基于转录组测序的茄子SSR标记开发.docVIP

基于转录组测序的茄子SSR标记开发 魏明明，陈钰辉、刘富中、张 映、连 勇 （中国农业科学院蔬菜花卉研究所北京 100081） 摘 要：应用Trinity软件对茄子转录组测序数据组装，得到总长度为47 910 660 bp的45 404条Unigenes，MISA从中检索到8 316个SSR位点，发生频率为18.32 %，平均5.63 kb一个位点。SSR位点中单碱基重复类型最多，为5 372个，占到64.60 %；其次为三碱基重复1 628个，占到19.58 %。三碱基重复中AAG/CTT是优势重复单元，占三碱基重复数的31.6 %；二碱基重复中AG/CT是优势重复单元，占二碱基重复数的42.3 %。利用Primer3设计引物，共得到858对SSR引物，随机选取100对引物对17份茄子材料进行扩增，结果表明：有84对可以扩增出条带清晰的片段，有47对引物扩增片段为多态性片段。对47对多态性引物进行分析，多态性信息含量范围为0.10~0.64之间，平均多态性信息含量为0.32，UPGMA聚类分析可将17份材料分为3类。以上结果表明，基于茄子转录组测序开发的SSR标记可以为茄子的遗传多样性分析和遗传图谱构建提供更加丰富的标记来源。 关键词：茄子；转录组；SSR；引物；多态性 Development of SSR Markers for Eggplant with Transcriptome Sequencing Data WEI Ming-ming，CHEN Yu-hui，LIU Fu-zhong，ZHANG Ying，and LIAN Yong (The Institute of Vegetables and Flowers，Chinese Academy of Agricultural Sciences，Beijing 100081，China） Abstract：The Trinity program was used to assemble the transcriptome sequences of eggplant. In total，45 404 Unigenes were obtained with the length of 4 791 066 bp. We detected 8 316 SSR loci from these Unigenes by using MISA software. The density of the SSR were 5.63 kb with the frequency of 18.32%. The single nucleotide SSR is the most abundant （52） type for 64. 60% the total loci and followed by the tri-nucleotide （1 628） for %. The tri-nucleotide repeat motifs of AAG/CTT was the predominant repeat types that accounting for 31.6% of the tri-nucleotide repeat motifs. The dinucleotide repeat motifs of AG/CT is the predominant repeat format in this types of repeat and accounting for 42.3%. A total of 858 pairs of SSR primers are designed by using primer3 online program and 100 pairs of SSR markers are randomly selected and verified by using 17 eggplant germplasms. Among of them，84 pairs of primers were able to amplify PCR products， of which pairs of primers produced polymorphic bands. The PIC values range was between 0.10 to 0.64，the average value was 0.32. The 17 eggplant germplasms could be divided into three phylogenetic groups by analysis with UPGMA method. The results indicated that the S