The estimation of hybrid rice seed purity is done conventionally by the grow out test (GOT), which is based on the assessment of morphological and floral characteristics in plants grown to maturity. For seed companies, large amounts of capital are locked up in the form of hybrid seed stock while awaiting the results of the GOT. With the objective of replacing the GOT with DNA based assays, cytoplasmic male sterile (CMS), restorer, and hybrid lines have been screened by means of microsatellite and sequence tagged site (STS) polymorphisms. A simple procedure for detecting heterozygosity and purity has been standardized and uses 6‐d‐old rice (Oryza sativa L.) seedlings, which could be used for detection of off‐types in hybrid seed lots. The extent of heterozygosity within parental lines of rice hybrids was assessed and the results suggest that a single, appropriately chosen microsatellite marker should be sufficient for assessing hybrid seed purity.

With the objective of identifying SSR markers that can distinguish parental lines of rice hybrids, we characterized 10 each of cytoplasmic male sterile (CMS) and restorer (R) lines along with 10 popular Indian rice varieties using a set of 48 hyperpolymorphic SSRs distributed uniformly across the rice genome. All the SSR markers were polymorphic, amplifying a total of 163 alleles, with an average of 3.36 § 1.3 allelic variants per locus. Twenty-seven SSR markers showed ampliWcation of an allele, which was very speciWc and unique to a particular parental line and not ampliWed in any other rice genotype tested. Through multiplex PCR, SSR marker combinations that were unique to a particular parental line or hybrid were also identiWed. With a set of 10 SSR markers, all the public bred Indian rice hybrids along with their parental lines could be clearly distinguished. To utilize these SSR markers eVectively for detection of impurities in parental lines, a two dimensional bulked DNA sampling strategy involving a 20 £ 20 grow-out matrix has been designed and used for detection of contaminants in a seed-lot of the popular CMS line IR58025A. We have also designed a multiplex PCR strategy involving single tube analysis using 2-3 markers for hybrid seed purity assessments and demonstrate its superiority over single marker analysis in accurate detection of impurities in hybrids. Implications of parental and hybrid speciWc SSR markers and strategies to utilize the informative SSR markers for detection of contaminants in a cost eVective manner are discussed.

Combining ability study on grain yield and its components from line x tester analysis over the locations of five well adapted CMS lines and twenty three testers of different eco-geographic origin revealed higher SCA variance than GCA variance for all the traits indicating the prevalence of non-additive gene action. The lines APMS 6A, PUSA 5A and CRMS 32A and testers 1096, 1005, IBL-57 and SC5 9-3 were the good general combiners for yield and its majority of the traits. IBL-57 was the only good general combiner among the male parents for earliness, dwarfness and grain yield per plant. The hybrids APMS 6A x SC5 9-3, APMS 6A x 1005 and APMS 6A x GQ 25 were identified as potential one for yield and desired traits based on sca effects.

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.

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