Background. Genetic traceability of seafood as well as population identification using molecular methods provide useful information about the fish origin and are important for protection of overfished populations, as well as for monitoring illegal, unreported, and unregulated (IUU) fisheries. The presently reported study focused on Indian mackerel, Rastrelliger kanagurta (Cuvier, 1816)—a pelagic species with a wide range of distribution—especially important for many tropical countries, such as India, Philippines, and Thailand. This paper is the first part of a larger project: ”Development of a genetic-based system for identification of food products from fisheries and aquaculture introduced to the European Union customs area”. Materials and Methods. Samples consisting of fin fragments of Indian mackerel were obtained from local markets in Thailand (MTH), Vietnam (SVN), Cambodia (SKH), and Madagascar (SMG) within 2012–2013. Two genes were analysed: nuclear rhodopsin gene (RH1) and mitochondrial D-loop (D-loop) region through RFLP analysis simulation and sequencing. Additionally, the samples from Cambodia and Madagascar were analysed with eight microsatellite loci (SSR). The data processing was aided by GenAlEx 6.5 and GeneClass2 software. Results. A comparison of the RH1 gene section revealed a total homology among the studied samples. A comparative analysis of D-loop sequences in the studied groups revealed intrapopulational diversity for MTH-, SKH-, SMG-, and SVN samples, at the level of 1, 1, 0.5, and 0.6 percentage points, respectively. Furthermore, the D-loop sequences identified a characteristic restriction site for SMG population. Based on the allele frequencies, we randomly assigned selected individuals to their original populations. GeneClass2 software correctly assigned only 16 out of 21 individuals to either the Cambodian or the Madagascar population, which jointly constituted 76% of all samples. We demonstrated, using AMOVA and GenAlEx 6.5, that the highest level of variability occurred among individuals within the respective populations, while the lowest interpopulation diversity was between the SMG and SKH populations. Conclusion. Our results may help the relevant authorities in the countries of the European Union to identify Indian mackerel and especially its products and trace them to the respective locality. Our findings may also be used for species-specific conservation measures hopefully undertaken by fisheries authorities of the countries where we took our samples. Results on other fish species, prepared in the frames of the same project, will be presented in other papers that will follow soon.
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