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Potential of (GATA)<sub>n</sub> microsatellites from rice for inter- and intra-specific variability studies

By Ranjekar Prabhakar K, Chowdari Venkat, Ramakrishna Wusirika, Davierwala Armaity P and Gupta Vidya S

Abstract

<p>Abstract</p> <p>Background</p> <p>The microsatellite, (GATA)<sub>n</sub> has been frequently used for DNA fingerprinting. However, very few attempts have been made to analyze (GATA)<sub>n</sub>-containing loci in rice.</p> <p>Results</p> <p>Three polymorphic (GATA)<sub>n</sub>-harboring loci viz. OS1A6, OS1H10 and OS2E7, containing 7–13 repeat motifs were identified from a genomic library of a cultivated rice, <it>Oryza sativa</it> var. Basmati-370 using oligonucleotide probe (GATA)<sub>4</sub>. When (GATA)<sub>n</sub> flanking primers were used to screen 26 wilds (representing different genomes of rice), 16 cultivars, 47 Indian elite rice varieties and 37 lines resistant/susceptible to bacterial blight, up to 22 alleles were obtained at an individual locus. Also, interestingly the bacterial blight resistant lines clustered into a separate group from the remaining rice genotypes, when a dendrogram was constructed based on the polymorphism obtained at the three loci. This may be due to the partial homology of the clones OS1H10 and OS2E7 to regions encoding <it>O. longistaminata</it> receptor kinase-like protein and pathogenesis-related protein. The ability of these <it>O. sativa</it> flanking primers to amplify DNA of maize, wheat, barley and oat indicates that these (GATA)<sub>n</sub>-containing loci are conserved across different cereal genera.</p> <p>Conclusions</p> <p>The large allele number obtained reveals the potential of (GATA)<sub>n</sub>-containing loci as powerful tools to detect simple sequence length polymorphism (SSLP). The (GATA)<sub>n</sub>-flanking primers were not only useful in distinguishing between closely related genotypes, but could also be used for cross-species amplification and are also conserved across different cereal genera. These loci could also cluster the bacterial blight resistant/susceptible lines into different groups based on the resistance genes present in them.</p

Topics: Evolution, QH359-425
Publisher: BMC
Year: 2001
DOI identifier: 10.1186/1471-2148-1-7
OAI identifier: oai:doaj.org/article:5048044182bb42efa488b82484c8532f
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