In the present study, de novo transcriptome analysis of Selaginella bryopteris in frond and root was performed to understand the regulation of flavonoid (FL) biosynthesis. High-quality data of 5.84 and 5.86 Gb was generated for frond and root, respectively, that assembled into 94,713 and 81,567 transcripts. A total of 87,471 and 73,395 unigenes were obtained from frond and root, respectively. A total of 41,267 and 31,048 CDS of frond and root, respectively, were annotated by BLASTX, which showed maximum hits against S. moellendorffii. Out of 11,285 differentially expressed genes, a total of 5639 genes were found to be down-regulated and 5628 genes up-regulated in frond as compared to those in root. In silico analysis of expression of genes in frond as compared to that in root was done for those related to phenylpropanoid (PP)/FL biosynthesis along with transcription factors (TFs) after DESeq and MapMan-based information. Results showed that genes of PP/FL biosynthesis pathway namely SbCHS, SbCHI, SbF3H, SbF3'H, SbDFR, SbUF3GT, SbCCOAMT, and SbCATOMT and TFs (SbMYB1, SbMYB2, SbMYB3, SbBHLH1, and SbWD40-5) were up-regulated in frond in comparison to those in root. Further, this in silico expression data was validated by RT-PCR analysis which showed predominant expression of most of these genes in frond and indicated their importance in the biosynthesis of flavonoids in S. bryopteris. A total of 9074 simple sequence repeats (SSRs) were also identified for frond and 3811 SSRs for root; these can be used for experimental validation.

‘Katarni Rice’ is a fine quality scented rice landrace of Bihar, India and has tremendous export potential and commercial value. This is a preferred rice in the state due to its flavour, palatability and popcorn like essence before and after cooking. But its area has been shrunken drastically in recent years due to its low yielding (25–30 Q/ha) ability caused due tall and week stature and lodging tendency at maturity. To overcome this problem, marker assisted introgression of semi-dwarfing (sd1) gene from semi-dwarf and high yielding rice varieties Rajendra Sweta and BPT5204 was attempted. Parental polymorphism was obtained through 109 SSR markers. The gene specific markers for fragrance and semi-dwarfing genes were used in the segregants to track their transfer. Recombinant selection was done for the donor genome segments flanking to the target gene i.e., sd1 followed by background selection through genome wide polymorphic SSR markers. More than 90% recurrent parent genome recovery was observed and the selected plants showed a reduction of plant height and flowering time in comparison to Katarni in the successive backcross generation along with the retention of aroma. The identified lines can be evaluated further in multilocation trials to release it as a sustainable high yielding aromatic genotype.

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