目的 采用生物信息学方法分析党参转录组文库EST序列简单重复序列（SSR）位点，快速、大规模鉴定党参功能性SSR。方法 使用MicroSAtellite（MISA）软件分析党参高通量转录组SSR的分布频率和重复基元的类型特征，利用软件Primer3设计引物，并通过SSRFinder校验SSR，筛选SSR引物。结果 从45 511条Unigenes中共搜到7 327个SSR位点，分布在6 017条Unigenes序列中，发生频率为12.22%，共有415种重复基元，平均每4 520 bp含1个SSR位点，二核苷酸重复占主要地位，发生频率为58.67%，在所有重复基元中，AG/CT出现频率最高。共获得4 329条SSR引物。结论 大规模的SSR分子标记开发将有助于党参遗传多样性与分子育种研究。

Objective To rapidly and largely identify the functional simple sequence repeat (SSR) in transcriptome dataset of Codonopsis pilosula based on bioinformatics analysis. Methods MicroSAtellite (MISA) sofeware was used to analyze the distributing frequency of high-flux transcriptome SSR and the basic characteristics of repeat motifs. Primers were designed using Primer3, and SSRFinder was used to check SSR and screen the SSR primers. Results SSR loci (7 327) were obtained from 45 511 unigenes, distributed in 6 017 unigenes (12.22%). There are 415 kinds of repeat motifs existing in C.pilosula transcriptome. On average, SSRs occurred every 4 520 bp in length. Dinucleotid repeats predominated with an occurrence frequency of 58.67%, and AG/CT was the most frequent one among all the repeat types. A total of 4 329 primer pairs were designed for marker development. Conclusion The large number of SSR genetic markers developed in the present study should contribute greatly to research into genetic diversity and germplasm characterization in C. pilosula.

国家自然科学基金资助项目（81072987）；国家“十二五”科技支撑计划（2011BAI07B07）