Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

<p>Abstract</p> <p>Background</p> <p>Earlier comparative maps between the genomes of rice (<it>Oryza sativa </it>L.), barley (<it>Hordeum vulgare </it>L.) and wheat (<it>Triticum aestivum </it>L.) were linkage maps based on cDNA-RFLP...

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Main Authors: Yu Ju-Kyung, Kantety Ramesh V, La Rota Mauricio, Sorrells Mark E
Format: Article
Language:English
Published: BMC 2005-02-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/6/23
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author Yu Ju-Kyung
Kantety Ramesh V
La Rota Mauricio
Sorrells Mark E
author_facet Yu Ju-Kyung
Kantety Ramesh V
La Rota Mauricio
Sorrells Mark E
author_sort Yu Ju-Kyung
collection DOAJ
description <p>Abstract</p> <p>Background</p> <p>Earlier comparative maps between the genomes of rice (<it>Oryza sativa </it>L.), barley (<it>Hordeum vulgare </it>L.) and wheat (<it>Triticum aestivum </it>L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps. Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes. The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine <it>in-silico </it>rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags.</p> <p>Results</p> <p>The proportions of SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) and motifs varied with the length of the SSRs within and among the three species, with trinucleotide SSRs being the most frequent. Distributions of genomic microsatellites (gSSRs), EST-derived microsatellites (EST-SSRs), and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated. More than 13,000 primer pairs were developed for use by the cereal research community as potential markers in wheat, barley and rice.</p> <p>Conclusion</p> <p>Trinucleotide SSRs were the most common type in each of the species; however, the relative proportions of SSR types and motifs differed among rice, wheat, and barley. Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome. Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals.</p>
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spelling doaj.art-edba5ba964f14ef582740738cb073cd12022-12-22T02:48:15ZengBMCBMC Genomics1471-21642005-02-01612310.1186/1471-2164-6-23Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barleyYu Ju-KyungKantety Ramesh VLa Rota MauricioSorrells Mark E<p>Abstract</p> <p>Background</p> <p>Earlier comparative maps between the genomes of rice (<it>Oryza sativa </it>L.), barley (<it>Hordeum vulgare </it>L.) and wheat (<it>Triticum aestivum </it>L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps. Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes. The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine <it>in-silico </it>rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags.</p> <p>Results</p> <p>The proportions of SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) and motifs varied with the length of the SSRs within and among the three species, with trinucleotide SSRs being the most frequent. Distributions of genomic microsatellites (gSSRs), EST-derived microsatellites (EST-SSRs), and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated. More than 13,000 primer pairs were developed for use by the cereal research community as potential markers in wheat, barley and rice.</p> <p>Conclusion</p> <p>Trinucleotide SSRs were the most common type in each of the species; however, the relative proportions of SSR types and motifs differed among rice, wheat, and barley. Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome. Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals.</p>http://www.biomedcentral.com/1471-2164/6/23
spellingShingle Yu Ju-Kyung
Kantety Ramesh V
La Rota Mauricio
Sorrells Mark E
Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
BMC Genomics
title Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
title_full Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
title_fullStr Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
title_full_unstemmed Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
title_short Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
title_sort nonrandom distribution and frequencies of genomic and est derived microsatellite markers in rice wheat and barley
url http://www.biomedcentral.com/1471-2164/6/23
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