Population Genetic Study Of Porcine Whole-genome Short Tandem Repeats And Their Effects On Gene Expression In Liver Tissues

Pigs are one of the most important agricultural animals,accounting for about 40% of the world’s total meat consumption.Wild boar originated in Southeast Asia and was domesticated independently in Asia and Europe.And constantly spread to the world,forming a wide variety of domestic pig breeds.The genetic study of pig genome is not only helpful to analyze the basic biological knowledge of pig population structure,genetic diversity,domestication and evolution,but also to analyze the causal mechanism of pig complex traits,and improve breeding efficiency and production performance.However,previous studies mainly focused on the functions of SNP,In Del,CNV and SV mutations in the pig genome,while ignoring the important role of short tandem repeat variation(STR)in the pig genome.STR,also known as simple repeat sequence(SSR),refers to the tandem repeated DNA sequence on the genome with a core motif length of1-6 base pairs.STR accounts for about 0.5% to 15.5% of the total length of the eukaryotic genome and is highly polymorphic.STR was once annotated as "junk DNA",but several recent studies have shown that STR plays an important role in gene expression and regulating complex traits in plants and animals.This study collected whole genome resequencing data of 394 samples from 22 domestic pig breeds,2 wild boar breeds,and 7 outgroups.Using TRF and lob STR software processes,a total of 878,967 polymorphism STR variants(p STR)were identified,which greatly enriched the database of porcine STR variants.We also found that(1)the p STR of the coding region was suffered from purification selection;Trinucleotide p STR was enriched in CDS,5’UTR and H3K4Me3 region.Among which,CCG,AGG,and AGC repeats were significantly enriched in CDS,5’UTR,and promoter regions,while ACAGCC repeats were significantly enriched in SINEs elements,suggesting that these STRs have important functions in the pig genome.(2)Population genetic analysis based on genome-wide p STR showed that Asian pigs had higher genetic diversity than European pigs.Among Chinese domestic pigs,Tibetan pigs had higher genetic diversity than other breeds.In addition,STR and SNP have similar or even higher population classification efficiency.(3)In this study,14125 p STRs were identified with an expansion score greater than 10,among which the p STRs located in the A3AGLT2 gene were highly differentiated among Eurasian pig populations.(4)1484 highly differentiated p STRs were identified between Asian boar and domestic pig,which involved TBX19,MSTN,SFT2D2 and AHR.A total of 1325 highly differentiated p STRs involving MFSD12,NR6A1,FAF1 and LAS1 L were identified between European boar and domestic pig.(5)In the environmental adaptation analysis of local pigs in China,a total of 3268 p STRs were significantly associated with annual mean temperature variation,involving EDA,METTL8 and FAM155 B genes.A total of 2692 p STRs were significantly associated with plateau adaptation,involving EPAS1,PDK1 and PIK3C2 B genes.Importantly,we also revealed that a number of p STRs show stronger signals in domestic pig – wild boar differentiation or association with the analyzed environmental variables than the flanking SNPs within a 100 kb window.In conclusion,this study provides the most comprehensive catalog of porcine genomic p STR to date,and illuminates the role of short tandem repeat variation in porcine evolution,domestication,and environmental adaptation.To explore the effect of STR variation on gene expression,whole-genome resequencing and liver gene expression data of an experimental design eight breeds mosaic pig population of its F6 and F7 generations were also obtained.Among them,the sample sizes of the F6 and F7 populations were 260 and 296,respectively.In liver tissues of the F6 and F7 generations,5,203 and 5,868 STRs(e STRs,FDR < 1%)were identified.Orthogonal validation analysis showed that the repeatability of significant e STR among different populations was 92%.Compared with e SNP,the heritability of e STR was about1/4 of that of cis-region.In F6 and F7,164 and 217 e STRs were significantly higher than e SNP,and 12 egenes were shared between the two populations,namely ABTB1,ASB5,NDUSF5,CARD19,MPG,KNJ18,RTTN,IL33,BCKDK,RAB4 B,SNX33 and ARPC5 genes.Based on the CAVIAR pipeline,235 and 298 significant FMe STRs have been identified in F6 and F7 populations,respectively.In addition,we found that FMe STR was significantly enriched in intron regions and epigenetic modification regions such as ATAC,HIC Compartment A and H3K4me3 in the pig genome.Finally,we observed hundreds of e STRs co-located with GWAS SNPs.Among them,20 FMe STR located near GWAS-SNP and overlapped with epigenetic modification peaks,suggesting that these STRs are more likely to be candidate causal variants.For example,a FMe STR on chromosome 9 is located on the conserved peaks of H3K4me3 H3K27 ac and ATAC,adjacent to the GWAS SNP of blood cell count,and significantly affects the expression of the CLPB gene.In summary,a comprehensive investigation of e STRS in porcine liver tissue confirmed the hypothesis that STR variation plays a significant regulatory role in gene expression and alternative splicing in porcine,providing important insights into the genetic basis of complex traits.