A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations

Abstract

Background Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs. Results This study screened 394 deep-sequenced genomes from 22 domesticated pig breeds/populations worldwide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identified a set of 878,967 polymorphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date. We found multiple lines of evidence that pSTRs in coding regions were affected by purifying selection. The enrichment of trinucleotide pSTRs in coding sequences (CDS), 5′UTR and H3K4me3 regions suggests that trinucleotide STRs serve as important components in the exons and promoters of the corresponding genes. We demonstrated that, compared to SNPs, pSTRs provide comparable or even greater accuracy in determining the breed identity of individuals. We identified pSTRs that showed significant population differentiation between domestic pigs and wild boars in Asia and Europe. We also observed that some pSTRs were significantly associated with environmental variables, such as average annual temperature or altitude of the originating sites of Chinese indigenous breeds, among which we identified loss-of-function and/or expanded STRs overlapping with genes such as AHR, LAS1L and PDK1. Finally, our results revealed that several pSTRs show stronger signals in domestic pig—wild boar differentiation or association with the analysed environmental variables than the flanking SNPs within a 100-kb window. Conclusions This study provides a genome-wide high-density map of pSTRs in diverse pig populations based on genome sequencing data, enabling a more comprehensive characterization of their roles in evolutionary and environmental adaptation.

Structural variants and tandem repeats in the founder individuals of four F2 pig crosses and implications to F2 GWAS results

“…The tetranucleotide repeats were the most abundant (27.93%), followed by the dinucleotide repeats (16.39%) (Figure SM 3 ). Given the cumulated length of 35.35 Mb, the library of TRs covered 1.56% of the autosomal reference genome, which was in line with previous reports [ 45 , 72 ]. In the founder data set, after genotype and sample-specific filters, we retained 844,558 high-quality TRs calls of which 103,730 loci had non-reference alleles, further denoted as pTR (polymorphic TR).…”

“…The number of TRs profiled was 844,556, from which 103,730 were categorized as polymorphic (pTR). Particular to this study was the augmentation of the usually targeted TRs, the STRs (2-6 bp) [ 45 , 72 ], by also including VNTRs (7-20 bp). From the total pTRs, the latter accounted for 7.02% and widened the pig TRs spectrum.…”

“…There is a growing body of evidence suggesting that TRs play a critical role in the regulation of gene expression [ 29 ] and splicing [ 33 ], as well as via DNA methylation [ 58 ]. Specifically for the pig, there have been efforts made to characterize TRs using WGS data with a focus on STRs [ 45 , 72 ].…”

A comparative investigation on H3K27ac enhancer activities in the brain and liver tissues between wild boars and domesticated pigs

“…To further explore the role of regulatory elements in pig domestication, we compiled 78 genes that were reported to be highly associated with domestication (Wu et al, 2021 ; Yang, Cui, et al, 2017 ; Yang, Yan, et al, 2017 ; Zhu et al, 2017 ) and the top 1% highly differentiated variants (SNPs and STRs) between wild boars and domestic pigs (Wu et al, 2021 ) (Figure S6 ). We examined their overlaps with the differentially active H3K27ac peaks of BMXs and CWBs identified in this study (Tables S6–S8 ).…”

“…We downloaded the results of Fst/Rst analysis on 19,249,347 SNPs and 296,831 STRs (Short Tandem Repeats) from 157 domestic pigs and 24 wild boars (Table S5 ) from Wu et al ( 2021 ). The fixation index (Rst) (Slatkin, 1995 ) of STRs was defined as: Rst = (St − Sw)/St, where Sw is the average sum of squares of the differences in allele length within each population, and St is the average sum of the squares of the differences in allele length across all individuals under investigation.…”