橡胶草转录组SSR信息分析与标记开发

Transcriptome Sequences SSR Information Analysis of Russian Dandelion

为了在总RNA水平上揭示橡胶草SSR分布规律和特性,利用GRAMENE网站提供的SSR鉴定工具SSRI T(Si mpl e Sequence Repeat I dent i f i cat i on Tool),对橡胶草6 756条无冗余的EST分别进行SSR鉴定。结果共搜查到2 761个1～6碱基SSR,出现频率最高的为单碱基重复基元类型,其次为三碱基重复基元类型与二碱基重复基元类型,分别为2 139、 338与219个,其出现频率分别为77. 5%、 12. 2%与7. 9%。AG/CT为二核苷酸中优势重复类型,占其总数的73. 1%;而AAG/CTT与ACC/GGT则为三核苷酸中优势重复类型,二者分别占三核苷酸SSR总数的24. 3%与23. 7%。设计了20对SSR引物并验证了它们在蒲公英属3个高度近缘种共24个不同个体中的存在情况。结果表明,引物扩增率为100%,多态率为95%,能够在DNA水平上将橡胶草(TKs)与其他2个高度近缘种短喙蒲公英(TB)及药用蒲公英(TO)有效地区分开。由此表明,将所开发的SSR标记用于橡胶草种质鉴定、蒲公英属不同种间多态性检测和彼此区分是可行的。

Russian dandelion is an important crop for natural rubber.In this study,simple sequence repeat identification tool was used to screen SSRs in Russian dandelion.A total of 2 761 SSRs were found in 6 756 unique root transcripts.Of the 2 761 SSRs,the most abundant SSR is the mon-nucleotide type,with the SSR numbers being 2 139,followed by the tri-and di-nucleotide ones,with 338 and219 SSR numbers,accounting for 77.5%,12.2%,and 7.9%,respectively.Among the di-nucleotide repeats,AG/CT was the most motifs and accounted for 73.1%.However,AAG/CTT and ACC/GGT were both the most frequent motif among the tri-nucleotide repeats,accounting for 24.3%and 23.7%,respectively.20 pairs of SSR primers were designed and tested for the presence of 24 individuals in 3 closely related species of Taraxacum.The results showed that the amplification efficiency was 100%,and the polymorphism efficiency was 95%.It could separate the Taraxacum kok-saghyz(TKs)from the other 2 relatives,Taraxacum brevirostre(TB)and Taraxacum officinale(TO),at DNA level.These results indicated that the developed SSR markers could be used for germplasm identification of TKs,and it was feasible to detect and differentiate different species between Taraxacum.