Comparative analysis of <i>draper</i> mutant alleles and RNAi expression systems in the ovary and brain of <i>Drosophila melanogaster</i>

The phagocytic receptor Draper (Drpr) mediates clearance of apoptotic cells in Drosophila melanogaster, yet how distinct drpr alleles and RNAi constructs differ in efficiency and phenotypic outcomes has not been systematically compared. Here, we evaluate multiple drprRNAi lines across UAS/GAL4, QUAS/QF2, and LexA/LexAop systems, alongside a newly generated CRISPR allele (drprCR1). Immunostaining confirmed efficient protein knockdown for all RNAi lines, while qRT-PCR revealed variable transcript reduction, with short-hairpin (SH) constructs more effective in glia and long-hairpin (LH) constructs likely acting at the translational level. Despite these differences, all RNAi lines caused strong phenotypes with persisting nurse cell nuclei in the ovary, and apoptotic cell persistence and neurodegenerative vacuoles in the brain, with SH constructs producing more severe defects. The newly generated drprCR1, which selectively deletes exons 5-6, abolished full-length Drpr-I while preserving shorter isoforms. Unlike the widely used drprΔ5 allele, drprCR1 uncouples ovarian and brain phenotypes: both alleles display ovarian defects, but drprCR1 shows markedly reduced neurodegeneration compared to drprΔ5. Together, our findings reveal construct- and allele-specific differences in RNAi knockdown and drpr isoform function, demonstrating that full-length Drpr is indispensable for ovarian cell clearance but less critical for neurodegeneration.