Identification of forty-five gene-derived polymorphic microsatellite loci for the sea cucumber, Apostichopus japonicus

Abstract

Sea cucumber (Apostichopus japonicus) is a common benthic detritus feeder of coastal sea habitats of East Asia, including Japan, China, Korea and fareastern Russia (Chang et al. 2009). Because of its high nutritive value and use in traditional medicine, sea cucumber is considered as one of the most valuable species in aquaculture markets in China. However, the number of wild sea cucumbers has severely declined owing to overexploitation and environment deterioration (Peng et al. 2009). To increase production of sea cucumber, artificial breeding techniques were established in China in the 1980s and sea cucumber aquaculture has been developing rapidly in recent years (Qiao and Cheng 2005). Because sea cucumber is an important aquaculture species in China, application of marker-assisted selection (MAS) or genomewide marker-assisted selection (G-MAS) in the A. japonicus breeding programme is expected to be a fertile research area. To apply MAS and G-MAS, a saturated linkage map should be constructed first, using large numbers of molecular markers. Unfortunately, progress in genetic and genomic research in sea cucumber has relatively slower than in other economically important marine species (Cecilia et al. 2010; Guo et al. 2011; Wang et al. 2011; Zhang et al. 2011). There is only one preliminary genetic map based on 37 amplified fragment length polymorphism (AFLP) primer combinations and 20 microsatellite (simple sequences repeat; SSR) markers from 88 individuals (Li et al. 2009). While this framework linkage map is useful, the marker density is still low. Mapping additional markers, especially appropriate codominant markers, is particularly important. Some microsatellite markers (Kanno et al. 2005; Zhan et al. 2007; Peng et al. 2009; Liao et al. 2011) and single-nucleotide polymorphism (SNPs) (Sun et al. 2010; Yang et al. 2012) have been developed for sea cucumber. However, the number