Establishment and Polymorphism Analysis of SNP Markers in the Gynogenic Blunt Snout Bream

The blunt snout bream (<i>Megalobrama amblycephala</i>, BSB) is a freshwater economic fish with Chinese characteristics, and its genetic characteristics have unique value for studying fish evolution. The gynogenetic blunt snout bream (GBSB) obtained through distant hybridization between cross-order species, which showed a faster growth rate than the female parent, but its appearance is similar to that of BSB and is difficult to distinguish. Therefore, by comparing the transcriptome sequencing data of BSB and GBSB (SRA number: PRJNA893089, not released yet), we identified 30 SNPs associated with genes related to muscle growth, protein synthesis, and glycolysis that are unique to GBSB. Through multi-sample PCR detection and sequencing analysis, 16 SNPs with stable differences in GBSB and BSB were obtained. The polymorphism analysis of 16 SNP sites showed that 9 SNP sites were polymorphic in GBSB, which could be used to identify GBSB and its female parent, BSB. In addition, the 9 SNP sites are located in the <i>myoz1a</i> (<i>myozenin 1a</i>) gene, which is related to muscle development, and may provide insights for further study of muscle growth regulation. Therefore, this study provides candidate marker resources for GBSB germplasm resource identification and molecular marker-assisted breeding, which is beneficial for improving the efficiency and reliability of selection and breeding work.