Zebrafish as a model system for studying cilia biology and ciliopathies

Cilia are highly conserved, microtubule-based, hair-like organelles that project from the surface of most eukaryotic cells. They perform essential functions in signal transduction, cellular motility, and the regulation of fluid flow within tissues. Foundational insights into ciliary biology have largely been derived from invertebrate models such as Chlamydomonas reinhardtii and Caenorhabditis elegans, which each possess a relatively uniform cilium type. In contrast, vertebrates display remarkable diversity in ciliary subtypes, with distinct structures and functions tailored to specific tissues. This diversity underlies the broad physiological importance of cilia, and it also explains why defects in ciliary assembly or function result in a wide spectrum of human genetic disorders collectively known as ciliopathies. As a result, vertebrate models have become indispensable for uncovering the roles of cilia in both normal development and disease pathogenesis. Among them, zebrafish has emerged as a particularly versatile and powerful model system. Its unique experimental advantages—including optical transparency during embryogenesis, external fertilization, high fecundity, and compatibility with large-scale genetic and pharmacological screening—make it ideally suited for studying ciliary biology in vivo. In this review, we summarize recent advances in our understanding of ciliary function using zebrafish, with particular emphasis on studies of ciliopathy-associated genes and newly uncovered roles of cilia in processes such as spinal development and meiosis. Finally, we discuss current challenges and outline future research directions, highlighting how zebrafish will continue to drive discoveries in cilia biology and ciliopathy research.