A Percent wild-type offspring in rDNA magnification assay from 10 µM rapamycin or control ethanol (EtOH) fed males. Animals in both conditions are bbZ9/Ybb+;; nos-Gal4 /+. p-values are determined by a two-sided chi-squared test. EtOH condition is the control for all comparisons between EtOH and rapamycin treatments (p = 0.0038 between control genotype samples; p = 0.5 between R2 RNAi samples). Control genotype is the control for comparison between rapamycin-fed treatments (p = 0.028). Data presented is the percentage of total animals exhibiting wild-type cuticles, with source data listed below, and ±95% CI. B rDNA copy number determined by ddPCR in offspring of 10 µM rapamycin or control EtOH-fed males. Animals in both conditions are bbZ9/Ybb+;; nos-Gal4/+. p-values were determined by two-tailed Welch’s t-test. The data presented is the mean ± 95% CI. C Percent R2 positive GSCs in 10 µM rapamycin or EtOH fed control males and inhibition of mTor factors. p-value determined by two-sided chi-squared test for samples to control condition (EtOH for rapamycin treatment (p = 2.2 × 10−16); No RNAi for Rictor RNAi (p = 1.0, Raptor RNAi (p = 6.11 × 10−5), and S6K DN (p = 0.003)) Data presented is the percent of total GSCs expressing R2, with source data listed below, and ±95% CI. D, E Images of phosphorylated S6 (pS6) in normal and low rDNA CN testes. All images are to scale. Scale bar: 5 µm. F Percent pS6 positive GSCs in low rDNA CN animals compared to normal rDNA CN control. p-value determined by a two-sided chi-squared test. Data presented is the percentage of GSCs with pS6 staining, with source data listed below, and ±95% CI. B, E Genotypes: bbZ9/Ybb+;; nos-Gal4 / + (EtOH control, rapamycin, no RNAi control, and normal rDNA), bbZ9/Ybb+;; nos-Gal4/UAS-Rictor RNAiHMS01588 (Rictor RNAi), bbZ9/Ybb+; nos-Gal4/UAS-Raptor RNAiJF01088 (Raptor RNAi), bbZ9/Ybb+; UAS-S6kK109Q/+; nos-Gal4/ + (S6K DN), bbZ9/Ybb0; nos-Gal4/ + (Low rDNA). Source data are provided as a Source Data file.