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引用本文:周小龙,朱靖华,董迎辉,林志华,富凯立,姚韩韩,齐晓艳.泥蚶(Tegillarca granosa)基因组SSR和EST-SSR的开发及比较研究.海洋与湖沼,2013,44(2):467-475.
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泥蚶(Tegillarca granosa)基因组SSR和EST-SSR的开发及比较研究
周小龙1,2, 朱靖华2, 董迎辉2, 林志华2, 富凯立2, 姚韩韩2, 齐晓艳3
1.上海海洋大学水产与生命学院;2.浙江万里学院 浙江省水产种质资源高效利用技术研究重点实验室;3.宁波大学海洋学院
摘要:
采用SSRHunter软件在泥蚶(Tegillarca granosa)磁珠富集文库和454转录组文库中搜索核心序列长度12bp以上的2—6核苷酸重复序列, 根据富集文库所得基因组SSR侧翼序列设计47对引物, 可成功扩增17对且均为多态性引物, 多态率100%, 平均等位基因数(Na)、观测杂合度(Ho)、期望杂合度(He)、多态性信息含量(PIC)分别为6.8、0.468、0.785、0.733。11344条EST序列中得到1683个SSR位点, 检出率14.83%, 平均每3.85kb出现1个位点。根据部分EST序列设计120对引物, 62对可扩增出目的片段, 其中29个位点具有多态性, 多态率为46.77%, 平均NaHoHe、PIC分别为4.2、0.372、0.554、0.500, 均低于基因组SSR。双变量相关性分析的结果表明, 46个多态性SSR位点的核心序列长度与其NaHoHe、PIC极显著正相关, Spearman相关系数分别为0.632、0.387、0.657、0.664。
关键词:  泥蚶  基因组SSR  EST-SSR
DOI:10.11693/hyhz201302032032
分类号:
基金项目:国家“863”计划项目, 2012AA10A410号; 国家现代贝类产业技术体系项目, CARS-48号; 宁波市科技创新团队项目, 2011B82017号; 宁波市科技局农业择优委托项目, 2010C10011号
附件
DEVELOPMENT AND COMPARATIVE STUDY OF GENOMIC-SSR AND EST-SSR IN TEGILLARCA GRANOSA
ZHOU Xiao-Long1,2, ZHU Jing-Hua2, DONG Ying-Hui2, LIN Zhi-Hua2, FU Kai-Li2, YAO Han-Han2, QI Xiao-Yan3
1.College of Fisheries and Life Science, Shanghai Ocean University;2.Zhejiang Key Laboratory of Aquatic Germplasm Resources, Zhejiang Wanli University;3.College of Marine Sciences, Ningbo University
Abstract:
47 pairs of primer were designed according to flanking sequence from magnetic bead enrichment library, 17 of them show amplification while 17 (100%) were polymorphic, the average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphism information content (PIC) were 6.8, 0.468, 0.785, 0.733. 1683 SSRs were detected by screening 11344 ESTs, the average density of SSRs was 1 per 3.86kb of EST. Of 120 pairs of primer designed, 62 pairs amplified expected fragment steadily while 29 (46.77%) were polymorphic after tested in 30 individuals of Tegillarca granosa. The average Na, Ho, He, PIC were 4.2, 0.372, 0.554, 0.500. The result of bivariate correlation analysis processed by SPSS showed: there were highly significant positive correlation between the length of SSR core sequence and Na, Ho, He, PIC at the 0.01 level, Spearman correlation coefficient were 0.632, 0.387, 0.657, 0.664, respectively.
Key words:  Tegillarca granosa  genomic-SSR  EST-SSR
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