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

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 this purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measureof 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 markerssignificantly associated with differential immune response. The results revealed significant SNPs associated with E2 anti-body response against CSF vaccination. The genome-wide informative SNPs for the humoral immune response againstCSF 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 forthese genes in order to gain maximum insights into the association of these genes with immune system functionality inpigs. The genetic makeup was associated with differential immune response against CSF vaccination in Landlly pigletswhile the identified informative SNPs may be used as suitable markers for determining variation in host immune responseagainst CSF vaccination in pigs.