Development and characterization of 68 SNP markers in red sea bream, Pagrus major

Abstract

Red sea bream is a commercially valuable fish that is used as ingredients in the food industry. To prevent a decrease in fishing yield, farmed red sea bream is released. However, this may cause a decrease in the genetic diversity of wild populations, so systematic resource management is required. In this study, 68 single nucleotide polymorphism (SNP) markers were developed using a genotyping-by-sequencing (GBS) analysis. The minor allele frequency (MAF) ranged from 0.1802 to 0.5000, the observed heterozygosity (H_o) ranged from 0.0864 to 0.5000, expected heterozygosity (H_e) ranged from 0.2955 to 0.5000, and the polymorphism information content (PIC) ranged from 0.2518 to 0.3750. Of these SNPs, 25 loci significantly deviated from the Hardy–Weinberg equilibrium after a Bonferroni correction (p < 0.00074). These SNP markers will be useful for the further genetic analysis of the red sea bream population.