Li Can, Zhang Yu, Ying Kai, Liang Xiaolei, Han Bin
National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China.
Theor Appl Genet. 2004 Feb;108(3):392-400. doi: 10.1007/s00122-003-1457-z. Epub 2003 Oct 17.
Computational screening of the chromosome-4 sequence of the rice cultivar Nipponbare ( Oryza sativa L. japonica) revealed 1,844 tandem simple sequence repeats (SSRs) or microsatellites with SSR motifs >/=20 bp and repeated unit length of 1-6 base pairs. Thus SSRs occur once in every 18.8 kb, on the average, on the chromosome with one SSR per 23.8 kb and 16 kb on the short and long arms, respectively. No SSR was detected in the core region of the centromere. Poly(AT)(n) repeats represented the most abundant and length polymorphic class of SSRs on the chromosome, but it did not occur in the exons. GC-rich trinucleotide repeats were most abundant in the coding regions, representing 71.69% of the SSRs identified in the exons. Two hundred and twenty four SSRs were associated with the repetitive DNA sequences, most of them were poly(AT)(n) tracts. Sequence variations of SSRs between two cultivars, representing the two subspecies of the Asian cultivated rice indica and japonica, were identified, revealing that divergence and convergence of the two subspecies could be traced by the analysis of SSRs. These results provide a great opportunity for SSR-based marker development and comparative genome analysis of the two subspecies of the Asian cultivated rice.
对水稻品种日本晴（Oryza sativa L. japonica）的4号染色体序列进行的计算筛选，揭示了1844个串联简单序列重复（SSR）或微卫星，其SSR基序≥20 bp，重复单元长度为1 - 6个碱基对。因此，平均每18.8 kb出现一次SSR，在染色体上，短臂和长臂上分别每23.8 kb和16 kb出现一个SSR。在着丝粒的核心区域未检测到SSR。聚（AT）（n）重复是染色体上最丰富且长度多态的SSR类别，但它不在外显子中出现。富含GC的三核苷酸重复在编码区最为丰富，占在外显子中鉴定出的SSR的71.69%。224个SSR与重复DNA序列相关，其中大多数是聚（AT）（n）片段。鉴定了代表亚洲栽培稻籼稻和粳稻两个亚种的两个品种之间SSR的序列变异，表明通过SSR分析可以追踪这两个亚种的分歧和趋同。这些结果为基于SSR的标记开发以及亚洲栽培稻两个亚种的比较基因组分析提供了巨大机会。
