Transcriptomics Uncovers Pathways Mediating Low-Nitrogen Stress Tolerance in Two Foxtail Millet Varieties

Nitrogen crucially impacts foxtail millet ( Setaria italica ) growth and development. Uncovering low nitrogen (LN) tolerance genes and mechanisms is vital for breeding high nitrogen use efficiency varieties. In this study, the LN tolerance of 50 foxtail millet genotypes was assessed through field trials and seedling hydroponic experiments. Subsequently, transcriptome analysis was performed on one highly sensitive genotype, named Maotigu, and on one highly tolerant genotype, named Dahuanggu, under LN (0.1 mmol/L) and control (5 mmol/L) conditions in seedling hydroponic experiments. Compared to the control treatment, 823 differentially expressed genes (DEGs) (350 upregulated, 473 downregulated) were identified in the roots of Dahuanggu, while 2427 DEGs (1703 upregulated, 724 downregulated) were detected in Maotigu under LN treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that a total of 3134 DEGs were associated with pathways including plant–pathogen interaction, amino sugar and nucleotide sugar metabolism, nitrogen metabolism, and others. A total of 116 DEGs were commonly identified between Dahuanggu and Maotigu, involving pathways like plant–pathogen interaction, galactose metabolism, and flavone and flavonol biosynthesis. The 28 of 116 DEGs showed opposite expression patterns between Dahuanggu and Maotigu; the expression of 18 genes was further validated using qRT-PCR. These offer valuable insights into the molecular mechanisms underlying LN stress responses in foxtail millet.