The chicken embryo as a model for developmental genomics

The chicken embryo has been a central model in developmental biology for centuries, prized for its experimental tractability and the ease with which embryonic tissues can be directly observed and manipulated. Its external development allows precise perturbations of cell fate, signaling, and morphogenesis that have defined core principles of vertebrate development. These strengths have taken on new significance with the advent of genomic technologies, which have largely offset the absence of robust forward genetics in the chick, repositioning it as a powerful platform for functional and regulatory genomics. The sequencing of the chicken genome, combined with high-throughput approaches to profile gene expression, chromatin accessibility, transcription factor binding, and genome organization, has opened new avenues for interrogating gene regulatory mechanisms directly in vivo. The chick is especially well-positioned for such studies: its compact genome supports high-quality genomic assays, its experimental throughput enables systematic perturbation, and its evolutionary placement among vertebrates makes it valuable for comparative analyses. In this review, we discuss how genomic and epigenomic approaches have reshaped the use of the chick embryo, highlighting advances in genome organization, regulatory element function, and comparative genomics, as well as the experimental toolkit that enables mechanistic studies of developmental gene regulation.