Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker

Larimichthys crocea (also known as the large yellow croaker) is one of the most economically important marine fishes in China, and research on the ecology and genetics of this species is of immense significance. In this study, we performed restriction site-associated DNA sequencing (RAD-seq) of 54 individuals collected from four sites in China to analyze the genetic structure and diversity of large yellow croaker at the genome level. It revealed that the large yellow croaker populations in the Ningde and Zhoushan coastal waters can be clearly distinguished. Different genetic diversity indices were used to analyze the genetic diversity of the large yellow croaker, which showed that there was a differentiation trend between the wild and farmed populations in Ningde. Moreover, we identified genetically differentiated genomic regions between the populations. GO gene enrichment analysis identified genes that are related to fatty acid metabolism and growth. These findings enhance our understanding of genetic differentiation and adaptation to different living environments, providing a theoretical basis for the preservation and restoration of the genetic resources of the large yellow croaker.

Automated summary

In this study, RAD-seq analysis was performed on 54 individuals of Larimichthys crocea to investigate its genetic structure and diversity at the genome level. The study revealed distinct genetic differentiation between the large yellow croaker populations in the Ningde and Zhoushan coastal waters. Different genetic diversity indices indicated a differentiation trend between wild and farmed populations in Ningde. Genetically differentiated genomic regions and genes related to fatty acid metabolism and growth were identified. These findings contribute to the understanding of genetic differentiation and adaptation in Larimichthys crocea, and provide a theoretical basis for the conservation and restoration of its genetic resources.