Development of genome-wide SNPs for population genetics of Collichthys lucidus

The assessment of genetic diversity and genetic structure is critical for fisheries management and conservation. Traditional markers may fail to reveal precise population genetic pattern in marine species. Nevertheless, the solution of this shortcoming could be solved by advanced high-throughput sequencing which allows genotyping thousands of markers on genome-wide scale. In this study, we generated single nucleotide polymorphism (SNP) dataset using restriction site-associated DNA sequencing for Collichthys lucidus of 55 individuals from three locations in the Chinese coastal waters. After applying careful filtering criteria, we obtained 169 624 genome-wide SNPs that performed well for population genetics and population assignment. Based on the SNPs, evident genetic differentiation was observed among C. lucidus populations. The SNPs identified in our study could be used as powerful tools in further genetic and evolutionary studies of C. lucidus.