Mechanisms of the Morphological Plasticity Induced by Phytohormones and the Environment in Plants

Water wisteria genome reveals environmental adaptation and heterophylly regulation in amphibious plants

Heterophylly is a phenomenon whereby an individual plant dramatically changes leaf shape in response to the surroundings. Hygrophila difformis (Acanthaceae; water wisteria), has recently emerged as a model plant to study heterophylly because of its striking leaf shape variation in response to various environmental factors. When submerged, H. difformis often develops complex leaves, but on land it develops simple leaves. Leaf complexity is also influenced by other factors, such as light density, humidity, and temperature. Here, we sequenced and assembled the H. difformis chromosome-level genome (scaffold N50: 60.43 Mb, genome size: 871.92 Mb), which revealed 36 099 predicted protein-coding genes distributed over 15 pseudochromosomes. H. difformis diverged from its relatives during the Oligocene climate-change period and expanded gene families related to its amphibious habit. Genes related to environmental stimuli, leaf development, and other pathways were differentially expressed in submerged and terrestrial conditions, possibly modulating morphological and physiological acclimation to changing environments. We also found that auxin plays a role in H. difformis heterophylly. Finally, we discovered candidate genes that respond to different environmental conditions and elucidated the role of LATE MERISTEM IDENTITY 1 (LMI1) in heterophylly. We established H. difformis as a model for studying interconnections between environmental adaptation and morphogenesis.

Diving into the Water: Amphibious Plants as a Model for Investigating Plant Adaptations to Aquatic Environments

Amphibious plants can grow and survive in both aquatic and terrestrial environments. This review explores the diverse adaptations that enable them to thrive in such contrasting habitats. Plants with amphibious lifestyles possess fascinating traits, and their phenotypic plasticity plays an important role in adaptations. Heterophylly, the ability to produce different leaf forms, is one such trait, with submerged leaves generally being longer, narrower, and thinner than aerial leaves. In addition to drastic changes in leaf contours, amphibious plants display significant anatomical and physiological changes, including a reduction in stomatal number and cuticle thickness and changes in photosynthesis mode. This review summarizes and compares the regulatory mechanisms and evolutionary origins of amphibious plants based on molecular biology studies actively conducted in recent years using novel model amphibious plant species. Studying amphibious plants will enhance our understanding of plant adaptations to aquatic environments.

A chromosome-level genome assembly for the amphibious plant Rorippa aquatica reveals its allotetraploid origin and mechanisms of heterophylly upon submergence

The ability to respond to varying environments is crucial for sessile organisms such as plants. The amphibious plant Rorippa aquatica exhibits a striking type of phenotypic plasticity known as heterophylly, a phenomenon in which leaf form is altered in response to environmental factors. However, the underlying molecular mechanisms of heterophylly are yet to be fully understood. To uncover the genetic basis and analyze the evolutionary processes driving heterophylly in R. aquatica, we assembled the chromosome-level genome of the species. Comparative chromosome painting and chromosomal genomics revealed that allopolyploidization and subsequent post-polyploid descending dysploidy occurred during the speciation of R. aquatica. Based on the obtained genomic data, the transcriptome analyses revealed that ethylene signaling plays a central role in regulating heterophylly under submerged conditions, with blue light signaling acting as an attenuator of ethylene signal. The assembled R. aquatica reference genome provides insights into the molecular mechanisms and evolution of heterophylly.

Cooperation of an external carbonic anhydrase and HCO3- transporter supports underwater photosynthesis in submerged leaves of the amphibious plant Hygrophila difformis

BACKGROUND AND AIMS

HCO3- can be a major carbon resource for photosynthesis in underwater environments. Here we investigate the underlying mechanism of uptake and membrane transport of HCO3- in submerged leaves of Hygrophila difformis, a heterophyllous amphibious plant. To characterize these mechanisms, we evaluated the sensitivity of underwater photosynthesis to an external carbonic anhydrase (CA) inhibitor and an anion exchanger protein inhibitor, and we attempted to identify components of the mechanism of HCO3- utilization.

METHODS

We evaluated the effects of the external CA inhibitor and anion exchanger protein inhibitor on the NaHCO3 response of photosynthetic O2 evolution in submerged leaves of H. difformis. Furthermore, we performed a comparative transcriptomic analysis between terrestrial and submerged leaves.

