Studying genetic variation of gene expression provides a powerful way to unravel the molecular components underlying complex traits. Expression QTL studies have been performed in several different model species, yet most of these linkage studies have been based on genetic segregation of two parental alleles. Recently we developed a multi-parental segregating population of 200 recombinant inbred lines (mpRILs) derived from four wild isolates (JU1511, JU1926, JU1931 and JU1941) in the nematode Caenorhabditis elegans. We used RNA-seq to investigate how multiple alleles affect gene expression in these mpRILs. We found 1,789 genes differentially expressed between the parental lines. Transgression, expression beyond any of the parental lines in the mpRILs, was found for 7,896 genes. For expression QTL mapping almost 9,000 SNPs were available. By combining these SNPs and the RNA-seq profiles of the mpRILs, we detected almost 6,800 eQTLs. Most trans-eQTLs (63%) co-locate in six newly identified trans-bands. The trans-eQTLs found in previous 2-parental allele eQTL experiments and this study showed some overlap (17.5%-46.8%), highlighting on the one hand that a large group of genes is affected by polymorphic regulators across populations and conditions, on the other hand it shows that the mpRIL population allows identification of novel gene expression regulatory loci. Taken together, the analysis of our mpRIL population provides a more refined insight into C. elegans complex trait genetics and eQTLs in general, as well as a starting point to further test and develop advanced statistical models for detection of multi-allelic eQTLs and systems genetics studying the genotype-phenotype relationship.

中文翻译：

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秀丽隐杆线虫多亲本重组自交系群体中基因表达的遗传学。

研究基因表达的遗传变异为揭示复杂性状的分子组成提供了一种有力的方法。已经在几种不同的模型物种中进行了表达QTL研究，但是大多数这些连锁研究都基于两个亲本等位基因的遗传分离。最近，我们从线虫秀丽隐杆线虫的四个野生分离株（JU1511，JU1926，JU1931和JU1941）中开发了200个重组自交系（mpRIL）的多亲分离群体。。我们使用RNA-seq来研究多个等位基因如何影响这些mpRILs中的基因表达。我们发现了1,789个基因在亲本系之间差异表达。发现了超过7,896个基因的超越，超出了mpRILs的任何亲本系的表达。对于表达QTL定位，近9,000个SNP可用。通过将这些SNP和mpRIL的RNA-seq谱图相结合，我们检测到了近6,800个eQTL。大多数trans-eQTL（63％）共位于六个新识别的跨频带中。在先前的2亲本等位基因eQTL实验中发现的trans-eQTL和这项研究显示出一些重叠（17.5％-46.8％），一方面强调了一大批基因受人群和条件的多态性调控因素的影响，另一方面，它表明mpRIL群体可以鉴定新的基因表达调控基因座。两者合计，对我们的mpRIL人群的分析为您提供了更精细的见解秀丽隐杆线虫的复杂性状遗传学和eQTL一般而言，也是进一步测试和开发用于检测多等位基因eQTL和系统遗传学以研究基因型与表型关系的高级统计模型的起点。