基于转录组的3种缬草SSR位点信息比较分析

Comparative analysis of SSR loci information of three Valeriana officinalis L.species based on transcriptome

为研究3种缬草SSR分子标记的差异,开发相应的引物用于缬草的鉴定及分子育种。本研究采用Excel和MISA软件对3种缬草转录组中SSR位点数据进行分析,利用Primer 3.0软件随机设计SSR引物,并进行PCR扩增及琼脂糖凝胶电泳验证引物的有效性和SSR的多态性。结果显示,缬草Valeriana officinalis L.(VOL)、Valeriana officinalis var.iatifolia Miq.(VOI)及Valeriana officinalis var.officinalis Linn.(VOO)的转录组数据分别包含29 462、40 840和29 280个序列总数(Unigene),这些Unigene分别包含7 515、8 046和7 330个SSR位点。3种缬草的SSR位点的发生频率为25.50%、19.71%、25.05%,平均距离为4.16 kb、4.20 kb、4.22 kb。SSR单碱基重复基元的主要类型为A/T型,占SSR总数的41.76%、41.30%、38.50%。VOL、VOI、VOO 3种缬草的独有重复基元数量分别是44种、45种、25种。随机设计的引物扩增SSR的有效率为77.78%,具有SSR高多态性的引物占比55.56%。总之,3种缬草的SSR位点具有分布密度高、出现频率高、重复基元类型多等特点,多态性好,可为3种缬草后续的鉴定及分子育种提供理论依据。

To study the differences in SSR molecular markers of three Valeriana officinalis L.species,the corresponding primers were developed for the identification and molecular breeding of Valeriana officinalis L.species.In this study,Excel and MISA software were used to analyze the SSR loci data in the transcriptome of three Valeriana officinalis L.species.Primer 3.0 software was used to randomly design SSR primers,and PCR amplification and agarose gel electrophoresis were performed to verify the effectiveness of the primers and the polymorphism of SSR.The results showed that the transcriptome data of Valeriana officinalis L.(VOL),Valeriana officinalis var.iatifolia Miq.(VOI),and Valeriana officinalis var.officinalis Linn.(VOO)contained 29462,40840,and 29280 Unigenes.These Unigenes included 7515,8046,and 7330 SSR loci,respectively.The occurrence frequency of SSR loci in the three Valeriana officinalis L.species was 25.50%,19.71%,and 25.05%,with average distance of 4.16 kb,4.20 kb,and 4.22 kb.The predominant type of single-nucleotide repeat units in SSR was A/T,accounting for 41.76%,41.30%,38.50%of the total SSR.The number of unique repeat units of VOL,VOI,VOO was 44,45 and 25,respectively.The effective rate of SSR amplification by randomly designed primers was 77.78%,and the proportion of highly polymorphic SSR primers was 55.56%.In conclusion,the SSR loci of three Valeriana officinalis L.species exhibited characteristics such as high distribution density,high occurrence frequency,and diverse types of repeat units,indicating good polymorphism.The results of this study can provide a theoretical basis for the subsequent identification and molecular breeding of the three Valeriana officinalis L.species.