Genome-wide population structure and genetic diversity of Japanese whiting (Sillago japonica) inferred from genotyping-by-sequencing (GBS): Implications for fisheries management

Abstract

Japanese whiting (Sillago japonica) is a relatively common marine fish inhabiting in the coastal shallow waters and the target species in an important commercial and recreational fishery. In this study, eighty-three specimens in five sites were collected along coasts of China and Japan, and genotyping-by-sequencing (GBS) technology was carried out to investigate the genetic structure and difference among them. Consistent with prior research conclusions, a relatively high genetic diversity was detected in S. japonica, and an increasing tendency of genetic variation level was detected as the latitude decreased in Chinese populations. Although estimated value of pairwise population differentiation (FST) was low, the genetic heterogeneity analysis demonstrated a certain amount of genetic differentiation among local populations of S. japonica. Samples from Rushan were differentiated from other Chinese populations, but closely correlate with Ise Bay (IB) and Tokoy Bay (TB) populations, indicating gene flow between Rushan population (RS) and Japanese populations to a certain extent. Isolation by distance (IBD) analysis showed that genetic differentiation was significantly affected by geographical isolation. While, the results of isolation by environment (IBE) test showed that genetic distance was correlated with seawater salinity, which might be a selective pressure promoting genetic variation in S. japonica. Given the complex pattern of genetic differentiation of Japanese whiting among Chinese and Japanese populations, we suggested treating them as different management units in utilization of offshore fisheries resources.