The modular Gal4 system has proven to be an extremely useful tool for conditional gene expression in Drosophila. One limitation has been the inability of the system to work in the female germline. A modified Gal4 system that works throughout oogenesis is presented here. To achieve germline expression, it was critical to change the basal promoter and 3'-UTR in the Gal4-responsive expression vector (generating UASp). Basal promoters and heterologous 3'-UTRs are often considered neutral, but as shown here, can endow qualitative tissue-specificity to a chimeric transcript. The modified Gal4 system was used to investigate the role of the Drosophila FGF homologue branchless, ligand for the FGF receptor breathless, in border cell migration. FGF signaling guides tracheal cell migration in the embryo. However, misexpression of branchless in the ovary had no effect on border cell migration. Thus border cells and tracheal cells appear to be guided differently.