Distinction of saffron cod (Eleginus gracilis) from several other gadid species by using microsatellite markers

The views and opinions expressed or implied in this article are those of the author (or authors) and do not necessarily reflect the position of the National Marine Fisheries Service, NOAA. Abstract—Nine microsatellite loci isolated in saffron cod (Eleginus gracilis) have potential applications for population genetics. Polymerase chain reaction products of samples of E. gracilis from northwestern Alaska amplified reliably, produced only one or two microsatellite bands, and had no apparent homozygote excess. A collection of E. gracilis sampled in the Gulf of Alaska (GOA) near Kodiak Island did not amplify reliably at one locus, and allele frequency profiles clustered distinctly (with principal component analysis [PCA]) from the northwestern Alaska collection. Northwestern Alaska and GOA E. gracilis collections were genetically different (on the basis of a standardized genetic differentiation measure [G′ST]=0.313, chord distance [Dchord]=0.078, P<0.0001) and differed in expected average heterozygosities at shared loci (0.859 and 0.689, respectively). We tested the microsatellite primers on other gadid species endemic to the northern Pacific Ocean, Bering Sea, and Arctic Ocean for cross-species amplification. Not all loci amplified reliably in navaga (E. nawaga), Pacific tomcod (Microgadus proximus), Arctic cod (Boreogadus saida), Pacific cod (Gadus macrocephalus), or walleye pollock (G. chalcogrammus). Reliable loci varied in microsatellite size profiles and produced distinct PCA clusters and accurate genotype assignments that allowed accurate species identification. The identifications support previous morphological and genetically determined systematic classifications and distinguished the geographically separated collections of E. gracilis. The saffron cod (Eleginus gracilis) is a gadid fish distributed from the northern Gulf of Alaska (GOA), around the Pacific Rim into the Sea of Okhotsk, and into the Arctic Ocean abutting the North Pacific Ocean (Cohen et al., 1990; Mecklenburg et al., 2016). Mature fish, which generally exceed 20 cm in fork length (FL) and may grow to more than 50 cm FL, are eaten by indigenous Alaskans and in Asia and have potential for commercial harvest in North America (Cohen et al., 1990; NPFMC1; Love et al.2).