Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs

Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.

Subcutaneous and intramuscular fat transcriptomes show large differences in network organization and associations with adipose traits in pigs

Subcutaneous fat(SCF)and intramuscular fat(IMF)deposition is relevant to health in humans,as well as meat production and quality in pigs.In this study,we generated RNA sequence data for 122 SCF,120 IMF,and 87 longissimus dorsi muscle(LDM)samples using 155 F6 pigs from a specially designed heterogeneous population generated by intercrossing four highly selected European commercial breeds and four indigenous Chinese pig breeds.The phenotypes including waist back fat thickness and intramuscular fat content were also measured in the 155 F6 pigs.We found that the genes in SCF and IMF differed largely in both expression levels and network connectivity,and highlighted network modules that exhibited strongest gain of connectivity in SCF and IMF,containing genes that were associated with the immune process and DNA double-strand repair,respectively.We identified 215 SCF genes related to kinase inhibitor activity,mitochondrial fission,and angiogenesis,and 90 IMF genes related to lipolysis and fat cell differentiation,displayed a tissue-specific association with back fat thickness and IMF content,respectively.We found that cis-expression QTL for trait-associated genes in the two adipose tissues tended to have tissuedependent predictability for the two adipose traits.Alternative splicing of genes was also found to be associated with SCF or IMF deposition,but the association was much less extensive than that based on expression levels.This study provides a better understanding of SCF and IMF gene transcription and network organization and identified critical genes and network modules that displayed tissue-specific associations with subcutaneous and intramuscular fat deposition.These features are helpful for designing breeding programs to genetically improve the two adipose traits in a balanced way.

Whole-genome sequence-based association study for immune cells in an eight-breed pig heterogeneous population

Pigs are an important domestic animal for meat production and animal models for biomedical research such as research on infectious diseases(Meurens et al.,2012).Immune cells,including T cells,B cells,monocytes,and macrophages,are among the major indicators of immune status in health and disease.Revealing the genetic basis of immune cell phenotypes would be helpful for improving the immunity of pigs genetically and reducing the disease occurrence,antibiotic usage.

Four genetic loci affecting swine lung lesions identified by whole-genome sequencing-based association studies

Dear Editor,Lung disease is a serious concern in humans and domestic animals.Huge economic losses are caused by enzootic pneumonia in the swine industry worldwide(Maes et al.,2018).The lung can be easily invaded by environmental pathogens,resulting in lung diseases usually accompanied by lung lesions.