玉米EST序列中微卫星的频率和分布

利用Tandem Repeats Finder程序,以大于15 bp,匹配值为80%的标准,对已经公布的1 162 745条玉米EST序列中的SSR进行查找,共发现一至六核苷酸重复的SSR序列84 314个,占1 162 745个EST序列的7.25%.组成这些SSR的主要基序有A,C,AG,GGC,AGG,AAC,AAGT,AAAT,ACAT,AGAT,AGGT,AGAGG,AAAAG,AGGGG,AAAGC,GCCGAG,CGGCGT,CGCCGG,GCGGCA和CGCTGC,且以单核苷酸重复的SSR数量最多,为75 917个,其次是六核苷酸重复,为2 903个,这两类重复的SSR占总数的93.48%,四、五核苷酸重复的SSR数量较少,分别为772和779个.值得注意的是,所有这些在玉米EST中发现的SSR序列的碱基数都大于24 hp.这暗示利用这些SSR序列有可能开发出一批扩增效果好,多态性高的SSR分子标记,有助于玉米高密度遗传图谱的构建、重要功能基因克隆及基因功能等研究.

Frequency and Distribution of Different Simple Sequence Repeats(SSRs) in the Maize ESTs

Different SSRs were searched in 1 162 745 maize ESTs downloaded from database by using the Tandem Repeats Finder program,with the criteria of SSR length>15 bp and 80% matches.The results showed that a total of 84 314 SSRs were observed in 1 162 745 ESTs,which accounted for 7.25%.A,C,AG,GGC,AGG,AAC,AAGT,AAAT,ACAT,AGAT,AGGT,AGAGG,AAAAG,AGGGG,AAAGC,GCCGAG,CGGCGT,CGCCGG,GCGGCA and CGCTGC were the major motifs,of which mononucleotide repeat was the most abundant,being 75 917,the next was the SSR of hexanucleotide repeat,being 2 903,SSR number of these 2 types accounted for 93.48% of total SSRs in maize ESTs;The SSRs with tetranucleotide and pentanucleotide repeats were less,only 772 and 779 numbers,respectively.It is worth noting that the length of the repeat motif is more than 24 bp,which implies that we can develop SSR markers with good polymorphism for genetic mapping,gene clone and gene functional research.