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

• Published in: Aquaculture 2013-08, Vol.404-405, p.1-7
• Main Authors: Yan, Jingjing, Jing, Jing, Mu, Xiaoyu, Du, Huixia, Tian, Meilin, Wang, Shi, Lu, Wei, Bao, Zhenmin
• Format: Article
• Language: English
• Subjects: Animal aquaculture; Animal productions; Apostichopus japonicus; Aquaculture; Aquatic plants; Biological and medical sciences; chromosome mapping; chromosome number; Chromosomes; Comparative analysis; Echinodermata; Fundamental and applied biological sciences. Psychology; General aspects; Genetic linkage map; Genetics; genomics; Holothurioidea; Invertebrates; linkage groups; loci; Microsatellite; microsatellite repeats; quantitative trait loci; single nucleotide polymorphism; SNP
• ISSN: 0044-8486; 1873-5622
• DOI: 10.1016/j.aquaculture.2013.04.011

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 1244.9cM, while the female map comprised 153 loci and spanned 1399.1cM. 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 1498.9cM with an average resolution of 7.0cM. 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. •The first genetic map for A. japonicus exclusively using co-dominant markers.•The sex-averaged map contained 22 linkage groups, which comprised 215 loci.•Sex difference in recombination rates was observed.