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RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids.

A panel of 60 genotypes comprising New Plant Types (NPTs) along with indica , tropical and temperate japonica genotypes was phenotypically evaluated for four seasons in irrigated situation for grain yield per se and component traits. Twenty NPT genotypes were found promising with an average grain yield varying from 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 8% within genotypes, 68% among the genotypes within the population and 24% among the populations were observed (AMOVA). This information may help in identification of potential parents for development of transgressive segregants with very high yield. The association analysis using GLM and MLM models led to the identification of 30 and 10 SSR markers associated with 70 and 16 QTLs, respectively. Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely tiller number ( qTL-6 . 1 , qTL-11 . 1 , qTL-4 . 1 ), panicle length ( qPL-1 . 1 , qPL-5 . 1 , qPL-7 . 1 , qPL-8 . 1 ), flag leaf length ( qFLL-8 . 1 , qFLL-9 . 1 ), flag leaf width ( qFLW-6 . 2 , qFLW-5 . 1 , qFLW-8 . 1 , qFLW-7 . 1 ), total no. of grains ( qTG-2 . 2 , qTG-a7 . 1 ), thousand-grain weight ( qTGW-a1 . 1 , qTGW-a9 . 2 , qTGW-5 . 1 , qTGW-8 . 1 ), fertile grains ( qFG-7 . 1 ), seed length-breadth ratio ( qSlb-3 . 1 ), plant height ( qPHT-6 . 1 , qPHT-9 . 1) , days to 50% flowering ( qFD-1 . 1 ) and grain yield per se ( qYLD-5 . 1 , qYLD-6 . 1a , ...

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