Genome-Wide Identification, Evolutionary Analysis and Expression Profiling of the BMP Gene Family in Qihe Gibel Carp

Bone morphogenetic proteins (BMPs), members of the transforming growth factor beta (TGF-β) superfamily, regulate diverse developmental and physiological processes. However, the BMP gene family has not been systematically characterized in the polyploid Qihe gibel carp (Carassius gibelio var. Qihe). We performed genome-wide identification, phylogenetic analysis, conserved motif and gene structure analysis, chromosomal mapping, and intra- and interspecific synteny analysis of BMP genes. Quantitative real-time PCR (qRT-PCR) was used to examine BMP expression in adult tissues and across developmental stages. Twenty-nine QhBMP genes were identified and assigned to 11 phylogenetic clades. Except for QhBMP1 proteins, most QhBMP proteins contained conserved motifs and characteristic TGF-β-related domains. Exon numbers ranged from 2 to 20, and the 29 genes were unevenly distributed across 24 chromosomes. Seventeen duplicated gene pairs were identified within the Qihe gibel carp genome, and conserved syntenic relationships were detected between Qihe gibel carp and seven reference vertebrates. In adult skeletal muscle, QhBMP4, QhBMP7, and QhBMP8 genes generally showed higher expression than QhBMP1, QhBMP2, and QhBMP6 genes. QhBMP6a and QhBMP6b showed similar temporal profiles, with the highest expression at 5 days post-hatching (dph), followed by a gradual decline and low, relatively stable expression after 45 dph. The developmental expression profiles identify QhBMP6a and QhBMP6b as candidate regulators of early development, although their specific biological functions require experimental validation. These results provide a genomic framework for functional studies of BMP genes in Qihe gibel carp. It should be noted that QhBMP1 paralogs belong to BMP1/Tolloid-like metalloproteases and do not encode canonical TGF-β-related BMP signaling ligands.