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Retrotransposon Insertion Polymorphisms (RIPs) in Pig Reproductive Candidate Genes
Zhanyu Du1, Enrico D'Alessandro2, Emmanuel Asare1
1College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
Genes
|August 26, 2022
Summary
Retrotransposon insertions (RIPs) in pig genomes influence reproductive traits. Specific SINE insertions in CWH43-9 and IDO2-9 genes show potential as molecular markers for pig breeding.
Area of Science:
- Genomics
- Molecular Biology
- Animal Genetics
Background:
- Retrotransposons constitute over a third of the pig genome.
- Structural variations (SVs) from retrotransposon indels may impact pig reproductive traits and production profitability.
Purpose of the Study:
- To identify and analyze retrotransposon-induced indels (RIPs) in pig genes related to reproductive performance.
- To investigate the association of specific RIPs with reproductive traits in different pig breeds.
Main Methods:
- Bioinformatics, genetics, and molecular biology techniques were employed.
- Predicted 100 SVs were annotated as retrotransposon indels in 20 reproductive genes.
- PCR detection identified 20 RIPs (12 SINE, 8 ERV) and analyzed their polymorphism across nine breeds.
Main Results:
- RIP-A1CF-4 showed homozygous genotypes in specific breeds, with moderate polymorphisms elsewhere.
- RIP-CWH43-9 and RIP-IDO2-9 exhibited rich polymorphism in Large White pigs.
- RIP-CWH43-9 SINE insertion positively impacted total number born (TNB) and number born alive (NBA) but negatively affected litter birthweight (LW).
- RIP-IDO2-9 SINE insertion negatively impacted LW in Large White pigs.
Conclusions:
- Specific retrotransposon indels (RIPs) are significant in pig genome research.
- RIP-CWH43-9 and RIP-IDO2-9 demonstrate potential as molecular markers for improving pig reproductive traits and breeding systems.
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