Can you explain your question, like, which part of apple fruit you want to examine? At what age and developmental condition do you want to perform the PCD assessment?
For TUNEL, you first have to fix the sample and then make a thin section, so the area selected for study is crucial. Also, you have to prepare a positive control by incubating your tissue of interest in DNAse-1 to induce DNA break in it. Before TUNEL, I will suggest checking several other methods such as DNA laddering, Caspase-like activity, DNA diffusion assay, Ethidium bromide- acridine orange double staining, and finally Tunel assay.
Vivek A., I'm focusing on the cortex of the apple. samples will be taken at different stages of fruit development. If you have any recommended readings, I am open to suggestions