ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2004
Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 29 citations in OpenAlex.
- Genetic diversity and population structure of 93 rice cultivars (lines) (Oryza sativa Xian group) in Qinba in China by 3 types of genetic markers.BMC genomics · 2022Article
- Development in rice genome research based on accurate genome sequence.International journal of plant genomics · 2008Article
- Rice functional genomics research in China.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2007Article
- A genome-wide microsatellite polymorphism database for the indica and japonica rice.DNA research : an international journal for rapid publication of reports on genes and genomes · 2007Article
- Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2006Article
- Microsatellite analysis in the genome of Acanthaceae: An in silico approach.Pharmacognosy magazineArticle
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5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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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