The dynamic nature of bud dormancy in trees: environmental control and molecular mechanisms

Above- and belowground phenology responses of subtropical Chinese fir (Cunninghamia lanceolata) to soil warming, precipitation exclusion and their interaction

Plant phenology plays an important role in nutrient cycling and carbon balance in forest ecosystems, but its response to the interaction of global warming and precipitation reduction remains unclear. In this study, an experiment with factorial soil warming (ambient, ambient +5 °C) and precipitation exclusion (ambient, ambient -50 %) was conducted in a subtropical Chinese fir (Cunninghamia lanceolata) plantation. We investigated the effects of soil warming, precipitation exclusion, and their interactions on Chinese fir phenology involving tree height and fine root growth. In the meantime, the impact of tree height growth and related climatic factors on fine root production was also assessed. The results showed that: (1) more variable phenology responses were observed in fine root growth than in tree height growth to the climatic treatments; the duration of fine root growth and tree height growth was significantly reduced by the precipitation exclusion and warming treatment, respectively; phenology differences of fine root and tree height growth caused by the solo warming and precipitation exclusion treatment were further enhanced by the combined treatment; and despite the greater inter-annual phenology stability of tree height growth than that of fine root growth, both of them showed insignificant response to all the climate treatments; (2) asynchrony of phenology between tree height and fine root growth was significantly enlarged by solo warming and precipitation exclusion treatments, and further enlarged by the combined treatment; (3) fine root production was significantly and positively correlated with air, and soil temperature, and tree height growth as well, which was altered by warming and precipitation exclusion treatments. Our results demonstrated that climatic changes significantly and differently alter phenology of, and extend the phenology asynchrony between, above and below ground plant components, and also highlight the climate-sensitive and variable nature of root phenology. Overall, these phenology responses to climatic change may weaken the close link between fine root production and tree height growth, which may result in temporal mismatch between nutrient demand and supply in Chinese fir plantation.

Toward uncovering an operating system in plant organs

Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell-cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.

Supplemental greenhouse lighting increased the water use efficiency, crop growth, and cutting production in Cannabis sativa

The expanding cannabis production sector faces economic challenges, intensified by freshwater scarcity in the main US production areas. Greenhouse cultivation harnesses sunlight to reduce production costs, yet the impact of greenhouse light levels on crucial production components, such as plant growth, branching, and water use efficiency (WUE), remains poorly understood. This study aimed to assess the effects of combined sunlight and supplemental lighting on the crop's main production components and leaf gas exchange of Cannabis sativa 'Suver Haze' in the vegetative stage. Within a greenhouse, LED lighting provided at intensities of ~150, 300, 500, and 700 µmol m-2 s-1 (18-hour photoperiod), combined with solar radiation, resulted in average daily light integrals of 17.9, 29.8, 39.5, and 51.8 mol m-2 d-1. Increasing light levels linearly increased biomass, leaf area, and the number of branches per plant and square meter, with respective rates of 0.26 g, 32.5 cm2, and 0.41 branches per mole of additional light. As anticipated, crop evapotranspiration increased by 1.8-fold with the increase in light intensity yet crop WUE improved by 1.6-fold when comparing the lowest and highest light treatments. Moreover, water requirements per unit of plant biomass decreased from 0.37 to 0.24 liters per gram when lighting increased from ~18 to 52 mol m-2 d-1, marking a 35% reduction in evapotranspiration. These results were supported by increments in leaf photosynthesis and WUE with light enhancement. Furthermore, our findings indicate that even 52 mol m-2 d-1 of supplemental lighting did not saturate any of the crop responses to light and can be economically viable for cannabis nurseries. In conclusion, light supplementation strongly enhanced photosynthesis and plant growth while increasing WUE. Additionally, a comprehensive discussion highlights the shared physiological mechanisms governing WUE in diverse plant species and their potential for water conservation under enhanced lighting conditions.

A tree peony RING-H2 finger protein, PsATL33, plays an essential role in cold-induced bud dormancy release by regulating gibberellin content

Bud dormancy is crucial for woody perennial plants to resist low-temperature stress in winter. However, the molecular regulatory mechanisms underlying bud dormancy release are largely unclear. Here, a tree peony (Paeonia suffruticosa) transcript ARABIDOPSIS TOXICOS EN LEVADURA 33 (PsATL33), encoding a RING-H2 finger protein, was selected from previously generated RNA sequencing data of chilling-treated buds. The objective of this study is to investigate the role of PsATL33 in the regulation of cold-induced bud dormancy release. Subcellular localization assay revealed that PsATL33 was localized to the nucleus and plasma membrane. Reverse transcription-quantitative PCR analysis showed that PsATL33 was dramatically upregulated during cold-triggered bud dormancy release. Exogenous treatments with gibberellin (GA3) increased, but abscisic acid (ABA) inhibited the transcription of PsATL33. Ectopic transformation assay indicated that overexpression of PsATL33 in petunia promoted seed germination, plant growth, and axillary bud break. Silencing of PsATL33 in tree peony through virus-induced gene silencing assay delayed bud dormancy release. tobacco rattle virus (TRV)-PsATL33-infected buds exhibited reduced expression levels of dormancy break-related genes EARLY BUD-BREAK 1 (PsEBB1) and CARBOXYLESTERASE 15 (PsCXE15). Silencing of PsATL33 decreased the accumulation of bioactive GAs, GA1 and GA3, rather than ABA. Transcript levels of several genes involved in GA biosynthesis and signaling, including GA20-OXIDASE 1 (PsGA20ox1), GA3-OXIDASE 1 (PsGA3ox1), PsGA3ox3, GA2-OXIDASE 1 (PsGA2ox1), and GA-INSENSITIVE 1A (PsGAI1A), were changed by PsATL33 silencing. Taken together, our data suggest that PsATL33 functions as a positive regulator of cold-induced bud dormancy release by modulating GA production.

