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

Abstract

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.