Li Jun-Ren, Chen Xiu-Zhen, Tang Xiao-Ting, He Rui, Zhan Ruo-Ting
Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou 510006, China.
Zhongguo Zhong Yao Za Zhi. 2018 Jun;43(12):2503-2508. doi: 10.19540/j.cnki.cjcmm.20180329.012.
To study the SSR loci information and develop molecular markers, a total of 43 683 Unigenes in transcriptome of Andrographis paniculata were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MicroSAtellite software, SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 14 135 SSR loci were found in the transcriptome of A. paniculata, which distributed in 9 973 Unigenes with a distribution frequency of 32.36%. Di-nucleotide and Tri-nucleotide repeat were the main types, accounted for 75.54% of all SSRs. The repeat motifs of AT/AT and CCG/CGG were the predominant repeat types of Di-nucleotide and Tri-nucleotide, respectively. A total of 4 740 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. Ten pairs of primers in 20 pairs of randomly picked primers produced fragments with expected molecular size. The gene function of Unigenes containing SSR were mostly related to the basic metabolism function of A. paniculata. The SSR markers in transcriptome of A. paniculata show rich type, strong specificity and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding.
为研究穿心莲转录组中简单序列重复（SSR）位点信息并开发分子标记，利用穿心莲转录组中的43683条单基因序列来探索SSR。使用MicroSAtellite软件分析SSR的分布频率和重复基序的基本特征，通过Primer 3.0软件设计SSR引物，然后通过聚合酶链式反应（PCR）进行验证。此外，通过Blast获得含SSR单基因的基因功能分析结果。结果表明，在穿心莲转录组中发现14135个SSR位点，分布于9973条单基因序列中，分布频率为32.36%。二核苷酸和三核苷酸重复是主要类型，占所有SSR的75.54%。AT/AT和CCG/CGG重复基序分别是二核苷酸和三核苷酸的主要重复类型。共设计了4740对具有产生多态性潜力的SSR引物用于标记开发。随机挑选的20对引物中有10对引物产生了预期大小的片段。含SSR单基因的基因功能大多与穿心莲的基本代谢功能相关。穿心莲转录组中的SSR标记类型丰富、特异性强且具有较高的多态性潜力，这将有助于候选基因挖掘和标记辅助育种。
