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题名: Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)
作者: Zhu, Chuankun1, 2; Cheng, Lei1; Tong, Jingou1; Yu, Xiaomu1
通讯作者: Tong, JG (reprint author), Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China.
关键词: common carp (Cyprinus carpio) ; expressed sequence tag (EST) ; single nucleotide polymorphism (SNP) ; validation ; genetic variations
刊名: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
发表日期: 2012-06-01
DOI: 10.3390/ijms13067343
卷: 13, 期:6, 页:7343-7353
收录类别: SCI
文章类型: Article
部门归属: [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
WOS标题词: Science & Technology ; Physical Sciences
资助者: MOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20]
类目[WOS]: Chemistry, Multidisciplinary
研究领域[WOS]: Chemistry
摘要: 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.
英文摘要: 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.
关键词[WOS]: ATLANTIC SALMON ; SNPS ; L. ; MICROSATELLITES ; EVOLUTION ; GENETICS ; GENOME ; DNA
语种: 英语
WOS记录号: WOS:000306188700050
ISSN号: 1422-0067
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/16915
Appears in Collections:鱼类生物学及渔业生物技术研究中心_期刊论文

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作者单位: 1.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:
Zhu, Chuankun; Cheng, Lei; Tong, Jingou; Yu, Xiaomu.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
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文件名: Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio).pdf
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