Novel effects of identified SNPs within the porcine Pregnancy-Associated Glycoprotein gene family (pPAGs) on the major reproductive traits in Hirschmann hybrid-line sows.

This is the first study describing identification of SNPs within the multiple and polymorphic Pregnancy-Associated Glycoprotein gene family (PAGs) in the genome of the domestic pig (pPAGs). We identified pPAG-like (pPAG-L) genotypes in primiparous and multiparous farmed hybrid-line JSR Hirschmann (Hrn) sows (N=159), in which various novel associations with their phenotypes for the major reproductive traits have been discovered. Genomic DNA templates were isolated from the blood and different pPAG-L primers were used to amplify various regions by PCR. Electrophoretically-separated amplicons were selected, purified and sequenced. All identified SNPs were verified for possible pPAG2-L genotype associations with the major reproductive traits. In total, 196 SNPs were identified within the entire structure of the pPAG2-Ls, encompassing 9 exons and 8 (A-H) introns, resembling all aspartic proteinases. It was discovered that among all SNPs, one diplotype localized in exon 6 (657C>T/749G>C; pPAG2 ORF cDNA numbering; L34361) caused amino acid substitutions (Asp220→Asn and Ser250→Thr) in the polypeptide precursors and was associated with an increase in the number of live-born piglets (P≤0.05) in Hrn sows. In turn, co-localized SNP (504g>a; KF537535 numbering) in the intron F of the pPAG2-Ls, but only in the homozygotic genotype (gg), was associated with an increased number of live-born (P≤0.01) and weaned (P≤0.05) piglets in the Hrn sows. These results qualify the pPAG2-Ls as candidate genes of the main QTLs. The novel pPAG SNP profiles provide the basis for a diagnostic genotyping test required for early pre-selection of female/male piglets, presumably mainly useful in various breeding herds.