PDF(Pubmed)
Abstract：
BACKGROUND: Integration of high throughput DNA genotyping and RNA-sequencing data enables the discovery of genomic regions that regulate gene expression, known as expression quantitative trait loci (eQTL). In pigs, efforts to date have been mainly focused on purebred lines for traits with commercial relevance as such growth and meat quality. However, little is known on genetic variants and mechanisms associated with the robustness of an animal, thus its overall health status. Here, the liver, lung, spleen, and muscle transcriptomes of 100 three-way crossbred female finishers were studied, with the aim of identifying novel eQTL regulatory regions and transcription factors (TFs) associated with regulation of porcine metabolism and health-related traits.
RESULTS: An expression genome-wide association study with 535,896 genotypes and the expression of 12,680 genes in liver, 13,310 genes in lung, 12,650 genes in spleen, and 12,595 genes in muscle resulted in 4,293, 10,630, 4,533, and 6,871 eQTL regions for each of these tissues, respectively. Although only a small fraction of the eQTLs were annotated as cis-eQTLs, these presented a higher number of polymorphisms per region and significantly stronger associations with their target gene compared to trans-eQTLs. Between 20 and 115 eQTL hotspots were identified across the four tissues. Interestingly, these were all enriched for immune-related biological processes. In spleen, two TFs were identified: ERF and ZNF45, with key roles in regulation of gene expression.
CONCLUSIONS: This study provides a comprehensive analysis with more than 26,000 eQTL regions identified that are now publicly available. The genomic regions and their variants were mostly associated with tissue-specific regulatory roles. However, some shared regions provide new insights into the complex regulation of genes and their interactions that are involved with important traits related to metabolism and immunity.
RESULTS: An expression genome-wide association study with 535,896 genotypes and the expression of 12,680 genes in liver, 13,310 genes in lung, 12,650 genes in spleen, and 12,595 genes in muscle resulted in 4,293, 10,630, 4,533, and 6,871 eQTL regions for each of these tissues, respectively. Although only a small fraction of the eQTLs were annotated as cis-eQTLs, these presented a higher number of polymorphisms per region and significantly stronger associations with their target gene compared to trans-eQTLs. Between 20 and 115 eQTL hotspots were identified across the four tissues. Interestingly, these were all enriched for immune-related biological processes. In spleen, two TFs were identified: ERF and ZNF45, with key roles in regulation of gene expression.
CONCLUSIONS: This study provides a comprehensive analysis with more than 26,000 eQTL regions identified that are now publicly available. The genomic regions and their variants were mostly associated with tissue-specific regulatory roles. However, some shared regions provide new insights into the complex regulation of genes and their interactions that are involved with important traits related to metabolism and immunity.
摘要：
背景：高通量DNA基因分型和RNA测序数据的整合使得能够发现调节基因表达的基因组区域，称为表达数量性状位点(eQTL)。在猪中,迄今为止的努力主要集中在纯种品系上，具有商业相关性的性状，例如生长和肉质。然而,对与动物健壮性相关的遗传变异和机制知之甚少，其整体健康状况。这里,肝脏,肺，脾,脾并研究了100个三向杂交雌性完成者的肌肉转录组，目的是鉴定与猪代谢和健康相关性状调控相关的新型eQTL调控区和转录因子(TFs)。
结果：对535,896个基因型和12,680个基因在肝脏中的表达进行了全基因组表达关联研究，肺13,310个基因,脾脏中的12,650个基因,肌肉中的12,595个基因导致这些组织中每个组织的4,293、10,630、4,533和6,871个eQTL区域，分别。尽管只有一小部分eQTL被注释为顺式eQTL，与反式eQTL相比,这些研究呈现每个区域更多的多态性,并且与靶基因的关联显著更强.在四个组织中鉴定了20至115个eQTL热点。有趣的是,这些都被富集用于免疫相关的生物过程.在脾脏中，确定了两种TFs：ERF和ZNF45，在基因表达调控中起关键作用。
结论：这项研究提供了一个全面的分析，确定了超过26,000个eQTL区域，现在是公开的。基因组区域及其变体主要与组织特异性调节作用相关。然而,一些共享区域为基因的复杂调控及其相互作用提供了新的见解，这些基因与代谢和免疫相关的重要特征有关。
结果：对535,896个基因型和12,680个基因在肝脏中的表达进行了全基因组表达关联研究，肺13,310个基因,脾脏中的12,650个基因,肌肉中的12,595个基因导致这些组织中每个组织的4,293、10,630、4,533和6,871个eQTL区域，分别。尽管只有一小部分eQTL被注释为顺式eQTL，与反式eQTL相比,这些研究呈现每个区域更多的多态性,并且与靶基因的关联显著更强.在四个组织中鉴定了20至115个eQTL热点。有趣的是,这些都被富集用于免疫相关的生物过程.在脾脏中，确定了两种TFs：ERF和ZNF45，在基因表达调控中起关键作用。
结论：这项研究提供了一个全面的分析，确定了超过26,000个eQTL区域，现在是公开的。基因组区域及其变体主要与组织特异性调节作用相关。然而,一些共享区域为基因的复杂调控及其相互作用提供了新的见解，这些基因与代谢和免疫相关的重要特征有关。