KEY RESULTS

Photosynthesis in the submerged leaves was decreased by both the external CA inhibitor and anion exchanger protein inhibitor, but no additive effect was observed. Among upregulated genes in submerged leaves, two α-CAs, Hdα-CA1 and Hdα-CA2, and one β-carbonic anhydrase, Hdβ-CA1, were detected. Based on their putative amino acid sequences, the α-CAs are predicted to be localized in the apoplastic region. Recombinant Hdα-CA1 and Hdβ-CA1 showed dominant CO2 hydration activity over HCO3- dehydration activity.

CONCLUSIONS

We propose that the use of HCO3- for photosynthesis in submerged leaves of H. difformis is driven by the cooperation between an external CA, Hdα-CA1, and an unidentified HCO3- transporter.

Avicennia germinans leaf traits in degraded, restored, and natural mangrove ecosystems of Guyana

Mangrove leaves have unique features that enable them to cope with shifting environmental conditions while preserving their general functionality and efficiency. We examined the morphological characteristics and chlorophyll content (spectroscopically) of 600 mature Avicennia germinans leaves selected from 30 trees located in one degraded, one restored, and one natural mangrove ecosystem along Guyana's coastline. Systematic sampling was carried out using the closest individual sampling method in the wet and dry seasons. We hypothesized that both habitat type and seasonality influence the leaf traits and chlorophyll content of A. germinans. Our findings showed that A. germinans leaves are mesophyllous, and traits such as leaf perimeter, area, length, width, dry mass, wet mass, turgid mass, leaf-specific area, and relative water content showed fluctuations in ecosystems (one-way ANOVA, p < .05) as well as seasonally (paired t-test, p < .05). Substantial, positive correlations (p < .05, R > .75) were also established for over 10 leaf parameters in both seasons while PCA and multiple regression analyses further confirmed the strong relationships between leaf morphological features and their respective locations. Changes in chlorophyll concentration were most noticeable in the degraded ecosystem while variations in leaf traits were more pronounced in the restored mangrove area. This may be due to the various disturbances found in each ecosystem coupled with fluctuations in the seasons. Our results demonstrate that mangroves, to some extent, alter their plant structures to cope with environmental stressors present in the various ecosystems they thrive in to maintain their survival.

Integrating genome-wide association and transcriptome analysis to provide molecular insights into heterophylly and eco-adaptability in woody plants

Heterophylly is regard as an important adaptive mechanism in response to different environments within plants. However, the genetic mechanisms responsible for heterophylly in woody plants are still poorly understood. Herein, the divergence of heterophyllous leaves was investigated at morphogenesis and using microdissection and physiological indexes in paper mulberry, and the genetic basis of heterophylly was further revealed combined with genome-wide association study (GWAS), transcriptome analysis and weighted gene coexpression network analysis (WGCNA). Our results revealed that the flavonoid content and antioxidant activity increased gradually from the entire leaf to the palmatisect leaf, while the hormone content and net photosynthetic rate decreased. Through GWAS and transcriptome analysis, a total of 98 candidate genes and 2338 differentially expressed genes associated with heterophylly were identified. Importantly, we uncovered critical variations in the candidate genes Bp07g0981 (WOX) and Bp07g0920 (HHO), along with significant differences in haplotypes and expression levels among heterophyllous leaves. Our results also suggested that the genes involved in hormone signaling pathways, antioxidant activity, and flavonoid metabolism might be closely related to the heterophylly of paper mulberry, which could account for the physiological data. Indeed, CR-wox mutant lines showed significant changes in leaf phenotypes, and differential expression profile analysis also highlighted the expression of genes related to phytohormones and transcription factors. Together, the genetic variations and candidate genes detected in this study provide novel insights into the genetic mechanism of heterophylly, and would improve the understanding of eco-adaptability in heterophyllous woody plants.

Cytokinin and Metabolites Affect Rhizome Growth and Development in Kentucky Bluegrass (Poa pratensis)

