Shared candidate genes associated with variation in egg size in cold-adapted and artificially selected Drosophila melanogaster.

The development of most multicellular organisms begins with oogenesis, the production of the egg. In D. melanogaster, egg size is a highly polygenic trait closely related to fitness. Elements of shifts in egg size have been widely studied and modeled, but the genes underlying this variation are still poorly understood. This study aimed to identify candidate genes associated with processes underlying egg-size variation using D. melanogaster as a model. In selection experiments, we generated large-egg populations from a shared ancestral population using both cold-adaptation and artificial selection, and identified candidate genes for the large-egg phenotype. Using whole-genome DNA sequencing and strict computational filtering, we uncovered single-nucleotide polymorphisms in 10 genes. Characterization of these candidates revealed functions in cytoskeletal dynamics, DNA replication and repair, intracellular signaling, and stem cell maintenance and differentiation. RT-PCR and qPCR were used to validate gene expression differences between cold-adapted lines and the Oregon R control (OrR) in a subset of the candidates. In RT-PCR, stathmin demonstrated a modified expression pattern in all cold-adapted lines relative to OrR controls. In qPCR experiments, Pde1c had significantly higher expression (p < 0.05) in the cold-adapted flies compared to OrR controls for all three fly cages tested. For Ino80, significantly higher expression was observed for one of three cages while one cage showed lower expression. We have assembled a candidate list we hope will be a useful resource for researchers across specialties, from germ cells to cytoskeletal dynamics, to further investigate the genetic and developmental aspects of variation in egg size in D. melanogaster.