Czech J. Genet. Plant Breed., X:X | DOI: 10.17221/25/2026-CJGPB

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

Tri Joko Santoso1, Reflinur Reflinur2, Zeeshan Ali1*, Tri Handayani1, Alberta Dinar Ambarwati1, Chotimatul Azmi1, Atmitri Sisharmini3, Aniversari Apriana3, Dwinita Wikan Utami1, Kristianto Nugroho1
1 Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia
2 Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Cibinong, Indonesia
3 Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia

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.

Keywords: DEGs; gene enrichment; gene expression; metabolic pathways; nitrogen use efficiency

Received: February 25, 2026; Revised: April 14, 2026; Accepted: April 30, 2026; Prepublished online: May 26, 2026 

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