Rhizome growth and development is regulated by phytohormone. However, endogenous phytohormones affect rhizome initiation, and sustained growth in perennial grass species remains elusive. In this study, we investigated the morphological characteristics and the content of indole-3-acetic acid (IAA), zeatin (ZT), gibberellic acid (GA3), and abscisic acid (ABA) in the rhizomes of two different Kentucky bluegrass. Using ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS), we performed metabolite analysis of two different rhizomes. In our study, the multi-rhizome Kentucky bluegrass material 'Yuzhong' had an average of 1113 rhizomes, while the few-rhizome material 'Anding' had an average of 347 rhizomes. The diameter of rhizome and length of rhizome internode in 'Yuzhong' were 1.68-fold and 1.33-fold higher than that of the 'Anding', respectively. The rhizome dry weight of 'Yuzhong' was 75.06 g, while the 'Anding' was 20.79 g. 'Yuzhong' had a higher ZT content (5.50 μg·g-1), which is 2.4-fold that of 'Anding' (2.27 μg·g-1). In contrast, the IAA, ABA, and GA3 content of rhizome were markedly higher in 'Anding' than 'Yuzhong'. Correlation analysis revealed significant correlations between ZT and ZT/ABA with the number of rhizomes, diameter of rhizome, and length of rhizome internode, whereas IAA, ABA, GA3, and IAA/ZT were opposite. In the metabolic profiles, we identified 163 differentially expressed metabolites (DEMs) (60 upregulated and 103 downregulated) in positive ion mode and 75 DEMs (36 upregulated and 39 downregulated) in negative ion mode. Histidine metabolism and ABC transporters pathways were the most significantly enriched in the positive and negative ion mode, respectively, both of which are involved in the synthesis and transport of cytokinin. These results indicate that cytokinin is crucial for rhizome development and promotes rhizome germination and growth of Kentucky bluegrass.

Optimizing lettuce yields and quality by incorporating movable downward lighting with a supplemental adjustable sideward lighting system in a plant factory

Background

Lettuce is a vegetable that is increasingly consumed globally, given its nutritional quality. Plant factories with artificial lighting can produce high-yield and high-quality plants. High plant density in these systems speeds up leaf senescence. Wasted energy and lower yield raised labor expenses are some of the bottlenecks associated with this farming system. In order to increase lettuce yields and quality in the plant factory, it is essential to develop cultivating techniques using artificial lighting.

Methods

Romaine lettuce was grown under a developed "movable downward lighting combined with supplemental adjustable sideward lighting system" (C-S) and under a system without supplemental sideward lighting (N-S) in a plant factory. The effects of C-S on lettuce's photosynthetic characteristics, plant yield, and energy consumption relative to plants grown under a system without N-S were studied.

Results

Romaine lettuce growth and light energy consumption in the plant factory were both influenced favorably by supplementary adjustable sideward lighting. The number of leaves, stem diameter, fresh and dry weights, chlorophyll a and b concentration, and biochemical content (soluble sugar and protein) all increased sharply. The energy consumption was substantially higher in the N-S treatment than the C-S.

SHOOT MERISTEMLESS participates in the heterophylly of Hygrophila difformis (Acanthaceae)

In heterophyllous plants, leaf shape shows remarkable plasticity in response to environmental conditions. However, transgenic studies of heterophylly are lacking and the molecular mechanism remains unclear. Here, we cloned the KNOTTED1-LIKE HOMEOBOX family gene SHOOT MERISTEMLESS (STM) from the heterophyllous plant Hygrophila difformis (Acanthaceae). We used molecular, morphogenetic, and biochemical tools to explore its functions in heterophylly. HdSTM was detected in different organs of H. difformis, and its expression changed with environmental conditions. Heterologous, ectopic expression of HdSTM in Arabidopsis (Arabidopsis thaliana) increased leaf complexity and CUP-SHAPED COTYLEDON (CUC) transcript levels. However, overexpression of HdSTM in H. difformis did not induce the drastic leaf change in the terrestrial condition. Overexpression of HdSTM in H. difformis induced quick leaf variations in submergence, while knockdown of HdSTM led to disturbed leaf development and weakened heterophylly in H. difformis. HdCUC3 had the same spatiotemporal expression pattern as HdSTM. Biochemical analysis revealed a physical interaction between HdSTM and HdCUC3. Our results provide genetic evidence that HdSTM is involved in regulating heterophylly in H. difformis.

Comparative physiological analyses and the genetic basis reveal heat stress responses mechanism among different Betula luminifera populations

Betula luminifera is a subtropical fast-growing timber species with high economic value. However, along with global warming, heat stress become one of the main environmental variables that limit the productivity of B. luminifera, and the response of diverse geographic populations to high temperatures is still unclear. In order to offer a comprehensive understanding of the behavior of B. luminifera under heat stress, the physiological responses of six B. luminifera populations (across the core distribution area) were described in this work in an integrated viewpoint. The results showed that a multi-level physiological regulatory network may exist in B. luminifera, the first response was the activity of resistant enzymes [e.g., peroxidase (POD)] at a preliminary stage of 2 h heat stress, and then the proline (osmoregulation substance) content began to increase after 24 h of continuous high-temperature treatment. In addition, photosynthesis was stronlgly affected by heat stress, and the net photosynthetic rate (P_n ) showed a downward trend under heat treatment in all six B. luminifera populations. Interestingly, although the physiological change patterns of the six B. luminifera populations were relatively consistent for the same parameter, there were obvious differences among different populations. Comprehensive analysis revealed that the physiological response of Rongshui (RS) was the most stable, and this was the representative B. luminifera population. Illumina RNA-seq analysis was applied to reveal the specific biological process of B. luminifera under heat stress using the RS population, and a total of 116,484 unigenes were obtained. The differentially expressed genes (DEGs) between different time periods under heat stress were enriched in 34 KEGG pathways, and the limonene and pinene degradation pathway was commonly enriched in all pairwise comparisons. Moreover, transcription factors including bHLH (basic helix-loop-helix), MYB, WRKY, and NAC (NAM, ATAF1/2, and CUC2) were identified. In this study, the physiological response and tolerance mechanisms of B. luminifera under high temperature stress were revealed, which can conducive to the basis of B. luminifera selection and resistance assessment for cultivation and breeding.

