Int. J. Mol. Sci. 2012, 13(6), 7343-7353; doi:10.3390/ijms13067343
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Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)

1 State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China 2 Graduate School of Chinese Academy of Sciences, Beijing 100039, China
* Author to whom correspondence should be addressed.
Received: 16 February 2012; in revised form: 17 May 2012 / Accepted: 22 May 2012 / Published: 14 June 2012
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Abstract: The common carp (Cyprinus carpio) is an important aquaculture fish worldwide but only limited single nucleotide polymorphism (SNP) markers are characterized from expressed sequence tags (ESTs) in this species. In this study, 1487 putative SNPs were bioinformatically mined from 14,066 online ESTs mainly from the European common carp, with the occurrence rate of about one SNP every 173 bp. One hundred and twenty-one of these SNPs were selected for validation using PCR fragment sequencing, and 48 out of 81 primers could amplify the expected fragments in the Chinese common carp genome. Only 26 (21.5%) putative SNPs were validated, however, 508 new SNPs and 68 indels were identified. The ratios of transitions to transversions were 1.77 for exon SNPs and 1.05 for intron SNPs. All the 23 SNPs selected for population tests were polymorphic, with the observed heterozygosity (Ho) ranging from 0.053 to 0.526 (mean 0.262), polymorphism information content (PIC) from 0.095 to 0.357 (mean 0.246), and 21 SNPs were in Hardy–Weinberg equilibrium. These results suggest that different common carp populations with geographic isolation have significant genetic variation at the SNP level, and these new EST-SNP markers are readily available for genetics and breeding studies in common carp.
Keywords: common carp (Cyprinus carpio); expressed sequence tag (EST); single nucleotide polymorphism (SNP); validation; genetic variations

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MDPI and ACS Style

Zhu, C.; Cheng, L.; Tong, J.; Yu, X. Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio). Int. J. Mol. Sci. 2012, 13, 7343-7353.

AMA Style

Zhu C, Cheng L, Tong J, Yu X. Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio). International Journal of Molecular Sciences. 2012; 13(6):7343-7353.

Chicago/Turabian Style

Zhu, Chuankun; Cheng, Lei; Tong, Jingou; Yu, Xiaomu. 2012. "Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)." Int. J. Mol. Sci. 13, no. 6: 7343-7353.

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