We have analyzed SSRs in mitochondrial and chloroplast genomes of rice. We identified 2528 SSRs in the mitochondrial genome and average 870 SSRs in the chloroplast genomes. About 8.7% of the mitochondrial and 27.5% of the chloroplast SSRs were observed in the genic region. Dinucleotides were the most abundant repeats in genic and intergenic regions of the mitochondrial genome while mononucleotides were predominant in the chloroplast genomes. The rps and nad gene clusters of mitochondria had the maximum repeats, while the rpo and ndh gene clusters of chloroplast had the maximum repeats. We identified SSRs in both organellar genomes and validated in different cultivars and species.

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IR 58025A is a very popular wild-abortive cytoplasmic male sterile (WA-CMS) line of rice and is extensively used for hybrid rice breeding. However, IR 58025A and many hybrids derived from it possess mild aroma (undesirable in some parts of India) and are highly susceptible to bacterial blight (BB) and blast diseases. To improve IR 58025A for BB and blast resistance, we have introgressed a major dominant gene conferring resistance against BB (i.e. Xa21) and blast (i.e. Pi54) into IR 58025B, the maintainer line of IR 58025A. An introgression line of Samba Mahsuri (i.e. SM2154) possessing Xa21 and Pi54 genes in homozygous condition and fine-grain type was used as donor parent, and backcross breeding strategy was adopted for targeted introgression of the resistance genes. PCR-based molecular markers tightly linked to Xa21 and Pi54 were used for selection of BB-and blast-resistant lines, while closely linked markers were used for identification of backcross-derived plants devoid of Rf4 and aroma. At BC 2 F 5 , four backcross-derived lines possessing resistance against BB and blast, devoid of aroma, high yield, short plant stature, long-slender grain type and with recurrent parent genome recovery ranging from 88.8% to 98.6% were selected and advanced for further evaluation. The improved versions of IR 58025B, viz. behaved as perfect maintainers when testcrossed with WA-CMS lines. Agronomically superior lines of improved IR 58025B are being converted to CMS line through backcrossing for developing high-yielding and biotic stress-resistant rice hybrids.

KMR-3R is a stable restorer line with medium-bold grain type and is the male parent of the popular public-bred Indian rice hybrid, KRH2. As both KMR-3R and KRH2 are highly susceptible to bacterial blight (BB) and possess undesirable bold-grain type, we crossed KMR-3R with a high-yielding, BB resistant, fine-grain-type variety, Improved Samba Mahsuri, possessing the major BB resistant gene, Xa21. The F 1 s were backcrossed to KMR-3R, and the BC 1 F 1 plants were subjected to marker-assisted selection (MAS) for Xa21 and two major fertility restorer genes, Rf3 and Rf4. ÔTripleÕ positive BC 1 F 1 plants were selfed and their progeny were subjected to MAS for Xa21 coupled with phenotype-based visual selection for agromorphological and grainquality traits. At BC 1 F 5 generation, three backcross derived lines (BK9, BK49 and BK61) possessing higher yield than KMR-3R, tall plant stature along with fine-grain type were identified and crossed with IR598025A, the female parent of KRH2. The hybrids were completely fertile, possessed long-slender grain type, exhibited resistance to BB and displayed a yield advantage of 24% over KRH2 under BB infection.

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 PCRbased 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.