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Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation.

机译:结合QTL和选择性扫描定位与编码SNP注释和顺式eQTL分析,揭示出PARK2和JAG2是肥胖调节的新候选基因。

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摘要

Very few causal genes have been identified by quantitative trait loci (QTLs) mapping because of the large size of QTLs, and most of them were identified thanks to functional links already known with the targeted phenotype. Here we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTLs identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for only one trait, the abdominal fat weight, in which several QTLs were previously mapped. Using a new haplotype-based statistics exploiting the very high SNP density generated through whole genome re-sequencing, we found 129 significant selective sweeps. Most of the QTLs co-localized with at least one sweep, which markedly narrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strong positional causal candidates with no presupposed function. We then focused on two of these QTLs/sweeps. The absence of non-synonymous SNPs in their coding regions strongly suggests the existence of causal mutations acting in cis on their expression, confirmed by cis-eQTL identification using either allele-specific expression or genetic mapping analyses. Additional expression analyses on those two genes in the chicken and mice contrasted for adiposity reinforces their link with this phenotype. This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. Moreover, it highlights two genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken and mice.
机译:由于QTL的大小较大,因此很少的因果基因已通过数量性状基因座(QTL)定位进行了鉴定,并且大多数归因于已知表型的功能联系而得以鉴定。在这里,我们建议结合选择签名检测,编码SNP注释和顺式表达QTL分析,以识别在不同系设计中鉴定的QTL潜在的因果基因。作为模型,我们选择了仅针对一项特征(腹部脂肪重量)而不同地选择的实验鸡系,其中先前已绘制了多个QTL。使用新的基于单倍型的统计数据,利用通过全基因组重新测序产生的非常高的SNP密度,我们发现了129个重要的选择性扫描。大多数QTL与至少一次扫描共定位,这显着缩小了候选区域的大小。这些扫描中的一些仅包含一个基因,因此使它们成为没有预设功能的强位置因果候选物。然后,我们专注于其中两个QTL /扫描。在其编码区中没有非同义SNP的存在强烈暗示了存在因果突变而顺式作用于它们的表达,这通过使用等位基因特异性表达或遗传图谱分析的顺式-eQTL鉴定得以证实。在鸡和小鼠中对这两个基因进行了另外的表达分析,对比了肥胖,这增强了它们与该表型的联系。这项研究首次显示了在选择针对特定性状的分歧系的背景下,结合选择性扫描定位,编码SNP注释和cis-eQTL分析来识别复杂性状的致病基因的兴趣。此外,它突出显示了两个基因,JAG2和PARK2,是鸡和小鼠肥胖的新的潜在的负性和正性肥胖关键调节因子。

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