Thirty novel microsatellite markers for the coastal pelagic fish, Scomber japonicus (Scombridae)

Abstract

Scomber japonicus (Scombridae: Scomber) is a wide-spread pelagic fish in the warm and temperate transition coastal areas and adjacent seas of Atlantic, Pacific and northwest Indian oceans (Collette and Nauen 1983). Although there are few studies on development of microsatellite markers that provide useful tool to evaluate population genetic diversity and structure of S. japonicus, the number of primer sets was relatively small and more microsatellite markers are needed for performing the comprehensive studies such as evolutionary biology and reproductive ecology, as S. japonicus is the most widely distributed and morphologically divergent among its populations in coastal regions and adjacent seas. In this study, we isolated and characterized 30 new microsatellite primer sets in S. japonicus using the combined biotin capture method. These loci included dinucleotide, trinucleotide and teranucleotide repeat motifs. All markers showed polymorphism when assessed in 60 individuals from two distant populations (Taizhou and Sanya) in the East China Sea and South China Sea, respectively. The numbers of alleles per locus for a single population ranged from 1 to 25, and the polymorphism information content (PIC) is from 0 to 0.946. The observed and expected heterozygosities (HO and HE) ranged from 0 to 0.933 and from 0 to 0.964, respectively. After the sequential Bonferroni correction, five out of 30 loci from Taizhou population and 12 loci from Sanya population (minimum adjusted alpha = 0.00167) showed significant deviation from Hardy– Weinberg equilibrium (HWE), while no significant linkage disequilibrium was detected for any pairs of loci. Results