Development of Gene‐derived SNP Markers and Their Application for the Assessment of Genetic Diversity in Wild and Cultured Populations in Sea Cucumber, Apostichopus japonicus

Abstract The Apostichopus japonicus is a valuable aquaculture species in China. In this study, 51 single nucleotide polymorphisms (SNPs) were identified from expressed sequence tags of sea cucumber using high‐resolution melting. The average observed heterozygosity (Ho) and expected heterozygosity (He) were 0.2462 and 0.2897, respectively. Thirty‐two of these loci were used for estimating the genetic similarity and variation between the five hatchery stocks from China and two wild stocks from Japan. No significant differences in Ho or He were observed between the wild and hatchery populations. The pairwise Fst (which ranged from 0.0119 to 0.0236) and the genetic identity (which varied from 0.9802 to 0.9915) showed no significant differentiation between the wild and cultured stocks. The analysis of molecular variance indicated the source of variation was at the level of “within the populations.” The information on the genetic variation and differentiation in cultured and wild populations of A. japonicus obtained in this study is useful for setting up suitable guidelines for founding and maintaining of cultured stocks and for future genetic improvement by selective breeding.