Development of 101 gene-based single nucleotide polymorphism markers in sea cucumber, Apostichopus japonicus

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 aqua...

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Bibliographic Details
Published in:International journal of molecular sciences 2012-06, Vol.13 (6), p.7080-7097
Main Authors: Du, Huixia, Bao, Zhenmin, Yan, Jingjing, Tian, Meilin, Mu, Xiaoyu, Wang, Shi, Lu, Wei
Format: Article
Language:English
Subjects:
Algorithms
Animals
Apostichopus japonicus
Aquaculture
Gene Frequency
Genetic Markers
Genotype
Heterozygote
Holothurioidea
Linkage Disequilibrium
Marine
Microsatellite Repeats
Polymorphism
Polymorphism, Single Nucleotide
Quantitative Trait Loci
Sea Cucumbers - genetics
Short Note
Transcriptome
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Summary: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.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms13067080