Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.

中文翻译：

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绵羊肝脏和肌肉中表达数量性状基因座的表达助长了肉质性状的变异

调节转录的变体，例如表达定量性状基因座（eQTL），已经在哺乳动物复杂性状的全基因组关联研究（GWAS）中得到了丰富。然而，尽管有许多复杂的肉类特征的GWAS已经用于绵羊的eQTL研究，但尚未有关于绵羊eQTL的报道。利用从149只绵羊的肝脏和肌肉产生的RNA序列数据以及估算的全基因组单核苷酸多态性（SNP），我们的目标是通过将绵羊基因型与包括基因表达（geQTL）在内的三种主要分子表型相关联，从而解剖转录组的遗传结构。 ，外显子表达（eeQTL）和RNA剪接（sQTL）。我们还检查了这三种类型的eQTL，它们丰富了多肉性状和脂肪酸谱的GWAS。相对较少的分子表型可遗传（h2> 0，P <0.05），肝脏的平均遗传力范围为0.67至0.73，肌肉的平均遗传度范围为0.71至0.77。在±1 Mb以内的分子表型和SNP之间的关联分析确定了许多重要的顺式-eQTL（错误发现率，FDR <0.01）。在三种eQTL类型之间，eQTL和转录起始位点（TSS）之间的中位距离为68到153 kb。每个组织内的geQTL，eeQTL和sQTL之间的常见变异数，以及每个eQTL类型内的肝脏和肌肉之间的常见变异数均显着大于（P <0.05）偶然达到的预期。鉴定出的eQTL富含GWAS命中（P <0.05），与56个car体性状和脂肪酸谱相关。例如，肌肉中的几个geQTL映射到FAM184B基因，肝中的数百个sQTL映射到CAST基因，肝中的数百个sQTL映射到C6基因。这三个基因与人体成分或脂肪酸谱有关。我们检测到大量重要的eQTL，发现eQTL类型和组织之间的变异重叠非常普遍。许多eQTL也是关于肉质性状的QTL。我们的研究填补了有关绵羊模型的调控变异及其在复杂性状中的作用的知识空白。我们检测到大量重要的eQTL，发现eQTL类型与组织之间的变异重叠非常普遍。许多eQTL也是关于肉质性状的QTL。我们的研究填补了有关绵羊模型的调控变异及其在复杂性状中的作用的知识空白。我们检测到大量重要的eQTL，发现eQTL类型和组织之间的变异重叠非常普遍。许多eQTL也是关于肉质性状的QTL。我们的研究填补了有关绵羊模型的调控变异及其在复杂性状中的作用的知识空白。