Unveiling the potential regulatory functions of long non-coding RNAs in potato tuberization through integrated analysis of transcriptomics and phytohormone profiles

BACKGROUND: Long non-coding RNAs (lncRNAs) are pivotal in plant development, including organ morphogenesis. However, currently, the biological significance of potato lncRNAs is still not fully known. This study delved into the cytological, transcriptomic, and phytohormonal dynamics that lie beneath potato tuberization. Special attention was given to the potential regulatory functions of lncRNAs. RESULTS: Cytological analysis indicated that tuber formation, encompassing non-swollen stolons (Stolon, stage 1), swelling stolons (Swelling, stage 2), tuber initiation (Initiation, stage 3), and small tubers (Tuber, stage 4), is marked by progressive cellular expansion, vascular disruption, and starch granule accumulation. Through RNA-seq analysis, 11,380 long non-coding RNA (lncRNAs) were identified across the four developmental stages, among which 520 were Arabidopsis homologs. Long intergenic non-coding RNAs (lincRNAs) predominated, accounting for 85.58%. The differentially expressed long non-coding RNAs (DELs) were predominantly enriched in processes related to auxin response, transcription factor activity, and signal transduction pathways. Phytohormonal profiles exhibited dynamic fluctuations in auxin (IAA), gibberellins (GAs), abscisic acid (ABA), and cytokinin (CTKs). The integration of phytohormone analysis with transcriptomics unveiled intricate regulatory networks among hormonal dynamics - particularly those involving GAs, ABA, and CTKs - transcription factors, and lncRNA genes. Upstream regulatory lncRNAs of crucial tuberization-related genes, including StSP6A, StPOTH1, StGA20OX1, StBRC1b, StAST1, and StSP5G, were identified. Moreover, both transient dual-LUC and GUS reporter assays were employed to verify the effect of StLNC_031680 on the expression of StHSFA6b. CONCLUSION: Overall, our findings comprehensively and for the first time globally uncovered the potentially crucial roles of lncRNAs in potato tuberization. These findings offer valuable insights into potato tuber formation and support advanced strategies for crop improvement.