doi:10.48130/forres-0026-0007

[1]

Ko D, Helariutta Y. 2017. Shoot–root communication in flowering plants. Current Biology 27:R973−R978

doi: 10.1016/j.cub.2017.06.054

[2]

Scheres B. 2007. Stem-cell niches: nursery rhymes across kingdoms. Nature Reviews Molecular Cell Biology 8:345−354

doi: 10.1038/nrm2164

[3]

Kitagawa M, Jackson D. 2019. Control of meristem size. Annual Review of Plant Biology 70:269−291

doi: 10.1146/annurev-arplant-042817-040549

[4]

Aichinger E, Kornet N, Friedrich T, Laux T. 2012. Plant stem cell niches. Annual Review of Plant Biology 63:615−636

doi: 10.1146/annurev-arplant-042811-105555

[5]

Wang Y, Jiao Y. 2023. Cell signaling in the shoot apical meristem. Plant Physiology 193:70−82

doi: 10.1093/plphys/kiad309

[6]

Mayer KFX, Schoof H, Haecker A, Lenhard M, Jürgens G, et al. 1998. Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell 95:805−815

doi: 10.1016/S0092-8674(00)81703-1

[7]

Daum G, Medzihradszky A, Suzaki T, Lohmann JU. 2014. A mechanistic framework for noncell autonomous stem cell induction in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 111:14619−14624

doi: 10.1073/pnas.1406446111

[8]

Yadav RK, Perales M, Gruel J, Girke T, Jönsson H, et al. 2011. WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex. Genes & Development 25:2025−2030

doi: 10.1101/gad.17258511

[9]

Li S, Meng S, Weng J, Wu Q. 2022. Fine-tuning shoot meristem size to feed the world. Trends in Plant Science 27:355−363

doi: 10.1016/j.tplants.2021.10.004

[10]

Brand U, Fletcher JC, Hobe M, Meyerowitz EM, Simon R. 2000. Dependence of stem cell fate in Arabidopsis on a feedback loop regulated by CLV3 activity. Science 289:617−619

doi: 10.1126/science.289.5479.617

[11]

Plong A, Rodriguez K, Alber M, Chen W, Reddy GV. 2021. CLAVATA3 mediated simultaneous control of transcriptional and post-translational processes provides robustness to the WUSCHEL gradient. Nature Communications 12:6361

doi: 10.1038/s41467-021-26586-0

[12]

Zhou Y, Liu X, Engstrom EM, Nimchuk ZL, Pruneda-Paz JL, et al. 2015. Control of plant stem cell function by conserved interacting transcriptional regulators. Nature 517:377−380

doi: 10.1038/nature13853

[13]

Zhou Y, Yan A, Han H, Li T, Geng Y, et al. 2018. HAIRY MERISTEM with WUSCHEL confines CLAVATA3 expression to the outer apical meristem layers. Science 361:502−506

doi: 10.1126/science.aar8638

[14]

Geng Y, Xie C, Zhang C, Liu X, Zhou Y. 2025. Functions and regulation of HAM family genes in meristems during gametophyte and sporophyte generations. Plant, Cell & Environment 48:2125−2131

doi: 10.1111/pce.15286

[15]

Takanashi H, Sumiyoshi H, Mogi M, Hayashi Y, Ohnishi T, et al. 2018. miRNAs control HAM1 functions at the single-cell-layer level and are essential for normal embryogenesis in Arabidopsis. Plant Molecular Biology 96:627−640

doi: 10.1007/s11103-018-0719-8

[16]

Han H, Geng Y, Guo L, Yan A, Meyerowitz EM, et al. 2020. The overlapping and distinct roles of HAM family genes in Arabidopsis shoot meristems. Frontiers in Plant Science 11:541968

doi: 10.3389/fpls.2020.541968

[17]

Jasinski S, Piazza P, Craft J, Hay A, Woolley L, et al. 2005. KNOX action in Arabidopsis is mediated by coordinate regulation of cytokinin and gibberellin activities. Current Biology 15:1560−1565

doi: 10.1016/j.cub.2005.07.023

[18]

Long JA, Moan EI, Medford JI, Barton MK. 1996. A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature 379:66−69

doi: 10.1038/379066a0

[19]

Yanai O, Shani E, Dolezal K, Tarkowski P, Sablowski R, et al. 2005. Arabidopsis KNOXI proteins activate cytokinin biosynthesis. Current Biology 15:1566−1571

doi: 10.1016/j.cub.2005.07.060

[20]

Su YH, Zhou C, Li YJ, Yu Y, Tang LP, et al. 2020. Integration of pluripotency pathways regulates stem cell maintenance in the Arabidopsis shoot meristem. Proceedings of the National Academy of Sciences of the United States of America 117:22561−22571

doi: 10.1073/pnas.2015248117

[21]