ELONGATED HYPOCOTYL 5a modulates FLOWERING LOCUS T2 and gibberellin levels to control dormancy and bud break in poplar

Photoperiod is a crucial environmental cue for phenological responses, including growth cessation and winter dormancy in perennial woody plants. Two regulatory modules within the photoperiod pathway explain bud dormancy induction in poplar (Populus spp.): the circadian oscillator LATE ELONGATED HYPOCOTYL 2 (LHY2) and GIGANTEA-like genes (GIs) both regulate the key target for winter dormancy induction FLOWERING LOCUS T2 (FT2). However, modification of LHY2 and GIs cannot completely prevent growth cessation and bud set under short-day (SD) conditions, indicating that additional regulatory modules are likely involved. We identified PtoHY5a, an orthologs of the photomorphogenesis regulatory factor ELONGATED HYPOCOTYL 5 (HY5) in poplar (Populus tomentosa), that directly activates PtoFT2 expression and represses the circadian oscillation of LHY2, indirectly activating PtoFT2 expression. Thus, PtoHY5a suppresses SD-induced growth cessation and bud set. Accordingly, PtoHY5a knockout facilitates dormancy induction. PtoHY5a also inhibits bud-break in poplar by controlling gibberellic acid (GA) levels in apical buds. Additionally, PtoHY5a regulates the photoperiodic control of seasonal growth downstream of phytochrome PHYB2. Thus, PtoHY5a modulates seasonal growth in poplar by regulating the PtoPHYB2-PtoHY5a-PtoFT2 module to determine the onset of winter dormancy, and by fine-tuning GA levels to control bud-break.

Integrated proteomic, transcriptomic, and metabolomic profiling reveals that the gibberellin-abscisic acid hub runs flower development in the Chinese orchid Cymbidium sinense

The seasonal flowering Chinese Cymbidium produce an axillary floral meristem and require a dormancy period during cold conditions for flower development. However, the bud activation mechanism remains elusive. This study evaluates the multi-omics across six stages of flower development, along with functional analysis of core genes to decipher the innate mechanism of floral bud initiation and outgrowth in the Chinese orchid Cymbidium sinense. Transcriptome and proteome analyses identified 10 modules with essential roles in floral bud dormancy and activation. Gene clusters in the early stages of flower development were mainly related to flowering time regulation and meristem determination, while the late stages were correlated with hormone signaling pathways. The metabolome identified 69 potential hormones in which gibberellin (GA) and abscisic acid (ABA) were the main regulatory hubs, and GA4 and GA53 exhibited a reciprocal loop. Extraneous GA application caused rapid elongation of flower buds and promoted the expression of flower development genes. Contrarily, exogenous ABA application extended the dormancy process and ABA inhibitors induced dormancy release. Moreover, CsAPETALA1 (CsAP1) was identified as the potential target of ABA for floral bud activation. Transformation of CsAP1 in Arabidopsis and its transient overexpression in C. sinense protoplasts not only affected flowering time and floral organ morphogenesis in Arabidopsis but also orchestrated the expression of flowering and hormone regulatory genes. The presence of ABA response elements in the CsAP1 promoter, rapid downregulation of CsAP1 after exogenous ABA application, and the activation of the floral bud after ABA inhibitor treatment suggest that ABA can control bud outgrowth through CsAP1.

Genetic and molecular regulation of chilling requirements in pear: breeding for climate change resilience

Pear (Pyrus spp.) is a deciduous fruit tree that requires exposure to sufficient chilling hours during the winter to establish dormancy, followed by favorable heat conditions during the spring for normal vegetative and floral budbreak. In contrast to most temperate woody species, apples and pears of the Rosaceae family are insensitive to photoperiod, and low temperature is the major factor that induces growth cessation and dormancy. Most European pear (Pyrus Communis L.) cultivars need to be grown in regions with high chilling unit (CU) accumulation to ensure early vegetative budbreak. Adequate vegetative budbreak time will ensure suitable metabolite accumulation, such as sugars, to support fruit set and vegetative development, providing the necessary metabolites for optimal fruit set and development. Many regions that were suitable for pear production suffer from a reduction in CU accumulation. According to climate prediction models, many temperate regions currently suitable for pear cultivation will experience a similar accumulation of CUs as observed in Mediterranean regions. Consequently, the Mediterranean region can serve as a suitable location for conducting pear breeding trials aimed at developing cultivars that will thrive in temperate regions in the decades to come. Due to recent climatic changes, bud dormancy attracts more attention, and several studies have been carried out aiming to discover the genetic and physiological factors associated with dormancy in deciduous fruit trees, including pears, along with their related biosynthetic pathways. In this review, current knowledge of the genetic mechanisms associated with bud dormancy in European pear and other Pyrus species is summarized, along with metabolites and physiological factors affecting dormancy establishment and release and chilling requirement determination. The genetic and physiological insights gained into the factors regulating pear dormancy phase transition and determining chilling requirements can accelerate the development of new pear cultivars better suited to both current and predicted future climatic conditions.

