Development of novel EST-SSR markers in common carp by data mining from public EST sequences
文献类型：期刊论文
| 作者 | Wang, Dan; Liao, Xiaolin; Cheng, Lei; Yu, Xiaomu; Tong, Jingou |
| 刊名 | AQUACULTURE
 |
| 出版日期 | 2007-10-03 |
| 卷号 | 271期号:1-4页码:558-574 |
| 关键词 | expressed sequence tag (EST) data mining EST-SSRs polymorphism cross-species amplification Cyprinus carpio |
| ISSN号 | 0044-8486 |
| 通讯作者 | Tong, JG, Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China |
| 中文摘要 | Expressed sequence tags (ESTs) are a source for microsatellite development. In the present study, EST-derived microsatelltes (EST-SSRs) were generated and characterized in the common carp (Cyprinus carpio) by data mining from updated public EST databases and by subsequent testing for polymorphism. About 5.5% (555) of 10,088 ESTs contain repeat motifs of various types and lengths with CA being the most abundant dinucleotide one. Out of the 60 EST-SSRs for which PCR primers were designed, 25 loci showed polymorphism in a common carp population with the alleles per locus ranging from 3 to 17 (mean 7). The observed (H-O) and expected (HE) heterozygosities of these EST-SSRs were 0.13-1.00 and 0.12-0.91, respectively. Six EST-SSR loci significantly deviated from the Hardy-Weinberg equilibrium (HWE) expectation, and the remaining 19 loci were in HWE. Of the 60 primer sets, the rates of polymorphic EST-SSRs were 42% in common carp, 17% in crucian carp (Carassius auratus), and 5% in silver carp (Hypophthalmichthys molitrix), respectively. These new EST-SSR markers would provide sufficient polymorphism for population genetic studies and genome mapping of the common carp and its closely related fishes. (c) 2007 Published by Elsevier B.V. |
| 英文摘要 | Expressed sequence tags (ESTs) are a source for microsatellite development. In the present study, EST-derived microsatelltes (EST-SSRs) were generated and characterized in the common carp (Cyprinus carpio) by data mining from updated public EST databases and by subsequent testing for polymorphism. About 5.5% (555) of 10,088 ESTs contain repeat motifs of various types and lengths with CA being the most abundant dinucleotide one. Out of the 60 EST-SSRs for which PCR primers were designed, 25 loci showed polymorphism in a common carp population with the alleles per locus ranging from 3 to 17 (mean 7). The observed (H-O) and expected (HE) heterozygosities of these EST-SSRs were 0.13-1.00 and 0.12-0.91, respectively. Six EST-SSR loci significantly deviated from the Hardy-Weinberg equilibrium (HWE) expectation, and the remaining 19 loci were in HWE. Of the 60 primer sets, the rates of polymorphic EST-SSRs were 42% in common carp, 17% in crucian carp (Carassius auratus), and 5% in silver carp (Hypophthalmichthys molitrix), respectively. These new EST-SSR markers would provide sufficient polymorphism for population genetic studies and genome mapping of the common carp and its closely related fishes. (c) 2007 Published by Elsevier B.V. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 学科主题 | Fisheries; Marine & Freshwater Biology |
| 类目[WOS] | Fisheries ; Marine & Freshwater Biology |
| 研究领域[WOS] | Fisheries ; Marine & Freshwater Biology |
| 关键词[WOS] | CATFISH ICTALURUS-PUNCTATUS ; GENETIC-LINKAGE MAP ; MICROSATELLITE MARKERS ; PENAEUS-MONODON ; TAGS ; REPEATS ; DNA ; L. ; DIVERSITY ; EVOLUTION |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000249874600060 |
| 公开日期 | 2010-10-13 |
| 源URL | [http://ir.ihb.ac.cn/handle/152342/8406]  |
| 专题 | 水生生物研究所_中科院水生所知识产出（2009年前）_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 | Wang, Dan,Liao, Xiaolin,Cheng, Lei,et al. Development of novel EST-SSR markers in common carp by data mining from public EST sequences[J]. AQUACULTURE,2007,271(1-4):558-574. |
| APA | Wang, Dan,Liao, Xiaolin,Cheng, Lei,Yu, Xiaomu,&Tong, Jingou.(2007).Development of novel EST-SSR markers in common carp by data mining from public EST sequences.AQUACULTURE,271(1-4),558-574. |
| MLA | Wang, Dan,et al."Development of novel EST-SSR markers in common carp by data mining from public EST sequences".AQUACULTURE 271.1-4(2007):558-574. |
入库方式： OAI收割
来源：水生生物研究所
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