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

Tri Joko Santoso, Reflinur Reflinur, Zeeshan Ali, Tri Handayani, Alberta Dinar Ambarwati, Chotimatul Azmi, Atmitri Sisharmini, Aniversari Apriana, Dwinita Wikan Utami and Kristianto Nugroho
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Tri Joko Santoso: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia
Reflinur Reflinur: Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Cibinong, Indonesia
Tri Handayani: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia
Alberta Dinar Ambarwati: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia
Chotimatul Azmi: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia
Atmitri Sisharmini: Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia
Aniversari Apriana: Research Center for Food Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia
Dwinita Wikan Utami: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia
Kristianto Nugroho: Research Center for Horticultural Crops, Research Organization for Agriculture and Food, National Research and Innovation Agency, Cibinong, Indonesia

Czech Journal of Genetics and Plant Breeding, vol. preprint

Abstract: 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 (search for similar items in EconPapers)
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Persistent link: https://EconPapers.repec.org/RePEc:caa:jnlcjg:v:preprint:id:25-2026-cjgpb

DOI: 10.17221/25/2026-CJGPB

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