IHB OpenIR  > 鱼类生物学及渔业生物技术研究中心  > 期刊论文
Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)
Zhu, Chuankun1,2; Cheng, Lei1; Tong, Jingou1; Yu, Xiaomu1; Tong, JG (reprint author), Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China.
2012-06-01
Source PublicationINTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN1422-0067
Volume13Issue:6Pages:7343-7353
AbstractThe 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.; 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.
SubtypeArticle
KeywordCommon Carp (Cyprinus Carpio) Expressed Sequence Tag (Est) Single Nucleotide Polymorphism (Snp) Validation Genetic Variations
Department[Zhu, Chuankun; Cheng, Lei; Tong, Jingou; Yu, Xiaomu] Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China; [Zhu, Chuankun] Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
DOI10.3390/ijms13067343
WOS HeadingsScience & Technology ; Physical Sciences
Funding OrganizationMOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20] ; MOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20] ; MOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20] ; MOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20]
Indexed BySCI
Language英语
WOS Research AreaChemistry
WOS SubjectChemistry, Multidisciplinary
WOS IDWOS:000306188700050
WOS KeywordATLANTIC SALMON ; SNPS ; L. ; MICROSATELLITES ; EVOLUTION ; GENETICS ; GENOME ; DNA
Funding OrganizationMOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20] ; MOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20] ; MOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20] ; MOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20]
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/16915
Collection鱼类生物学及渔业生物技术研究中心_期刊论文
Corresponding AuthorTong, JG (reprint author), Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China.
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China
2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
Recommended Citation
GB/T 7714
Zhu, Chuankun,Cheng, Lei,Tong, Jingou,et al. Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2012,13(6):7343-7353.
APA Zhu, Chuankun,Cheng, Lei,Tong, Jingou,Yu, Xiaomu,&Tong, JG .(2012).Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio).INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,13(6),7343-7353.
MLA Zhu, Chuankun,et al."Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 13.6(2012):7343-7353.
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