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. 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 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. 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.

中文翻译：

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绘制肝脏基因表达性状的短串联重复序列有助于优先考虑猪复杂性状的潜在因果变异

最近发现短串联重复序列 (STR) 对人类的基因表达和疾病有重大影响，但它们对猪的基因表达和复杂性状的作用仍未得到探索。本研究基于 260 个 F6 个体的发现队列和 296 个 F7 个体的验证群体的全基因组序列和 RNA-Seq 数据，研究 STR 对肝组织中基因表达的影响，该群体来自八种杂交产生的异质群体。猪品种。我们分别在 F6 和 F7 群体中鉴定了 5203 和 5868 个显着表达 STR（eSTR，FDR < 1%），其中大部分可以相互验证（π1 = 0.92）。eSTR 平均解释了基因表达性状的 27.5% 的顺式遗传率。我们进一步通过贝叶斯精细定位方法分别在 F6 和 F7 猪中鉴定了 235 和 298 个精细定位的 STR，它们在内含子、ATAC 峰、隔室 A 和 H3K4me3 区域中显着富集。我们确定了 20 个精细映射的 STR，位于已发表的复杂性状相关 SNP 上游和下游的 100 kb 窗口中，这些 SNP 与 H3K27ac 和 ATAC 峰等表观遗传标记共定位。其中包括 CLPB、PGLS、PSMD6 和 DHDH 基因的 eSTR，它们分别与血液相关性状、腿部构象、生长相关性状和肉质性状的全基因组关联研究 (GWAS) SNP 相关联。这项研究提供了有关 STR 对基因表达特征的影响的见解。确定的 eSTR 是为猪的复杂性状优先考虑因果 STR 的宝贵资源。