response to classical swine fever vaccination in pigs using immunogenomics approach

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Abstract

The host genetic makeup plays a significant role in causing the within-breed variation among individuals after vaccination. The present study was undertaken to elucidate the genetic basis of differential immune response between high and low responder Landlly (Landrace X Ghurrah) piglets vis-à-vis CSF vaccination. For the purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measure of humoral immune response. Double-digestion restriction associated DNA (ddRAD) sequencing was undertaken on 96 randomly chosen Landlly piglets using Illumina HiSeq platform. SNP markers were called using standard methodology. Genome-wide association study (GWAS) was undertaken in PLINK program to identify the informative SNP markers significantly associated with differential immune response. The results revealed significant SNPs associated with E2 antibody response against CSF vaccination. The genome-wide informative SNPs for the humoral immune response against CSF vaccination were located on SSC10, SSC17, SSC9, SSC2, SSC3 and SSC6. The overlapping and flanking genes (500Kb upstream and downstream) of significant SNPs were CYB5R1, PCMTD2, WT1, IL9R, CD101, TMEM64, TLR6, PIGG, ADIPOR1, PRSS37, EIF3M, and DNAJC24. Functional enrichment and annotation analysis were undertaken for these genes in order to gain maximum insights into the association of these genes with immune system functionality in pigs. The genetic makeup was associated with differential immune response against CSF vaccination in Landlly piglets while the identified informative SNPs may be used as suitable markers for determining variation in host immune response against CSF vaccination in pigs.

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Data Availability

The data in the current study are available from the corresponding author upon reasonable request.

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Funding

This work was supported by the Indian Council of Agricultural Research, Centre for Agricultural Bioinformatics project CABin/100644/16103/801/10133.

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Authors and Affiliations

  1. Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India

    Satish Kumar, Bharat Bhushan, Amit Kumar, Manjit Panigrahi, Soni Kumari, Kaisa Kaiho, A. Karthikeyan & Rajni Chaudhary

  2. Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P, 243122, India

    G. K. Gaur & Triveni Dutt

  3. ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India

    Satish Kumar, Jaya Bharati & Santanu Banik

Authors
  1. Satish Kumar
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  2. Bharat Bhushan
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  3. Amit Kumar
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Contributions

Conceptualization: Amit Kumar, Bharat Bhushan and Satish Kumar; Methodology: Satish Kumar, Rajni Chaudhary, Jaya Bharati; Formal analysis and investigation: Satish Kumar, Jaya Bharati, A. Karthikeyan; Writing - original draft preparation: Satish Kumar, Jaya Bharati; Writing - review and editing: Manjit Panigrahi, Kaisa Kaiho, Soni Kumari; Funding acquisition: Amit Kumar; Resources: Amit Kumar, Santanu Banik, G. K. Gaur, Triveni Dutt; Supervision: Amit Kumar, Bharat Bhushan.

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Correspondence to Satish Kumar, Bharat Bhushan or Amit Kumar.

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Competing interests

The authors declare no competing interests.

Ethics approval

All the experimental procedures were performed in accordance with the guidelines of the Committee for the Purpose of Control and Supervision of Experimentation in Animals (CPCSEA), Ministry of Environment, Forest and Climate Change, Government of India. The methods and protocol had prior approval of Institutional Animal Ethics Committee of ICAR-IVRI with approval no. No. F.I-53/2012- 13/JD(R).

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Kumar, S., Bhushan, B., Kumar, A. et al. Elucidation of novel SNPs affecting immune response to classical swine fever vaccination in pigs using immunogenomics approach. Vet Res Commun 48, 941–953 (2024). https://doi.org/10.1007/s11259-023-10262-3

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