Zebrafish hoxba and hoxbb clusters are redundantly required for posterior pharyngeal pouch development

Pharyngeal pouch formation is fundamental to vertebrate craniofacial development, but molecular mechanisms underlying posterior pouch formation remain incompletely understood. Retinoic acid (RA) signaling is required for posterior pharyngeal development, and Hox genes are established RA targets. However, their genetic requirement in posterior pouch formation has not been established.

Zebrafish lacking both hoxba and hoxbb clusters-teleost-specific duplicates of the ancestral HoxB cluster-exhibited severe loss of posterior pharyngeal pouches and associated pharyngeal skeletal elements, accompanied by reduced expression of the pouch marker pax1a. Alcian blue analysis revealed highly similar losses of posterior pharyngeal skeletal elements in hoxba;hoxbb and RA-deficient aldh1a2 mutants. Pharyngeal expression of hoxb1a and hoxb1b was reduced in aldh1a2 mutants. Combined knockdown of hoxb1a and hoxb1b caused variable, incompletely penetrant posterior pouch abnormalities, supporting their contribution to HoxB-cluster function.

These results provide genetic evidence that the hoxba and hoxbb clusters are redundantly required for posterior pharyngeal pouch development. The highly similar posterior pharyngeal abnormalities in hoxba;hoxbb and aldh1a2 mutants, together with reduced hoxb1a and hoxb1b expression, support a functional association between RA signaling and HoxB-cluster activity. Together, these findings identify the duplicated HoxB-derived clusters as important genetic components of RA-associated posterior pharyngeal development.