川党参转录组EST-SSR位点分析  

Analysis of EST-SSR locus in Codonopsis tangshen transcriptome

作　　者：蒋小刚 周武先 王华 由金文 张美德 JIANG Xiao-gang;ZHOU Wu-xian;WANG Hua;YOU Jin-wen;ZHANG Mei-de(Institute of Chinese Herbal Medicines,Hubei Academy of Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medi-cine,Ministry of Agriculture and Rural Affairs,P.R.,Enshi,Hubei 445000,China)

机构地区：[1]湖北省农业科学院中药材研究所/农业农村部中药材生物学与栽培重点实验室,湖北恩施445000

出　　处：《西南农业学报》2023年第6期1132-1140,共9页Southwest China Journal of Agricultural Sciences

基　　金：现代农业产业技术体系(CARS-21);湖北省农业科技创新中心2020年度重大科技研发项目(2020-620-000-002-04);湖北省重点研发计划项目(2020BCA059);湖北省农业科学院青年科学基金项目(2021NKYJJ19);恩施州科技计划研究与开发项目(D20210035)。

摘　　要：[目的]探究川党参转录组SSR位点信息和分布特征。[方法]对川党参叶片进行转录组测序,通过MISA软件鉴定川党参转录组序列SSR位点,并对含有SSR位点的Unigenes进行功能注释。采用Primer3.0设计EST-SSR引物,基于不同产地的川党参种质DNA模板,验证EST-SSR引物的扩增稳定性。[结果]从川党参转录组序列中共鉴定124179个Unigene,其中26084个Uni-gene序列包含35827个SSR位点,SSR发生频率为21.01%。这些SSR位点共有165种SSR重复基元类型,从重复基元分布比例来看,单核苷酸重复基元A/T占SSR位点总数比例最高,为37.59%;从核苷酸重复基元平均距离来看,五核苷酸平均距离最大,为1288.54kb;从基元重复次数比例来看,重复10次的最多,有7722个,占SSR总数的21.55%。川党参转录组SSR序列长度集中在12~19bp,共19628个,频率为54.79%,SSR长度在20bp以上的潜在多态性位点有6933个,占总数的19.35%。筛选出27对扩增稳定的SSR引物,对川党参基因组DNA进行扩增,扩增片段大小范围为124~393bp。基于不同产地川党参种质资源的基因组DNA模板,筛选了部分多态性标记,扩增条带清晰,多态性较好。此外对26084个含有SSR序列的Unigenes进行Go和KEGG注释,这些Unigenes极显著富集于转录调控、DNA结合、催化、信号转导等生物过程。[结论]川党参转录组SSR序列具有较高的潜能多态性,挖掘的潜能SSR标记将为川党参遗传多样性分析、种质鉴定、辅助育种等提供研究基础。[Objective]The study aimed to explore the SSR locus and distribution characteristics of Codonopsis tangshen Oliv transcriptome.[Method]Transcriptome sequencing was performed on C.tangshen leaves.The SSR locus of the transcriptome sequence was identified by MISA software,and functional annotation was performed on the Unigenes containing the SSR locus.Primer 3.O was used to design EST-SSR primers,and the amplification stability of EST-SSR primers was verified based on C.tangshen germplasm from different regions.[Result]A total of 124179 Unigenes were identified from the transcriptome sequences of C.tangshen,of which 26084 Unigenes contained 35827 SSR locus,with a SSR occurrence frequency of 21.01%.There were165 types of SSR repeat elements in these SSR locus.From the distribution ratio of repeat elements in all the SSRs,the single nucleotide repeat elements A/T accounted for the highest percentage of 37.59%.In re-spect of the average distance of nucleotide repeat units,pentanucleotide showed the largest distance of 1288.54 kb.Concerning the proportion of primitive repetition times,the SSRs with that of ten accounted for the largest percentage of 21.55%(7722).The base count of SSR se-quences was concentrated between 12 and 19 bp,with a total of 19628 sequences(54.79%).There were 6933 potential polymorphic SSRs above 20 bp,accounting for 19.35%of all.27 SSR primers with stable amplification were selected to amplify the genomic DNA of C.tangshen,with the amplified fragment size ranging from 124 to 393 bp.Based on germplasm resources from different regions of C.tangshen,partial polymorphic markers with clear bands were selected.In addition,26084 Unigenes containing SSR locus were annotated by Go and KEGG analysis.These genes were highly enriched in biological processes such as transcriptional regulation,DNA binding,cataly-sis,and signal transduction.[Conclusion]SSR locus of C.tangshen transcriptome have high potential polymorphism,and developed potential polymorphic SSR markers will be used in research on genetic diver

关 键 词：川党参 转录组 功能注释 EST-SSR 分子标记 

分 类 号：S567[农业科学—中草药栽培]