Reveal the Population Genetic Characteristics of Bombay Duck (Harpadon nehereus) in Coastal Waters of China with Genotyping-by-Sequencing Technique

Bombay duck (Harpadon nehereus) is an economically important species in the estuarine and coastal offshore waters of the Indo-West Pacific. This study aims to reveal the genome-wide genetic characteristics of five populations of H. nehereus from the coastal areas of China by using the genotyping-by-sequencing technique. After strict filtering, 32088 high-quality single-nucleotide polymorphism markers were detected and analyzed. The average observed heterozygosity and expected heterozygosity ranged from 0.41651 to 0.56725 and from 0.30998 to 0.45531, respectively, indicating that heterozygosity excess occurred in H. nehereus populations. The nucleotide diversity ranged from 0.63664 to 0.74868, which was larger than those from other marine fishes. No obvious genetic structure was detected among H. nehereus populations, and the genetic variation originated within individuals. Extensive gene exchange caused by longshore currents in the reproductive season might be the primary reason for the weak genetic differentiation. Among various environmental factors, water temperature might be the key element affecting the genetic structure of H. nehereus. Due to the destruction and overfishing of spawning grounds, the fishery resources declined in recent years. This study could serve as a reference for the resource protection and rational utilization of H. nehereus.