Genetic variation and population genetic structure of the large yellow croaker (Larimichthys crocea) based on genome-wide single nucleotide polymorphisms in farmed and wild populations

Populations of marine fishes are show relatively weak genetic differentiation due to the lack of geographical barriers and the potential for the strong diffusion ability favoring high levels of gene flow. The large yellow croaker (Larimichthys crocea) is a commercially important fish species with high gene flow, and its aquaculture production ranks first among all marine fishes cultured in China. To better understand the population structure of L. crocea, a total of 7161 quality-filtered SNP markers were identified in 120 individuals from five farmed and wild populations by using restriction site-associated DNA sequencing (RAD-seq). Our population genetic inferences suggest the existence of two genetic lineages of this croaker in the wild populations in the coastal waters of China. We suggested that an allopatric speciation mechanism is typically characterized by the formation of the Taiwan Strait between the South and East China Sea. The farmed and wild populations present in Ningde City exhibit similar genetic ancestry, which implies that the latter population may represent escaped farmed fish with a higher discharge frequency, rather than areal wild population.