The genetic basis of natural variation in the timing of vegetative phase change in Arabidopsis thaliana

Juvenile-to-adult phase transition in a common wheat cultivar Norin 61, and accompanying changes in leaf transcriptome

Higher plants experience morphological and physiological changes during the vegetative stage called juvenile-to-adult (JA) phase transition. Despite the advanced studies in Arabidopsis, maize, and rice, the JA phase transition remains unexplored in wheat. This study aimed to elucidate when and how the transition occurs in wheat by investigating the temporal changes in leaf morphology, expression of its regulators, transcriptome, and photosynthetic activity in the common wheat cultivar Norin 61. As a result, leaf blade size, leaf tip shape, and trichome density on leaf blades exhibited major changes from the first to second leaf stages. The expression level of microRNA 156, a regulator of JA phase transition in plants, was the highest in the first leaf stage and decreased following the plant growth, whereas that of its targets, SQUAMOSA PROMOTER BINDING PROTEIN-like (SPL) genes, increased. Additionally, transcriptome profiles dramatically changed from the second to third leaf stages and from the fourth to fifth leaf stages, which could be characterized by the change in activity of photoreactions, material transport, and phytohormone signaling. Unlike rice, wheat showed high photosynthetic rates per unit area even in the first leaf, which may be a unique and noteworthy characteristic in wheat. Taken together, we conclude that wheat initiates the JA phase transition after the first leaf stage and reaches the adult phase before the fourth leaf stage; it subsequently enters the reproductive stage. The present study will provide a foundation for advanced studies on wheat JA phase transition.

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

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.

Proper activity of the age-dependent miR156 is required for leaf heteroblasty and extrafloral nectary development in Passiflora spp

Passion flower extrafloral nectaries (EFNs) protrude from leaves and facilitate mutualistic interactions with insects; however, how age cues control EFN growth remains poorly understood. Here, we examined leaf and EFN morphology and development of two Passiflora species with distinct leaf shapes, and compared the phenotype of these to transgenics with manipulated activity of the age-dependent miR156, which targets several SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) transcription factors. Low levels of miR156 correlated with leaf maturation and EFN formation in Passiflora edulis and P. cincinnata. Accordingly, manipulating miR156 activity affected leaf heteroblasty and EFN development. miR156-overexpressing leaves exhibited less abundant and tiny EFNs in both Passiflora species. EFN abundance remained mostly unchanged when miR156 activity was reduced, but it led to larger EFNs in P. cincinnata. Transcriptome analysis of young leaf primordia revealed that miR156-targeted SPLs may be required to properly express leaf and EFN-associated genes. Importantly, altered miR156 activity impacted sugar profiles of the nectar and modified ecological relationships between EFNs and ants. Our work provides evidence that the miR156/SPL module indirectly regulates EFN development in an age-dependent manner and that the EFN development program is closely associated with the heteroblastic developmental program of the EFN-bearing leaves.

Age-associated growth control modifies leaf proximodistal symmetry and enabled leaf shape diversification

Biological shape diversity is often manifested in modulation of organ symmetry and modification of the patterned elaboration of repeated shape elements.1,2,3,4,5 Whether and how these two aspects of shape determination are coordinately regulated is unclear.5,6,7 Plant leaves provide an attractive system to investigate this problem, because they often show asymmetries along the proximodistal (PD) axis of their blades, along which they can also produce repeated marginal outgrowths such as serrations or leaflets.1 One aspect of leaf shape diversity is heteroblasty, where the leaf form in a single genotype is modified with progressive plant age.8,9,10,11 In Arabidopsis thaliana, a plant with simple leaves, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9) controls heteroblasty by activating CyclinD3 expression, thereby sustaining proliferative growth and retarding differentiation in adult leaves.12,13 However, the precise significance of SPL9 action for leaf symmetry and marginal patterning is unknown. By combining genetics, quantitative shape analyses, and time-lapse imaging, we show that PD symmetry of the leaf blade in A. thaliana decreases in response to an age-dependent SPL9 expression gradient, and that SPL9 action coordinately regulates the distribution and shape of marginal serrations and overall leaf form. Using comparative analyses, we demonstrate that heteroblastic growth reprogramming in Cardamine hirsuta, a complex-leafed relative of A. thaliana, also involves prolonging the duration of cell proliferation and delaying differentiation. We further provide evidence that SPL9 enables species-specific action of homeobox genes that promote leaf complexity. In conclusion, we identified an age-dependent layer of organ PD growth regulation that modulates leaf symmetry and has enabled leaf shape diversification.

