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bioRxiv · 10.1101/2025.05.21.653756

TypeSINE: Genome-Wide Detection of SINE Retrotransposon Polymorphisms Reveals Functional Variants Linked to Body Size Variation in Pigs

Zheng, Y.·Yang, N.·Chen, C.·Zong, W.·Chen, H.·Shi, S.·Wang, X.·Murani, E.·Reyer, H.·Gao, B.·Zhang, L.·Wimmers, K.·Song, C.
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Abstract

The genotyping of Short Interspersed Element (SINE) retrotransposon insertion polymorphisms (RIPs) from large-scale sequencing data remains technically challenging. To overcome this limitation, we developed TypeSINE to genotype SINE-RIPs from short-read sequencing data. Analyzing 362 porcine genomes, we identified 749,835 SINE-RIPs (>85% accuracy), including 65,917 common variants (5-95% frequency). These showed uniform genomic distribution ([~]22/Mb), with 40% in introns. Population analyses based on SINE-RIPs revealed independent domestication of Asian and European pigs from local wild populations, followed by introgression. GWAS detected body size-associated regions using SINE-RIPs. We created pigRIPdb (82,227 curated SINE-RIPs) with browsing and visualization tools. The methods cross-species applicability is supported by conserved SINE evolutionary patterns, enabling polymorphism discovery of SINEs in livestock and humans. TypeSINE represents an efficient, scalable solution for genome-wide SINE-RIP analysis, advancing population genomics research. TeaserAn integrated SINE-RIP genotyping platform with companion database enables large-scale analysis of SINE evolution and population genetics in swine

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Zheng, Y., Yang, N., Chen, C., Zong, W., Chen, H., Shi, S., Wang, X., Murani, E., Reyer, H., Gao, B., Zhang, L., Wimmers, K., Song, C.. 2025-05-26. TypeSINE: Genome-Wide Detection of SINE Retrotransposon Polymorphisms Reveals Functional Variants Linked to Body Size Variation in Pigs. https://doi.org/10.1101/2025.05.21.653756

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