Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes

Zhanyu Du; Enrico D'Alessandro; Emmanuel Asare; Yao Zheng; Mengli Wang; Cai Chen; Xiaoyan Wang; Chengyi Song

doi:10.3390/genes13081359

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes

Genes (Basel). 2022 Jul 28;13(8):1359. doi: 10.3390/genes13081359.

Authors

Zhanyu Du¹, Enrico D'Alessandro², Emmanuel Asare¹, Yao Zheng¹, Mengli Wang¹, Cai Chen¹, Xiaoyan Wang¹, Chengyi Song¹

Affiliations

¹ College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
² Department of Veterinary Sciences, University of Messina, Via Palatucci snc, 98168 Messina, Italy.

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 retrotranspos-on-generated deletion or insertion (indel) 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 indel in 20 genes related to reproductive performance. The PCR detection based on these predicted SVs revealed 20 RIPs in 20 genes, that most RIPs (12) were generated by SINE indel, and eight RIPs were generated by the ERV indel. We selected 12 RIPs to make the second round 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 traits 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.

Keywords: pig genome; polymorphism; reproductive traits; retrotransposon.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Female
Genome
Litter Size / genetics
Polymorphism, Genetic*
Pregnancy
Reproduction / genetics
Retroelements* / genetics
Swine / genetics

Substances

Retroelements

Grants and funding

This work was supported through grants from the NSFC (31872977 and 32002146), the Revitalization of Seed Industry (JBGS) in Jiangsu province [JBGS(2021)028], the Independent Innovation Fund Project of Agricultural Science and Technology in Jiangsu Province [CX(19)2016], the Priority Academic Program Development of Jiangsu Higher Education Institutions, China Postdoctoral Science Foundation [2020M671630] to Cai Chen, and the High-end Talent Support Program of Yangzhou University to Chengyi Song.