Reverse transcription quantitative real-time PCR (RT-qPCR) is arguably the most prevalent and accurate quantitative gene expression analysis. However, selection of reliable reference genes for RT-qPCR in rice (Oryza sativa) is still limited, especially for a specific tissue type or growth condition. In this study, we took the advantage of our RNA-seq datasets encompassing data from five rice varieties with diverse treatment conditions, identified 12 novel candidate reference genes, and conducted rigorous evaluations of their suitability across typical rice tissues. Comprehensive analysis of the leaves, shoots, and roots of two rice seedlings subjected to salt (30 mmol/L NaCl) and drought (air-dry) stresses have revealed that OsMED7, OsACT1, and OsOS-9 were the robust reference genes for leaf samples, while OsACT1, OsZOS3-23, and OsGDCP were recommended for shoots and OsMED7, OsOS-9, and OsGDCP were the most reliable reference genes for roots. Comparison results produced by different sets of reference genes revealed that all these newly recommended reference genes displayed less variation than previous commonly used references genes under the experiment conditions. Thus, selecting appropriate reference genes from RNA-seq datasets leads to identification of reference genes suitable for respective rice tissues under drought and salt stress. The findings offer valuable insights for refining the screening of candidate reference genes under diverse conditions through the RNA-seq database. This refinement serves to improve the accuracy of gene expression in rice under similar conditions.

Maintaining rice yield and reducing nitrogen (N) input are two important targets in sustainable agriculture practices. The adoption of a nitrogen-saving variety (NSV) provides a unique opportunity to achieve this. However, limited options in NSV japonica rice and a lack of information on their responses to N reduction make management decisions difficult. This study aims to explore the responses of yield and nitrogen use efficiency (NUE) in NSV to N reduction. Two newly released NSVs and two popular general varieties (GVs) of japonica rice were field tested in Yangzhou, located at the lower reaches of Yangtze River of China, in two consecutive years. The results showed that for NSVs, with a 40–60% reduction in common practice N rate (300 Kg ha⁻¹), the rice yield could maintain a record average level (p < 0.05), whereas the yield for the GV would drop 20–30% (p < 0.05). This indicates that combining the practices of adoption of NSV and N reduction to 120–180 Kg N ha⁻¹ could balance the yield and N consumption. Moderate N reduction promotes the N accumulation and NUE, and it increases the number of tillers, the productive tiller percentage and the total amount of spikelets in the population, and increases the carbon and N metabolism of the population in the NSV. Compared with GV, NSV showed higher NUE and non-structural carbohydrate re-mobilization in the reduced N rate. The results showed that the practice of N reduction has to adopt NSV at the same time in order to maintain the grain yield level in rice.