Genome-Wide Analysis of the Growth-Regulating Factor (GRF) Family in Aquatic Plants and Their Roles in the ABA-Induced Turion Formation of Spirodela polyrhiza

Growth-regulating factors (GRFs) are plant-specific transcription factors that play essential roles in regulating plant growth and stress response. The GRF gene families have been described in several terrestrial plants, but a comprehensive analysis of these genes in diverse aquatic species has not been reported yet. In this study, we identified 130 GRF genes in 13 aquatic plants, including floating plants (Azolla filiculoides, Wolffia australiana, Lemna minuta, Spirodela intermedia, and Spirodela polyrhiza), floating-leaved plants (Nymphaea colorata and Euryale ferox), submersed plants (Zostera marina, Ceratophyllum demersum, Aldrovanda vesiculosa, and Utricularia gibba), an emergent plant (Nelumbo nucifera), and an amphibious plant (Cladopus chinensis). The gene structures, motifs, and cis-acting regulatory elements of these genes were analyzed. Phylogenetic analysis divided these GRFs into five clusters, and ABRE cis-elements were highly enriched in the promoter region of the GRFs in floating plants. We found that abscisic acid (ABA) is efficient at inducing the turion of Spirodela polyrhiza (giant duckweed), accompanied by the fluctuated expression of SpGRF genes in their fronds. Our results provide information about the GRF gene family in aquatic species and lay the foundation for future studies on the functions of these genes.

Mechanisms of elevated CO2-induced thermotolerance in plants: the role of phytohormones

Rising atmospheric CO₂ is a key driver of climate change, intensifying drastic changes in meteorological parameters. Plants can sense and respond to changes in environmental parameters including atmospheric CO₂ and temperatures. High temperatures beyond the physiological threshold can significantly affect plant growth and development and thus attenuate crop productivity. However, elevated atmospheric CO₂ can mitigate the deleterious effects of heat stress on plants. Despite a large body of literature supporting the positive impact of elevated CO₂ on thermotolerance, the underlying biological mechanisms and precise molecular pathways that lead to enhanced tolerance to heat stress remain largely unclear. Under heat stress, elevated CO₂-induced expression of respiratory burst oxidase homologs (RBOHs) and reactive oxygen species (ROS) signaling play a critical role in stomatal movement, which optimizes gas exchange to enhance photosynthesis and water use efficiency. Notably, elevated CO₂ also fortifies antioxidant defense and redox homeostasis to alleviate heat-induced oxidative damage. Both hormone-dependent and independent pathways have been shown to mediate high CO₂-induced thermotolerance. The activation of heat-shock factors and subsequent expression of heat-shock proteins are thought to be the essential mechanism downstream of hormone and ROS signaling. Here we review the role of phytohormones in plant response to high atmospheric CO₂ and temperatures. We also discuss the potential mechanisms of elevated CO₂-induced thermotolerance by focusing on several key phytohormones such as ethylene. Finally, we address some limitations of our current understanding and the need for further research to unveil the yet-unknown crosstalk between plant hormones in mediating high CO₂-induced thermotolerance in plants.

