Single-Cell Transcriptomic Profiling Reveals Cellular Changes Associated with bmp6 Deficiency During Intermuscular Bone Development in Zebrafish

Intermuscular bones (IBs) are small mineralized structures embedded in fish muscle tissue that complicate processing and are therefore regarded as a quality drawback in cultured cyprinids. Although bmp6 has been implicated in IB development, the cellular changes associated with its loss remain incompletely characterized. Here, we performed single-cell transcriptomic analysis of IB-associated muscle tissues from wild-type and bmp6-knockout zebrafish. In the mutant samples analyzed here, the proportion of osteoblasts was lower and the inferred transcriptional trajectory between tendon stem/progenitor cells (TSPCs) and osteoblasts was altered. In addition, a distinct mutant-specific runx2+/ctsk+ population with osteoclast-associated transcriptional features was identified. CellChat analysis further predicted altered LAMININ-associated cell–cell communication involving LAMC1 and DAG1 in bmp6 mutants. These findings further characterize the cellular changes associated with bmp6 deficiency and provide insights into the cellular regulation of intermuscular bone development in zebrafish.