灯盏花转录组中SSR位点信息分析及其多态性研究

SSR information in Erigeron breviscapus transcriptome and polymorphism analysis

目的:通过对灯盏花转录组中SSR位点信息的分析,设计SSR引物,为开发新的SSR标记奠定了基础。方法:利用MISA工具筛选灯盏花转录组测序获得的52 060条unigenes,对其SSR位点信息进行了分析;Primer3设计SSR引物,随机选取36对引物对13株采自不同地方的灯盏花进行多态性扩增分析。结果:灯盏花转录组搜索到3 639个SSR位点,分布于3 260条unigenes上,SSR位点出现频率是6.99%。其中,二核苷酸重复是主要的类型,占总SSR的34.41%,其次是单核苷酸和三核苷酸重复基元,分别占总SSR的31.41%,30.04%。二核苷酸重复基元中以AT/AT和AC/GT为优势重复基元,占总SSRs的28.71%,三核苷酸重复基元以AAT/ATT为主,占7.94%。随机选取36对引物进行PCR扩增,其中34对(94.44%)扩增出清晰、可重复的条带,19对(52.78%)表现出多态性差异。利用UPGMA作图,将13个材料分为2类。结论:灯盏花转录组中SSR位点出现频率高,类型丰富;大量的SSR为其遗传多样性分析和遗传图谱构建提供了丰富的候选分子标记。

Objective： The SSR information in the transcriptome of Erigeron breviscapus was analyzed in this study, in order to further develop new functional genes SSR markers laid a solid foundation. Method： SSR loci were searched in all of 52,060 unigenes by using est_timmer. Perl program and SSR primers were designed by Primer3. Furthermore, 36 pairs of primers were randomly selected for the polymorphism analysis on 13 Erigeron breviscapus plants collected from different places. Result： A total of 3639 SSRs were found in the transcriptome of Erigeron breviscapus, distributed in 3260 unigenes with the distribution frequency of 6.99%. Di-nucleotide repeat was the main type, account for as much as 34.41% of all SSRs, followed by mono-nucleotide （31.41%） and tri-nucleotide repeat motif （28.08%）. The di-nucleotide repeat motifs of AT/AT and AC/GT were the predominant repeat types （28.71%）. The tri-nucleotide repeat motifs of AAT/ATT was the predominant repeat types（7.94%）. For validation the availability of those SSR primers, we randomly selected 36 pairs of primers for PCR amplification. Among them, 34 pair primers （94.44%） produced clear and reproductive bands, 19 pair primers showed polymorphism （52.78%）, and 13 Erigeron breviscapus plants were divided into 2 groups. Conclusion： There are numerous SSRs in Erigeron breviscapus transcriptome with high frequency and various types, this will provide abundant candidate molecular markers for genetic diversity study and genetic map in this plant.