This study was undertaken to assess the comparative potential of 25 Expressed Sequence Tag derived simple sequence repeats (EST-SSRs) and 25 genomic SSRs in the prediction of grain yield heterosis using a set of nine cytoplasmic male sterile (CMS) lines and 32 restorer lines of rice. EST-SSRs and genomic SSRs exhibited an average Polymorphism Information Content value of 0.37 and 0.45, respectively. The coefficient of marker polymorphism among parental lines with respect to a set of hypervariable EST and genomic SSRs was correlated with standard heterosis for grain yield of six public bred rice hybrids. ESTSSRs gave a better correlation (r = 0.75) as compared with genomic SSRs (r = 0.09). When 10 ÔkeyÕ informative EST-SSR markers which showed a higher positive correlation with grain yield heterosis were validated in a new set of 14 experimental hybrids, the markers exhibited a higher correlation (r = 0.79), indicating the predictive value of these EST-SSRs. We recommend these 10 ÔkeyÕ informative EST-SSR markers for analysis of genetic diversity of parental lines and prediction of heterosis in hybrid rice breeding programmes.

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Evaluation of a set of 10 F 1 hybrids along with their female (27A and 7A) and male parents (C 43, RS 673, RS 627, CB 26, and CB 29) for grain yield and its component traits revealed that grain yield/plant followed by panicle weight, primary branches/panicle, and 100-seed weight exhibited high levels of heterosis. Eight hybrids exhibited 50% or more mid-parent heterosis for grain yield/plant, of which, one hybrid (27A × RS673) recorded heterobeltiosis above 50% (73.61%). Differential display analysis generated about 2995 reproducible transcripts, which were categorized as UPF 1 -expressed in any one of the parents and F 1 (10.53-14.76%), BPnF 1 -expressed in both parents but not in F 1 (4.56-11.44%), UPnF 1 -expressed in either of the parents and not in F 1 (17.95-27.40%), F 1 nBP-expressed only in F 1 but not in either of the parents (14.39-20.54%), and UET-expressed in both parents and F 1 (34.52-42.43%). A comparison between high and low heterotic hybrids revealed that the proportions of UPF 1 and F 1 nBP transcript patterns were much higher in the former (21.31% and 45.24%) as compared to the latter (16.67% and 32.14%) at the booting and flowering stage, respectively, indicating the role of over-dominance and dominance in the manifestation of grain yield heterosis. Significant positive correlations were observed for differential transcript patterns with mid-parent and better-parent heterosis for the components of grain yield such as primary branches (0.63 and 0.61 at p < 0.01) and 100-seed weight (0.64 and 0.52 at p < 0.01). Cloning and sequence analysis of 16 transcripts that were differentially expressed in hybrids and their parental lines revealed that they code for genes involved in basic cellular processes, cellulose biosynthesis, and assimilate partitioning between various organs and allocation between various pathways, pyrimidine, and polyamine biosynthesis, enhancing ATP production and regulation of plant growth and development.

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