Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes

Abstract

Retrotransposons account for more than one-third of the pig reference genome. On account of the genome variability in different breeds, structural variation (SV) caused by retrotransposon-generated deletion or insertion may have a function in the genome. Litter size is one of the most important reproductive traits and significantly impacts profitability in terms of pig production. We used the method of bioinformatics, genetics, and molecular biology to make an analysis among different pig genomes. Predicted 100 SVs were annotated as retrotransposon in 20 genes related to reproduction. The PCR detection based on these predicted SVs revealed 20 RIPs in 20 genes, that most RIPs (12) were generated by SINE insertion or deletion (indel), and nine RIPs were generated by the ERV indel. We selected 12 RIPs to make the second PCR detection in 24 individuals among nine pig breeds. The PCR detection results revealed that the RIP-A1CF-4 insertion in the breed of Bama, Large White, and Meishan only had the homozygous genotype but low to moderately polymorphisms were present in other breeds. We found that RIP-CWH43-9, RIP-IDO2-9, RIP-PRLR-6, RIP-VMP1-12, and RIP-OPN-1 had a rich polymorphism in the breed of Large White pigs. The statistical analysis revealed that RIP-CWH43-9 had a SINE insertion profitable to the reproductive traits of TNB and NBA but was significantly affected (p < 0.01) and (p < 0.05) in the reproductive traits of litter birthweight (LW) in Large White. On the other hand, the SINE insertion in IDO2-9 may be a disadvantage to the reproductive trait of LW, which was significantly affected (p < 0.05) in Large White. These two RIPs are significant in pig genome research and could be useful molecular markers in the breeding system.

Effect of SNPs on Litter Size in Swine

“…It has been reported that FSH β short interspersed nuclear elements (SINEs) and 212T>C both affect pig LS [24]. The PRLR SINE also affects pig LS [29]. Another study reported that GDF9 affects swine LS and identified 12 SNPs, of which 3 are associated with LS [27].…”

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

“…Despite the potential advantages of TEs, many insertions result in a disease state, or even a lethal allele. For instance, the SINE insertion in IDO2 had a negative impact on the reproductive traits of litter birth-weight, which was significantly (p < 0.05) affected in the Large White pig breed [13]. A recent study on the swamp buffalo (Bubalus bubalis) [14] reported that the 2809-bp-long LINE-1 insertion in the agouti signaling protein (ASIP) gene is the causative mutation for the white coat phenotype.…”

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

“…Retrotransposon can be classified into long terminal repeat (LTR) elements, which mainly contain endogenous retrovirus (ERV) and non-LTR elements (Long interspersed nuclear elements, LINEs; Short interspersed nuclear elements, SINEs). Retrotransposons contribute to genetic diversity [22][23][24] and generate rich polymorphism [25][26][27] in the mammal genome. By changing gene expression patterns, retrotransposon insertion can result in human neurologic and psychiatric disorders [28][29][30], genetic disorders [31,32], and cancer [33,34].…”

“…RIPs were utilized to evaluate the genetic variation and population structure of different pig breeds [41,42]. Additionally, RIPs in important protein-coding genes were conducted to determine their association with porcine phenotypes, including coat color [43], reproductive traits [25,44], growth traits [45,46], and immunity [47]. Based on the genetic variation and population structure evaluations conducted in previous studies, as well as the importance of PPARs in lipid metabolism, RIPs in these genes were identified in this study.…”