Time to budbreak is not enough: cold hardiness evaluation is necessary in dormancy and spring phenology studies

BACKGROUND

Dormancy of buds is an important phase in the life cycle of perennial plants growing in environments where unsuitable growth conditions occur seasonally. In regions where low temperature defines these unsuitable conditions, the attainment of cold hardiness is also required for survival. The end of the dormant period culminates in budbreak and flower emergence, or spring phenology, one of the most appreciated and studied phenological events - a time also understood to be most sensitive to low-temperature damage. Despite this, we have a limited physiological and molecular understanding of dormancy, which has negatively affected our ability to model budbreak. This is also true for cold hardiness.

SCOPE

Here we highlight the importance of including cold hardiness in dormancy studies that typically only characterize time to budbreak. We show how different temperature treatments may lead to increases in cold hardiness, and by doing so also (potentially inadvertently) increase time to budbreak.

CONCLUSIONS

We present a theory that describes evaluation of cold hardiness as being key to clarifying physiological changes throughout the dormant period, delineating dormancy statuses, and improving both chill and phenology models. Erroneous interpretations of budbreak datasets are possible by not phenotyping cold hardiness. Changes in cold hardiness were very probably present in previous experiments that studied dormancy, especially when those included below-freezing temperature treatments. Separating the effects between chilling accumulation and cold acclimation in future studies will be essential for increasing our understanding of dormancy and spring phenology in plants.

Tree post-drought recovery: scenarios, regulatory mechanisms and ways to improve

Efficient post-drought recovery of growth and assimilation enables a plant to return to its undisturbed state and functioning. Unlike annual plants, trees suffer not only from the current drought, but also from cumulative impacts of consecutive water stresses which cause adverse legacy effects on survival and performance. This review provides an integrated assessment of ecological, physiological and molecular evidence on the recovery of growth and photosynthesis in trees, with a view to informing the breeding of trees with a better ability to recover from water stress. Suppression of recovery processes can result not only from stress damage but also from a controlled downshift of recovery as part of tree acclimation to water-limited conditions. In the latter case, recovery processes could potentially be activated by turning off the controlling mechanisms, but several obstacles make this unlikely. Tree phenology, and specifically photoperiodic constraints, can limit post-drought recovery of growth and photosynthesis, and targeting these constraints may represent a promising way to breed trees with an enhanced ability to recover post-drought. The mechanisms of photoperiod-dependent regulation of shoot, secondary and root growth and of assimilation processes are reviewed. Finally, the limitations and trade-offs of altering the photoperiodic regulation of growth and assimilation processes are discussed.

Stable water isotopes reveal the onset of bud dormancy in temperate trees, whereas water content is a better proxy for dormancy release

Earlier spring growth onset in temperate forests is a visible effect of global warming that alters global water and carbon cycling. Consequently, it becomes crucial to accurately predict the future spring phenological shifts in vegetation under different climate warming scenarios. However, current phenological models suffer from a lack of physiological insights of tree dormancy and are rarely experimentally validated. Here, we sampled twig cuttings of five deciduous tree species at two climatically different locations (270 and 750 m a.s.l., ~ 2.3 °C difference) throughout the winter of 2019-20. Twig budburst success, thermal time to budburst, bud water content and short-term 2H-labelled water uptake into buds were quantified to link bud dormancy status with vascular water transport efficacy, with the objective of establishing connections between the dormancy status of buds and their effectiveness in vascular water transport. We found large differences in the dormancy status between species throughout the entire investigation period, likely reflecting species-specific environmental requirements to initiate and release dormancy, whereas only small differences in the dormancy status were found between the two studied sites. We found strong 2H-labelled water uptake into buds during leaf senescence, followed by a sharp decrease, which we ascribed to the initiation of endodormancy. However, surprisingly, we did not find a progressive increase in 2H-labelled water uptake into buds as winter advanced. Nonetheless, all examined tree species exhibited a consistent relationship between bud water content and dormancy status. Our results suggest that short-term 2H-labelled water uptake may not be a robust indicator of dormancy release, yet it holds promise as a method for tracking the induction of dormancy in deciduous trees. By contrast, bud water content emerges as a cost-effective and more reliable indicator of dormancy release.

Allelic variation of PmCBF03 contributes to the altitude and temperature adaptability in Japanese apricot (Prunus mume Sieb. et Zucc.)

Japanese apricot is an important subtropical deciduous fruit tree in China, widely distributed in different altitude areas. How does it adapt to the different temperature environments in these areas? In this study, we identified a low-temperature transcription factor PmCBF03 on chromosome 7 through adaptive analysis of populations at different altitudes, which has an early termination single nucleotide polymorphism mutation. There were two different types of variation, PmCBF03A type in high-altitude areas and PmCBF03T type in low-altitude areas. PmCBF03A gene increased the survival rate, Fv/Fm values, antioxidant enzyme activity, and expression levels of antioxidant enzyme genes, and reducing electrolyte leakage and accumulation of reactive oxygen species in transgenic Arabidopsis under low temperature and freezing stress. Simultaneously, PmCBF03A gene promoted the dormancy of transgenic Arabidopsis seeds than wild-type. Biochemical analysis demonstrated that PmCBF03A directly bound to the DRE/CRT element in the promoters of the PmCOR413, PmDAM6 and PmABI5 genes, promoting their transcription and enhanced the cold resistance and dormancy of the overexpressing PmCBF03A lines. While PmCBF03T gene is unable to bind to the promoters of PmDAM6 and PmABI5 genes, leading to early release of dormancy to adapt to the problem of insufficient chilling requirement in low-altitude areas.

