Development of SNP markers associated with defense mechanism of sea cucumber, Apostichopus japonicas
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TECHNICAL NOTE
Development of SNP markers associated with defense mechanism of sea cucumber, Apostichopus japonicas Lin-lin Gao • Meng Chen • Ya-Qing Chang Nan-Jing Ji • Cheng-Ze Li
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Received: 31 December 2012 / Accepted: 3 January 2013 / Published online: 16 January 2013 Ó Springer Science+Business Media Dordrecht 2013
Abstract Tewenty six Single nucleotide polymorphism (SNPs) markers were developed of sea cucumber (Apostichopus japonicas) by the high resolution melting assays. All loci were involved in defense mechanism. The results of genotyping revealed that all loci had two alleles and the minor allele frequency ranged from 0.038 to 0.500. The observed and expected heterozygosity ranged from 0.054–0.792 to 0.064–0.547, respectively. Two loci significantly depart from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was detected. As far as we know, this is the first report about defense mechanism of sea cucumber at molecular level. These SNP markers should be useful for the construction of genetic linkage map and comparative genome analysis in A. japonicus. Keywords Single nucleotide polymorphism (SNPs) Defense mechanism Apostichopus japonicus High resolution melting (HRM)
The sea cucumber (Apostichopus japonicus) is a common benthic detritus feeder of coastal sea habitats of East Asia, including Japan, China, Korea, and Far Eastern Russia (Chang et al. 2009). Due to its high nutritional and medicinal properties, sea cucumber has long been exploited as an economically important aquaculture species in China. However, the number of wild sea cucumber has severely declined because of over-exploitation and environment deterioration (Peng et al. 2009). Thus, it is necessary to implement research on sea cucumber genetics to L. Gao M. Chen Y.-Q. Chang (&) N.-J. Ji C.-Z. Li Key laboratory of Mariculture, DaLian Ocean University, DaLian 116023, Liaoning, China e-mail: [email protected]
protect sea cucumber resource. Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variations in eukaryotic genomes (Cho et al. 1999), which makes it to be a research hotspot currently. Compared with anonymous genomic markers, SNPs developed from the functional genes potentially held responsible for economically important traits, such as growth, reproduction and have greater transferability between species. Due to its advantages, SNPs have been characterized and used in several aquaculture species, such as Atlantic salmon (Hayes et al. 2007), oyster (Wang et al. 2011) and Zhikong scallop (Jiang et al. 2011). However, the number of SNP markers reported in A. japonicus is limited (Sun et al. 2010; Kang et al. 2011; Yang et al. 2012; Du et al. 2012). In this study, we choose defense mechanism functionassociated unigene sequences which was sequenced and annotated by our laboratory (explanation below) to develop SNPs markers in A. japonicus. Recently, sea cucumber’s defense mechanism research at cell level has been reported (Eliseikina and Magarlamov 2002; Jans et al. 1996), bu
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