基于转录组测序的茄子SSR标记开发  

Development of SSR Markers for Eggplant with Transcriptome Sequencing Data

作　　者：魏明明[1] 陈钰辉[1] 刘富中[1] 张映[1] 连勇[1] WEI Ming-ming CHEN Yu-hui LIU Fu-zhong ZHANG Ying LIAN Yong(The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences ,Beijing 100081)

机构地区：[1]中国农业科学院蔬菜花卉研究所,北京100081

出　　处：《植物遗传资源学报》2016年第6期1082-1091,共10页Journal of Plant Genetic Resources

基　　金：国家科技支撑计划项目(2012BAD02B02);国家"863"计划项目(2012AA100103);中央级公益性科研院所基本科研业务费专项(1610092015002-01);中国农业科学院创新工程项目;农业部园艺作物生物学与种质创制重点试验室项目

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47919660 bp的45404条Unigenes,MISA从中检索到8316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5372个,占到64.60%;其次为三碱基重复1628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Primer 3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,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。The transcriptome sequences of eggplant were assembled by using Trinity program. The 45404 Unigenes were obtained with the length of 47919660 bp in total and 8316 SSR loci were detected from these Unigenes by using MISA software. The density of the SSR were 5. 63 kb with the frequency of 18. 32%. The type of single nucleotide SSR was the most abundant（5372） which counted for 64. 60%,and tri-nucleotide（1628） counted for19. 58%. The tri-nucleotide repeat motifs of AAG/CTT were the predominant repeat types that counted for 31. 6% in the tri-nucleotide repeat motifs. The dinucleotide repeat motifs of AG/CT was the predominant repeat types that counted for 42. 3%. A total of 858 pairs of SSR primers were designed by using primer3 program. Among of them,the 100 pairs of SSR markers were randomly selected and verified by using 17 eggplant germplasms. The results showed that 84 pairs of primers were able to amplify PCR products,of which 47 pairs of primers produced polymorphic bands. Through analysis the 47 pairs of polymorphic primers,the result showed that the PIC values ranged between 0. 10 and 0. 64 with average of 0. 32. The 17 eggplant germplasms could be divided into three phylogenetic groups with UPGMA method.The results indicated that the development of SSR markers based on the transcriptome sequencing of eggplant will provide more reliable markers for map structure and analysis of genetic polymorphism in eggplant.

关 键 词：茄子 转录组 SSR 引物 多态性 

分 类 号：S641.1[农业科学—蔬菜学]