Abscisic acid-induced transcription factor PsMYB306 negatively regulates tree peony bud dormancy release

Bud dormancy is a crucial strategy for perennial plants to withstand adverse winter conditions. However, the regulatory mechanism of bud dormancy in tree peony (Paeonia suffruticosa) remains largely unknown. Here, we observed dramatically reduced and increased accumulation of abscisic acid (ABA) and bioactive gibberellins (GAs) GA1 and GA3, respectively, during bud endodormancy release of tree peony under prolonged chilling treatment. An Illumina RNA sequencing study was performed to identify potential genes involved in the bud endodormancy regulation in tree peony. Correlation matrix, principal component, and interaction network analyses identified a downregulated MYB transcription factor gene, PsMYB306, the expression of which positively correlated with 9-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (PsNCED3) expression. Protein modeling analysis revealed 4 residues within the R2R3 domain of PsMYB306 to possess DNA binding capability. Transcription of PsMYB306 was increased by ABA treatment. Overexpression of PsMYB306 in petunia (Petunia hybrida) inhibited seed germination and plant growth, concomitant with elevated ABA and decreased GA contents. Silencing of PsMYB306 accelerated cold-triggered tree peony bud burst and influenced the production of ABA and GAs and the expression of their biosynthetic genes. ABA application reduced bud dormancy release and transcription of ENT-KAURENOIC ACID OXIDASE 1 (PsKAO1), GA20-OXIDASE 1 (PsGA20ox1), and GA3-OXIDASE 1 (PsGA3ox1) associated with GA biosynthesis in PsMYB306-silenced buds. In vivo and in vitro binding assays confirmed that PsMYB306 specifically transactivated the promoter of PsNCED3. Silencing of PsNCED3 also promoted bud break and growth. Altogether, our findings suggest that PsMYB306 negatively modulates cold-induced bud endodormancy release by regulating ABA production.

Transcription factors BZR2/MYC2 modulate brassinosteroid and jasmonic acid crosstalk during pear dormancy

Bud dormancy is an important physiological process during winter. Its release requires a certain period of chilling. In pear (Pyrus pyrifolia), the abscisic acid (ABA)-induced expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes represses bud break, whereas exogenous gibberellin (GA) promotes dormancy release. However, with the exception of ABA and GA, the regulatory effects of phytohormones on dormancy remain largely uncharacterized. In this study, we confirmed brassinosteroids (BRs) and jasmonic acid (JA) contribute to pear bud dormancy release. If chilling accumulation is insufficient, both 24-epibrassinolide (EBR) and methyl jasmonic acid (MeJA) can promote pear bud break, implying that they positively regulate dormancy release. BRASSINAZOLE RESISTANT 2 (BZR2), which is a BR-responsive transcription factor, inhibited PpyDAM3 expression and accelerated pear bud break. The transient overexpression of PpyBZR2 increased endogenous GA, JA, and JA-Ile levels. In addition, the direct interaction between PpyBZR2 and MYELOCYTOMATOSIS 2 (PpyMYC2) enhanced the PpyMYC2-mediated activation of Gibberellin 20-oxidase genes PpyGA20OX1L1 and PpyGA20OX2L2 transcription, thereby increasing GA3 contents and accelerating pear bud dormancy release. Interestingly, treatment with 5 μm MeJA increased the bud break rate, while also enhancing PpyMYC2-activated PpyGA20OX expression and increasing GA3,4 contents. The 100 μm MeJA treatment decreased the PpyMYC2-mediated activation of the PpyGA20OX1L1 and PpyGA20OX2L2 promoters and suppressed the inhibitory effect of PpyBZR2 on PpyDAM3 transcription, ultimately inhibiting pear bud break. In summary, our data provide insights into the crosstalk between the BR and JA signaling pathways that regulate the BZR2/MYC2-mediated pathway in the pear dormancy release process.

Molecular Mechanisms of Seasonal Gene Expression in Trees

In trees, the annual cycling of active and dormant states in buds is closely regulated by environmental factors, which are of primary significance to their productivity and survival. It has been found that the parallel or convergent evolution of molecular pathways that respond to day length or temperature can lead to the establishment of conserved periodic gene expression patterns. In recent years, it has been shown in many woody plants that change in annual rhythmic patterns of gene expression may underpin the adaptive evolution in forest trees. In this review, we summarize the progress on the molecular mechanisms of seasonal regulation on the processes of shoot growth, bud dormancy, and bud break in response to day length and temperature factors. We focus on seasonal expression patterns of genes involved in dormancy and their associated epigenetic modifications; the seasonal changes in the extent of modifications, such as DNA methylation, histone acetylation, and histone methylation, at dormancy-associated loci have been revealed for their actions on gene regulation. In addition, we provide an outlook on the direction of research on the annual cycle of tree growth under climate change.

Advancing tree genomics to future proof next generation orchard production

The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.

