A rare 24-bp in-frame deletion in porcine PRNP identified in a Berkshire pig

Abstract Background Prion diseases are transmissible neurodegenerative disorders that have been reported in humans and several major food-producing animal species. No cases of natural prion infection have been reported in pigs, although susceptibility to prion infection has been demonstrated under certain experimental inoculation conditions. Several studies have identified genetic polymorphisms in the prion protein gene ( PRNP ), which encodes the cellular prion protein (PrP C ), the precursor of the pathogenic prion protein (PrP Sc ). However, previous studies have identified only limited genetic variation in the porcine PRNP gene, with few variants predicted to affect the amino acid sequence of PrP. Therefore, this study investigated genetic variation in the porcine PRNP gene across multiple swine breeds. Methods We conducted an analysis of genetic variants in the swine PRNP gene using polymerase chain reaction (PCR) and amplicon sequencing in 170 pigs from five breeds, including Berkshire, Duroc, Yorkshire, Korean native pigs, and Jeju black pigs. The distributions of the genetic variants were analyzed across these five pig breeds using Fisher’s exact test. Results We identified three novel genetic variants, including two synonymous SNPs: c.198T>C (p.(Gly66=)) and c.354C>T (p.(Gly118=)), and one 24-bp in-frame deletion variant: NM_001008687.1:c.219_242del (NP_001008687.1:p.(Trp84_Gly91del)). Notably, the deletion variant was located in the tandem repeat region and was predicted to remove one octapeptide from the full-length swine PrP precursor. Conclusion To the best of our knowledge, this is the first reported naturally occurring in-frame deletion predicted to alter the amino acid sequence of porcine PrP.