SREL Reprint #3537

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

Noel Sme1, Sarah Lyon1, Michael Canino2, Natalia Chernova3, Jason O’Bryhim4, Stacey Lance4,
Kenneth Jones5, Franz Mueter1, and Anthony Gharrett1

1Juneau Center, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks,
17101 Point Lena Loop Road, Juneau, Alaska 99801
2Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA,
7600 Sand Point Way NE, Seattle, Washington 98115
3Zoological Institute of the Russian, Academy of Sciences, Universitetskaja Naberezhnaya 1,
St. Petersburg, Russia 199034
4Savannah River Ecology Laboratory, University of Georgia, P.O. Drawer E,
Aiken, South Carolina 29802
5Section of Hematology-Oncology, Department of Pediatrics, University of Colorado School of Medicine,
12800 East 19th Ave, RC-1 North, Room 4129, Aurora, Colorado 80045

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.

Keywords: aquatic ecology; seasonal wetland; ephemeral wetland; rivers; streams; lakes; biota, fauna; habitat

SREL Reprint #3537

Sme, N., S. Lyon, M. Canino, N. Chernova, J. O'Bryhim, S. L. Lance, K. Jones, F. Mueter, and A. Gharrett. 2018. Distinction of saffron cod (Eleginus gracilis) from several other gadid species by using microsatellite markers. Fishery Bulletin 116(1): 60-68.

This information was provided by the University of Georgia's Savannah River Ecology Laboratory (srel.uga.edu).