Daylength predominates the bud growth initiation of winter deciduous forest trees in the monsoon region of China

Climate warming has induced significant shifts in spring phenology over both temperate and boreal forests. The timing of bud growth resuming from dormancy is crucial for predicting spring phenology. However, the mechanisms by which environmental cues, other than chilling accumulation, initiate bud growth remains unclear. By constructing a revised process-based spring phenology model incorporating photoperiod and temperature triggers of bud growth, we simulated the first leaf unfolding and first flowering dates of four deciduous forest trees during 1981-2014 at 102 stations across China's monsoon regions. Then, we revealed spatial patterns of the two triggers. Moreover, we compared fitting precision and robustness of the revised model with three mainstream models. Results show that the revised models can effectively simulate all spring phenology time series. Growth initiation of foliar and floral buds was induced by photoperiod lengthening in 80.8% and 77.7% of time series, and by temperature increasing in remaining 19.2% and 22.3% of time series, respectively. The proportions of time series with photoperiod- and temperature-initiated bud growth significantly increase and decrease from northern to southern climatic zones, respectively. Chilling exposure controls the predominant bud growth triggers in different climate zones. Specifically, in regions with long and severe winters where chilling requirement is easily fulfilled, rising temperature in spring alleviates the cold constraint and initiate bud growth. Conversely, in regions with short and mild winters, prolonged daylength in spring compensates the lack of chilling exposure to initiate bud growth. These findings suggest that photoperiod may limit spring phenology response to temperature in low-latitudes. Overall, our model slightly outperforms other models in terms of efficiency, accuracy, and robustness in modeling leaf unfolding and flowering dates. Therefore, this study deepens our understanding of the mechanisms of spring phenology, and improves the predicting capability of spring phenology models in the face of ongoing global warming.

Transcriptomic landscape of staminate catkins development during overwintering process in Betula platyphylla

Betula platyphylla, belonging to the cold-specialized lineage Betulaceae, exhibits a unique reproductive strategy where staminate catkins emerge in the first summer and undergo an overwintering process, culminating in flowering in the following year. However, the underlying regulatory mechanism remains unclear. In this study, we investigated the male germline development of B. platyphylla in four distinct stages: microsporocytes in Oct. (S1), uninuclear microspores from Dec. (S2) to Mar. of the following year (S3), and bicellular microspores in Apr. (S4). We performed RNA sequencing on mature pollen and the four stages of staminate catkins. Using weighted gene co-expression network analysis (WGCNA), we identified five highly correlated gene modules with distinct expression profiles. These modules exhibited strong correlations with sugar metabolism, cell cycle, flowering, and cell wall dynamics, highlighting their dynamic roles during male germline developmental stages. During the overwintering process, we observed that the expression of transcription factors such as BpDUO1 and BpAMS at the appropriate developmental stages, suggests their significant roles in male germline development. The expression patterns of BpFLC and BpFT suggest their potential involvement in temperature perception during male reproductive development. These findings offer valuable insights into the reproductive success of plants adapting to cold environments.

Unveiling the effect of gibberellin-induced iron oxide nanoparticles on bud dormancy release in sweet cherry (Prunus avium L.)

Hydrogen cyanide has been extensively used worldwide for bud dormancy break in fruit trees, consequently enhancing fruit production via expedited cultivation, especially in areas with controlled environments or warmer regions. A novel and safety nanotechnology was developed since the hazard of hydrogen cyanide for the operators and environments, there is an urgent need for the development of novel and safety approaches to replace it to break bud dormancy for fruit trees. In current study, we have systematically explored the potential of iron oxide nanoparticles, specifically α-Fe2O3, to modulate bud dormancy in sweet cherry (Prunus avium). The synthesized iron oxide nanoparticles underwent meticulous characterization and assessment using various techniques, including Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and ultraviolet-visible infrared (UV-Vis) spectroscopy. Remarkably, when applied at a concentration of 10 mg L-1 alongside gibberellin (GA4+7), these iron oxide nanoparticles exhibited a substantial 57% enhancement in bud dormancy release compared to control groups, all achieved within a remarkably short time span of 4 days. Our RNA-seq analyses further unveiled that 2757 genes within the sweet cherry buds were significantly up-regulated when treated with 10 mg L-1 α-Fe2O3 nanoparticles in combination with GA, while 4748 genes related to dormancy regulation were downregulated in comparison to the control. Moreover, we discovered an array of 58 transcription factor families among the crucial differentially expressed genes (DEGs). Through hormonal quantification, we established that the increased bud burst was accompanied by a reduced concentration of abscisic acid (ABA) at 761.3 ng/g fresh weight in the iron oxide treatment group, coupled with higher levels of gibberellins (GAs) in comparison to the control. Comprehensive transcriptomic and metabolomic analyses unveiled significant alterations in hormone contents and gene expression during the bud dormancy-breaking process when α-Fe2O3 nanoparticles were combined with GA. In conclusion, our findings provide valuable insights into the intricate molecular mechanisms underlying the impact of iron oxide nanoparticles on achieving uniform bud dormancy break in sweet cherry trees.

Perenniality: From model plants to applications in agriculture

To compensate for their sessile nature, plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing environments. One such prominent feature is the evolution of diverse life history strategies, particularly such that annuals reproduce once followed by seasonal death, while perennials live longer by cycling growth seasonally. This intrinsic phenology is primarily genetic and can be altered by environmental factors. Although evolutionary transitions between annual and perennial life history strategies are common, perennials account for most species in nature because they survive well under year-round stresses. This proportion, however, is reversed in agriculture. Hence, perennial crops promise to likewise protect and enhance the resilience of agricultural ecosystems in response to climate change. Despite significant endeavors that have been made to generate perennial crops, progress is slow because of barriers in studying perennials, and many developed species await further improvement. Recent findings in model species have illustrated that simply rewiring existing genetic networks can lead to lifestyle variation. This implies that engineering plant life history strategy can be achieved by manipulating only a few key genes. In this review, we summarize our current understanding of genetic basis of perenniality and discuss major questions and challenges that remain to be addressed.

