Combined transcriptome and metabolome analysis reveals nitrogen-responsive genes and metabolites in sugar beet (Beta vulgaris L.) seedlings

Abstract

Nitrogen (N) is an essential macronutrient for the growth and yield of sugar beet (Beta vulgaris L.); however, the molecular mechanisms governing its responses to varying N supply levels have not been fully characterized. Sugar beet seedlings were cultivated under low nitrogen (LN, 0.35 g N kg-1) and high nitrogen (HN, 0.42 g N kg-1) conditions on the same nutrient-soil background. Leaf and root tissues were collected at 30 days after emergence (DAE) for RNA sequencing and untargeted metabolomics analysis. HN treatment increased plant height by 18.60%, fresh weight by 23.31%, and SPAD values by 27.98% at 35 DAE (P < 0.05). RNA-seq detected 1, 472 differentially expressed genes (DEGs) and 148 differentially accumulated metabolites (DAMs) in leaves, and 1, 224 DEGs and 261 DAMs in roots. KEGG co-enrichment analysis identified nitrogen metabolism, amino acid biosynthesis, and alanine-aspartate-glutamate metabolism as pathways jointly enriched by DEGs and DAMs. Fourteen nitrogen metabolism-related DEGs exhibited tissue-specific expression patterns: five DEGs encoding nitrogen assimilation enzymes (GLT1, NIA, and NIR) were upregulated in leaves under HN, participating in the stepwise conversion of nitrate to glutamate; eight DEGs predominantly encoding high-affinity nitrate transporters (NRT2.1 and NRT2.5) were uniformly downregulated in roots under HN. Pearson correlation analysis linked leaf nitrogen assimilation genes to O-phospho-L-serine and D-erythrose-4-phosphate (positive), whereas root NRT2 family genes showed negative correlations with these metabolites. qRT-PCR results supported the expression patterns of key DEGs. Our results illustrate the coordinated transcriptome-metabolome responses in leaves and roots of sugar beet seedlings to different nitrogen levels and provide potential candidate genes and metabolites for future functional validation aimed at improving nitrogen use efficiency in sugar beet.