Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes

Effect of SNPs on Litter Size in Swine

Although sows do not directly enter the market, they play an important role in piglet breeding on farms. They consume large amounts of feed, resulting in a significant environmental burden. Pig farms can increase their income and reduce environmental pollution by increasing the litter size (LS) of swine. PCR-RFLP/SSCP and GWAS are common methods to evaluate single-nucleotide polymorphisms (SNPs) in candidate genes. We conducted a systematic meta-analysis of the effect of SNPs on pig LS. We collected and analysed data published over the past 30 years using traditional and network meta-analyses. Trial sequential analysis (TSA) was used to analyse population data. Gene set enrichment analysis and protein-protein interaction network analysis were used to analyse the GWAS dataset. The results showed that the candidate genes were positively correlated with LS, and defects in PCR-RFLP/SSCP affected the reliability of candidate gene results. However, the genotypes with high and low LSs did not have a significant advantage. Current breeding and management practices for sows should consider increasing the LS while reducing lactation length and minimizing the sows' non-pregnancy period as much as possible.

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

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.

A body map of super-enhancers and their function in pig

Introduction

Super-enhancers (SEs) are clusters of enhancers that act synergistically to drive the high-level expression of genes involved in cell identity and function. Although SEs have been extensively investigated in humans and mice, they have not been well characterized in pigs.

Methods

Here, we identified 42,380 SEs in 14 pig tissues using chromatin immunoprecipitation sequencing, and statistics of its overall situation, studied the composition and characteristics of SE, and explored the influence of SEs characteristics on gene expression.

Results

We observed that approximately 40% of normal enhancers (NEs) form SEs. Compared to NEs, we found that SEs were more likely to be enriched with an activated enhancer and show activated functions. Interestingly, SEs showed X chromosome depletion and short interspersed nuclear element enrichment, implying that SEs play an important role in sex traits and repeat evolution. Additionally, SE-associated genes exhibited higher expression levels and stronger conservation than NE-associated genes. However, genes with the largest SEs had higher expression levels than those with the smallest SEs, indicating that SE size may influence gene expression. Moreover, we observed a negative correlation between SE gene distance and gene expression, indicating that the proximity of SEs can affect gene activity. Gene ontology enrichment and motif analysis revealed that SEs have strong tissue-specific activity. For example, the CORO2B gene with a brain-specific SE shows strong brain-specific expression, and the phenylalanine hydroxylase gene with liver-specific SEs shows strong liver-specific expression.

Discussion

In this study, we illustrated a body map of SEs and explored their functions in pigs, providing information on the composition and tissue-specific patterns of SEs. This study can serve as a valuable resource of gene regulatory and comparative analyses to the scientific community and provides a theoretical reference for genetic control mechanisms of important traits in pigs.

Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs

PPARs are essential regulators of mammalian fatty acid and lipid metabolism. Although the effects of genetic variations, including single nucleotide polymorphisms (SNPs) in PPARs genes on the phenotype of domestic animals have been investigated, there is limited information on the impact of retrotransposon insertion polymorphisms (RIPs). In this study, a combined comparative genome and polymerase chain reaction (PCR) was used to excavate the RIPs in porcine PPARs. We also investigated the potential effects of retrotransposon insertion on phenotype and expression patterns. This study identified the two RIPs in PPARs genes, namely an ERV in intron 1 of PPARα and a combined retrotransposon in intron 2 of PPARγ, designated as PPARα-ERV-RIP and PPARγ-COM-RIP, respectively. These RIPs exhibited different distribution patterns among Chinese indigenous breeds and Western commercial breeds. Individuals with the PPARα-ERV-RIP^+/+ genotype (+/+ indicated homozygous with insertion) among Large White pigs had significantly higher (p < 0.05) corrected backfat thickness compared to those with the other two genotypes. Similarly, those with the PPARγ-COM-RIP^-/- genotype had significantly higher (p < 0.05) corrected backfat thickness than those with the other two genotypes in Large White pigs. Moreover, in 30-day-old Sujiang piglets, the PPARγ gene expression in the backfat of those with the PPARγ-COM-RIP^-/- genotype (-/- indicated homozygous without insertion) was significantly greater (p < 0.01) than those with other genotypes. The dual luciferase reporter gene assay demonstrated that the combined retrotransposon insertion significantly reduced the activity of the MYC promoter in both C2C12 and 3T3-L1 cells (p < 0.01). Therefore, the combined retrotransposon insertion could function as a repressor to decrease the expression of PPARγ, making PPARγ-COM-RIP a valuable molecular marker for assisted selection of backfat thickness in pig breeding.

Feeding and meat qualities of young pigs of different genotypes according to melanocortin 4 receptor (Mc4r) gene and interbreed differentiation according to the coefficient of decrease in growth intensity in early ontogenesis

The paper presents the results of studies of fattening and meat qualities of young large white pigs of different genotypes for the melanocortin receptor 4 (Mc4r) gene and the decline in growth intensity in early ontogeny. The research was carried out in the agricultural formations of the Dnipropetrovsk region, the Jazz meat processing plant, the laboratory of the genetics of the Institute of Pig Breeding and APV of the National Academy of Sciences, and the laboratory of animal husbandry of the State Institution “Institute of Grain Crops of the National Academy of Sciences”. The work was carried out following the scientific research program of the National Academy of Sciences No. 30, “Innovative technologies of breeding, industrial and organic production of pig farming products” (“Pig farming”). Assessment of animals for fattening and meat quality was carried out taking into account the following characteristics: average daily gain of live weight during the period of control fattening, g; the age of reaching 100 kg live weight, days, length of the chilled carcass, cm; length of the bacon half of the cooled carcass, cm; thickness of lard at the level of 6–7 thoracic vertebrae, mm. The coefficient of decline in growth intensity was calculated according to the method of Yu. K. Sviechin. Biometric research results were processed using generally accepted methods. It was established that according to live weight at 4 and 6 months of age, fattening and meat qualities (age of reaching a live weight of 100 kg, days; lard thickness at the level of 6–7 thoracic vertebrae, mm; length of the chilled carcass, cm) young pigs the controlled population belongs to the I class and the elite class. The coefficient of growth decline in animals of the controlled population ranges from 108.57 to 142.51 points. The data analysis shows that according to the live weight at 4 and 6 months of age, the age of reaching the live weight of 100 kg, the fat thickness at the level of 6–7 thoracic vertebrae, and the length of the chilled carcass, the young pigs of the controlled population belong to the I class and the elite class. Animals of the Mc4r АГ genotype prevail over peers of the Mc4r AA genotype in terms of fattening and meat qualities by an average of 5.90 %. The interbreed differentiation of young pigs by the coefficient of the intensity of growth decline (∆K) shows that the difference between the animals of the experimental groups in terms of the average daily gain in live weight is 23.3 g (td = 2.62), the age of reaching 100 kg live weight is 2.7 days (td = 1.59), the length of the cooled carcass is 1.4 mm (td = 2.12). The number of reliable correlations between fattening and meat qualities, coefficient of the intensity of growth decline (∆K), and Tyler B. index is 75.0 %, which indicates the possibility of their use in selection and breeding work. The use of young pigs of the Mc4r АG genotype and animals of the I group, in which the coefficient of the intensity of growth decline (∆K) ranges from 115.61 to 123.27 points, provides additional production at the level of +3.68 – +1.75 % respectively.