Warming nondormant tree roots advances aboveground spring phenology in temperate trees

Climate warming advances the onset of tree growth in spring, but above- and belowground phenology are not always synchronized. These differences in growth responses may result from differences in root and bud dormancy dynamics, but root dormancy is largely unexplored. We measured dormancy in roots and leaf buds of Fagus sylvatica and Populus nigra by quantifying the warming sum required to initiate above- and belowground growth in October, January and February. We furthermore carried out seven experiments, manipulating only the soil and not air temperature before or during tree leaf-out to evaluate the potential of warmer roots to influence budburst timing using seedlings and adult trees of F. sylvatica and seedlings of Betula pendula. Root dormancy was virtually absent in comparison with the much deeper winter bud dormancy. Roots were able to start growing immediately as soils were warmed during the winter. Interestingly, higher soil temperature advanced budburst across all experiments, with soil temperature possibly accounting for c. 44% of the effect of air temperature in advancing aboveground spring phenology per growing degree hour. Therefore, differences in root and bud dormancy dynamics, together with their interaction, likely explain the nonsynchronized above- and belowground plant growth responses to climate warming.

Age-dependent seasonal growth cessation in Populus

In temperate and boreal regions, perennial plants adapt their annual growth cycle to the change of seasons. In natural forests, juvenile seedlings usually display longer growth seasons compared to adult trees to ensure their establishment and survival under canopy shade. However, how trees adjust their annual growth according to their age is not known. In this study, we show that age-dependent seasonal growth cessation is genetically controlled and found that the miR156-SPL3/5 module, a key regulon of vegetative phase change (VPC), also triggers age-dependent growth cessation in Populus trees. We show that miR156 promotes shoot elongation during vegetative growth, and its targets SPL3/5s function in the same pathway but as repressors. We find that the miR156-SPL3/5s regulon controls growth cessation in both leaves and shoot apices and through multiple pathways, but with a different mechanism compared to how the miR156-SPL regulon controls VPC in annual plants. Taken together, our results reveal an age-dependent genetic network in mediating seasonal growth cessation, a key phenological process in the climate adaptation of perennial trees.

Transport capacity is uncoupled with endodormancy breaking in sweet cherry buds: physiological and molecular insights

Introduction

To avoid the negative impacts of winter unfavorable conditions for plant development, temperate trees enter a rest period called dormancy. Winter dormancy is a complex process that involves multiple signaling pathways and previous studies have suggested that transport capacity between cells and between the buds and the twig may regulate the progression throughout dormancy stages. However, the dynamics and molecular actors involved in this regulation are still poorly described in fruit trees.

Methods

Here, in order to validate the hypothesis that transport capacity regulates dormancy progression in fruit trees, we combined physiological, imaging and transcriptomic approaches to characterize molecular pathways and transport capacity during dormancy in sweet cherry (Prunus avium L.) flower buds.

Results

Our results show that transport capacity is reduced during dormancy and could be regulated by environmental signals. Moreover, we demonstrate that dormancy release is not synchronized with the transport capacity resumption but occurs when the bud is capable of growth under the influence of warmer temperatures. We highlight key genes involved in transport capacity during dormancy.

Discussion

Based on long-term observations conducted during six winter seasons, we propose hypotheses on the environmental and molecular regulation of transport capacity, in relation to dormancy and growth resumption in sweet cherry.

Rapid response of nonstructural carbohydrate allocation and photosynthesis to short photoperiod, low temperature, or elevated CO2 in Pinus strobus

During autumn, decreasing photoperiod and temperature temporarily perturb the balance between carbon uptake and carbon demand in overwintering plants, requiring coordinated adjustments in photosynthesis and carbon allocation to re-establish homeostasis. Here we examined adjustments of photosynthesis and allocation of nonstructural carbohydrates (NSCs) following a sudden shift to short photoperiod, low temperature, and/or elevated CO2 in Pinus strobus seedlings. Seedlings were initially acclimated to 14 h photoperiod (22/15°C day/night) and ambient CO2 (400 ppm) or elevated CO2 (800 ppm). Seedlings were then shifted to 8 h photoperiod for one of three treatments: no temperature change at ambient CO2 (22/15°C, 400 ppm), low temperature at ambient CO2 (12/5°C, 400 ppm), or no temperature change at elevated CO2 (22/15°C, 800 ppm). Short photoperiod caused all seedlings to exhibit partial nighttime depletion of starch. Short photoperiod alone did not affect photosynthesis. Short photoperiod combined with low temperature caused hexose accumulation and repression of photosynthesis within 24 h, followed by a transient increase in nonphotochemical quenching (NPQ). Under long photoperiod, plants grown under elevated CO2 exhibited significantly higher NSCs and photosynthesis compared to ambient CO2 plants, but carbon uptake exceeded sink capacity, leading to elevated NPQ; carbon sink capacity was restored and NPQ relaxed within 24 h after shift to short photoperiod. Our findings indicate that P. strobus rapidly adjusts NSC allocation, not photosynthesis, to accommodate short photoperiod. However, the combination of short photoperiod and low temperature, or long photoperiod and elevated CO2 disrupts the balance between photosynthesis and carbon sink capacity, resulting in increased NPQ to alleviate excess energy.

