(A) Autophagosomes of oocytes and pre-implantation embryos of mice with GFP-tagged LC3 were visualized by fluorescence microscopy and autophagosomes per embryo counted. Relative mtDNA content (AU for arbitrary units) was assessed by single embryo qPCR. The mtDNA of these mice is wild type C57BL/6N and each embryo was individually lysed using an alkaline lysis protocol. After neutralization using tricine, the Taqman quantitative PCR was run for mtDNA along with standards to quantify the mtDNA content per embryo. The results show that mtDNA declines during active autophagy. (B) Two-cell embryos have been treated with rapamicin (red bars), phenanthroline (green bars) or not (blue bars) for 4 h to activate mitophagy; rapamycin 100 nM increased autophagosomes number per embryo and mtDNA dropped after exposure to 10 uM phenanthroline. Key *P<0.05, **P<0.01, ***P<0.001 t test. t tests where distribution was normal, Mann–Whitney elsewhere.