Different Metabolic Roles for Alternative Oxidase in Leaves of Palustrine and Terrestrial Species

The alternative oxidase pathway (AOP) is associated with excess energy dissipation in leaves of terrestrial plants. To address whether this association is less important in palustrine plants, we compared the role of AOP in balancing energy and carbon metabolism in palustrine and terrestrial environments by identifying metabolic relationships between primary carbon metabolites and AOP in each habitat. We measured oxygen isotope discrimination during respiration, gas exchange, and metabolite profiles in aerial leaves of ten fern and angiosperm species belonging to five families organized as pairs of palustrine and terrestrial species. We performed a partial least square model combined with variable importance for projection to reveal relationships between the electron partitioning to the AOP (τa) and metabolite levels. Terrestrial plants showed higher values of net photosynthesis (AN) and τa, together with stronger metabolic relationships between τa and sugars, important for water conservation. Palustrine plants showed relationships between τa and metabolites related to the shikimate pathway and the GABA shunt, to be important for heterophylly. Excess energy dissipation via AOX is less crucial in palustrine environments than on land. The basis of this difference resides in the contrasting photosynthetic performance observed in each environment, thus reinforcing the importance of AOP for photosynthesis.

Arsenic Toxicity-Induced Physiological and Metabolic Changes in the Shoots of Pteris cretica and Spinacia oleracea

Arsenic is a ubiquitous toxic element that can be accumulated into plant parts. The present study investigated the response of Pteris cretica and Spinacia oleracea to As treatment through the analysis of selected physiological and metabolic parameters. Plants were grown in pots in As(V) spiked soil (20 and 100 mg/kg). Plants’ physiological condition was estimated through the determination of elements, gas-exchange parameters, chlorophyll fluorescence, water potential, photosynthetic pigments, and free amino acid content. The results confirmed differing As accumulation in plants, as well as in shoots and roots, which indicated that P. cretica is an As-hyperaccumulator and that S. oleracea is an As-root excluder. Variations in physiological and metabolic parameters were observed among As treatments. Overall, the results revealed a significant effect of 100 mg/kg As treatment on the analysed parameters. In both plants, this treatment affected growth, N, Mg, S, Mn, and Zn content, as well as net photosynthetic rate, chlorophyll fluorescence, and total free amino acid content. In conclusion, the results reflect the similarity between P. cretica and S. oleracea in some aspects of plants’ response to As treatment, while physiological and metabolic parameter changes related to As treatments indicate the higher sensitivity of S. oleracea.

Auxin and Cytokinin Interplay during Leaf Morphogenesis and Phyllotaxy

Auxins (IAA) and cytokinins (CKs) are the most influential phytohormones, having multifaceted roles in plants. They are key regulators of plant growth and developmental processes. Additionally, their interplay exerts tight control on plant development and differentiation. Although several reviews have been published detailing the auxin-cytokinin interplay in controlling root growth and differentiation, their roles in the shoot, particularly in leaf morphogenesis are largely unexplored. Recent reports have provided new insights on the roles of these two hormones and their interplay on leaf growth and development. In this review, we focus on the effect of auxins, CKs, and their interactions in regulating leaf morphogenesis. Additionally, the regulatory effects of the auxins and CKs interplay on the phyllotaxy of plants are discussed.

Genome-Wide Characterization of Dirigent Proteins in Populus: Gene Expression Variation and Expression Pattern in Response to Marssonina brunnea and Phytohormones

Marssonina brunnea causes a major disease that limits poplar growth. Lignin and lignan play essential roles in protecting plants from various biological stresses. Dirigent (DIR) proteins are thought to control the stereoselective coupling of coniferyl alcohol in the formation of lignan and lignin. DIR family members have been well studied in several plant species, but no previous detailed genome-wide analysis has been carried out in forest trees, such as poplar. We identified 40 PtDIR genes in Populus trichocarpa and classified them into three subgroups (DIR-a, DIR-b/d, and DIR-e) based on phylogenetic analyses. These genes are distributed on 11 poplar chromosomes, and 80% of PtDIRs (32/40) are intronless. The cis-element analysis inferred that PtDIRs possess many types of biological and abiotic stress-response cis-elements. We also analyzed intra- and inter-specific collinearity, which provided deep insights into the evolutionary characteristics of the poplar DIR genes. Analyses of the protein tertiary structure and critical amino acid residues showed that PtDIR7–10 and PtDIR13–16, which belong to the DIR-a subfamily, might be involved in the regio- and stereo-selectivity of bimolecular phenoxy radical coupling in poplars. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis revealed different expression patterns for the PtDIR genes of P. trichocarpa and the PeDIR genes of ‘Nanlin 895’ in various tissues. Additionally, we analyzed responses of PeDIRs to M. brunnea and different phytohormone treatments (abscisic acid, salicylic acid, methyl jasmonate, and ethylene) in ‘Nanlin 895’. The results showed that at least 18 genes responded strongly to M. brunnea, and these PeDIRs also showed significant responses to phytohormones. These results suggest that DIR genes are involved in the poplar defense response against M. brunnea, and this study will provide fundamental insights for future research on poplar DIR genes.