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Muscular dystrophies are genetic diseases characterized by progressive muscle degeneration and muscular weakening. Defects in glycosylation of α-dystroglycan are responsible for certain congenital muscular dystrophies to be called α-dystroglycanopathies. The structure of glycans in α-dystroglycan is Siaα2-3Galβ1-4GlcNAcβ1- 2Manα1-Ser/Thr and required for binding basal lamina proteins. The first step of O-mannosyl glycan synthesis on α-dystroglycan is catalyzed by protein O-mannosyltransferases (POMT1 and POMT2), and detect in POMT1 or POMT2 result in Walker-Warburg syndrome one of the α-dystroglycanopathies. Next step is catalyzed by O-mannose β-1,2-N-acetylglucosaminyltransferase 1 (POMGnT1) and it is responsible for muscle-eye-brain disease. We have previously reported that protein O-mannosylation is necessary for normal embryonic development in zebrafish and revealed that zebrafish is a useful model for α-dystroglycanopathies. In this study, we focused on zebrafish POMGnT1. Zebrafish POMGnT1 revealed high level of expression in ovary and ubiquitously throughout early developmental stage as well as zebrafish POMT1 and POMT2. Morpholino experiments of zebrafish POMGnT1 in juvenile zebrafish showed several phenotypes of bended body, small eyes and edematous pericardium. More importantly, morpholino-injected zebrafish had reduction of the reactivity to the monoclonal antibody IIH6 that recognizes a glycosylated α-dystroglycan. Furthermore, phenotypes observed by knockdown of zebrafish POMGnT1 were similar to zebrafish POMT2 rather than zebrafish POMT1. Finally, in order to measure POMGnT1 activity, we cloned and expressed zebrafish POMGnT1 in human embryonic kidney 293T cells. As a result, zebrafish POMGnT1 had the enzymatic activity to transfer GlcNAc from UDP-GlcNAc to O-mannosyl peptide, indicating that O-mannosylation pathway of α-dystroglycan is conserved in zebrafish.