# A space for time. Exploring temporal regulation of plant development across spatial scales

**Authors:** Yadhusankar Sasidharan, Vijayalakshmi Suryavanshi, Margot E. Smit

PMC · DOI: 10.1111/tpj.70130 · 2025-03-31

## TL;DR

This paper reviews how plant development is regulated over time, from whole-plant processes to cell-level changes, and explores the mechanisms controlling these transitions.

## Contribution

The paper systematically reviews temporal regulation of plant development across spatial scales, highlighting gaps and mechanisms.

## Key findings

- Developmental timing in plants is tightly regulated at the whole-organism scale, including germination, flowering, and senescence.
- Cell-level transitions in plants are also temporally regulated, though less is known about the specific mechanisms.
- Environmental and cellular factors like temperature, photoperiod, and tissue context influence developmental timing.

## Abstract

Plants continuously undergo change during their life cycle, experiencing dramatic phase transitions altering plant form, and regulating the assignment and progression of cell fates. The relative timing of developmental events is tightly controlled and involves integration of environmental, spatial, and relative age‐related signals and actors. While plant phase transitions have been studied extensively and many of their regulators have been described, less is known about temporal regulation on a smaller, cell‐level scale. Here, using examples from both plant and animal systems, we outline time‐dependent changes. Looking at systemic scale changes, we discuss the timing of germination, juvenile‐to‐adult transition, flowering, and senescence, together with regeneration timing. Switching to temporal regulation on a cellular level, we discuss several instances from the animal field in which temporal control has been examined extensively at this scale. Then, we switch back to plants and summarize examples where plant cell‐level changes are temporally regulated. As time cannot easily be separated from signaling derived from the environment and tissue context, we next discuss factors that have been implicated in controlling the timing of developmental events, reviewing temperature, photoperiod, nutrient availability, as well as tissue context and mechanical cues on the cellular scale. Afterwards, we provide an overview of mechanisms that have been shown or implicated in the temporal control of development, considering metabolism, division control, mobile signals, epigenetic regulation, and the action of transcription factors. Lastly, we look at remaining questions for the future study of developmental timing in plants and how recent technical advancement can enable these efforts.

Developmental timing in plants is tightly regulated at the whole‐organism scale, from germination to flowering. Less is known about when and how local transitions are temporally regulated. Not every cell or tissue change happens at any time, and by now, several examples are known where there appears to be regulation of the timing of these decisions. In this review, we explore examples of developmental transitions whose timing is being controlled and the underlying mechanisms.

