Functional Genomics in Zoology: Harnessing CRISPR-Cas Mechanisms and Applications
The advent of CRISPR–Cas genome editing has changed the study of animal biology, turning functional genomics from a discipline constrained by slow forward-genetic screens and bespoke, species-specific reagents into one capable of rapid, programmable, and broadly portable genetic manipulation. This review critically synthesises the past decade of progress in applying CRISPR-based tools across zoology, spanning classical vertebrate model organisms, emerging non-model invertebrates, livestock and aquaculture species, and wildlife populations of direct conservation concern. We examine the expanding molecular toolkit, from nuclease-mediated knockouts through base and prime editing to transcriptional and epigenetic modulation, and consider how these tools have been adapted to taxa as different as zebrafish, cephalopods, reef-building corals, lepidopteran insects, poultry, and large-bodied mammals. Particular attention is given to three areas where functional genomics meets applied zoology and conservation biology most directly: genetic rescue and de-extinction science aimed at restoring genetic diversity or ecological function to imperilled or vanished species; gene drive technologies designed to suppress or modify wild populations of disease vectors and invasive pests; and genome-edited livestock, poultry, and aquaculture stocks engineered for disease resistance, welfare improvement, and production efficiency. We further evaluate methodological advances in detecting and mitigating off-target mutagenesis, the welfare and biosafety implications of intentionally altering the genomes of sentient animals, and the evolving regulatory landscape governing genome-edited organisms in agriculture, biomedicine, and the environment. Throughout, we take a critical stance, weighing demonstrated efficacy against persistent technical limitations, ecological uncertainty, and unresolved ethical questions. We conclude that CRISPR-based functional genomics has reshaped zoological enquiry in ways unlikely to be reversed, yet its translation into field-deployed conservation and agricultural interventions remains constrained by incomplete ecological risk assessment, uneven regulatory harmonisation, and the biological idiosyncrasies of non-model taxa that resist easy extrapolation from laboratory systems.