Abstract
Single nucleotide polymorphisms (SNPs) are currently the marker of choice in a variety of genetic studies. Using the high resolution melting (HRM) genotyping approach, 101 gene-based SNP markers were developed for Apostichopus japonicus, a sea cucumber species with economic significance for the aquaculture industry in East Asian countries. HRM analysis revealed that all the loci showed polymorphisms when evaluated using 40 A. japonicus individuals collected from a natural population. The minor allele frequency ranged from 0.035 to 0.489. The observed and expected heterozygosities ranged from 0.050 to 0.833 and 0.073 to 0.907, respectively. Thirteen loci were found to depart significantly from Hardy–Weinberg equilibrium (HWE) after Bonferroni corrections. Significant linkage disequilibrium (LD) was detected in one pair of markers. These SNP markers are expected to be useful for future quantitative trait loci (QTL) analysis, and to facilitate marker-assisted selection (MAS) in A. japonicus.
Highlights
The sea cucumber Apostichopus japonicus (Selenka 1867), naturally distributes along the coasts ofChina, Japan, Korea and Russia [1]
During the initial high resolution melting (HRM) screen, 63.5% (101) of the 159 successfully amplified loci showed polymorphisms in 48 individuals collected from 4 natural populations, 21.4%
We showed that minor allele frequency (MAF) can serve as an important selection criterion to distinguish true SNPs from sequencing errors when performing SNP mining from 454 sequencing data (Figure 1)
Summary
The sea cucumber Apostichopus japonicus (Selenka 1867), naturally distributes along the coasts of. The aquaculture of A. japonicus has become widespread along the coasts of China, due to increasing market demand and over-exploitation of wild sea cucumbers [2]. To perform MAS, a large number of genetic markers are usually needed to determine the quantitative trait loci (QTLs) associated with economically important traits. SNP validation was performed using 48 A. japonicus individuals collected from four natural populations. Genetic parameters of the validated SNP markers were evaluated using 40 A. japonicus individuals from a single natural population. These SNP markers will be useful for future QTL analysis in order to facilitate MAS in A. japonicus
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