Uncovering the complex regulatory network of spring bud sprouting in tea plants: insights from metabolic, hormonal, and oxidative stress pathways

The sprouting process of tea buds is an essential determinant of tea quality and taste, thus profoundly impacting the tea industry. Buds spring sprouting is also a crucial biological process adapting to external environment for tea plants and regulated by complex transcriptional and metabolic networks. This study aimed to investigate the molecular basis of bud sprouting in tea plants firstly based on the comparisons of metabolic and transcriptional profiles of buds at different developmental stages. Results notably highlighted several essential processes involved in bud sprouting regulation, including the interaction of plant hormones, glucose metabolism, and reactive oxygen species scavenging. Particularly prior to bud sprouting, the accumulation of soluble sugar reserves and moderate oxidative stress may have served as crucial components facilitating the transition from dormancy to active growth in buds. Following the onset of sprouting, zeatin served as the central component in a multifaceted regulatory mechanism of plant hormones that activates a range of growth-related factors, ultimately leading to the promotion of bud growth. This process was accompanied by significant carbohydrate consumption. Moreover, related key genes and metabolites were further verified during the entire overwintering bud development or sprouting processes. A schematic diagram involving the regulatory mechanism of bud sprouting was ultimately proposed, which provides fundamental insights into the complex interactions involved in tea buds.

Late autumn warming can both delay and advance spring budburst through contrasting effects on bud dormancy depth in Fagus sylvatica L

The current state of knowledge on bud dormancy is limited. However, expanding such knowledge is crucial in order to properly model forest responses and feedback to future climate. Recent studies have shown that warming can decrease chilling accumulation and increase dormancy depth, thereby inducing delayed budburst in European beech (Fagus sylvatica L). Whether fall warming can advance spring phenology is unclear. To investigate the effect of warming on endodormancy of deciduous trees, we tested the impact of mild elevated temperature (+2.5-3.5 °C; temperature, on average, kept at 10 °C) in mid and late autumn on the bud dormancy depth and spring phenology of beech. We studied saplings by inducing periods of warming in greenhouses over a 2-year period. Even though warming reduced chilling accumulation in both years, we observed that the response of dormancy depth and spring budburst were year-specific. We found that warming during endodormancy peak could decrease the bud dormancy depth and therefore advance spring budburst. This effect appears to be modulated by factors such as the date of senescence onset and forcing intensity during endodormancy. Results from this study suggest that not only chilling but also forcing controls bud development during endodormancy and that extra forcing in autumn can offset reduced chilling.

Temporal transcriptome and metabolite analyses provide insights into the biochemical and physiological processes underlying endodormancy release in pistachio (Pistacia vera L.) flower buds

Pistachio (Pistacia vera L.), an economically and nutritionally important tree crop, relies on winter chill for bud endodormancy break and subsequent blooming and nut production. However, insufficient winter chill poses an increasing challenge in pistachio growing regions. To gain a better understanding of the physiological and biochemical responses of endodormant pistachio buds to chilling accumulation, we investigated the global gene expression changes in flower buds of pistachio cv. Kerman that were cultivated at three different orchard locations and exposed to increasing durations of winter chill. The expression of genes encoding β-1,3-glucanase and β-amylase, enzymes responsible for breaking down callose (β-1,3-glucan) and starch (α-1,4-glucan), respectively, increased during the endodormancy break of pistachio buds. This result suggested that the breakdown of callose obstructing stomata as well as the release of glucose from starch enables symplasmic trafficking and provides energy for bud endodormancy break and growth. Interestingly, as chilling accumulation increased, there was a decrease in the expression of nine-cis-epoxycarotenoid dioxygenase (NCED), encoding an enzyme that uses carotenoids as substrates and catalyzes the rate-limiting step in abscisic acid (ABA) biosynthesis. The decrease in NCED expression suggests ABA biosynthesis is suppressed, thus reducing inhibition of endodormancy break. The higher levels of carotenoid precursors and a decrease in ABA content in buds undergoing endodormancy break supports this suggestion. Collectively, the temporal transcriptome and biochemical analyses revealed that the degradation of structural (callose) and non-structural (starch) carbohydrates, along with the attenuation of ABA biosynthesis, are critical processes driving endodormancy break in pistachio buds.

Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature

Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive "switches"; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.

From endodormancy to ecodormancy: the transcriptional landscape of apple floral buds

This study endeavors to explore the transcriptomic profiles of two apple cultivars, namely, 'Honeycrisp' and 'Cripps Pink,' which represent late and early-blooming cultivars, respectively. Using RNA-sequencing technology, we analyzed floral bud samples collected at five distinct time intervals during both endodormancy and ecodormancy. To evaluate the transcriptomic profiles of the 30 sequenced samples, we conducted principal component analysis (PCA). PC1 explained 43% of the variance, separating endodormancy and ecodormancy periods, while PC2 explained 16% of the variance, separating the two cultivars. The number of differentially expressed genes (DEGs) increased with endodormancy progression and remained elevated during ecodormancy. The majority of DEGs were unique to a particular time point, with only a few overlapping among or between the time points. This highlights the temporal specificity of gene expression during the dormancy transition and emphasizes the importance of sampling at multiple time points to capture the complete transcriptomic dynamics of this intricate process. We identified a total of 4204 upregulated and 7817 downregulated DEGs in the comparison of endodormancy and ecodormancy, regardless of cultivar, and 2135 upregulated and 2413 downregulated DEGs in the comparison of 'Honeycrisp' versus 'Cripps Pink,' regardless of dormancy stage. Furthermore, we conducted a co-expression network analysis to gain insight into the coordinated gene expression profiles across different time points, dormancy stages, and cultivars. This analysis revealed the most significant module (ME 14), correlated with 1000 GDH and consisting of 1162 genes. The expression of the genes within this module was lower in 'Honeycrisp' than in 'Cripps Pink.' The top 20 DEGs identified in ME 14 were primarily related to jasmonic acid biosynthesis and signaling, lipid metabolism, oxidation-reduction, and transmembrane transport activity. This suggests a plausible role for these pathways in governing bud dormancy and flowering time in apple.

