Comparative Physiological and Transcriptomic Characterisation of Two Japonica Rice Cultivars Under Low Nitrogen Stress

Nitrogen (N) is an essential nutrient for the growth and development of rice. However, excessive N fertiliser application and low N Use Efficiency (NUE) have led to serious environmental problems and threatened agricultural sustainability. In this study, we compared the physiological and transcriptomic profiles of roots of two cultivars exposed to normal nitrogen (NN) and low nitrogen (LN). The results showed that the LN treatment suppressed root growth and severely affected enzymatic activities in the roots of both rice cultivars compared to the NN treatment. Moreover, HJ753 exhibited significantly higher activities of NITRATE REDUCTASE (NR) and GLUTAMINE SYNTHETASE (GS) in its roots than DJ8 under both LN and NN conditions. Transcriptomic analysis identified 23,205 genes across all samples, with more than 5000 differentially expressed genes (DEGs) detected in response to LN stress in both cultivars. The KEGG analysis revealed that the DEGs were primarily involved in DNA replication, tryptophan metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and N metabolism. Under LN stress, most genes associated with tryptophan metabolism and phenylpropanoid biosynthesis pathways remained stable or were upregulated in both cultivars. In contrast, genes related to auxin signalling transduction, N metabolism, and N utilisation exhibited significant genotype-specific expression patterns between HJ753 and DJ8. In conclusion, this study elucidated the genotypic differences in root development and N response mechanisms under LN stress at the molecular level, providing new insights into the regulatory mechanisms of N efficiency that may be used to develop and support the breeding of N-efficient rice cultivars.