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.
Highlights
Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals
Young short interspersed nuclear elements (SINEs) retrotransposon insertions are highly polymorphic in the pig genomes Three pig-specific SINE families (SINEA, SINEB, and SINEC), with different evolutionary histories, were identified in a previous study showing that SINEA represents the youngest family with some of its subfamilies still displaying activity in the last 10 million years [9]
Insertion age analysis revealed that SINEA1–SINEA3 displayed activity 2 million years ago (Mya); the activity of SINEA4 was hard to detect in the last 2 million years, while the activity of other subfamilies (SINEA5–SINEA11), SINEB, and SINEC was totally extinct in this period (Fig. 1 A and Additional file 1: Fig. S2)
Summary
Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Retrotransposons—a heterogeneous group of genetic sequences that have the ability to be transcribed into RNA, reverse-transcribed into DNA, and inserted into a new site in a genome—account for 30–50 % of mammalian genomes and represent major genomic parasites of mammals [1]. They play key roles in the structural organization of the genome, in the orchestration. SINE insertions can play roles in gene regulation by diverse mechanisms: by acting on the promoters, enhancers [12], or transcription factor binding sites [13] of corresponding genes. When a SINE is inserted into a lncRNA, it can promote translation of partially overlapping sense protein-coding mRNAs (designated a SINEUP), leading to regulation of the expression of the target gene [23, 24]
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