The Drosophila melanogaster Genetic Reference Panel (DGRP) is a community resource of 205 sequenced inbred lines, derived to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show higher deletion than insertion mutation rates and stronger purifying selection on deletions. Weaker selection on insertions than deletions is consistent with our observed distribution of genome size determined by flow cytometry, which is skewed toward larger genomes. Insertion/ deletion and single nucleotide polymorphisms are positively correlated with each other and with local recombination, suggesting that their nonrandom distributions are due to hitchhiking and background selection. Our cytogenetic analysis identified 16 polymorphic inversions in the DGRP. Common inverted and standard karyotypes are genetically divergent and account for most of the variation in relatedness among the DGRP lines. Intriguingly, variation in genome size and many quantitative traits are significantly associated with inversions. Approximately 50% of the DGRP lines are infected with Wolbachia, and four lines have germline insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP, and genome-wide analyses of quantitative traits identify novel candidate genes. The DGRP lines, sequence data, genotypes, quality scores, phenotypes, and analysis and visualization tools are publicly available.[Supplemental material is available for this article.]Studies in Drosophila melanogaster have revealed basic principles and mechanisms underlying fundamental genetic concepts of linkage and recombination and were instrumental in identifying canonical and evolutionarily conserved cell signaling pathways.Most D. melanogaster genes are evolutionarily conserved, leading to fly models for understanding common human diseases and behavioral disorders, dipteran disease vectors, and insects impacting agriculture, medicine, and forensics. Despite nearly a century of research on D. melanogaster, however, a large fraction of its coding and noncoding sequence has no known function (McQuilton et al. 2012). Recent efforts to induce mutations in every protein coding gene utilize transposable elements (Bellen et al. 2004(Bellen et al. , 2011, which have a different spectrum of allelic effects than SNPs and small insertions and deletions (indels). Comprehensive efforts to identify regulatory DNA elements in Drosophila (The Ó 2014 Huang et al.

We determined female genome sizes using flow cytometry for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel, and found significant conspecific and intrapopulation variation in genome size. We also compared several life history traits for 25 lines with large and 25 lines with small genomes in three thermal environments, and found that genome size as well as genome size by temperature interactions significantly correlated with survival to pupation and adulthood, time to pupation, female pupal mass, and female eclosion rates. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Expression data implicate differences in metabolism that correspond to genome size variation. These results indicate that significant genome size variation exists within D. melanogaster and this variation may impact the evolutionary ecology of the species. Genome size variation accounts for a significant portion of life history variation in an environmentally dependent manner, suggesting that potential fitness effects associated with genome size variation also depend on environmental conditions.

Genes encoding members of the p24 family of intracellular trafficking proteins are present throughout animal and plant lineages. However, very little is known about p24 developmental, spatial, or sex-specific expression patterns or how localized expression affects function. We investigated these problems in Drosophila melanogaster, which contains nine genes encoding p24 proteins. One of these genes, logjam (loj), is expressed in the adult female nervous system and ovaries and is essential for oviposition. Nervous system-specific expression of loj, but not ovary-specific expression, rescues the behavioral defect of mutants. The Loj protein localizes to punctate structures in the cellular cytoplasm. These structures colocalize with a marker specific to the intermediate compartment and cis-Golgi, consistent with experimental evidence from other systems suggesting that p24 proteins function in intracellular transport between the endoplasmic reticulum and Golgi. Our findings reveal that Drosophila p24 transcripts are developmentally and tissue-specifically expressed. CG31787 is male-specifically expressed gene that is present during the larval, pupal, and adult stages. Female CG9053 mRNA is limited to the head, whereas males express this gene widely. Together, our studies provide experimental evidence indicating that some p24 genes have sex-specific expression patterns and tissue-and sex-limited functions. Developmental Dynamics 236:544 -555, 2007.

Behavior is influenced by an organism's genes and environment, including its interactions with same or opposite sex individuals. Drosophila melanogaster perform innate, yet socially modifiable, courtship behaviors that are sex specific and require rapid integration and response to multiple sensory cues. Furthermore, males must recognize and distinguish other males from female courtship objects. It is likely that perception, integration, and response to sex-specific cues is partially mediated by changes in gene expression. Reasoning that social interactions with members of either sex would impact gene expression, we compared expression profiles in heads of males that courted females, males that interacted with other males, or males that did not interact with another fly. Expression of 281 loci changes when males interact with females, whereas 505 changes occur in response to male-male interactions. Of these genes, 265 are responsive to encounters with either sex and 240 respond specifically to male-male interactions. Interestingly, 16 genes change expression only when a male courts a female, suggesting that these changes are a specific response to male-female courtship interactions. We supported our hypothesis that sociallyresponsive genes can function in behavior by showing that egghead (egh) expression, which increases during social interactions, is required for robust male-to-female courtship. We predict that analyzing additional socially-responsive genes will give us insight into genes and neural signaling pathways that influence reproductive and other behavioral interactions.

BackgroundBehavior is a complex process resulting from the integration of genetic and environmental information. Drosophila melanogaster rely on multiple sensory modalities for reproductive success, and mating causes physiological changes in both sexes that affect reproductive output or behavior. Some of these effects are likely mediated by changes in gene expression. Courtship and mating alter female transcript profiles, but it is not known how mating affects male gene expression.ResultsWe used Drosophila genome arrays to identify changes in gene expression profiles that occur in mated male heads. Forty-seven genes differed between mated and control heads 2 hrs post mating. Many mating-responsive genes are highly expressed in non-neural head tissues, including an adipose tissue called the fat body. One fat body-enriched gene, female-specific independent of transformer (fit), is a downstream target of the somatic sex-determination hierarchy, a genetic pathway that regulates Drosophila reproductive behaviors as well as expression of some fat-expressed genes; three other mating-responsive loci are also downstream components of this pathway. Another mating-responsive gene expressed in fat, Juvenile hormone esterase (Jhe), is necessary for robust male courtship behavior and mating success.ConclusionsOur study demonstrates that mating causes changes in male head gene expression profiles and supports an increasing body of work implicating adipose signaling in behavior modulation. Since several mating-induced genes are sex-determination hierarchy target genes, additional mating-responsive loci may be downstream components of this pathway as well.