Transcriptomic profiling of shallots (Allium cepa var. aggregatum) reveals differential gene expression patterns under nitrogen deficiency

Nitrogen (N) is essential for crop productivity, yet excessive fertilisation decreases the nitrogen use efficiency and increases the environmental risks. Despite the economic and medicinal importance of the shallot, its molecular response to N deficiency remains unclear. We performed transcriptome profiling of two cultivars (Bima-0 and Bima 1) under N deficient and N-sufficient conditions. The RNA sequencing identified 438 differentially expressed genes (DEGs). The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed significant modulation of the nitrogen metabolism, amino acid biosynthesis, glutathione metabolism, and stress responses pathways, indicating coordinated metabolic reprogramming under N limitation. The cultivar-specific expression patterns suggested differential adaptive strategies. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of fifteen DEGs confirmed the reliability of the RNA-Seq results. The nitrogen deficiency predominantly repressed the photosynthetic and growth-linked genes while activating the stress-responsive pathways. These findings provide the first transcriptome-level insights into the N deficiency responses in shallots and identify candidate genes and pathways for improving the nitrogen use efficiency (NUE) and developing the sustainable fertiliser management of Allium crops.