Development of EST-SSR markers derived from transcriptome of Saccharina japonica and their application in genetic diversity analysis
Development of EST-SSR markers derived from transcriptome of Saccharina japonica and their application in genetic diversity analysis
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糖精转录组EST-SSR标记的建立及其在遗传多样性分析中的应用
DOI：
10.1007/s10811-017-1354-5
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发表时间：
2018-06
影响因子：
3.3
通讯作者：
芮凤萍
中科院分区：
文献类型：
--
作者：
张静;刘涛;芮凤萍
利用转录组数据，开发了表达序列标签（EST）衍生的简单重复序列（SSR）标记，并对其进行了表征。利用微卫星搜索模块（MISA）对98，627个EST进行SSR筛选。在8039条ESTs中共检测到9688个SSR，其中三核苷酸SSR占57.69%，是主要的SSR类型。最终设计了1120对EST-SSR引物，其中146对引物可用于4个拟南芥DNA的多态性分析。本研究选择了52个代表性较好的EST-SSR标记对10个中国菌株进行遗传分析。共检测到139个等位基因，每个位点的等位基因数为2 ~ 5个。多态位点百分率（P）为28.85 ~ 73.08%，遗传多样性（H）为0.1207 ~ 0.3376，Shannon信息指数（I）为0.1819 ~ 0.5267。根据获得的EST-SSR数据，我们还进行了菌株的遗传一致性和聚类分析。遗传结构分析表明，10个菌株可分为3个类群，这与它们的亲本来源有关。这些EST-SSR标记的获得将有助于对该属植物的遗传分析和分子标记辅助育种。
Expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers were developed and characterized for Saccharina japonica using transcriptome data. A total of 98,627 ESTs were screened for SSRs using microsatellite search module (MISA) tool. From those, 9688 SSRs in 8039 ESTs were identified and trinucleotides accounted for 57.69% were the predominant types. Among these EST-SSRs, 1120 SSR primer pairs were ultimately designed and 146 could be used for genetic study by polymorphism tests using four Saccharina DNAs as templates. In the present study, 52 EST-SSR markers with good representativeness were selected to conduct genetic analyses of ten Chinese strains. A total of 139 alleles were detected and alleles per locus ranged from 2 to 5. The percentage of polymorphic loci (P) per strain ranged from 28.85 to 73.08%, Nei’s genetic diversity (H) ranged from 0.1207 to 0.3376 and Shannon’s information index (I) from 0.1819 to 0.5267. Genetic identity and cluster analysis of Saccharina strains were also performed based on the obtained EST-SSR data in our work. As shown by genetic structure analysis, ten strains could be classified into three groups which associated with their parental origin. These obtained EST-SSR markers will be helpful for genetic analysis and molecular marker assisted breeding in Saccharina.
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影响因子：
3.3
作者：
J. K. Pritchard;Matthew Stephens;Peter Donnelly
通讯作者：
J. K. Pritchard;Matthew Stephens;Peter Donnelly
使用 Illumina 测序对橡胶树 (Hevea brasiliensis Muell. Arg.) 中的树皮转录组进行从头组装和表征以及 EST-SSR 标记的开发
影响因子：
4.4
作者：
Li D;Deng Z;Qin B;Liu X;Men Z
通讯作者：
Men Z
影响因子：
3.3
作者：
Porse, Hans;Rudolph, Brian
通讯作者：
Rudolph, Brian
影响因子：
1
作者：
P. Gupta;H. Balyan;P. C. Sharma
通讯作者：
P. Gupta;H. Balyan;P. C. Sharma
DOI：
--
发表时间：
2005
期刊：
Acta Agronomica Sinica
影响因子：
--
作者：
C. Jun;R. Zheng
通讯作者：
C. Jun;R. Zheng