Development of gene-associated single nucleotide polymorphisms for Japanese anchovy Engraulis japonicus through cross-species amplification

Cross-species amplification is a fast and cost-effective approach for the discovery of genetic markers in non-model species that have a phylogenetically close species with developed markers. The present study employed this method to discover new single nucleotide polymorphism (SNP) markers in the Japanese anchovy Engraulis japonicus . We selected 482 mitochondrial and nuclear SNPs described in the European anchovy Engraulis encrasicolus ; primer and probe sets developed for this species were used for genotyping 35 individuals of E. japonicus . A total of 451 SNPs (93.6%) were successfully cross-amplified, of which 176 SNPs (36.5%) were polymorphic in E. japonicus . The mean expected heterozygosity was 0.102, and no marker deviated significantly from Hardy–Weinberg proportions. Two mitochondrial SNPs were identified as a set of species diagnosing markers since, compared to four other species from the genus Engraulis , they formed a haplotype only present in E. japonicus . The new SNP set presented here constitutes the first SNP-type marker developed for E. japonicus , which is suitable for a range of applications including traceability and population genetics studies.