Developmental Stage Shapes Acute Transcriptional Responses to Operational Chemical Euthanasia Formulations in Zebrafish Embryos and Larvae

Chemical euthanasia protocols are routinely applied across zebrafish developmental stages, but the effects of formulation, time exposure, and developmental stage remain unclear and could introduce variability in transcriptional results and interfere with interlaboratory reproducibility of molecular endpoints. Wild-type AB zebrafish were exposed at three developmental windows (6 hpf, gastrulation; 30 hpf, pharyngula; 100 hpf, pre-feeding larva) to three operational euthanasia formulations (clove oil 0.1% v/v, tricaine/MS-222 1 g/L, or lidocaine 1 g/L), for 3, 10, or 25 min. Expression of ten genes covering immediate-early activation, cellular stress, metabolism, neuroendocrine signalling, apoptosis, and inflammation was quantified by qPCR. Expression responses were analysed using a three-way factorial framework including the developmental phase, formulation, and exposure time. The developmental phase explained substantial developmental context in several genes. The Phase × Treatment interaction was significant after global FDR correction for nine of ten genes, whereas treatment main effects did not provide a stable cross-stage ranking of formulations. Descriptively, gene expression varied across formulations and stages, with several Phase III markers showing positive shifts, but no operational formulation showed universally consistent effects after multiple-testing correction, while effect-size magnitudes should be interpreted cautiously. Acute transcriptional responses to operational chemical euthanasia formulations in zebrafish embryos and larvae were context-dependent. Developmental stage, rather than a universal formulation effect, emerged as the most consistent modulator. Because euthanasia efficacy and non-recovery were not experimental endpoints, these transcriptional data do not identify a best formulation for each developmental phase. These results support stage-aware reporting of euthanasia conditions.