Integrated Transcriptomic and Metabolomic Analysis of Starch Biosynthesis in Different Spatial Regions of Tetraploid Potato Tubers.

Potato tubers exhibit prominent spatial heterogeneity in starch accumulation across distinct anatomical zones, yet the underlying transcriptional and metabolic regulatory mechanisms remain unclear, especially the molecular basis for divergent starch deposition between high- and low-starch tetraploid cultivars. In this study, the high-starch cultivar Atlantic (DX) and low-starch cultivar Dingshu No. 1 (D) were used as experimental materials. Dynamic starch contents of the tuber cortex (CR), perimedullary region (PMR), and inner medullary region (IMR) were measured throughout starch biosynthetic stages. Integrated untargeted metabolomics and RNA-seq transcriptomics were performed to compare transcriptional and metabolic differentiation between CR and IMR with the largest starch gap, followed by qRT-PCR verification of hub genes. Physiological results showed that starch content in both cultivars followed the gradient CR > PMR > IMR, and inter-regional starch disparities expanded continuously with tuber development; low-starch D had lower overall starch levels and milder tissue differences than DX. Transcriptomic analysis revealed massive transcriptional activation in the cortex of both cultivars, while D displayed far more dramatic transcriptional divergence between CR and IMR than DX. Core transcription factors including AP2/ERF, bHLH and MYB were identified to mediate tissue-specific starch synthesis. Metabolomic data demonstrated severe carbon metabolic polarization in D (hyperactive cortex, weak inner medulla), whereas DX maintained balanced sugar metabolism across whole tuber tissues. Integrated multi-omics analysis of the starch and sucrose pathway (ko00500) screened 18 key structural genes. High-starch DX upregulated starch synthetic and sugar transport genes while repressing starch hydrolysis and carbon diversion genes, realizing coordinated whole-tuber carbon flux toward starch production. In contrast, D showed disrupted regulatory networks, excessive carbon shunting to secondary metabolism and aggravated starch degradation, limiting starch accumulation. Three conserved negative regulatory candidate genes, LOC102593331 (TPS), LOC102584887 (AMY), and LOC102580651 (EN), were characterized via tissue expression profiling: TPS dominates upstream carbon flux allocation, EN competes for starch precursors during cell wall synthesis, and AMY accelerates starch breakdown. This study systematically uncovered the molecular framework of spatial starch heterogeneity in tetraploid potato tubers, clarified the essential distinctions in carbon partitioning strategies between high- and low-starch cultivars, and provided valuable gene resources and theoretical support for high-starch potato molecular design breeding.