A genetic linkage map of the sea cucumber (Apostichopus japonicus) based on microsatellites and SNPs

The sea cucumber (Apostichopus japonicus) belongs to the phylum Echinodermata, which includes approximately 7000 living species. It is one of the most important aquacultural species in China. A linkage map is an essential framework for mapping traits of interest and a basic tool needed in many fields of genetic studies. In this study, we constructed a consensus genetic map of Apostichopus japonicus exclusively based on microsatellites and SNP markers using two F1 families. The consensus male linkage map comprised 157 loci and spanned 1244.9 cM, while the female map comprised 153 loci and spanned 1399.1 cM. 22 linkage groups were identified both in the male and female consensus maps which agreed with the haploid chromosome number of A. japonicus. The sex-averaged map contained 215 loci, and spanned 1498.9 cM with an average resolution of 7.0 cM. The estimated coverage for the consensus linkage map was 79.2%. Large differences in recombination rate existed in some linkage groups between the two families, which may be attributable to chromosomal rearrangements. This map will facilitate further sea cucumber genetic studies such as quantitative trait loci (QTL) mapping and comparative genomic analysis.