{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T08:23:15Z","timestamp":1787732595705,"version":"build-2784847793"},"reference-count":44,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Project of Central Guiding Local Technology Development","award":["202407AB110005"],"award-info":[{"award-number":["202407AB110005"]}]},{"name":"Yunnan Fundamental Research Projects","award":["202601AS070108"],"award-info":[{"award-number":["202601AS070108"]}]},{"name":"Yunnan University and the Yunnan Education Department","award":["KC-252514039"],"award-info":[{"award-number":["KC-252514039"]}]},{"award":["KC-252514039"],"award-info":[{"award-number":["KC-252514039"]}],"id":[{"id":"https:\/\/ror.org\/0040axw97","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Potato stolon research has emphasized stolon-tip tuberization, leaving the transition of basal axillary buds into subterranean stolons poorly characterized. Using cv. D\u00e9sir\u00e9e, 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\u2013IS9, 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\u2013IS5 and IS9\u2013IS11. 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.<\/jats:p>","DOI":"10.3390\/ijms27177633","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T08:11:15Z","timestamp":1787731875000},"page":"7633","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Time-Resolved Developmental and Transcriptomic Profiling of Potato Stolon Initiation from Basal Axillary Buds Following Soil Covering"],"prefix":"10.3390","volume":"27","author":[{"given":"Kaiyuan","family":"Zhao","sequence":"first","affiliation":[{"name":"School of Agriculture, Yunnan University, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7332-1783","authenticated-orcid":false,"given":"Baozhen","family":"Jiao","sequence":"additional","affiliation":[{"name":"School of Agriculture, Yunnan University, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Agriculture, Yunnan University, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Vegetables, Anhui Academy of Agricultural Sciences, Hefei 230001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongchao","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Agriculture, Yunnan University, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Binquan","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Agriculture, Yunnan University, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1146\/annurev-arplant-080720-084456","article-title":"Tuber and tuberous root development","volume":"72","author":"Zierer","year":"2021","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"uhae360","DOI":"10.1093\/hr\/uhae360","article-title":"Regulation of storage organ formation by long-distance tuberigen signals in potato","volume":"12","author":"Bao","year":"2025","journal-title":"Hortic. Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00344-023-11053-5","article-title":"Transcriptional and post-transcriptional regulation of tuberization in potato (Solanum tuberosum L.)","volume":"43","author":"Dutta","year":"2024","journal-title":"J. Plant Growth Regul."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1007\/s12229-023-09289-7","article-title":"Critical factors responsible for potato tuberization","volume":"89","author":"Singh","year":"2023","journal-title":"Bot. Rev."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nature10431","article-title":"Control of flowering and storage organ formation in potato by FLOWERING LOCUS T","volume":"478","author":"Navarro","year":"2011","journal-title":"Nature"},{"key":"ref_6","first-page":"365","article-title":"Potato tuber induction is regulated by interactions between components of a tuberigen complex","volume":"58","author":"Teo","year":"2017","journal-title":"Plant Cell Physiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1016\/j.cub.2019.02.018","article-title":"Source\u2013sink regulation is mediated by interaction of an FT homolog with a SWEET protein in potato","volume":"29","author":"Abelenda","year":"2019","journal-title":"Curr. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1016\/j.cub.2016.01.066","article-title":"Potato StCONSTANS-like1 suppresses storage organ formation by directly activating the FT-like StSP5G repressor","volume":"26","author":"Abelenda","year":"2016","journal-title":"Curr. Biol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1104\/pp.15.01314","article-title":"Targets of the StBEL5 transcription factor include the FT ortholog StSP6A that mediates tuber formation","volume":"170","author":"Sharma","year":"2016","journal-title":"Plant Physiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"100547","DOI":"10.1016\/j.xplc.2023.100547","article-title":"Long-distance control of potato storage organ formation by SELF PRUNING 3D and FLOWERING LOCUS T-like 1","volume":"4","author":"Jing","year":"2023","journal-title":"Plant Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/s41477-022-01112-2","article-title":"Spatial control of potato tuberization by the TCP transcription factor BRANCHED1b","volume":"8","author":"Nicolas","year":"2022","journal-title":"Nat. Plants"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1111\/nph.12217","article-title":"The role of the potato (Solanum tuberosum) CCD8 gene in stolon and tuber development","volume":"198","author":"Pasare","year":"2013","journal-title":"New Phytol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4539","DOI":"10.1093\/jxb\/ers132","article-title":"The effects of auxin and strigolactones on tuber initiation and stolon architecture in potato","volume":"63","author":"Roumeliotis","year":"2012","journal-title":"J. Exp. Bot."