Abstract
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.
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Acknowledgements
The authors acknowledge the support for rice functional genome study (Grant No. 2002AA2Z1003) from the Ministry of Science and Technology of China.
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fig01.jpg
Supplementary Figure 1 A total of 1844 SSRs in Nipponbare chromosome 4. Chromosome is indicated in the blue vertical line. SSRs are indicated in Orange, and markers are indicated in red. The scale (kb) is indicated in black.
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Li, C., Zhang, Y., Ying, K. et al. Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice. Theor Appl Genet 108, 392–400 (2004). https://doi.org/10.1007/s00122-003-1457-z
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DOI: https://doi.org/10.1007/s00122-003-1457-z