Abstract
Sugarcane (Saccharum spp.) is globally considered an important crop for sugar and biofuel production. During sugarcane production, the heavy reliance on chemical nitrogen fertilizer has resulted in low nitrogen use efficiency (NUE) and high loss. Up until now, there has been extensive research on the transcriptomic dynamics during sugarcane response to low nitrogen (LN) stress. However, the specific contribution of S. spontaneum to the NUE of modern sugarcane remains unclear. In the present study, the comparative transcriptome analysis of two contrasting sugarcane cultivars in response to nitrogen deficiency was performed via the combination of genomes of S. spontaneum and S. officinarum. Sub-genome analysis indicated that S. spontaneum supports the high NUE of modern sugarcane by providing genes related to nitrogen and carbohydrate metabolism, photosynthesis, and amino acid metabolism. Additionally, the key genes involved in nitrogen metabolism from the S. spontaneum were successfully identified through weighted gene co-expression network analyses (WGCNA), and a high-affinity nitrate transporter named ScNRT2.3 was subsequently cloned. Heterogeneous expression of the ScNRT2.3, a cell membrane-localized protein, could enhance the growth of Arabidopsis under low nitrate conditions. Furthermore, a conserved protein module known as NAR2.1/NRT2.3 was shown to regulate the response to LN stress in sugarcane roots through molecular interaction. This work helps to clarify the contribution of S. spontaneum to the NUE in modern sugarcane, and the function of the ScNRT2.3 in sugarcane.