微卫星序列完整性与多态性的关系

Relationship between Sequence Completeness and Polymorphism of Microsatellites

微卫星或简单序列重复（SSR）是指以1~6个碱基为单位的串联重复序列.SSR 包括完整型和不完整型两种.不完整型 SSR 是指其序列中存在个别不符合基序的碱基.SSR 作为一种用途广泛的分子标记,其多态性水平越高则应用价值越大.本研究利用模式植物水稻的两个品种（籼稻93-11和粳稻日本晴）和拟南芥的两个生态型（Columbia 和 Lansberg）的基因组序列,以及稻瘟菌中245个 SSR 标记的试验结果,对 SSR 序列完整性与多态性之间的关系进行了分析.结果表明,总体上三个物种都表现为不完整型 SSR 的多态性比完整型 SSR 低,其中以稻瘟菌最为显著.水稻和拟南芥表现出相似的规律,其 SSR 序列完整性对多态性的影响都是以二核苷酸重复最为显著,而五核苷酸重复序列则基本不受影响;另外,SSR 多态性水平与序列完整程度呈正相关关系,但轻微的序列不完整一般并不会降低 SSR 的多态性,甚至在拟南芥中还提高多态性.本研究结果对 SSR 标记的开发和 SSR 进化研究提供了有用的信息,具有重要的参考价值.

Microsatellites or simple sequence repeats （SSRs） are tandem repeats of 1 to 6 base pairs. There are two types of SSRs, namely, perfect SSR and imperfect SSR. An imperfect SSR contains one or more bases that do not follow the motif. As a widely utilized molecular marker, the higher polymorphism level of SSR is, the greater ap-plication value of SSR will be. In this study, the relationship between sequence completeness and polymorphism of SSR was investigated by using the genome sequences of two rice varieties （indica rice 93-11 and japonica rice Ni-pponbare） and two ecotypes of Arabidopsis （Columbia and Lansberg） as well as the experimental results of 245 SSR markers in rice blast pathogen Magnaporthe grisea. The results indicated that in general the imperfect SSRs had lower polymorphism levels than that of the perfect SSRs in all the three species, with M. grisea being the most ap-parent. Rice and Arabidopsis exhibited similar results. In both species, the influence of sequence completeness on polymorphism was the most significant for dinucleotide repeats, but little for pentanucleotide repeats; in addition, there is positive correlation between SSR polymorphism and sequence completeness, but slight incompleteness did not reduce the polymorphism level, in contrast, increased the polymorphism in Arabidopsis. The results of this study may provide useful information and valuable reference for the development of SSR markers and the study of SSR evolution.