Population structure of large yellow croaker (Larimichthys crocea) revealed by single nucleotide polymorphisms

• Population structure of large yellow croaker (Larimichthys crocea) revealed by single nucleotide polymorphisms is innovative.
• The genotyping determined by Sequenom MassARRAY in large yellow croaker are effective.
• There are some distinctive SNP markers for identificating the large yellow croaker populations.

The large yellow croaker, Larimichthys crocea, is one of the most commercially important marine species native to China Seas. In this study, Sequenom MassARRAY was used to analyze 120 individuals from three geographic populations in the East and South China Seas and a cultured stock. Forty-four of 60 single nucleotide polymorphism (SNP) loci were ascertained. Eleven loci, scf117, scf708, scf247, scf595, scf100, scf166, scf305, scf664, scf117, scf187 and scf511 each showed population-specific genotypes. A total of 127 alleles were detected. Averagely, the effective number of alleles was between 1.328 and 1.341, expected heterozygosity and observed heterozygosity ranged from 0.273 to 0.320, and 0.190 to 0.235, respectively, Pic value ranged from 0.215 to 0.247, and FIS ranged from 0.174 to 0.279. The neighbor-joining tree based on calculated genetic distances showed a concordant topology with the traditional morphological characterization. When the population size of wild large yellow croaker drastically has shrunk over the past 20 years, the genetic diversity in both wild and farmed stocks has declined as well.