Natural variation in CYCLIC NUCLEOTIDE-GATED ION CHANNEL 4 reveals a novel role of calcium signaling in vegetative phase change in Arabidopsis

The timing of vegetative phase change (VPC) in plants is regulated by a temporal decline in the expression of miR156. Both exogenous cues and endogenous factors, such as temperature, light, sugar, nutrients, and epigenetic regulators, have been shown to affect VPC by altering miR156 expression. However, the genetic basis of natural variation in VPC remains largely unexplored. Here, we conducted a genome-wide association study on the variation of the timing of VPC in Arabidopsis. We identified CYCLIC NUCLEOTIDE-GATED ION CHANNEL 4 (CNGC4) as a significant locus associated with the diversity of VPC. Mutations in CNGC4 delayed VPC, accompanied by an increased expression level of miR156 and a corresponding decrease in SQUAMOSA PROMOTER BINDING-LIKE (SPL) gene expression. Furthermore, mutations in CNGC2 and CATION EXCHANGER 1/3 (CAX1/3) also led to a delay in VPC. Polymorphisms in the CNGC4 promoter contribute to the natural variation in CNGC4 expression and the diversity of VPC. Specifically, the early CNGC4 variant promotes VPC and enhances plant adaptation to local environments. In summary, our findings offer genetic insights into the natural variation in VPC in Arabidopsis, and reveal a previously unidentified role of calcium signaling in the regulation of VPC.

Ca2+ regulates developmental timing in Arabidopsis

This article is a Commentary on Wang et al. (2024), 242: 1043–1054.

Temporal regulation of vegetative phase change in plants

During their vegetative growth, plants reiteratively produce leaves, buds, and internodes at the apical end of the shoot. The identity of these organs changes as the shoot develops. Some traits change gradually, but others change in a coordinated fashion, allowing shoot development to be divided into discrete juvenile and adult phases. The transition between these phases is called vegetative phase change. Historically, vegetative phase change has been studied because it is thought to be associated with an increase in reproductive competence. However, this is not true for all species; indeed, heterochronic variation in the timing of vegetative phase change and flowering has made important contributions to plant evolution. In this review, we describe the molecular mechanism of vegetative phase change, how the timing of this process is controlled by endogenous and environmental factors, and its ecological and evolutionary significance.

Vegetative phase change causes age-dependent changes in phenotypic plasticity

Phenotypic plasticity allows organisms to optimize traits for their environment. As organisms age, they experience diverse environments that benefit from varying degrees of phenotypic plasticity. Developmental transitions can control these age-dependent changes in plasticity, and as such, the timing of these transitions can determine when plasticity changes in an organism. Here, we investigate how the transition from juvenile-to adult-vegetative development known as vegetative phase change (VPC) contributes to age-dependent changes in phenotypic plasticity and how the timing of this transition responds to environment using both natural accessions and mutant lines in the model plant Arabidopsis thaliana. We found that the adult phase of vegetative development has greater plasticity in leaf morphology than the juvenile phase and confirmed that this difference in plasticity is caused by VPC using mutant lines. Furthermore, we found that the timing of VPC, and therefore the time when increased plasticity is acquired, varies significantly across genotypes and environments. The consistent age-dependent changes in plasticity caused by VPC suggest that VPC may be adaptive. This genetic and environmental variation in the timing of VPC indicates the potential for population-level adaptive evolution of VPC.

Reproductive competence is regulated independently of vegetative phase change in Arabidopsis thaliana

A long-standing question in plant biology is how the acquisition of reproductive competence is related to the juvenile-to-adult vegetative transition. We addressed this question by examining the expression pattern and mutant phenotypes of two families of miRNAs-miR156/miR157 and miR172-that operate in the same pathway and play important roles in these processes. The phenotype of mutants deficient for miR156/miR157, miR172, and all three miRNAs demonstrated that miR156/miR157 regulate the timing of vegetative phase change but have only a minor effect on reproductive competence, whereas miR172 has a minor role in vegetative phase change but has a major effect on reproductive competence. MIR172B is directly downstream of the miR156/SPL module, but temporal variation in the level of miR156 in the shoot apex and leaf-to-leaf variation in miR156 expression in young primordia was not associated with a change in the level of miR172 in these tissues. Additionally, although miR172 levels increase from leaf to leaf later in leaf development, this variation is largely insensitive to changes in the abundance of miR156. Our results indicate that the acquisition of reproductive competence in Arabidopsis is regulated by miR172 through a mechanism that is independent of the vegetative phase change pathway.

Integrated Transcriptome and Targeted Metabolite Analysis Reveal miRNA-mRNA Networks in Low-Light-Induced Lotus Flower Bud Abortion

Most Nelumbo nucifera (lotus) flower buds were aborted during the growing season, notably in low-light environments. How lotus produces so many aborted flower buds is largely unknown. An integrated transcriptome and targeted metabolite analysis was performed to reveal the genetic regulatory networks underlying lotus flower bud abortion. A total of 233 miRNAs and 25,351 genes were identified in lotus flower buds, including 68 novel miRNAs and 1108 novel genes. Further enrichment analysis indicated that sugar signaling plays a potential central role in regulating lotus flower bud abortion. Targeted metabolite analysis showed that trehalose levels declined the most in the aborting flower buds. A potential regulatory network centered on miR156 governs lotus flower bud abortion, involving multiple miRNA-mRNA pairs related to cell integrity, cell proliferation and expansion, and DNA repair. Genetic analysis showed that miRNA156-5p-overexpressing lotus showed aggravated flower bud abortion phenotypes. Trehalose-6-P synthase 1 (TPS1), which is required for trehalose synthase, had a negative regulatory effect on miR156 expression. TPS1-overexpression lotus showed significantly decreased flower bud abortion rates both in normal-light and low-light environments. Our study establishes a possible genetic basis for how lotus produces so many aborted flower buds, facilitating genetic improvement of lotus' shade tolerance.