## Full-text entities

- **Genes:** EMF2 (VEFS-Box of polycomb protein) [NCBI Gene 835198] {aka AT5G51240, AtEMF2, CYR1, CYTOKININ RESISTANT 1, EMBRYONIC FLOWER 2, MWD22.18}, ftz (fushi tarazu) [NCBI Gene 40834] {aka BG:DS07876.1, CG2047, Dm-Ftz, Dm-ftz, DmFtz, Dmel\CG2047}, TFL1 (PEBP (phosphatidylethanolamine-binding protein) family protein) [NCBI Gene 831683] {aka MED24.6, TERMINAL FLOWER 1, TFL-1}, FIE (Transducin/WD40 repeat-like superfamily protein) [NCBI Gene 821622] {aka FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE1, FIS3}, Zc3h12d (zinc finger CCCH type containing 12D) [NCBI Gene 237256] {aka D730019B10Rik, TFL}, Adgrl1 (adhesion G protein-coupled receptor L1) [NCBI Gene 330814] {aka 2900070I05Rik, CLIBA, Lec2, Lphn1, mKIAA0821}, Spl (plasma serotonin level) [NCBI Gene 104153], Cse1 (Chromosome segregation 1) [NCBI Gene 35016] {aka BcDNA:LD14270, CAS, CG13281, Cas, Dcas, Dmel\CG13281}, FT (PEBP (phosphatidylethanolamine-binding protein) family protein) [NCBI Gene 842859] {aka F5I14.3, F5I14_3, FLOWERING LOCUS T, REDUCED STEM BRANCHING 8, RSB8}, Abi3 (ABI family member 3) [NCBI Gene 66610] {aka 2210414K06Rik, NESH}, hubb (hyper-unconjugated bilirubinemia) [NCBI Gene 15570] {aka hub, jaundice}, DML1 (demeter-like 1) [NCBI Gene 818224] {aka AtROS1, F1O11.12, F1O11_12, REPRESSOR OF SILENCING1, ROS1, demeter-like 1}, MAF1 (K-box region and MADS-box transcription factor family protein) [NCBI Gene 844042] {aka AGAMOUS-like 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1}, HAT1 (histone acetyltransferase 1) [NCBI Gene 8520] {aka KAT1}, CLV3 (CLAVATA3) [NCBI Gene 817267] {aka AtCLV3, CLAVATA3, F12K2.17, F12K2_17}, PHO2 (phosphate 2) [NCBI Gene 817943] {aka ATUBC24, T1B8.8, T1B8_8, UBC24, UBIQUITIN-CONJUGATING ENZYME 24, phosphate 2}, CESA6 (cellulose synthase 6) [NCBI Gene 836595] {aka E112, ISOXABEN RESISTANT 2, IXR2, MVP7.7, MVP7_7, PRC1}, hb (hunchback) [NCBI Gene 41032] {aka CG9786, Dm-Hb, Dm-hb, Dmel\CG9786, Hunchback, R-pbx}, ABI3 (AP2/B3-like transcriptional factor family protein) [NCBI Gene 822061] {aka ABA INSENSITIVE 3, ABSCISIC ACID INSENSITIVE 3, AtABI3, SIS10, SUGAR INSENSITIVE 10}, FLD (protein FLOWERING locus D-like protein) [NCBI Gene 820202] {aka FLOWERING LOCUS D, RSI1, Reduced Systemic immunity 1}, Dmbx1 (diencephalon/mesencephalon homeobox 1) [NCBI Gene 140477] {aka Atx, Cdmx, Mbx, Otx3}, LFY (floral meristem identity control protein LEAFY (LFY)) [NCBI Gene 836307] {aka LEAFY, LEAFY 3, LFY3, MAC9.13, MAC9_13}, DOG1 (delay of germination 1) [NCBI Gene 834623] {aka ATDOG1, DELAY OF GERMINATION 1, GAAS5, GLUCOSE SENSING QTL 5, GSQ5, K15I22.3}, MIR164a (ncRNA) [NCBI Gene 3768750] {aka MICRORNA 164, MIR164, microRNA164A, p_MI0000197}, cas (castor) [NCBI Gene 44018] {aka CG2102, Dmel\CG2102, l(3)j1C2, l(3)neo33, ming}, Kr (Kruppel) [NCBI Gene 38012] {aka CG3340, Dm-Kr, Dmel\CG3340, If, Kru}, SPT (basic helix-loop-helix (bHLH) DNA-binding superfamily protein) [NCBI Gene 829847] {aka AP22.25, AP22_25, SPATULA}, Atox1 (antioxidant 1 copper chaperone) [NCBI Gene 11927] {aka Atx1}, CLE45 (CLAVATA3/ESR-RELATED 45) [NCBI Gene 5007842] {aka CLAVATA3/ESR-RELATED 45}, FUS3 (AP2/B3-like transcriptional factor family protein) [NCBI Gene 822293] {aka FUSCA 3}, SPL (sporocyteless (SPL)) [NCBI Gene 828841] {aka F27G19.11, NOZZLE, NZZ, SPOROCYTELESS}, ICE1 (basic helix-loop-helix (bHLH) DNA-binding superfamily protein) [NCBI Gene 822287] {aka A. THALIANA INDUCER OF CBP EXPRESSION 1, ATICE1, INDUCER OF CBF EXPRESSION 1, SCREAM, SCRM}, Zfp282 (zinc finger protein 282) [NCBI Gene 101095] {aka E430019K09Rik, HUB1}, Paf1 (Paf1, RNA polymerase II complex component) [NCBI Gene 54624] {aka 5730511K23Rik}, MIR165a (ncRNA) [NCBI Gene 3766638] {aka MICRORNA 165, MIR165, microRNA165A, p_MI0000199}, CMT3 (chromomethylase 3) [NCBI Gene 843313] {aka T6C23.3, T6C23_3, chromomethylase 3}, AP1 (K-box region and MADS-box transcription factor family protein) [NCBI Gene 843244] {aka AGAMOUS-like 