Development of SNP markers with genome sequencing method for trachurus species (Trachurus mediterraneus, Trachurus trachurus, Trachurus picturatus, Perciformes: Carangidae) distributed in Turkish seas

The difficulty in morphologically distinguishing between Trachurus species (Trachurus mediterraneus, Trachurus trachurus, and Trachurus picturatus) found in Turkish seas has led to confusion between species and the use of incorrect species names. This situation stems from the inadequate definition of species and the lack of sufficient scientific data on the mixed stocks of these species in our seas. In this context, it is of great importance to identify species-specific SNPs and develop molecular markers for these SNPs, which will enable the correct identification of the Trachurus species in question. In our study, whole genome sequence data of three species were taken for the differentiation of Trachurus species and intraspecific primers and interspecific primers and probes were designed according to gene regions containing specific SNP loci. Species discrimination was successfully achieved with the designed primers and probes. The primer-probe designs developed in this study, based on universal probes and using the intermediate primer triggered qPCR (UPIP-qPCR) approach, have potential as a new analytical method that can be used in stock assessment studies to determine the regions where three mackerel species are mixed and the mixing ratios of the stocks. In conclusion, the development of genetic markers for the reliable identification of fish species and the detection of potential hybridization states is increasingly important for legal regulations established within the scope of sustainable fisheries management in our country. This study will serve as a reference not only for Trachurus species but also for other species with similar problems.