两种黄连转录组中SSR位点信息分析与多态性引物开发

SSR Loci Information Analysis and Polymorphism Primers Development in Two Kinds of Coptidis transcriptome

本研究通过对两种黄连,即黄连（Coptis chinensis Franch.）和云南黄连（C.teeta Wall.）转录组中SSR位点信息的分析,设计SSR引物,为开发新的SSR标记提供理论基础。利用MISA工具筛选黄连及云南黄连转录组测序获得的55 903和49 741条Unigenes,对其SSR位点信息进行了分析;Primer3设计SSR引物,随机选取60对引物对两种黄连,每种20株,共40株进行多态性扩增分析。黄连和云南黄连转录组分别搜索到4 071和4 041个SSR位点。两种黄连中二核苷酸和三核苷酸重复皆是主要的类型,分别占总SSR的87.71%和87.58%。黄连中,二核苷酸重复基元出现最多的为AG/CT,共953个,占总SSR的23.40%,三核苷酸重复基元出现最多的为AAG/CTT,共746个,占总SSR的18.3%;在云黄连中,AG/CT和AAG/CTT分别为934（23.10%）和773（19.10%）。随机选取60对引物进行PCR扩增,其中12对（20.00%）表现出多态性差异。利用Populations软件作图,将40个材料分为2类。两种黄连转录组中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。

In this study,through the analysis of the SSR loci information in the transcriptomes of two kinds of Coptis chinensis which were Coptis chinensis Franch.and C.teeta Wall.,the SSR primers were designed to lay the foundation for the development of new SSR markers.By using MISA,we screened sequencing of transcriptomes of Coptis chinensis Franch.and C.teeta Wall.to obtain 55 903 and 49 741 unigenes,and then analyzed their SSR loci information.SSR primers were designed by Primer 3.Furthermore,60 pairs of primers were randomly selected for the polymorphism analysis on a total of 40 Coptidis（20 of each kind of Coptidis） plants.4 071 and 4 041 SSRs were found in the Coptis chinensis Franch.and C.teeta Wall.,respectively.Di-nucleotide repeat and Trinucleotide repeat were the main types,which accounted for as much as 87.71% and 87.58% of the total SSRs in Coptis chinensis Franch.and C.teeta Wall.,res pectively.In Coptis chinensis Franch.,the di-nucleotide repeat motifs of AG/CT were the predominant repeat types,a total of 953,accounting for 23.40% of the total SSR.The tri-nucleotide repeat motifs of AAG/CTT were the predominant repeat types,a total of 746,accounting for 18.3%of the total SSR;in C.teeta Wall.,AG/CT and AAG/CTT were 934（23.10%） and 773（19.10%） respectively.We randomly selected 60 pairs of primers for PCR amplification.Among them,12 pair primers showed polymorphism difference（20.00%）.And 40 Coptidis plants were divided into 2 groups by using Populations software.There were numerous SSRs in Coptidis transcriptomes with high frequency and various types.It would provide abundant candidate molecular markers for genetic diversity analysis and genetic map construction of this plant.