Identification and mapping of SNPs associated with number of intermuscular bone in blunt snout bream

Most of the freshwater aquaculture fish species in the world, especially cyprinid fishes, contain intermuscular bones (IBs). Different number of IBs had been indicated among different species and strains or individuals of same species, which suggested that the trait of IBs counts has the possibility of genetic improvement through selective breeding program. In this study, two groups with extreme differences for IB number were constructed to identify IB number-associated SNPs and genes in blunt snout bream (Megalobrama amblycephala), which is one of the most important aquaculture species in China. Through whole genome resequencing and bulked segregant analysis (BSA) for two groups with extreme IBs number (IB-more group with IBs number ≥130; IB-less group with IBs number ≤100), a total of 6074 high quality SNPs with |Delta-Index|≥0.5 were screened out by chi-square test and index analysis. The sliding-window analysis subsequently obtained two SNP enrichment regions, which located on chromosome 06 (32 M–34 M) and chromosome 11 (12 M–16 M), respectively, containing 21 and 300 candidate SNPs. Besides, 181 candidate SNPs with |Delta-Index|≥0.8 were detected and annotated within the genome-wide range beyond above two regions. Finally, 52 SNPs were used for data reliability verification. Genotyping of SNPs in IB-less individuals and IB-more individuals and correlation analysis between candidate SNPs and IB number traits indicated that five SNPs were significantly associated with the trait of IB number. The sequences or flanking sequences where SNPs located were then annotated to different genes, which maybe closely related to IB number trait. This is the first study to explore SNPs/genes related to the number of IBs in fish by BSA. The identified dataset provides an extensive resource for understanding the molecular mechanisms underlying IB counts in teleosts and also lays the foundation for the marker assisted breeding of IB number traits in M. amblycephala.