Comparative transcriptome analysis of different nitrogen responses in low-nitrogen sensitive and tolerant maize genotypes

Although previous researches have greatly increased our general knowledge on plant responses to nitrogen (N) stress, a comprehensive understanding of the different responses in crop genotypes is still needed. This study evaluated 304 maize accessions for low-N tolerance under field conditions, and selected the low-N sensitive Ye478 and low-N tolerant Qi319 for further investigations. After a 5-day low-N treatment, the typical N-deficient phenotype with yellowing older leaves was observed in Ye478 but not in Qi319. After the 5-day low-N stress, 16 RNA libraries from leaf and root of Ye478 and Qi319 were generated. The differentially expressed genes (DEGs) in the root of Qi319 up-regulated by special N deficiency were mainly enriched in energy-related metabolic pathways, including tricarboxylic acid metabolic process and nicotinamide metabolic process. Consistent with yellowing older leaves only observed in Ye478, the special N deficiency-responsive DEGs related to thylakoid, chloroplast, photosynthetic membrane, and chloroplast stroma pathways were repressed by low-N stress in Ye478. A total of 216 transcription factors (TFs), including ZmNLP5, were identified as special N deficiency-responsive TFs between Qi319 and Ye478, indicating the importance of transcriptional regulation of N stress-responsive pathway in different tolerance to low-N stress between crop genotypes. In addition, 15 miRNAs were identified as DEGs between Qi319 and Ye478. Taken together, this study contributes to the understanding of the genetic variations and molecular basis of low-N tolerance in maize.