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SSR markers targeting (GATA) n motifs are known to be highly polymorphic and useful in many organisms. (GATA) n motif specific SSR markers covering the whole rice genome are not available. The present study was carried out with an objective to identify class I rice microsatellites in the rice genome with (GATA)n motifs, in-silico, and validate their potential as molecular markers. A total of 243 such motifs were identified; 65 of these were present in the genic region, 59 were in the upstream region and the remaining motifs were found in the intergenic regions. Many of the (GATA) n motifs were found within and/or upstream of genes associated with biotic or abiotic stress tolerance. A total of 230 PCR-based markers targeting all the class I (GATA) n microsatellites were developed and 35 of these markers spread across the rice genome were validated in a set of 24 representative rice varieties belonging to five distinct cultivar groups. All the markers were polymorphic, with average polymorphism information content (PIC) value of 0.61, and the rice cultivars could be uniquely distinguished into different cultivar groups based on marker analysis. These informative markers targeting (GATA) n motifs representing a new set of markers in rice will be highly useful for genetic studies and marker-assisted selection. [ABSTRACT FROM AUTHOR]

APMS 6B is the stable maintainer of the CMS line APMS 6A, which is the female parent of the popular Indian rice hybrid DRRH 3. APMS 6B has good combining ability and plant stature but is highly susceptible to bacterial blight (BB) disease. In order to improve the BB resistance of APMS 6B, we pyramided two major, dominant BB resistance genes, Xa21 and Xa38, through marker-assisted backcross breeding (MABB). Improved Samba Mahsuri (ISM) was used as the donor for Xa21 while PR 114 (Xa38) served as the donor for Xa38. Individual crosses [APMS 6B/ISM and APMS 6B/PR 114 (Xa38)] were performed, and true F1 plants were then backcrossed with APMS 6B and the MABB process was continued till BC3. A single positive BC3F1 plant identified from both the crosses with maximum genotypic and phenotypic similarity with APMS 6B was selfed to generate BC3F2s. At BC3F2 generation, plants homozygous for either Xa21 or Xa38 were identified and further confirmed for the absence of two major fertility restorer genes, Rf3 and Rf4. A single such homozygous BC3F2 plant, each from both the crosses, was then inter-mated to generate ICF1s (inter-cross F1s). Selected ICF1 plants possessing both the BB resistance genes were selfed to generate ICF2s. A total of 42 ICF2 plants homozygous for both Xa21 and Xa38 were identified and screened with parental polymorphic SSR markers to identify the best F2 plants having the maximum recurrent parent genome recovery. Twelve best ICF2 plants were advanced up to ICF5. The ICF5 lines displayed very high level of BB resistance and were similar to APMS 6B in terms of agro-morphological characters. Further, most of these lines also showed complete maintenance ability and such lines are being advanced for conversion to WA-CMS lines. [ABSTRACT FROM AUTHOR]