Retroviral Insertion Polymorphism (RIP) of Porcine Endogenous Retroviruses (PERVs) in Pig Genomes.

Simple Summary: Retrotransposons in pigs account for approximately 37.13% of the genome, while long terminal repeats (LTRs) make up 7.56%. These LTR retrotransposons consist of two identical sequences that flank an internal protein-coding region, known as an endogenous retrovirus (ERV). When an insertion polymorphism integrates into a genomic region that harbors functional ERV elements, such as promoters, enhancers, and insulators, it may contribute to phenotypic variation. In this study, we explored the insertion polymorphisms generated by the mobilization of full-length ERVs (Fl-ERVs). Through comparative genomic analysis, we identified 18 insertion polymorphic sites that were generated by Fl-ERVs, and evaluated the genetic impact of one Fl-ERV insertion polymorphism in the STAB2-like gene. Endogenous retroviruses (ERVs) are one of the superfamilies of long terminal repeat retrotransposons (LTRs) in mice and humans. Approximately 8% of the pig genome is composed of sequences derived from LTRs. While the majority of ERVs in pigs have decayed, a small number of full-length copies can still mobilize within the genome. This study investigated the unexplored retroviral insertion polymorphisms (RIPs) generated by the mobilization of full-length ERVs (Fl-ERVs), and evaluated their impact on phenotypic variation to gain insights into the biological role of Fl-ERVs in pigs. Overall, 39 RIPs (insertions or deletions relative to the pig reference genome) generated by Fl-ERVs were predicted by comparative genomic analysis, and 18 of them were confirmed by PCR detection. Four RIP sites (D5, D14, D15, and D18) were further evaluated by population analysis, and all of them displayed polymorphisms in multiple breeds. The RIP site of ERV-D14, which is a Fl-ERV inserted in the STAB2-like gene, was further confirmed by sequencing. Population analysis of the polymorphic site of ERV-D14 reveals that it presents moderate polymorphism information in the Large White pig breed, and the association analysis reveals that the RIP of ERV-D14 is associated with age variations at 30 kg body weight (p < 0.05) and 100 kg body weight (p < 0.01) in the population of Large White pigs (N = 480). Furthermore, the ERV-D14 RIP is associated with changes in the expression of the target gene STAB2-like in the liver, backfat, and leaf fat in Sushan pigs. These data suggest that some Fl-ERVs are still mobilizing in the pig's genome, and contribute to genomic and phenotypic variations. [ABSTRACT FROM AUTHOR]