Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley
| Autor: | Mauricio La Rota, Ramesh V. Kantety, Ju-Kyung Yu, Mark E. Sorrells |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2005 |
| Předmět: |
Genetic Markers
Transcription Genetic lcsh:QH426-470 Genetic Linkage lcsh:Biotechnology Amino Acid Motifs Biology Genes Plant Polymerase Chain Reaction Genome Chromosomes Plant DNA sequencing lcsh:TP248.13-248.65 Genetics Triticum DNA Primers Expressed Sequence Tags Expressed sequence tag Models Statistical Polymorphism Genetic Oryza sativa Models Genetic Nucleotides Chromosome Mapping food and beverages Hordeum Oryza lcsh:Genetics Genetic marker Regression Analysis Microsatellite Hordeum vulgare Restriction fragment length polymorphism Genome Plant Polymorphism Restriction Fragment Length Research Article Microsatellite Repeats Biotechnology |
| Zdroj: | BMC Genomics, Vol 6, Iss 1, p 23 (2005) BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | Background Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum 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 in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags. Results 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. Conclusion 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. |
| Databáze: | OpenAIRE |
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