A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. This question is best addressed in a genetic mapping population in which all molecular polymorphisms are known and for which molecular endophenotypes and complex traits are assessed on the same genotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and for which phenotypes of many quantitative traits have been evaluated. We mapped expression quantitative trait loci for annotated genes, novel transcribed regions, transposable elements, and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, as well as genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses.

中文翻译：

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果蝇遗传参考面板中的基因表达网络。


现代生物学的一个主要挑战是了解 DNA 序列自然发生的变异如何通过中间分子表型网络影响复杂的生物体特征。这个问题最好在遗传作图群体中得到解决，其中所有分子多态性都是已知的，并且在相同基因型上评估分子内表型和复杂性状。在这里，我们对 200 个果蝇遗传参考面板自交系进行了深度 RNA 测序，这些自交系具有完整的基因组序列，并且已经评估了许多数量性状的表型。我们绘制了注释基因、新转录区域、转座元件和微生物物种的表达数量性状基因座。我们确定了影响转座元件表达的宿主变异，与其拷贝数以及微生物组组成无关。我们构建了性别特异性表达数量性状基因座调控网络。这些网络富含异染色质和重组减少的常染色质区域中的新转录区域和靶基因，以及调节转座元件表达的基因。这项研究提供了关于自然遗传变异在调节基因表达中的作用的新见解，并为未来的功能分析提供了可检验的假设。