Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates

Abstract

The genetic basis for nitrogen (N)-response and N use efficiency (NUE) must be found in N-responsive gene expression or protein regulation. Our transcriptomic analysis of nitrate response in two contrasting rice genotypes of Oryza sativa ssp. Indica (Nidhi with low NUE and Panvel1 with high NUE) revealed the processes/functions underlying differential N-response/NUE. The microarray analysis of low nitrate response (1.5 mM) relative to normal nitrate control (15 mM) used potted 21-days old whole plants. It revealed 1,327 differentially expressed genes (DEGs) exclusive to Nidhi and 666 exclusive to Panvel1, apart from 70 common DEGs, of which 10 were either oppositely expressed or regulated to different extents. Gene ontology analyses revealed that photosynthetic processes were among the very few processes common to both the genotypes in low N response. Those unique to Nidhi include cell division, nitrogen utilization, cytoskeleton, etc. in low N-response, whereas those unique to Panvel1 include signal transduction, protein import into the nucleus, and mitochondria. This trend of a few common but mostly unique categories was also true for transporters, transcription factors, microRNAs, and post-translational modifications, indicating their differential involvement in Nidhi and Panvel1. Protein-protein interaction networks constructed using DEG-associated experimentally validated interactors revealed subnetworks involved in cytoskeleton organization, cell wall, etc. in Nidhi, whereas in Panvel1, it was chloroplast development. NUE genes were identified by selecting yield-related genes from N-responsive DEGs and their co-localization on NUE-QTLs revealed the differential distribution of NUE-genes between genotypes but on the same chromosomes 1 and 3. Such hotspots are important for NUE breeders.

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

“…To understand the genome-wide effects of urea, two indica rice genotypes Nidhi (low NUE) and Panvel1 (high NUE), were grown for 21 days in nutrient-depleted soil containing normal (15 mM) and low (1.5 mM) urea and used for microarray analyses, as described earlier [ 10 , 11 , 16 ]. The raw data were deposited in NCBI GEO (GSE140257).…”

“…Post-transcriptional regulation by miRNAs is implicated in many important traits in rice development, growth, stress tolerance [ 52 , 53 ] and yield [ 54 ], including NUE [ 14 , 16 ]. However, they have not been characterized for urea response in NUE.…”

“…To construct the protein-protein interaction (PPI) networks, DEG-associated interactors detected experimentally were retrieved from STING, PRIN, MCDRP and BioGRID databases, as described earlier [ 16 ]. The interactors were used to construct PPI networks for each genotype and the expression values of the DEGs were mapped onto the networks in Cytoscape ( Supplementary Figures S3 and S4 ).…”

“…Functional genomics revealed various N-responsive genes/processes in rice (reviewed in [ 14 , 16 , 17 ]). Most of them were nitrate-based and only one each was based on urea [ 18 ] or thiourea-based (GSE71492).…”

“…Comparative transcriptomic studies focused on nitrate response in genotypes with contrasting yield [ 13 , 40 ] or NUE in rice [ 16 ], but such studies are lacking for urea, except one field study described by Neerja et al [ 41 ]. In view of the difficulties associated with interpreting the effects of dynamic mixtures of N-forms in field soils, we report here the first controlled study of urea response in contrasting rice genotypes that were field-validated for NUE.…”