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SINE jumping contributes to large-scale polymorphisms in the pig genomes
Cai Chen1, Enrico D'Alessandro2, Eduard Murani3
1College of Animal Science & Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China.
Mobile DNA
|June 29, 2021
Summary
Short interspersed nuclear elements (SINEs) are highly polymorphic in pig genomes, with SINEA1 being the most variable. Over 35,000 SINE retrotransposon insertion polymorphism (RIP) markers were identified, offering potential for genetic analysis and QTL mapping in pigs.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Retrotransposon insertion polymorphisms (RIPs) are established molecular markers in various species.
- Short interspersed nuclear elements (SINEs) significantly influence gene activity and phenotypes.
- SINE RIP profiles in livestock, particularly pigs, remain largely unexplored.
Purpose of the Study:
- To characterize SINE RIP profiles in pig genomes.
- To develop a genome-wide SINE RIP mining protocol.
- To evaluate the potential of SINE RIPs as genetic markers for pig population genetics and trait mapping.
Main Methods:
- Development of a genome-wide SINE RIP mining protocol.
- Analysis of SINEA1, SINEA2, and SINEA3 insertion polymorphisms.
- Genome-wide identification and characterization of SINE RIPs.
- Application of selected SINE RIPs for population genetic analysis in 23 pig breeds.
Main Results:
- SINEA1, SINEA2, and SINEA3 elements exhibit significant polymorphism, with SINEA1 showing the highest rates.
- A total of 36,284 SINE RIPs were identified with high accuracy and even chromosomal distribution.
- Over 65% of pig SINE RIPs overlap with genes, primarily within introns, affecting approximately 23% of all genes.
- Phylogenetic analysis using 16 SINE RIPs correlated with the geographical distribution of Chinese native pig breeds.
Conclusions:
- SINEA1-3 elements, especially SINEA1, are major drivers of structural variation in pig genomes.
- Over 35,000 SINE RIP markers were successfully generated.
- SINE RIPs are valuable genetic markers for population genetic analysis and quantitative trait locus (QTL) mapping in pigs, highlighting their role in generating genetic diversity and shaping pig genome evolution.
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