Moderate nitrogen with medium planting density enhances sweet potato storage root growth via hormone signaling and carbon metabolism: A multi-omics perspective

Optimizing nitrogen (N) and planting density is essential for sustainable sweet potato production, but the molecular mechanisms underlying their combined effects remain unclear. This study combined field and pot experiments with transcriptomic and metabolomic analyses to compare low-density, high-nitrogen (LDHN) and medium-density, moderate-nitrogen (MDMN) treatments. Across two seasons, MDMN increased yield by 15–25% compared to LDHN by enhancing storage root number without affecting individual root weight. MDMN accelerated cambial ring formation and increased xylem vessel density at 15–30 days after planting, facilitating assimilate transport during root initiation. Transcriptome analysis identified 9856 differentially expressed genes. Under MDMN, starch/sucrose metabolism genes ( SUS , glgC , WAXY , GBE1 ), MAPK signaling, and hormone transduction were upregulated, while phenylpropanoid and flavonoid biosynthesis genes were downregulated, indicating a shift from nitrogen-intensive defense to carbon storage. Nitrogen metabolism analysis revealed 85 DEGs; most uptake and assimilation genes were downregulated, whereas nitrate reductase genes ( NR ) and nitrate transporter NRT were upregulated, which may suggest altered nitrate reduction under reduced nitrogen supply. Metabolomic profiling identified 1240 differentially accumulated metabolites, including elevated glucose, trehalose, D -fructose, and increased auxin, cytokinin, and jasmonate conjugates supporting root development. Weighted gene co-expression network analysis highlighted WRKY , NAC , bHLH , and TCP transcription factors and confirmed hub genes ( ASMT1 , HIPL2 , EL22Y , MSS1 , GDH1 ) positively correlated with storage root biomass. These findings demonstrate that MDMN establishes a sink-optimized strategy through coordinated hormone signaling, carbon reallocation, and secondary metabolism suppression, providing molecular targets associated with nitrogen metabolism under high-density, low-input systems. • MDMN boosts sweet potato yield 15–25% by increasing storage root number, not individual root weight. • MDMN accelerates cambial ring formation and vascular development, forming efficient transport roots during early initiation. • Multi-omics reveal MDMN shifts carbon from phenylpropanoid/flavonoid defense to starch/sucrose storage. • MDMN modulates auxin, cytokinin, jasmonate, ABA pathways transcriptionally and metabolically, promoting sink establishment. • WGCNA identifies hub genes ( ASMT1 , HIPL2 , EL22Y , MSS1 , GDH1 ) and TFs ( WRKY , NAC , bHLH , TCP ) regulating biomass under MDMN.