芦笋EST资源的SSR信息分析  

Analysis of SSR information in EST resource of asparagus

作　　者：吴建霞[1] 李亚玲[2] 张智俊[1] 管雨[1] 

机构地区：[1]浙江农林大学亚热带森林培育技术国家重点实验室培育基地,杭州临安311300 [2]浙江农林大学农业与食品科学学院,杭州临安311300

出　　处：《生物信息学》2012年第2期96-100,共5页Chinese Journal of Bioinformatics

基　　金：国家"863"项目(2007AA021403);浙江省自然科学基金资助项目(Y307469);浙江农林大学人才启动基金

摘　　要：为了在芦笋中开发EST-SSR功能性标记,对来源于NCBI公共数据库的8590条芦笋(AsparagusofficinalisL.)EST序列进行简单重复序列SSR搜索。剔除冗余序列,得到非冗余序列8377条。在非冗余序列中共挖掘出469个EST-SSR,平均相隔14.80kb出现1个SSR。在所有的重复基序中,二核苷酸重复基序的SSR所占比例最高40.51%(190/469),其次是三核苷酸34.97%(164/469),六核苷酸21.11%(99/469)。在所有基序里,CT/AG出现的频率最高有62次,占全部重复基序的13.22%(62/469)。选取含SSR的EST序列30条,并利用primer5软件设计引物,进行SSR位点的扩增,其中27对引物扩增产物,24对有较清晰可靠的目标扩增条带,占引物数的80%,且所检测出的芦笋等位基因数量较丰富,平均4.93个/对。这些EST-SSR标记的开发将有助于芦笋群体遗传多样性、遗传图谱构建、基因定位、分子标记和系谱分析等方面的研究。To develop asparagus EST -SSRs function of molecular marker, Simple sequence repeats （SSRs） were investigated in 8590 qualified ESTs downloaded from Nucleotide ESTs database of Lentinula edodes in NCBI . After eliminated redundancy, we got 8377 sequence of nonredundancy, in which there were 469 EST - SSRs, the mean distance was 14.80 kb in non- redundant ESTs. Of the total EST- SSRs, 40.51% （190/469） were dinucleotides repeats （DNRs） , 34.79 % （ 164/469 ） were trinucleotide repeats （TNRs） and 21.11% （99/469） were hexanucleotide repeats （HNRs）. In which the repeat motifs CT/AG were the most abundant up to 13.22% （62/469）. Ran- dom filter out 30 EST - SSR sequences, then using primer5 software designed its primers for PCR amplification. 27 of primers showed amplifications, in which 21 pairs could amplify distinct bands , accounted for 80% （24/30）. Alleles in asparagus were abundant , average 4.93 each pair. These EST - SSR markers will be useful in studies of population genetics, linkage mapping, molecular mapping, gene tagging, and pedigree analysis and other aspects for this species.

关 键 词：芦笋 EST—SSRs 引物 

分 类 号：S664.1[农业科学—果树学]