Gordon SP, Chickarmane VS, Ohno C, Meyerowitz EM. 2009. Multiple feedback loops through cytokinin signaling control stem cell number within the Arabidopsis shoot meristem. Proceedings of the National Academy of Sciences of the United States of America 106:16529−16534

doi: 10.1073/pnas.0908122106

[22]

Chickarmane VS, Gordon SP, Tarr PT, Heisler MG, Meyerowitz EM. 2012. Cytokinin signaling as a positional cue for patterning the apical–basal axis of the growing Arabidopsis shoot meristem. Proceedings of the National Academy of Sciences of the United States of America 109:4002−4007

doi: 10.1073/pnas.1200636109

[23]

Meng WJ, Cheng ZJ, Sang YL, Zhang MM, Rong XF, et al. 2017. Type-B ARABIDOPSIS RESPONSE REGULATORs specify the shoot stem cell niche by dual regulation of WUSCHEL. The Plant Cell 29:1357−1372

doi: 10.3410/f.727683202.793535470

[24]

Wang J, Tian C, Zhang C, Shi B, Cao X, et al. 2017. Cytokinin signaling activates WUSCHEL expression during axillary meristem initiation. The Plant Cell 29:1373−1387

doi: 10.1105/tpc.16.00579

[25]

Zhang TQ, Lian H, Zhou CM, Xu L, Jiao Y, et al. 2017. A two-step model for de novo activation of WUSCHEL during plant shoot regeneration. The Plant Cell 29:1073−1087

doi: 10.1105/tpc.16.00863

[26]

Zubo YO, Blakley IC, Yamburenko MV, Worthen JM, Street IH, et al. 2017. Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 114:E5995−E6004

doi: 10.1073/pnas.1620749114

[27]

Snipes SA, Rodriguez K, DeVries AE, Miyawaki KN, Perales M, et al. 2018. Cytokinin stabilizes WUSCHEL by acting on the protein domains required for nuclear enrichment and transcription. PLoS Genetics 14:e1007351

doi: 10.1371/journal.pgen.1007351

[28]

Leibfried A, To JPC, Busch W, Stehling S, Kehle A, et al. 2005. WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators. Nature 438:1172−1175

doi: 10.1038/nature04270

[29]

Ma J, Wang Y, Chen S, Xu T. 2025. The central role of auxin in orchestrating apical stem cells in plants. Plant, Cell & Environment 48:5053−5072

doi: 10.1111/pce.15464

[30]

Ma Y, Miotk A, Šutiković Z, Ermakova O, Wenzl C, et al. 2019. WUSCHEL acts as an auxin response rheostat to maintain apical stem cells in Arabidopsis. Nature Communications 10:5093

doi: 10.1038/s41467-019-13074-9

[31]

Luo L, Zeng J, Wu H, Tian Z, Zhao Z. 2018. A molecular framework for auxin-controlled homeostasis of shoot stem cells in Arabidopsis. Molecular Plant 11:899−913

doi: 10.1016/j.molp.2018.04.006

[32]

Ince YÇ, Sugimoto K. 2023. Illuminating the path to shoot meristem regeneration: Molecular insights into reprogramming cells into stem cells. Current Opinion in Plant Biology 76:102452

doi: 10.1016/j.pbi.2023.102452

[33]

Xu C, Chang P, Guo S, Yang X, Liu X, et al. 2024. Transcriptional activation by WRKY23 and derepression by removal of bHLH041 coordinately establish callus pluripotency in Arabidopsis regeneration. The Plant Cell 36:158−173

doi: 10.1093/plcell/koad255

[34]

Bao Y, Dharmawardhana P, Arias R, Allen MB, Ma C, et al. 2009. WUS and STM-based reporter genes for studying meristem development in poplar. Plant Cell Reports 28:947−962

doi: 10.1007/s00299-009-0685-3

[35]

Sang YL, Cheng ZJ, Zhang XS. 2018. iPSCs: a comparison between animals and plants. Trends in Plant Science 23:660−666

doi: 10.1016/j.tplants.2018.05.008

[36]

Gordon SP, Heisler MG, Reddy GV, Ohno C, Das P, et al. 2007. Pattern formation during de novo assembly of the Arabidopsis shoot meristem. Development 134:3539−3548

doi: 10.1242/dev.010298

[37]

Paul LK, Rinne PL, van der Schoot C. 2014. Shoot meristems of deciduous woody perennials: self-organization and morphogenetic transitions. Current Opinion in Plant Biology 17:86−95

doi: 10.1016/j.pbi.2013.11.009

[38]

