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学科主题: Fisheries; Marine & Freshwater Biology
题名: Development of novel EST-SSR markers in common carp by data mining from public EST sequences
作者: Wang, Dan; Liao, Xiaolin; Cheng, Lei; Yu, Xiaomu; Tong, Jingou
通讯作者: Tong, JG, Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China
关键词: expressed sequence tag (EST) ; data mining ; EST-SSRs ; polymorphism ; cross-species amplification ; Cyprinus carpio
刊名: AQUACULTURE
发表日期: 2007-10-03
DOI: 10.1016/j.aquaculture.2007.06.001
卷: 271, 期:1-4, 页:558-574
收录类别: SCI
文章类型: Article
部门归属: Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China; Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
类目[WOS]: Fisheries ; Marine & Freshwater Biology
研究领域[WOS]: Fisheries ; Marine & Freshwater Biology
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.
关键词[WOS]: CATFISH ICTALURUS-PUNCTATUS ; GENETIC-LINKAGE MAP ; MICROSATELLITE MARKERS ; PENAEUS-MONODON ; TAGS ; REPEATS ; DNA ; L. ; DIVERSITY ; EVOLUTION
语种: 英语
WOS记录号: WOS:000249874600060
ISSN号: 0044-8486
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/152342/8406
Appears in Collections:中科院水生所知识产出(2009年前)_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:
Wang, Dan; Liao, Xiaolin; Cheng, Lei; Yu, Xiaomu; Tong, Jingou.Development of novel EST-SSR markers in common carp by data mining from public EST sequences,AQUACULTURE,2007,271(1-4):558-574
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