基于水稻基因组序列SSR的多态性分析

Analysis of SSR Polymorphism by Genome-Scale Comparing Between Varieties in Rice

根据Monsanto公司所发布的6655个序列[由简单重复序列(SSR)及其两翼各100个碱基组成],通过生物信息学的方法,找到了在籼稻(Oryzasativasubsp.indica)品种93-11与粳稻(Oryzasativasubsp.japonica)品种日本晴的基因组序列中匹配最好的1453个同源位点。在这些位点中,93-11和日本晴中分别搜索到了1449个和1451个SSR。通过对SSR的分类比较,发现在93-11和日本晴的相同位点存在1175个具有相同基序的SSR,其中371个具有相同的基序和重复个数,804个具有相同的基序但重复次数有差异。具有相同基序但重复次数有差异的SSR类型中,频率最高的是2个核苷酸的重复子,占62.94%,基序为5个和6个核苷酸的SSR则较少。对水稻这两个品种相应区域SSR的多态性比较分析,揭示了用这些特定类型的SSR可以在这两个品种的特定区域发展新的SSR标记,并为研究这两个品种之间遗传变异、基因组功能之间的差异等提供依据。

One thousand four hundred and fifty three loci were identified the same as in two rice varieties, indica rice 93-11 and japonica rice Nipponbare, by using bioinformatics tools based on 6655 sequences released by Monsanto enterprise which consisted of perfect repeats flanked by 100 bp on either side of the simple sequence repeat (SSR). Among those sequence hits, 1449 and 1451 SSRs were detected in 93-11 and Nipponbare, respectively. Among those, 371 SSRs had the same repeat units and the same repeat count, while 804 SSRs had the same special motifs with different repeat counts. In addition, in the same repeat units with different repeat counts SSR class,di-nucleotide SSRs were the most abundant, occupying 62.94% identified, while penta- and hexa-nucleotide SSRs were the least frequent. Polymorphism of SSR between two varieties in the collinear region were identified, revealing that new SSR markers could be developed for the further research of the genetic variation and genome analysis of the two varieties.