Nilsson O. 2022. Winter dormancy in trees. Current Biology 32:R630−R634

doi: 10.1016/j.cub.2022.04.011

[39]

Ding J, Wang K, Pandey S, Perales M, Allona I, et al. 2024. Molecular advances in bud dormancy in trees. Journal of Experimental Botany 75:6063−6075

doi: 10.1093/jxb/erae183

[40]

Gao Y, Chen Z, Feng Q, Long T, Ding J, et al. 2024. ELONGATED HYPOCOTYL 5a modulates FLOWERING LOCUS T2 and gibberellin levels to control dormancy and bud break in poplar. The Plant Cell 36:1963−1984

doi: 10.1093/plcell/koae022

[41]

Böhlenius H, Huang T, Charbonnel-Campaa L, Brunner AM, Jansson S, et al. 2006. CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312:1040−1043

doi: 10.1126/science.1126038

[42]

Ding J, Böhlenius H, Rühl MG, Chen P, Sane S, et al. 2018. GIGANTEA-like genes control seasonal growth cessation in Populus. New Phytologist 218:1491−1503

doi: 10.1111/nph.15087

[43]

IbÁñez C, Kozarewa I, Johansson M, Ögren E, Rohde A, et al. 2010. Circadian clock components regulate entry and affect exit of seasonal dormancy as well as winter hardiness in Populus trees. Plant Physiology 153:1823−1833

doi: 10.1104/pp.110.158220

[44]

Ramos-Sánchez JM, Triozzi PM, Alique D, Geng F, Gao M, et al. 2019. LHY2 integrates night-length information to determine timing of poplar photoperiodic growth. Current Biology 29:2402−2406.e4

doi: 10.1016/j.cub.2019.06.003

[45]

Suárez-López P, Wheatley K, Robson F, Onouchi H, Valverde F, et al. 2001. CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410:1116−1120

doi: 10.1038/35074138

[46]

Luo A, Xu X, Liu Y, Li Y, Su X, et al. 2023. Spatio-temporal patterns in the woodiness of flowering plants. Global Ecology and Biogeography 32:384−396

doi: 10.1111/geb.13627

[47]

Liu S, Xu H, Wang G, Jin B, Cao F, et al. 2025. Tree longevity: multifaceted genetic strategies and beyond. Plant, Cell & Environment 48:244−259

doi: 10.1111/pce.15146

[48]

Fischer U, Kucukoglu M, Helariutta Y, Bhalerao RP. 2019. The dynamics of cambial stem cell activity. Annual Review of Plant Biology 70:293−319

doi: 10.1146/annurev-arplant-050718-100402

[49]

Fletcher JC, Brand U, Running MP, Simon R, Meyerowitz EM. 1999. Signaling of cell fate decisions by CLAVATA3 in Arabidopsis shoot meristems. Science 283:1911−1914

doi: 10.1126/science.283.5409.1911

[50]

Maes L, Inzé D, Goossens A. 2008. Functional specialization of the TRANSPARENT TESTA GLABRA1 network allows differential hormonal control of laminal and marginal trichome initiation in Arabidopsis rosette leaves. Plant Physiology 148:1453−1464

doi: 10.1104/pp.108.125385

[51]

Vidal EA, Araus V, Lu C, Parry G, Green PJ, et al. 2010. Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America 107:4477−4482

doi: 10.1073/pnas.0909571107

[52]

Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, et al. 2015. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Molecular Plant 8:1274−1284

doi: 10.1016/j.molp.2015.04.007

[53]

Zhang Z, Zhang R, Meng F, Chen Y, Wang W, et al. 2023. A comprehensive atlas of long non-coding RNAs provides insight into grain development in wheat. Seed Biology 2:12

doi: 10.48130/seedbio-2023-0012

[54]

Kim S, Park JS, Lee J, Lee KK, Park OS, et al. 2021. The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection. Proceedings of the National Academy of Sciences of the United States of America 118:e2026806118

doi: 10.1073/pnas.2026806118

[55]

Ohyama K, Shinohara H, Ogawa-Ohnishi M, Matsubayashi Y. 2009. A glycopeptide regulating stem cell fate in Arabidopsis thaliana. Nature Chemical Biology 5:578−580

doi: 10.1038/nchembio.182

[56]

Ma T, Li E, Li LS, Li S, Zhang Y. 2021. The Arabidopsis R-SNARE protein YKT61 is essential for gametophyte development. Journal of Integrative Plant Biology 63:676−694

doi: 10.1111/jipb.13017

[57]

Liu JH, Dong WC, Fei FF, Li XT, Zhang XH, et al. 2022. Regulation of WOX11 expression represents the difference between direct and indirect shoot regeneration. Frontiers in Plant Science 13:850726

doi: 10.3389/fpls.2022.850726

[58]

