Time-Resolved Developmental and Transcriptomic Profiling of Potato Stolon Initiation from Basal Axillary Buds Following Soil Covering

Potato stolon research has emphasized stolon-tip tuberization, leaving the transition of basal axillary buds into subterranean stolons poorly characterized. Using cv. Désirée, we characterized this transition at IS0 immediately before soil covering and at 5, 7, 9, and 11 d thereafter (IS5, IS7, IS9, and IS11) by morphological, histological, and transcriptomic analyses. At IS5, external morphology changed little, although internal tissue reorganization was evident. During IS7–IS9, buds progressively reoriented, enlarged basally, and established a subterranean lateral axis. By IS11, white stolons had formed and entered post-initiation elongation without visible stolon-tip swelling. PCA separated IS0 and IS11 from the intermediate stages, and adjacent-stage differential expression identified the largest DEG sets in IS0–IS5 and IS9–IS11. Direction-resolved GO and KEGG enrichment distinguished successive transitions: early oxidative/defense and phenylpropanoid-related categories; intermediate changes in transport, photosynthesis, redox metabolism, and cytoskeletal organization; and later enrichment of translation-, proteasome-, and cell-division-related categories. Mfuzz clustering provided a complementary overview of broad temporal trajectories, including IS5-associated C6, distinct C3 and C5 patterns during initiation, and IS11-associated C2. RT-qPCR profiles of StBRC1b, StWUS, StWOX5, StCCD8, StSP6A, and StSP3D were broadly consistent with the RNA-Seq trends. These results establish a time-resolved framework for soil-covering-induced stolon initiation and subsequent elongation.