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

Zhongzi Wu,Bin Yang,Zhimin Zhou,Huanfa Gong,Jing Li,Ziqi Lin,Shijun Xiao,Tao Jiang,Lusheng Huang

doi:10.1186/s40104-021-00658-z

Zhongzi Wu, Bin Yang + Show 7 more

Open Access

https://doi.org/10.1186/s40104-021-00658-z

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Abstract

BackgroundShort 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.ResultsWe 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 cis-heritability 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.ConclusionsThis 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.

Highlights

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
The reciprocal π 1 statistics of the Expression STR (eSTR) in the two populations reached an average of 92% (Additional file 6: Fig. S4)
We compared the distribution and enrichment of eSTRs/Fine-mapping expression STR (FMeSTR) in these functional areas, and the results showed that most FMeSTRs and eSTRs were located in active chromatin interaction areas (TAD and High-through chromosome conformation capture (HIC) compartment A) (Fig. 4c)

Summary

Introduction

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. Expression quantitative trait loci (eQTL) mapping studies identify DNA variants linked to gene expression traits, is a powerful approach for identifying target genes that mediate the effects of genetic variations on complex traits [1]. Most genome-wide association mapping studies on gene expression traits have focused on SNPs and InDels, while other forms of mutations such as Short tandem repeats (STRs) and structural variations, have been ignored, leading the QTLs driven by these variants to be overlooked. STRs were found to have a significant impact on gene expression traits in both humans [7,8,9] and plants [10, 11], and the results of association analyses of STRs with gene expression traits provide valuable resources to prioritize causal variants for complex traits

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