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1111\/nph.71253","article-title":"StLAX5 regulates stolon initiation to control the tuber number and productivity of potato","volume":"251","author":"Wang","year":"2026","journal-title":"New Phytol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1093\/plphys\/kiab071","article-title":"The molecular and genetic regulation of shoot branching","volume":"187","author":"Luo","year":"2021","journal-title":"Plant Physiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"100028","DOI":"10.1016\/j.ncrops.2024.100028","article-title":"The hormonal, metabolic, and environmental regulation of plant shoot branching","volume":"1","author":"Liu","year":"2024","journal-title":"New Crops"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1093\/plphys\/kiab421","article-title":"Woodland strawberry axillary bud fate is dictated by a crosstalk of environmental and endogenous factors","volume":"187","author":"Caruana","year":"2021","journal-title":"Plant Physiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.molp.2025.12.001","article-title":"Integrative regulation of axillary meristem maturation and stolon fate determination in strawberry by light, gibberellin, and ZFP6","volume":"19","author":"Guo","year":"2026","journal-title":"Mol. Plant"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Luo, Z., Jones, D., Philp-Wright, S., Putterill, J., and Snowden, K.C. (2023). Transcriptomic analysis implicates ABA signaling and carbon supply in the differential outgrowth of petunia axillary buds. BMC Plant Biol., 23.","DOI":"10.1186\/s12870-023-04505-3"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1007\/s00299-020-02511-5","article-title":"WUSCHEL: A master regulator in plant growth signaling","volume":"39","author":"Jha","year":"2020","journal-title":"Plant Cell Rep."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/s44318-024-00302-2","article-title":"Deciphering the molecular logic of WOX5 function in the root stem cell organizer","volume":"44","author":"Zhang","year":"2025","journal-title":"EMBO J."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Hu, J., Hu, J., Duan, S., Xiang, C., Duan, Y., Zhang, S., and Li, G. (2025). Transcriptome analysis reveals co-expression regulation of sugar transport and signaling networks in initiating stolon-to-tuber transition in potato. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26115278"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1111\/tpj.16056","article-title":"Leaves and stolons transcriptomic analysis provides insight into the role of phytochrome F in potato flowering and tuberization","volume":"113","author":"Wang","year":"2023","journal-title":"Plant J."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4838","DOI":"10.1111\/pce.15459","article-title":"Cell fate determination of the potato shoot apex and stolon tips revealed by single-cell transcriptome analysis","volume":"48","author":"Guo","year":"2025","journal-title":"Plant Cell Environ."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"19122","DOI":"10.1038\/s41598-025-02215-4","article-title":"Transcriptomic profiles reveal hormonal regulation of sugar-induced stolon initiation in potato","volume":"15","author":"Wang","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"4665","DOI":"10.1038\/s41467-023-40366-y","article-title":"ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana","volume":"14","author":"Zubrycka","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3057","DOI":"10.1093\/plcell\/koab180","article-title":"Cross-talk between clathrin-dependent post-Golgi trafficking and clathrin-mediated endocytosis in Arabidopsis root cells","volume":"33","author":"Yan","year":"2021","journal-title":"Plant Cell"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"kiae541","DOI":"10.1093\/plphys\/kiae541","article-title":"SYNTAXIN OF PLANTS 132 underpins secretion of cargoes associated with salicylic acid signaling and pathogen defense","volume":"197","author":"Waghmare","year":"2025","journal-title":"Plant Physiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1093\/plcell\/koab249","article-title":"Cell biology of primary cell wall synthesis in plants","volume":"34","author":"Gu","year":"2022","journal-title":"Plant Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1111\/nph.17358","article-title":"A plant-unique ESCRT component, FYVE4, regulates multivesicular endosome biogenesis and plant growth","volume":"231","author":"Liu","year":"2021","journal-title":"New Phytol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1093\/plphys\/kiae138","article-title":"TCP transcription factor StAST1 represses potato tuberization by regulating tuberigen complex activity","volume":"195","author":"Sun","year":"2024","journal-title":"Plant Physiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1676","DOI":"10.1111\/nph.19426","article-title":"The tuber-specific StbHLH93 gene regulates proplastid-to-amyloplast development during stolon swelling in potato","volume":"241","author":"Yang","year":"2024","journal-title":"New Phytol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"giaa100","DOI":"10.1093\/gigascience\/giaa100","article-title":"Construction of a chromosome-scale long-read reference genome assembly for potato","volume":"9","author":"Pham","year":"2020","journal-title":"GigaScience"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"5","DOI":"10.6026\/97320630002005","article-title":"Mfuzz: A software package for soft clustering of microarray data","volume":"2","author":"Kumar","year":"2007","journal-title":"Bioinformation"},{"key":"ref_40","first-page":"100141","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"The Gene Ontology Consortium, Aleksander, S.A., Balhoff, J., Carbon, S., Cherry, J.M., Drabkin, H.J., Ebert, D., Feuermann, M., Gaudet, P., and Harris, N.L. (2023). The Gene Ontology knowledgebase in 2023. Genetics, 224, iyad031.","DOI":"10.1093\/genetics\/iyad031"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"D672","DOI":"10.1093\/nar\/gkae909","article-title":"KEGG: Biological systems database as a model of the real world","volume":"53","author":"Kanehisa","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2\u2212\u0394\u0394CT method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1093\/clinchem\/hvaf043","article-title":"MIQE 2.0: Revision of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments Guidelines","volume":"71","author":"Bustin","year":"2025","journal-title":"Clin. Chem."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7633\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T08:14:37Z","timestamp":1787732077000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/17\/7633"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,26]]},"references-count":44,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ijms27177633"],"URL":"https:\/\/doi.org\/10.3390\/ijms27177633","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,26]]}}}