Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.)

Temnykh, Svetlana V.; Park, William D.; Ayres, Nicola M.; Cartinhour, Sam; Hauck, Nathanael R.; Lipovich, Leonard; Cho, Y. G.; Ishii, Takashige; McCouch, Susan R.

doi:10.1007/s001220051342

Cited by 779 publications

(570 citation statements)

References 41 publications

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“…Markers derived from genomic libraries also contained more repeat units as well as a greater range of allele sizes and genetic diversity than markers isolated from EST libraries. The striking difference of polymorphism between the soybean SSRs derived from the two sources is consistent with differences reported in rice (Temnykh et al 1999;Cho et al 2000), sugarcane (Cordeiro et al 2001), tomato (Arshchenkova and Ganal 2002), wheat (Eujayl et al 2002), and barley (Thiel et al 2003). For example, Arshchenkova and Ganal (2002) reported that only 20 of 27,000 tomato ESTs contained microsatellites of more than ten repeat units.…”

Section: Discussionsupporting

confidence: 81%

A new integrated genetic linkage map of the soybean

Song¹,

et al. 2004

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Section: Discussionsupporting

confidence: 81%

A new integrated genetic linkage map of the soybean

Song¹,

et al. 2004

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“…Similar to tall fescue ESTs , orchardgrass trinucleotide repeats containing C and G in the first two positions were more abundant than those containing A and T, accounting for 33% of all SSRs. However, no single trinucleotide repeattype accounted for more than 5% of the SSRs (Supplemental Table 1), which is similar to that found in rice and barley (Temnykh et al 2000;Thiel et al 2003). Among the 94 dinucleotide repeats, the most abundant motifs, accounting for 25%, were AG/TC.…”

Section: Discussionsupporting

confidence: 62%

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

et al. 2011

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Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties.

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“…Twenty two published drought and salt tolerance linked SSR markers were selected (Akagi et al 1996;Panaud et al 1996;Temnykh et al 2000;McCouch et al 2002) which were reported in different indica rice lines. Detailed information of these markers was collected from Gramene database (www.gramene.org), a freely available comparative web data resource for cereal crops.…”

Section: Marker Selection For Genotypingmentioning

confidence: 99%

Profiling of selected indigenous rice (Oryza sativa L.) landraces of Rarh Bengal in relation to osmotic stress tolerance

Karmakar

Roychowdhury

Kar

et al. 2012

Physiol Mol Biol Plants

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A total of ten rare indigenous rice landraces of West Bengal were screened for germination potential and seedling growth under varying concentrations of sodium chloride (NaCl) and polyethylene glycol (PEG) solutions as osmotic stress inducing agents. Among the studied rice landraces Kelas and Bhut Moori showed highest degree of tolerance to induced osmotic stresses. Proline content of the studied lines was also determined. Genetic relationship among the studied rice landraces was assessed with 22 previously reported osmotic stress tolerance linked Simple Sequence Repeat (SSR) markers. The identified allelic variants in form of amplified products size (molecular weight) for each SSR marker were documented to find out allele mining set for the linked markers of the studied genotypes in relation to osmotic stress tolerance. A Microsatellite Panel was constructed for the different allelic forms (size of amplified products) of each used marker. Among 22 SSR markers, ten showed unique alleles in form of single specific amplified product for the studied four genotypes which can be used for varietal identification. Genetic relationship among the studied rice lines was determined and a dendrogram was constructed to reveal their genetic inter-relationship. Polymorphism Information Content (PIC) for each used marker was also calculated for the studied rice lines.

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Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.)

Cited by 779 publications

References 41 publications

A new integrated genetic linkage map of the soybean

A new integrated genetic linkage map of the soybean

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

Profiling of selected indigenous rice (Oryza sativa L.) landraces of Rarh Bengal in relation to osmotic stress tolerance

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