ArticleMobile DNA2021
SINE jumping contributes to large-scale polymorphisms in the pig genomes.
Article in Mobile DNA, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 29 citations in OpenAlex.
- A 280 bp SINE insertion within the pig PLA2G16 could potentially modify gene expression through integration with its transcript.Journal of applied genetics · 2025Article
- Multi-omics analysis reveals criticaliScience · 2025Article
- Population structure and genetic diversity of Mi pigs based on SINE-RIPs.Frontiers in veterinary science · 2025Article
- Construction of the porcine genome mobile element variations and investigation of its role in population diversity and gene expression.Journal of animal science and biotechnology · 2024Article
- Article
- Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Retroviral Insertion Polymorphism (RIP) of Porcine Endogenous Retroviruses (PERVs) in Pig Genomes.Animals : an open access journal from MDPI · 2024Article
- Interspecific Comparison of Orthologous Short Interspersed Elements Loci Using Whole-Genome Data.Genes · 2023Article
- Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs.Journal of animal science and biotechnology · 2023Article
- Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits.Communications biology · 2023Article
- Taming transposable elements in livestock and poultry: a review of their roles and applications.Genetics, selection, evolution : GSE · 2023Review
- Insertion of 643bp Retrotransposon Upstream ofAnimals : an open access journal from MDPI · 2023Article
- SINE Insertion in the Pig Carbonic Anhydrase 5BAnimals : an open access journal from MDPI · 2023Article
- Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs.iScience · 2023Article
- Characterization of the Nero Siciliano Pig Fecal Microbiota after a Liquid Whey-Supplemented Diet.Animals : an open access journal from MDPI · 2023Article
- Structural variants and tandem repeats in the founder individuals of four FBMC genomics · 2022Article
- Article
- Allele-biased expression of the bovine APOB gene associated with the cholesterol deficiency defect suggests cis-regulatory enhancer effects of the LTR retrotransposon insertion.Scientific reports · 2022Article
- Genetic Evaluation and Population Structure of Jiangsu Native Pigs in China Revealed by SINE Insertion Polymorphisms.Animals : an open access journal from MDPI · 2022Article
- Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes.Animals : an open access journal from MDPI · 2022Article
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Authors and funding
11 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundMolecular 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.
resultsOur 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, most of them (> 95 %) are in introns. Overall, about one forth (23.09 %) of the total genes contain SINE RIPs. Significant biases of SINE RIPs in the transcripts of protein coding genes were observed. 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.
conclusionsOur 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.
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