SINE jumping contributes to large-scale polymorphisms in the pig genomes

Abstract

Background: Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene activity and even on phenotypes. However, SINE RIP profiles in livestock remain largely unknown, and not be revealed in pigs. Results: Our data revealed that SINEA1 displayed the most polymorphic insertions (22.5% intragenic and 26.5% intergenic), followed by SINEA2 (10.5% intragenic and 9% intergenic) and SINEA3 (12.5% intragenic and 5.0% intergenic). We developed a genome-wide SINE RIP mining protocol and obtained a large number of SINE RIPs (36,284), with over 80% accuracy and an even distribution in chromosomes (14.5/Mb), and 74.34% of SINE RIPs generated by SINEA1 element. Over 65% of pig SINE RIPs overlap with genes, with significant enrichment in the first and second introns of protein-coding and long non-coding RNA genes. Nearly half of the RIPs are common in these pig breeds. Sixteen SINE RIPs were applied for population genetic analysis in 23 pig breeds, the phylogeny tree and cluster analysis were generally consistent with the geographical distributions of native pig breeds in China. Conclusions: Our analysis revealed that SINEA1–3 elements, particularly SINEA1, are high polymorphic across different pig breeds, and generate large-scale structural variations in the pig genomes. And over 35, 000 SINE RIP markers were obtained. These data indicate that young SINE elements play important roles in creating new genetic variations and shaping the evolution of pig genome, and also provide strong evidences to support the great potential of SINE RIPs as genetic markers, which can be used for population genetic analysis and quantitative trait locus (QTL) mapping in pig.

SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor

“…This may be because there is less chance that the retrotransposons inserted into the conserved region will be retained after insertion [53]. Furthermore, our recent study revealed that young SINEs generated a large-scale SINE RIPs occurrence (over 35,000) with an even distribution across chromosomes (14.5 Mb) [54], indicating that SINE may play important roles in genomic variation and evolution in pigs. Here, we found that out of a total of five RIPs confirmed by PCR in the GHR and IGF1 genes, four were derived from SINE insertions, providing additional evidence that SINEs may have an impact on genetic variations in pig.…”