title: Potential of (GATA)n microsatellites from rice for inter- and intra-specific variability studies.
abstract: BACKGROUND
  The microsatellite, (GATA)n has been frequently used for DNA fingerprinting. However, very few attempts have been made to analyze (GATA)n-containing loci in rice.
  
  
  RESULTS
  Three polymorphic (GATA)n-harboring loci viz. OS1A6, OS1H10 and OS2E7, containing 7-13 repeat motifs were identified from a genomic library of a cultivated rice, Oryza sativa var. Basmati-370 using oligonucleotide probe (GATA)4. When (GATA)n 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 O. longistaminata receptor kinase-like protein and pathogenesis-related protein. The ability of these O. sativa flanking primers to amplify DNA of maize, wheat, barley and oat indicates that these (GATA)n-containing loci are conserved across different cereal genera.
  
  
  CONCLUSIONS
  The large allele number obtained reveals the potential of (GATA)n-containing loci as powerful tools to detect simple sequence length polymorphism (SSLP). The (GATA)n-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.
authors.affiliation: Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune 411008, India. adavierwata@yahoo.com
authors.forename: A P
authors.initials: AP
authors.lastname: Davierwala
authors.forename: W
authors.initials: W
authors.lastname: Ramakrishna
authors.forename: V
authors.initials: V
authors.lastname: Chowdari
authors.forename: P K
authors.initials: PK
authors.lastname: Ranjekar
authors.forename: V S
authors.initials: VS
authors.lastname: Gupta
mesh_terms: D000225:Adenine; D000483:Alleles; D003001:Cloning, Molecular / Q000379:methods; D016000:Cluster Analysis; D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D005838:Genotype; D006147:Guanine; D007113:Immunity, Innate / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000382:microbiology; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D011110:Polymorphism, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods / Q000706:statistics & numerical data; D013045:Species Specificity; D013941:Thymine
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers; D006147:Guanine; D000225:Adenine; D013941:Thymine