Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency

Abstract

Rice is an ideal crop for improvement of nitrogen use efficiency (NUE), especially with urea, its predominant fertilizer. There is a paucity of studies on rice genotypes contrasting for NUE. We compared low urea-responsive transcriptomes of contrasting rice genotypes, namely Nidhi (low NUE) and Panvel1 (high NUE). Transcriptomes of whole plants grown with media containing normal (15 mM) and low urea (1.5 mM) revealed 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors (TFs) and better photosynthesis, water use efficiency and post-translational modifications. Many of their genes co-localized to NUE-QTLs on chromosomes 1, 3 and 9. A field evaluation under different doses of urea revealed better agronomic performance including grain yield, transport/uptake efficiencies and NUE of Panvel1. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and TFs, among others, contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE.

Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice

“…In the meantime, there have been several attempts to validate the candidate genes with varying success (Madan et al., 2022, Raghuram et al., 2022 ), indicating further scope for identification and shortlisting of more candidates. Important recent progress in this regard has been in the comparative transcriptomics of contrasting NUE genotypes in rice, which projected some potentially important genes ( Neeraja et al., 2021 ; Sharma et al., 2022 ; Sharma et al., 2023 ).…”