# Genetic Basis of Transcriptome Diversity in Drosophila melanogaster

## TL;DR

This study explores how genetic differences in fruit flies affect gene expression, revealing patterns and regulatory variants that influence transcriptome diversity.

## Contribution

The study provides a comprehensive analysis of the genetic basis of transcriptome diversity in Drosophila using population-scale data.

## Key findings

- A substantial fraction of the Drosophila transcriptome is genetically variable and organized into modules.
- Regulatory variants for gene expression mean and variance were identified, with variance often explained by epistasis.
- Expression quantitative trait loci for mean gene expression are concentrated near genes.

## Abstract

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.