Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Abstract

Understanding the relationship between genetic and phenotypic variation is one of the great outstanding challenges in biology. To meet this challenge, comprehensive genomic variation maps of human as well as of model organism populations are required. Here, we present a nucleotide resolution catalog of single-nucleotide, multi-nucleotide, and structural variants in 39 Drosophila melanogaster Genetic Reference Panel inbred lines. Using an integrative, local assembly-based approach for variant discovery, we identify more than 3.6 million distinct variants, among which were more than 800,000 unique insertions, deletions (indels), and complex variants (1 to 6,000 bp). While the SNP density is higher near other variants, we find that variants themselves are not mutagenic, nor are regions with high variant density particularly mutation-prone. Rather, our data suggest that the elevated SNP density around variants is mainly due to population-level processes. We also provide insights into the regulatory architecture of gene expression variation in adult flies by mapping cis-expression quantitative trait loci (cis-eQTLs) for more than 2,000 genes. Indels comprise around 10% of all cis-eQTLs and show larger effects than SNP cis-eQTLs. In addition, we identified two-fold more gene associations in males as compared to females and found that most cis-eQTLs are sex-specific, revealing a partial decoupling of the genomic architecture between the sexes as well as the importance of genetic factors in mediating sex-biased gene expression. Finally, we performed RNA-seq-based allelic expression imbalance analyses in the offspring of crosses between sequenced lines, which revealed that the majority of strong cis-eQTLs can be validated in heterozygous individuals.

Sex-Specific Effects ofCis-Regulatory Variants inDrosophila melanogaster

“…Interactions between sexually dimorphic trans-regulatory environments and species-specific cis-regulatory alleles also were recently observed between D. simulans and D. mauritiana using a different experimental design (Meiklejohn et al 2013), indicating that these effects are not limited to cis-regulatory variants segregating within a species. Furthermore, while our observations are based on a small subset of the genome, the genes used are not enriched for particular functional groups, chromosomal location, or magnitude of cis-regulatory differences (data not shown), suggesting that the set is unbiased and that sex3cis-regulatory variant interactions are common, consistent with Massouras et al (2012). These types of interactions can result, for example, from cis-regulatory variants that affect binding sites for trans-regulatory factors that differ between the two sexes Cooley et al 2012), as was reported for the Drosophila desatF gene (Shirangi et al 2009).…”

“…Or, put another way, how often do cis-regulatory variants have sex-specific effects? A recent QTL study of expression variation in D. melanogaster found that sex-specific trans-regulatory factors appear to often have different effects on alternative cis-regulatory alleles (Massouras et al 2012).Here, we investigate the magnitude of such cis-by-sex effects and compare them to the frequency and magnitude of cis-by-trans effects from other sources. To do this, we used pyrosequencing (Ahmadian et al 2000) to measure relative allele-specific expression for 11 randomly selected autosomal genes in male and female F 1 progeny from reciprocal crosses between the highly inbred Drosophila melanogaster lines zhr and z30 (Begun and Aquadro 1993;Sawamura et al 1993;Wu et al 1995;Ferree and Barbash 2009;Coolon et al 2012).…”

“…Or, put another way, how often do cis-regulatory variants have sex-specific effects? A recent QTL study of expression variation in D. melanogaster found that sex-specific trans-regulatory factors appear to often have different effects on alternative cis-regulatory alleles (Massouras et al 2012).…”

Genetic perturbation of key central metabolic genes extends lifespan in Drosophila and affects response to dietary restriction

“…Moreover, these activity differences are representative of the range of much of the cis-associated SNP expression variation seen in natural populations [34,38]. The observation that metabolic genes, when perturbed modestly in activity, have an effect on lifespan is certainly relevant to discussions of the maintenance of genetic variation in these genes in natural populations, especially as nutrient levels vary geographically and seasonally [38,39].…”

Effects of larval crowding on quantitative variation for development time and viability in Drosophila melanogaster

“…The DGRP strains are characterized by high genetic (Mackay et al., 2012; Massouras et al., 2012) and phenotypic variation (Ayroles et al., 2009; Durham, Magwire, Stone, & Leips, 2014; Ellis et al., 2014; Harbison, McCoy, & Mackay, 2013; Mackay et al., 2012; Unckless, Rottschaefer, & Lazzaro, 2015). Fly stocks were ordered from the Bloomington Stock Center and are kept in standard molasses/soy‐corn flour/agar media‐containing vials.…”