Wang Xueyong, Zhou Xiaoli, Gao Wei, Cui Guanghong, Huang Luqi, Liu Chunsheng
Beijing University of Chinese Medicine, Beijing 100102, China.
Zhongguo Zhong Yao Za Zhi. 2011 Feb;36(3):289-93.
To establish the new EST-SSR markers for analyzing the genetic variation of different population of Salvia miltiorrhiza.
It was dealt with ESTs newly downloaded from Genbank and that of acquired from HMPL lab EGassembler software, and then carried out SSR loci search and SSR type analysis by SSRIT software. After that, it was designed the EST-SSR primer pairs for PCR amplification condition optimization.
Abundant and high coverage of SSR loci distribution were found in S. miltiorrhiza with having one SSR per 5.8 kb ESTs. Among them, the occurrences of different repeat units were mainly the di- (63.0%) and tri- (35.5%). The CT/AG was the most frequent motif in dinucleotide motif type and the GAA/TCC was the most frequent motif in trinucleotide repeats. Out off 36 primer pairs, 29 primer pairs (80.5%) were successfully amplified in all samples of S. miltiorrhiza while the rest failed to give PCR products at various annealing temperature and Mg2+ concentrations. The selected primer pairs also showed the polymorphism in samples from different S. miltiorrhiza populations.
The newly establishment of EST-SSR markers showed high SSR loci coverage and genetic polymorphisms in S. miltiorrhiza population. It could be used for genetic variation analysis.
建立新的EST-SSR标记，用于分析不同丹参种群的遗传变异。
处理从Genbank新下载的ESTs以及从HMPL实验室获取的ESTs，使用EGassembler软件，然后通过SSRIT软件进行SSR位点搜索和SSR类型分析。之后，设计EST-SSR引物对并优化PCR扩增条件。
在丹参中发现了丰富且高覆盖率的SSR位点分布，每5.8 kb ESTs中有一个SSR。其中，不同重复单元的出现主要是二核苷酸（63.0%）和三核苷酸（35.5%）。CT/AG是二核苷酸基序类型中最常见的基序，GAA/TCC是三核苷酸重复中最常见的基序。在36对引物中，29对引物（80.5%）在所有丹参样品中成功扩增，其余引物在不同退火温度和Mg2+浓度下未能获得PCR产物。所选引物对在不同丹参种群的样品中也表现出多态性。
新建立的EST-SSR标记在丹参种群中显示出高SSR位点覆盖率和遗传多态性。可用于遗传变异分析。
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