Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Sus scrofa)

The interferon-induced guanylate-binding protein 1 gene (GBP1) plays an important role in host defense against viral, bacterial and protozoan infections. To explore novel genetic variants in this gene, we re-sequenced a 587-bp fragment spanning the exon 2 of the GBP1 gene in a sample panel consisting of 34 wild boars and 59 local domestic pigs from three geographic regions (China, Iberian Peninsula, and Central Europe) and 12 individuals of three commercial breeds (Pietrain, Landrace, and Large White). In a final 543-bp sequence fragment, there were 14 single nucleotide polymorphisms (SNPs), of which five were coding (three novel mutations). A total of 19 haplotypes were reconstructed and most haplotypes were shared by two or more sample groups. Those shared haplotypes revealed a clear signature of genetic introgression from Chinese domestic pigs into European domestic pigs. In addition, there were six haplotypes with frequencies below 1%, but none of them were present in the three commercial breeds (Pietrain, Landrace, and Large White). Although a limited number of individuals and breeds were analyzed, the absence of rare alleles (or haplotypes) in the commercial breeds is an indication that a significant proportion of genetic diversity in domestic species is not present in commercial breeds. This study demonstrated the potential to find sufficient genetic variation for population genetic analyses of demography versus selection, in functional candidate genes of domestic pigs and wild boars worldwide.