Heisler MG, Ohno C, Das P, Sieber P, Reddy GV, et al. 2005. Patterns of auxin transport and gene expression during primordium development revealed by live imaging of the Arabidopsis inflorescence meristem. Current Biology 15:1899−1911

doi: 10.1016/j.cub.2005.09.052

[59]

Qiu D, Bai S, Ma J, Zhang L, Shao F, et al. 2019. The genome of Populus alba x Populus tremula var. glandulosa clone 84K. DNA Research 26:423−431

doi: 10.1093/dnares/dsz020

[60]

Han H, Zhang G, Wu M, Wang G. 2016. Identification and characterization of the Populus trichocarpa CLE family. BMC Genomics 17:174

doi: 10.1186/s12864-016-2504-x

[61]

Liu Z, Yang N, Lv Y, Pan L, Lv S, et al. 2016. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior 11:e1191734

doi: 10.1080/15592324.2016.1191734

[62]

Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI, et al. 2022. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nature Biotechnology 40:1023−1025

doi: 10.1038/s41587-021-01156-3

[63]

Laux T, Mayer KFX, Berger J, Jürgens G. 1996. The WUSCHEL gene is required for shoot and floral meristem integrity in Arabidopsis. Development 122:87−96

doi: 10.1242/dev.122.1.87

[64]

Reddy GV, Meyerowitz EM. 2005. Stem-cell homeostasis and growth dynamics can be uncoupled in the Arabidopsis shoot apex. Science 310:663−667

doi: 10.1126/science.1116261

[65]

Singh RK, Svystun T, AlDahmash B, Jönsson AM, Bhalerao RP. 2017. Photoperiod- and temperature-mediated control of phenology in trees – a molecular perspective. New Phytologist 213:511−524

doi: 10.1111/nph.14346

[66]

Fan C, Wu Y, Yang Q, Yang Y, Meng Q, et al. 2014. A novel single-nucleotide mutation in a CLAVATA3 gene homolog controls a multilocular silique trait in Brassica rapa L. Molecular Plant 7:1788−1792

doi: 10.1093/mp/ssu090

[67]

Kieffer M, Stern Y, Cook H, Clerici E, Maulbetsch C, et al. 2006. Analysis of the transcription factor WUSCHEL and its functional homologue in Antirrhinum reveals a potential mechanism for their roles in meristem maintenance. The Plant Cell 18:560−573

doi: 10.1105/tpc.105.039107

[68]

Meng Y, Liu H, Wang H, Liu Y, Zhu B, et al. 2019. HEADLESS, a WUSCHEL homolog, uncovers novel aspects of shoot meristem regulation and leaf blade development in Medicago truncatula. Journal of Experimental Botany 70:149−163

doi: 10.1093/jxb/ery346

[69]

Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB. 2017. Engineering quantitative trait variation for crop improvement by genome editing. Cell 171:470−480.e8

doi: 10.1016/j.cell.2017.08.030

[70]

Stuurman J, Jäggi F, Kuhlemeier C. 2002. Shoot meristem maintenance is controlled by a GRAS-gene mediated signal from differentiating cells. Genes & Development 16:2213−2218

doi: 10.1101/gad.230702

[71]

Xu C, Liberatore KL, MacAlister CA, Huang Z, Chu YH, et al. 2015. A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nature Genetics 47:784−792

doi: 10.1038/ng.3309

[72]

Demesa-Arevalo E, Narasimhan M, Simon R. 2024. Intercellular communication in shoot meristems. Annual Review of Plant Biology 75:319−344

doi: 10.1146/annurev-arplant-070523-035342

[73]

Wybouw B, Zhang X, Mähönen AP. 2024. Vascular cambium stem cells: past, present and future. New Phytologist 243:851−865

doi: 10.1111/nph.19897

[74]

Atkins PA, Voytas DF. 2020. Overcoming bottlenecks in plant gene editing. Current Opinion in Plant Biology 54:79−84

doi: 10.1016/j.pbi.2020.01.002

[75]

Bouchabké-Coussa O, Obellianne M, Linderme D, Montes E, Maia-Grondard A, et al. 2013. Wuschel overexpression promotes somatic embryogenesis and induces organogenesis in cotton (Gossypium hirsutum L.) tissues cultured in vitro. Plant Cell Reports 32:675−686

doi: 10.1007/s00299-013-1402-9

[76]

Lowe K, Wu E, Wang N, Hoerster G, Hastings C, et al. 2016. Morphogenic regulators Baby boom and Wuschel improve monocot transformation. The Plant Cell 28:1998−2015

doi: 10.1105/tpc.16.00124