Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)
文献类型：期刊论文
| 作者 | Zhu, Chuankun1,2; Cheng, Lei1; Tong, Jingou1; Yu, Xiaomu1 |
| 刊名 | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
 |
| 出版日期 | 2012-06-01 |
| 卷号 | 13期号:6页码:7343-7353 |
| 关键词 | common carp (Cyprinus carpio) expressed sequence tag (EST) single nucleotide polymorphism (SNP) validation genetic variations |
| ISSN号 | 1422-0067 |
| 通讯作者 | Tong, JG (reprint author), Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China. |
| 中文摘要 | 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. |
| 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. |
| WOS标题词 | Science & Technology ; Physical Sciences |
| 类目[WOS] | Chemistry, Multidisciplinary |
| 研究领域[WOS] | Chemistry |
| 关键词[WOS] | ATLANTIC SALMON ; SNPS ; L. ; MICROSATELLITES ; EVOLUTION ; GENETICS ; GENOME ; DNA |
| 收录类别 | SCI |
| 资助信息 | MOST973 Program[2010CB126305]; MOA Special Programs[200903045, 2011-G12]; SKL-FEBL of China[2011FBZ20] |
| 语种 | 英语 |
| WOS记录号 | WOS:000306188700050 |
| 公开日期 | 2012-09-25 |
| 源URL | [http://ir.ihb.ac.cn/handle/342005/16915]  |
| 专题 | 水生生物研究所_鱼类生物学及渔业生物技术研究中心_期刊论文 |
| 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 |
| 推荐引用方式 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.(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. |
入库方式： OAI收割
来源：水生生物研究所
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