Sequencing of two groups with extreme differences for IB number

Intermuscular bones (IBs), which are ossified from tendons in the myosepta of lower teleosts, are attracting more attention because of their unique developmental mechanisms and adverse effects on food and commercial value. Previous studies have shown that there are differences in the number of IBs between different individuals, and genetic techniques such as crossbreeding can reduce the IBs number of fish, which suggested that the traits of IBs number has the possibility of genetic improvement through selective breeding program. In this study, two groups with extreme differences for IB number (IB-more group: IB number ≥130; IB-less group: IB number≤100) were constructed to identify IB number-associated SNPs and genes in Blunt snout bream (Megalobrama amblycephala), which is one of the most important species in stock enhancement programs of China.Through whole genome resequencing and bulked segregant analysis, two associated chromosome regions were identified using the SNP-index method after 21802 SNPs being screened. 21 and 300 candidate SNPs were detected in these two regions, respectively, located in chromosome 06 and chromosome 11. Detection and annotation of SNPs within the genome-wide range also revealed three key SNPs annotated to skeletal development genes. These discoveries indicated a potential correlation between the SNPs produced in this study and IB development. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying number of IBs in blunt snout bream. It also lays the foundation for the molecular selective breeding of IB number traits.