ArticleMolecular genetics and genomics : MGG2007
Biased distribution of microsatellite motifs in the rice genome.
Article in Molecular genetics and genomics : MGG, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 76 citations in OpenAlex.
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- Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (3 Biotech · 2023Article
- Development of genome-wide polymorphic microsatellite markers for Trichinella spiralis.Parasites & vectors · 2020Article
- Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes.Scientific reports · 2018Article
- Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India.Rice (New York, N.Y.) · 2016Article
- An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice.Frontiers in plant science · 2016Article
- De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis.BMC genomics · 2015Article
- Identification, validation and cross-species transferability of novel Lavandula EST-SSRs.Planta · 2015Article
- Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource.Frontiers in plant science · 2015Article
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- Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera.BMC plant biology · 2014Article
- Analysis of Jatropha curcas transcriptome for oil enhancement and genic markers.Physiology and molecular biology of plants : an international journal of functional plant biology · 2014Article
- In silico genome comparison and distribution analysis of simple sequences repeats in cassava.International journal of genomics · 2014Article
- Association of microsatellite pairs with segmental duplications in insect genomes.BMC genomics · 2013Article
- In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB.BMC genomics · 2013Article
- Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.).PloS one · 2013Article
- Article
- Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome.International journal of evolutionary biology · 2012Article
- Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.).DNA research : an international journal for rapid publication of reports on genes and genomes · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microsatellites are useful tools to study the extent of divergence between two taxonomic groups that show high sequence similarity. We have compared microsatellite distribution to illustrate genetic variation between the two rice genomes, Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. Microsatellite distribution proved to be non random as certain regions of very high microsatellite density have been identified. Microsatellite density in the subspecies japonica was computed marginally higher than in the subspecies indica in the genomic regions compared between the two subspecies. Unexpectedly high microsatellite densities were observed in 5'-untranslated regions of genes. These regions also displayed a clear motif bias. Some of the longest microsatellite repeats were found in intron sequences. Frequency, as well as motif bias was also noted with respect to the association of microsatellites with transposable elements. Microsatellite mutability values were exemplarily estimated for 90 loci by aligning the microsatellite containing regions between the two genomes. Poor rates of finding an orthologue corresponded with high microsatellite mutability in rice. These insights are likely to play a significant role in selecting microsatellite loci to be used in molecular breeding and studying evolutionary dynamics of the two subspecies.
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