Identification of key candidate genes and pathways responding to nitrogen stress in sugarcane

Nitrogen is a vital element for the growth and development of sugarcane, and nitrogen stress severely impairs these processes. Significant differences exist in nutrient utilization among various sugarcane genotypes. Therefore, it is crucial to investigate the molecular mechanisms underlying nitrogen stress tolerance across different genotypes. In this study, morphological, physiological, and transcriptomic analyses were conducted on seedlings of two sugarcane genotypes (TAGZ, Saccharum officinarum and 51NG3, Saccharum robustum) under low- and high-nitrogen. Under nitrogen stress, 51NG3 exhibited greater plant height and higher activities of glutamine synthetase (GS) and nitrate reductase (NR) compared to TAGZ. Transcriptome analysis revealed that 51NG3 exhibited a broader and more diverse gene expression response, with thousands of genes up- and down-regulated in leaves and roots, while TAGZ showed fewer changes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that 51NG3 emphasized photosynthesis optimization and nitrogen metabolism, whereas TAGZ focused on energy conservation by modulating glycolysis and suppressing core photosynthesis genes. In addition, we identified that the transcription factor ScMYB61.1 exhibited opposite expression patterns in the two sugarcane genotypes. Overexpression of ScMYB61.1 in Arabidopsis improved leaf growth, plant height, and root development under nitrogen-deficient conditions. These findings uncover distinct adaptive strategies among sugarcane genotypes and identify ScMYB61.1 as a promising genetic target for improving nitrogen use efficiency (NUE) and breeding high-NUE cultivars.