利用生物信息学方法进行基于表达序列标签的玉 米单核苷酸多态性标记的开发

针对简单重复序列（SSR）标记密度不足、单核苷酸多态性（SNP）标记开发一般只基于2种基因型的序列差异，用以检测其他基因型的材料时多态性不高，不能满足玉米基因精细定位需要的现状，本研究从公共数据库下载来自不同遗传背景的玉米表达序列标签（EST），结合运用各种生物信息学软件，开发基于EST序列的高多态性SNP标记。通过对2018530条EST序列的比对分析，拼接发掘出遍布全基因组的80363个SNP位点。在SNP位点两侧保守序列上设计PCR引物，开发出12388 个SNP标记（www.sicau.edu.cn/web/yms/snp/snp.html），包含34721个SNP位点。其中，6008个标记只含单一SNP位点，12762个位点的多态性信息含量（PIC）大于04，具有高度多态性。

THE DEVELOPMENT OF SNP MARKERS BASED ON EST BY BIOINFORMATIC APPROACH IN MAIZE

Due to the inadequate density of simple repeat sequence (SSR) markers and the inadequate polymorphism of single nucleotide polymorphism (SNP) markers, which are developed based on sequence difference between only two genotypes, these two kinds of DNA molecular markers do not meet the requirement of fine mapping for maize genes. In this study, expressed sequence tags with different genetic background were downloaded from public databases, and used for development of highly polymorphic SNP markers with the help of different bioinformatical softwares. On the basis of alignment among 2018530 pieces of EST sequences, 80363 SNP sites were found out throughout all the genome. According to flanking conserved sequences beyond these SNP sites, 12388 pairs of PCR primers were designed to amplify sequences involving 34721 SNP sites, and provided to be used as SNP markers, among which 6008 contain only one SNP site. For 12762 of these SNP sites, the polymorphism information content (PIC) is more than 0.4, showing their high polymorphism. All the relative information about these SNP markers is available from our web page (www.sicau.edu.cn/web/yms/snp/snp.html).