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

• Published in: Veterinary research communications Vol. 48; no. 2; pp. 941 - 953
• Main Authors: Kumar, Satish, Bhushan, Bharat, Kumar, Amit, Panigrahi, Manjit, Bharati, Jaya, Kumari, Soni, Kaiho, Kaisa, Banik, Santanu, Karthikeyan, A., Chaudhary, Rajni, Gaur, G. K., Dutt, Triveni
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-04-2024; Springer Nature B.V
• Subjects: Animals; Antibody response; Biomedical and Life Sciences; Classical Swine Fever - genetics; Classical Swine Fever - prevention & control; DNA sequencing; Genome-wide association studies; Genome-Wide Association Study - methods; Genome-Wide Association Study - veterinary; Genomes; Hog cholera; Hogs; Humans; Immune response (humoral); Immunity, Humoral; Interleukin 9 receptors; Life Sciences; Polymorphism, Single Nucleotide; Single-nucleotide polymorphism; Swine; Swine Diseases; Vaccination; Vaccination - veterinary; Veterinary Medicine/Veterinary Science; Viral Vaccines; Zoology; Landly; GWAS; Immune Response; E2 antibody; CSF
• ISSN: 0165-7380; 1573-7446
• DOI: 10.1007/s11259-023-10262-3

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.