目的 探究黄连Coptis chinensis转录组中简单重复序列（simple sequence repeat，SSR）位点信息，进而开发可用于黄连资源遗传多样性评价的SSR分子标记。方法 采用MISA软件对黄连叶片转录组获得的93 629条Unigene进行SSR位点数据挖掘，利用Primer 3.0软件进行引物设计，以64株不同形态的黄连作为分析样本，通过聚丙烯酰胺凝胶电泳筛选多态性引物。结果 黄连转录组中的12 848个SSR位点分布于10 016条Unigene序列中，SSR位点的出现频率为13.72%。单核苷酸和三核苷酸重复是SSR序列中最主要的重复类型，分别占SSR总数的53.81%和25.01%。SSR序列中共包含115种重复基元，优势重复基元为A/T、AG/CT、AAG/CTT。随机筛选的180对引物中，94对可扩增出清晰条带，其中的7对引物具有明显多态性，能够将64份黄连样本分成4个类群，其生物性状与遗传多样性聚类结果基本吻合。结论 黄连转录组中SSR位点出现频率较高，重复类型丰富，多态性较高，可为黄连资源研究提供候选分子标记。开发的7个SSR标记可用于黄连资源遗传多样性评价、种质鉴定、分子辅助育种等研究。

Objective To explore the simple sequence repeat (SSR) site information in the transcriptome of Coptis chinensis and develop the SSR molecular markers which can be used for the genetic diversity evaluation of C. chinensis resource. Methods MISA software was used to mine the SSR site data of 93 629 Unigenes obtained from the transcriptome of C. chinensis leaves. SSR primers were designed through Primer 3.0 software. A total of 64 samples of C. chinensis with different morphological features were used to select the polymorphic primers through polyacrylamide gel electrophoresis (PAGE). Results A total of 12 848 SSR loci in the transcriptome of C. chinensis were distributed in 10 016 Unigenes, with a SSR loci frequency of 13.72%. Mono-nucleotide and tri-nucleotide repeats were the main repeat types in SSR sequences, accounting for 53.81% and 25.01% of the total SSRs, respectively. The SSR sequence contained 115 repeat motifs, with dominant motifs being A/T, AG/CT, and AAG/CTT. Among the 180 pairs of primers randomly selected, 94 pairs could be used to amplify expected bands and seven pairs exhibited significant polymorphism. A total of 64 samples of C. chinensis could be divided into four groups, and their biological characteristics were basically consistent with the clustering results of genetic diversity. Conclusion The SSR loci in the transcriptome of C. chinensis are high in frequency, rich in repetition type, high in polymorphism, which can provide candidate molecular markers for the research on C. chinensis resources. The seven SSR molecular markers screened in this study can be used for genetic diversity evaluation, variety identification, molecular assisted breeding of C. chinensis.

R286.12

国家重点研发计划项目(2022YFD1201600)