Isolation and characterization of 30 SNP markers in Guangdong bream (Megalobrama terminalis) by next-generation sequencing

Abstract

Guangdong bream (Megalobrama terminalis) is an economically important species. However, wild Guangdong bream resources have declined sharply in recent years as a result of human disturbance and habitat destruction. Thus, it is crucial that the current resources of Guangdong bream are protected. In this study, 30 novel single nucleotide polymorphism (SNP) markers were developed based on restriction site-associated DNA sequencing (RAD-seq). The results showed that the minor allele frequency varied from 0.021 to 0.489 and that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.043 to 0.638 and 0.042 to 0.506, respectively. The PIC ranged from 0.041 to 0.375. Seven loci showed significant deviations from the HWE after Bonferroni correction (p < 0.05), but no significant linkage disequilibrium was found. These SNP markers will serve as a useful tool for genetic studies and population evaluation aimed at the conservation of Guangdong bream.