Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential.
By S. Temnykh, G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour, Susan McCouch. Genome Research, 2001
1,564 citations recorded by the source corpus.
A total of 57.8 Mb of publicly available rice (Oryza sativa L.) DNA sequence was searched to determine the frequency and distribution of different simple sequence repeats (SSRs) in the genome. SSR loci were categorized into two groups based on the length of the repeat motif. Class I, or hypervariable markers, consisted of SSRs > or =20 bp, and Class II, or potentially variable markers, consisted of SSRs > or =12 bp <20 bp. The occurrence of Class I SSRs in end-sequences of EcoRI- and HindIII-digested BAC clones was one SSR per 40 Kb, whereas in continuous genomic sequence (represented by 27 fully sequenced BAC and PAC clones), the frequency was one SSR every 16 kb. Class II SSRs were estimated to occur every 3.7 kb in BAC ends and every 1.9 kb in fully sequenced BAC and PAC clones. GC-rich trinucleotide repeats (TNRs) were most abundant in protein-coding portions of ESTs and in fully sequenced BACs and PACs, whereas AT-rich TNRs showed no such preference, and di- and tetranucleotide repeats were most frequently found in noncoding, intergenic regions of the rice genome. Microsatellites with poly(AT)n repeats represented the most abundant and polymorphic class of SSRs but were frequently associated with the Micropon family of miniature inverted-repeat transposable elements (MITEs) and were difficult to amplify. A set of 200 Class I SSR markers was developed and integrated into the existing microsatellite map of rice, providing immediate links between the genetic, physical, and sequence-based maps. This contribution brings the number of microsatellite markers that have been rigorously evaluated for amplification, map position, and allelic diversity in Oryza spp. to a total of 500.
Subfields: Genetics, Plant Science
View Paper: https://www.semanticscholar.org/paper/3a616b306c372e9b3c2832287d5d66cc9e49b3bd
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Citations in the corpus
- Marker-assisted improvement of bacterial blight resistance in parental lines of Pusa RH10, a superfine grain aromatic rice hybrid (2010, methodology): “Information regarding chromosomal location and sequences of primers were obtained from www.gramene.org, Panaud et al. (1996), Temnykh et al. (2000, 2001) and McCouch et al. (2002).”
- Quantitative trait loci for phytate in rice grain and their relationship with grain micronutrient content (2007, methodology): “Further details of development of SSRs and construction of the linkage map for the Azucena · IR64 population are reported in Causse et al. (1994), Panaud et al. (1996), Temnykh et al. (2000, 2001).”
- Microsatellite markers: what they mean and why they are so useful (2016, methodology): “Using publicly available DNA sequence information on the rice genome, Temnykh et al. (2001) categorized microsatellites based on length and noticed that longer perfect repeats ( 20 nucleotides) were highly polymorphic.”
- Methods for Development of Microsatellite Markers: An Overview (2014, neutral): “Two types of SSRs (Temnykh et al., 2001): a.”
- Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa (2004, methodology): “In rice, Temnykh et al. (2001) reported one simple perfect SSR per 40 kb of random genomic DNA based on in silico surveys of BAC-end sequences available at the time.”
- GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein (2006, methodology): “The SSR primers of the RM-series were designed according to Temnykh et al. (2000, 2001) , and those of the MRG-series were according to the rice genome sequences of Monsanto Company that were made available by McCouch et al. (2002).”
- Ghd7 (Ma6) Represses Sorghum Flowering in Long Days: Ghd7 Alleles Enhance Biomass Accumulation and Grain Production (2014, methodology): “07007 BC1F1 populations using polymorphisms developed from SSR markers (SSRIT) (Temnykh et al., 2001), CAPS markers, SNPS, and INDELS.”
- Microsatellite markers: an overview of the recent progress in plants (2011, background): “Microsatellite generation was found to be accompanied by retrotransposition events by analysis of a portion-sequenced human and rice genome DNA (Nadir et al. 1996; Temnykh et al. 2001).”
- Genetic Diversity and Population Structure in Landraces and Improved Rice Varieties from India (2015, positive): “Numerous SSR markers have been identified in rice (Temnykh et al, 2001; McCouch et al, 2002), and along with ISSR markers they have been used to assess genetic diversity (Joshi et al, 2000; Saini et al, 2004; Lapitan et al, 2007; Pervaiz et al, 2010; Sivaranjani et al, 2010; Ghaley et al, 2012;…”
- Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers (2011, positive): “2 Tree Genetics & Genomes (2012) 8:205–220 207 5,720 unigenes were generated and used for SSR exploitation using SSRIT software (Temnykh et al. 2001).”
- Genic Molecular Markers in Plants: Development and Applications (2007, background): “Rice Oriza sativa EST-SSR, EST-SNP, cDNA-RFLP, Intron Length Polymorphism (ILP) Causse et al. 1994, Harushima et al. 1998, Temnykh et al. 2001, Feltus et al. 2004, Wang et al. 2005”
- In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. (2002, background): “Overall, the results in the present study are in contrast to earlier studies where the motifs AT were reported to be dominant in plant genomes [8, 24, 25].”