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

Abstract

AbstractWe 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 FST 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