The large yellow croaker is an important marine economic fish species in China. In the mid to late 20th century, as overfishing led to the decline of large yellow croaker resources and the rise of the aquaculture industry, a large number of aquaculture-derived large yellow croakers entered the sea through artificial restocking or aquaculture escapees. Accurate differentiation of wild and aquaculture-derived individuals in the natural environment is crucial, whether for evaluating the benefits of artificial restocking or assessing the genetic diversity risks posed by the invasion of farmed populations to natural stocks. Therefore, developing a method that can accurately identify the genetic background of wild-caught large yellow croakers has become a critical issue needs to be addressed urgently.

Based on the significant differentiation in the genome sequences between aquaculture and wild populations of the large yellow croaker, we screened their genomes and found four SNP loci showing significant allele frequency differences between wild and farmed groups. By combining these SNP loci with the mitochondrial haplotype data of large yellow croaker, we successfully constructed a method that can accurately identify the origin of individuals captured in the wild. Furthermore, we developed a simple PCR-based genotyping step to identify SNP alleles, which further improves the identification efficiency of this method. Through validation against resequencing results, the accuracy of this method reaches over 99%. This method has strong operability and provides a new approach for distinguishing farmed and wild yellow croakers.
 

Larimichthys crocea, molecular marker, SNP, genetic identification