7, AGL7, APETALA1, AtAP1, F4N2.9, F4N2_9}, Mmel1 (membrane metalloendopeptidase like 1) [NCBI Gene 27390] {aka Mell1, NEP2, NEP2(m), NEPII, NL-1, NL2}, VIN3 (Fibronectin type III domain-containing protein) [NCBI Gene 835844] {aka MSF19.4, MSF19_4, VERNALIZATION INSENSITIVE 3}, TRIM3 (tripartite motif containing 3) [NCBI Gene 10612] {aka BERP, HAC1, RNF22, RNF97}, AT2G32710 (Cyclin-dependent kinase inhibitor family protein) [NCBI Gene 817831] {aka ACK2, CYCLIN-DEPENDENT KINASE INHIBITOR 2, F24L7.15, F24L7_15, ICK7, INTERACTORS OF CDC2 KINASE 7}, REV (Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein) [NCBI Gene 836190] {aka HOMEODOMAIN-LEUCINE ZIPPER PROTEIN, HOMEODOMAIN-LEUCINE ZIPPER PROTEIN IFL1, IFL, IFL1, INTERFASCICULAR FIBERLESS, INTERFASCICULAR FIBERLESS 1}, AP2 (Integrase-type DNA-binding superfamily protein) [NCBI Gene 829845] {aka AP22.49, AP22_49, APETALA 2, AtAP2, FL1, FLO2}, Hes7 (hes family bHLH transcription factor 7) [NCBI Gene 84653] {aka bHLHb37}, FRI (FRIGIDA-like protein) [NCBI Gene 828044] {aka F6N23.25, F6N23_25, FLA, FLOWERING LOCUS A, FRIGIDA, REDUCED STEM BRANCHING 7}, FLC (K-box region and MADS-box transcription factor family protein) [NCBI Gene 830878] {aka AGAMOUS-like 25, AGL25, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F, MADS BOX PROTEIN FLOWERING LOCUS F}, Adgrl2 (adhesion G protein-coupled receptor L2) [NCBI Gene 99633] {aka CIRL-2, Gm619, Lec1, Lphh1, Lphn2, mKIAA0786}, EMF1 (embryonic flower 1 (EMF1)) [NCBI Gene 831025] {aka F15N18.120, F15N18_120, embryonic flower 1}, ER (Leucine-rich receptor-like protein kinase family protein) [NCBI Gene 817173] {aka ERECTA, QRP1, QUANTITATIVE RESISTANCE TO PLECTOSPHAERELLA 1, T1D16.3, T1D16_3}, Spata6 (spermatogenesis associated 6) [NCBI Gene 67946] {aka 1700062C23Rik, Hash, KRP, Mash}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, TOR (target of rapamycin) [NCBI Gene 841427] {aka F2J10.19, F2J10_19, target of rapamycin}, BBX13 (B-box type zinc finger protein with CCT domain-containing protein) [NCBI Gene 839698] {aka B-box domain protein 13, F13K9.15, F13K9_15}, PIF4 (phytochrome interacting factor 4) [NCBI Gene 818903] {aka AtPIF4, MFL8.13, MFL8_13, SRL2, phytochrome interacting factor 4}, AT5G02220 (cyclin-dependent kinase inhibitor) [NCBI Gene 831792] {aka SIAMESE-RELATED 4, SMR4, T7H20.270, T7H20_270}, DME (HhH-GPD base excision DNA repair family protein) [NCBI Gene 830335] {aka AT5G04570, AT5G04580, DEMETER, T32M21.160, T32M21_160}, LEC2 (AP2/B3-like transcriptional factor family protein) [NCBI Gene 839724] {aka AtLEC2, F3H9.5, F3H9_5, LEAFY COTYLEDON 2}, MIR399f (ncRNA) [NCBI Gene 5007930] {aka MIR399, microRNA399F, p_MI0001025}, Scr (scruffy) [NCBI Gene 109559], REF6 (relative of early flowering 6) [NCBI Gene 824002] {aka JMJ12, Jumonji domain-containing protein 12, relative of early flowering 6}
- **Diseases:** TEMPORAL (MESH:C536956), MECHANISMS (MESH:D041781)
- **Chemicals:** N (MESH:D009584), ethylene (MESH:C036216), CO (MESH:D002248), gibberellic acid (MESH:C007842), nitrate (MESH:D009566), phosphate (MESH:D010710), P (MESH:D010758), ABA (MESH:D000040), Aux (-), Auxin (MESH:D007210), ROS (MESH:D017382), glucose (MESH:D005947), GA (MESH:D005708), NAD(H) (MESH:D009243), GSH (MESH:D005978), Cytokinins (MESH:D003583)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Melanogaster (genus) [taxon 80614], Homo sapiens (human, species) [taxon 9606], Danio rerio (leopard danio, species) [taxon 7955], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Ambystoma mexicanum (axolotl, species) [taxon 8296], Drosophila melanogaster (fruit fly, species) [taxon 7227], Gallus gallus (bantam, species) [taxon 9031], Oryza sativa (Asian cultivated rice, species) [taxon 4530], Brachypodium distachyon (annual false brome, species) [taxon 15368]

## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC11956849/full.md

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Source: https://tomesphere.com/paper/PMC11956849