Transcriptomic Insights into the Molecular Cross-Talk Between Nitrogen and Phosphorus Use Efficiency in Roots and Shoots of Rice Recombinant Inbred Lines (RILs) BV24 and BV148 (BPT 5204* Varadhan)

Two recombinant inbred lines (RILs) viz. BV 24 (efficient for NUE, PUE) and BV148 (inefficient for NUE, PUE) derived from the cross BPT 5204 Varadhan, exhibiting contrasting responses to nitrogen use efficiency (NUE) and phosphorus use efficiency (PUE), were selected for a detailed transcriptomic study. The RILs were initially grown for 14 days in hydroponics Yoshida media and subsequently transferred to treatments with low nitrogen (no N source), low phosphorus (no P source), combined low N and P (no N and P sources), and a control condition (recommended N and P sources) for 21 days, with three biological replicates for each treatment. On day 35, RNA was extracted separately from roots and shoots, reverse-transcribed into cDNA, and processed using the Illumina paired-end (150 x 2 bp) library preparation protocol. Sequencing was performed on the Illumina NovaSeq 6000 platform, generating high-quality reads. The reads were pre-processed to retain high-quality sequences, aligned to the rice reference genome, and subjected to differential gene expression analysis using standardized bioinformatics tools and pipelines tailored for rice transcriptomic studies. The analysis aimed to elucidate the molecular mechanisms underpinning NUE and PUE in both roots and shoots under varying nutrient conditions.