Nitrate-responsive transcriptome analysis of rice RGA1 mutant reveals the role of G-protein alpha subunit in negative regulation of nitrogen-sensitivity and use efficiency

Abstract

Nitrogen (N) use e ciency (NUE) is important for sustainable agriculture. G-protein signalling was implicated in N-response/NUE in rice, but needs genetic characterization of the role of α subunit (RGA1). We found that RGA1 knock-out mutant in japonica rice exhibited lesser nitrate-dose sensitivity, higher yield and NUE relative to the wild type (WT). We investigated its genomewide basis using nitrateresponsive rga1 transcriptome relative to WT. It revealed 3,416 differentially expressed genes (DEGs), including 719 associated with development, grain yield and phenotypic traits for NUE. The upregulated DEGs were related to photosynthesis, chlorophyll, tetrapyrrole and porphyrin biosynthesis, while the downregulated DEGs belonged to cellular protein metabolism and transport, small GTPase signalling, cell redox homeostasis etc. RT-qPCR validated 26 nitrate-responsive DEGs across functional categories. Physiological validation of nitrate-response in the mutant and WT at 1.5 and 15 mM doses revealed higher chlorophyll and stomatal length but decreased stomatal density, conductance and transpiration.The consequent increase in photosynthesis and water use e ciency may contribute to higher yield and NUE in the mutant, whereas the WT was N-dose sensitive. The mutant was not as N dose-responsive as WT in shoot/root growth, productive tillers and heading date, but equally responsive as WT in total N and protein content. RGA1mutant is less impacted by higher N-dose or salt stress in terms of yield, protein content, photosynthetic performance, relative water content, water use e ciency and catalase activity. PPI-network analyses revealed known NUE-related proteins as RGA1 interactors. Therefore, RGA1 regulates N-dose sensitivity and NUE in rice. Key MessageNitrate-responsive transcriptomic, phenotypic and physiological analyses of rice RGA1 mutant revealed many novel RGA1-regulated genes/processes/traits related to nitrogen use e ciency, and provided robust genetic evidence of RGA1-regulation of NUE.