RT Journal Article SR Electronic T1 Genetic Basis of Transcriptome Diversity in Drosophila melanogaster JF bioRxiv FD Cold Spring Harbor Laboratory SP 018325 DO 10.1101/018325 A1 Wen Huang A1 Mary Anna Carbone A1 Michael M. Magwire A1 Jason A. Peiffer A1 Richard F. Lyman A1 Eric A. Stone A1 Robert R. H. Anholt A1 Trudy F. C. Mackay YR 2015 UL http://biorxiv.org/content/early/2015/04/21/018325.abstract AB Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive, but is essential for predicting adaptive evolution, selecting agriculturally important animals and crops, and personalized medicine. Here, we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP). We found that a substantial fraction of the Drosophila transcriptome is genetically variable and organized into modules of genetically correlated transcripts, which provide functional context for newly identified transcribed regions. We identified regulatory variants for the mean and variance of gene expression, the latter of which could often be explained by an epistatic model. Expression quantitative trait loci for the mean, but not the variance, of gene expression were concentrated near genes. This comprehensive characterization of population scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation.