Development Of SSR Markers And SNPs Markers Associated With Defense Mechanism Based On Transcriptome Sequencing Of Apostichopus Japonicus

Sea cucumber (Apostichopus japonicus) belongs to the Holothurioider of Echinodermata,mainly distributed in the northern coast of China, Japan, Korea, and Far Eastern Russia. Due toits high nutritional and medicinal properties, sea cucumber has long been exploited as aneconomically important aquaculture species in China. However, the number of wild seacucumber has severely declined because of over-exploitation and environment deterioration.Thus, it is necessary to implement research on sea cucumber genetics to protect sea cucumberresource. It’s useful to keep the good trait and improve economic returns.（1）From more than12000unigene sequences were obtained from a transcriptome ofApostichopus japonicus using the Illumina HiSeq2000Sequencing Technology, total355microsatellite loci were identified,110primer pairs synthesized and45amplified expectedproducts and showed polymorphism using50field specimens tested. The number of allelesranged from2to20with an average of5.53alleles per locus, and the observed and expectedheterozygosities varied from0.1333to0.8668and from0.1266to0.9463with an average of0.4486and0.6579, respectively. No significant linkage disequilibrium (LD) between pairs ofloci was found and17loci significantly deviated from the Hardy-Weinberg equilibrium (HWE).（2）In this study,34Single nucleotide polymorphism (SNPs) sites related to defensemechanism of the sea cucumber were found by the high resolution melting (HRM) assays.Among them, the percentage of transition is70.56%while the transversion is23.53%, thenumber of A/G(C/T), A/C(G/T), A/T and C/G mutation type is20,4,1and7, accounting for58.82%,11.76%,2.94%and20.59%of the total, respectively;1site is tri-base deletion and onesite is fuzzy base substitution type. In these34SNP sites,26sites could be used to geneotypingby small amplicon method. The results of genotyping revealed that11sites were genopypeed tothree genetypes while the other15sites were were genopypeed to two genetypes; all loci hadtwo alleles and the minor allele frequency ranged from0.038to0.500; The observed andexpected heterozygosity ranged from0.054to0.792and0.064to0.547, respectively; Two locisignificantly depart from Hardy Weinberg equilibrium and no significant linkage disequilibrium(LD) was detected.These SSR markers and SNP markers should be useful for the construction of geneticlinkage map and comparative genome analysis in A. japonicus.