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Development of novel EST-SSR markers in common carp by data mining from public EST sequences
Wang, Dan; Liao, Xiaolin; Cheng, Lei; Yu, Xiaomu; Tong, Jingou; Tong, JG, Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China
2007-10-03
Source PublicationAQUACULTURE
ISSN0044-8486
Volume271Issue:1-4Pages:558-574
AbstractExpressed 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.; 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.
SubtypeArticle
KeywordExpressed Sequence Tag (Est) Data Mining Est-ssrs Polymorphism Cross-species Amplification Cyprinus Carpio
DepartmentChinese 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
Subject AreaFisheries ; Marine & Freshwater Biology
DOI10.1016/j.aquaculture.2007.06.001
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Indexed BySCI
Language英语
WOS Research AreaFisheries ; Marine & Freshwater Biology
WOS SubjectFisheries ; Marine & Freshwater Biology
WOS IDWOS:000249874600060
WOS KeywordCATFISH ICTALURUS-PUNCTATUS ; GENETIC-LINKAGE MAP ; MICROSATELLITE MARKERS ; PENAEUS-MONODON ; TAGS ; REPEATS ; DNA ; L. ; DIVERSITY ; EVOLUTION
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/152342/8406
Collection期刊论文
Corresponding AuthorTong, JG, 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
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,&Tong, JG, Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China.(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.
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