Genetic Structure and Diversity of Japanese Chum Salmon Populations Inferred from Single-Nucleotide Polymorphism Markers

Abstract

We estimated the genetic structure and diversity of Japanese Chum Salmon Oncorhynchus keta populations using single-nucleotide polymorphism (SNP) markers to support the management and assessment of the Japanese salmon hatchery program. A total of 5,571 individuals from 57 Japanese Chum Salmon populations were genotyped with 52 markers. A neighbor-joining tree, principal coordinate analysis, analysis of molecular variance, and average pairwise F_ST values indicated the existence of eight regional groups, six in Hokkaido and two in Honshu. Weak but significant isolation by distance was found within the populations of Hokkaido and the Pacific Ocean coast of Honshu. These results suggest that the genetic differentiation among the eight regional groups is small but distinct and occurred through low or restricted gene flow. Furthermore, our results also suggest the persistence of the historical genetic structure (or remnants of it) in extant populations in Japan despite the operation of a hatchery program for about 120 years. The genetic framework of the Japanese Chum Salmon populations that we observed using SNP markers is basically similar to that found by previous studies using other molecular markers but the populations along the western Pacific Ocean coast of Hokkaido are separated into two regional groups.

Received September 19, 2013; accepted February 10, 2014

ACKNOWLEDGMENTS

We would like to thank the technical staffs of Hokkaido National Fisheries Research Institute, Tohoku National Fisheries Research Institute, and Japan Sea National Fisheries Research Institute, Fisheries Research Agency, for their help in sampling tissues of Chum Salmon. We are also grateful to two anonymous reviewers and one associate editor for valuable advice as well as to Christian T. Smith, Alaska Department of Fish and Game; Carita Pascal, University of Washington; and Yukiko Fujisaki, Hokkaido National Fisheries Research Institute, Fisheries Research Agency, for their help in DNA extraction, SNP genotyping, and data analysis. Itsuro Koizumi, Hokkaido University, kindly assisted in the DPR analysis. We are grateful to Fred Utter, University of Washington, for his editorial assistance. This study was primarily supported by a grant from the Fisheries Agency of Japan. L.W.S. and J.E.S. were supported by a grant from the Gordon and Betty Moore Foundation.