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Development of 101 Gene-based Single Nucleotide Polymorphism Markers in Sea Cucumber, Apostichopus japonicus
Key Laboratory of Marine Genetics and Breeding, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
* Author to whom correspondence should be addressed.
Received: 25 April 2012; in revised form: 25 May 2012 / Accepted: 25 May 2012 / Published: 8 June 2012
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.
Keywords: single nucleotide polymorphism (SNP); Apostichopus japonicus; high resolution melting (HRM) analysis; marker-assisted selection (MAS)
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Du, H.; Bao, Z.; Yan, J.; Tian, M.; Mu, X.; Wang, S.; Lu, W. Development of 101 Gene-based Single Nucleotide Polymorphism Markers in Sea Cucumber, Apostichopus japonicus. Int. J. Mol. Sci. 2012, 13, 7080-7097.
Du H, Bao Z, Yan J, Tian M, Mu X, Wang S, Lu W. Development of 101 Gene-based Single Nucleotide Polymorphism Markers in Sea Cucumber, Apostichopus japonicus. International Journal of Molecular Sciences. 2012; 13(6):7080-7097.
Du, Huixia; Bao, Zhenmin; Yan, Jingjing; Tian, Meilin; Mu, Xiaoyu; Wang, Shi; Lu, Wei. 2012. "Development of 101 Gene-based Single Nucleotide Polymorphism Markers in Sea Cucumber, Apostichopus japonicus." Int. J. Mol. Sci. 13, no. 6: 7080-7097.