CRISPR/Cas9 mutants delineate roles of Populus FT and TFL1/CEN/BFT family members in growth, dormancy release and flowering

Vegetative and reproductive phase change and phenology are economically and ecologically important traits. Trees typically require several years of growth before flowering and, once mature, seasonal control of the transition to flowering and flower development is necessary to maintain vegetative meristems and for reproductive success. Members of two related gene subfamilies, FLOWERING LOCUST (FT) and TERMINAL FLOWER1 (TFL1)/CENTRORADIALIS (CEN)/BROTHER OF FT AND TFL1 (BFT), have antagonistic roles in flowering in diverse species and roles in vegetative phenology in trees, but many details of their functions in trees have yet to be resolved. Here, we used CRISPR/Cas9 to generate single and double mutants involving the five Populus FT and TFL1/CEN/BFT genes. The ft1 mutants exhibited wild-type-like phenotypes in long days and short days, but after chilling, to release dormancy, they showed delayed bud flush and GA3 could compensate for the ft1 mutation. After rooting and generating some phytomers in tissue culture, both cen1 and cen1ft1 mutants produced terminal as well as axillary flowers, indicating that the cen1 flowering phenotype is independent of FT1. The CEN1 showed distinct circannual expression patterns in vegetative and reproductive tissues and comparison with the expression patterns of FT1 and FT2 suggests that the relative levels of CEN1 compared with FT1 and FT2 regulate multiple phases of vegetative and reproductive seasonal development.

Light on perenniality: Para-dormancy is based on ABA-GA antagonism and endo-dormancy on the shutdown of GA biosynthesis

Perennial para- and endo-dormancy are seasonally separate phenomena. Whereas para-dormancy is the suppression of axillary buds (AXBs) by a growing shoot, endo-dormancy is the short-day elicited arrest of terminal and AXBs. In hybrid aspen (Populus tremula x P. tremuloides) compromising the apex releases para-dormancy, whereas endo-dormancy requires chilling. ABA and GA are implicated in both phenomena. To untangle their roles, we blocked ABA biosynthesis with fluridone (FD), which significantly reduced ABA levels, downregulated GA-deactivation genes, upregulated the major GA3ox-biosynthetic genes, and initiated branching. Comprehensive GA-metabolite analyses suggested that FD treatment shifted GA production to the non-13-hydroxylation pathway, enhancing GA₄ function. Applied ABA counteracted FD effects on GA metabolism and downregulated several GA_3/4 -inducible α- and γ-clade 1,3-β-glucanases that hydrolyze callose at plasmodesmata (PD), thereby enhancing PD-callose accumulation. Remarkably, ABA-deficient plants repressed GA₄ biosynthesis and established endo-dormancy like controls but showed increased stress sensitivity. Repression of GA₄ biosynthesis involved short-day induced DNA methylation events within the GA3ox2 promoter. In conclusion, the results cast new light on the roles of ABA and GA in dormancy cycling. In para-dormancy, PD-callose turnover is antagonized by ABA, whereas in short-day conditions, lack of GA₄ biosynthesis promotes callose deposition that is structurally persistent throughout endo-dormancy.

Genome-Wide Analysis of the BBX Genes in Platanus × acerifolia and Their Relationship with Flowering and/or Dormancy

The B-BOX (BBX) gene family is widely distributed in animals and plants and is involved in the regulation of their growth and development. In plants, BBX genes play important roles in hormone signaling, biotic and abiotic stress, light-regulated photomorphogenesis, flowering, shade response, and pigment accumulation. However, there has been no systematic analysis of the BBX family in Platanus × acerifolia. In this study, we identified 39 BBX genes from the P. × acerifolia genome, and used TBtools, MEGA, MEME, NCBI CCD, PLANTCARE and other tools for gene collinearity analysis, phylogenetic analysis, gene structure, conserved domain analysis, and promoter cis-element analysis, and used the qRT-PCR and transcriptome data for analyzing expression pattern of the PaBBX genes. Collinearity analysis indicated segmental duplication was the main driver of the BBX family in P. × acerifolia, and phylogenetic analysis showed that the PaBBX family was divided into five subfamilies: I, II, III, IV and V. Gene structure analysis showed that some PaBBX genes contained super-long introns that may regulate their own expression. Moreover, the promoter of PaBBX genes contained a significant number of cis-acting elements that are associated with plant growth and development, as well as hormone and stress responses. The qRT-PCR results and transcriptome data indicated that certain PaBBX genes exhibited tissue-specific and stage-specific expression patterns, suggesting that these genes may have distinct regulatory roles in P. × acerifolia growth and development. In addition, some PaBBX genes were regularly expressed during the annual growth of P. × acerifolia, corresponding to different stages of flower transition, dormancy, and bud break, indicating that these genes may be involved in the regulation of flowering and/or dormancy of P. × acerifolia. This article provided new ideas for the study of dormancy regulation and annual growth patterns in perennial deciduous plants.

Comprehensive analysis and expression profiles of the AP2/ERF gene family during spring bud break in tea plant (Camellia sinensis)

BACKGROUND

AP2/ERF transcription factors (AP2/ERFs) are important regulators of plant physiological and biochemical metabolism. Evidence suggests that AP2/ERFs may be involved in the regulation of bud break in woody perennials. Green tea is economically vital in China, and its production value is significantly affected by the time of spring bud break of tea plant. However, the relationship between AP2/ERFs in tea plant and spring bud break remains largely unknown.

RESULTS

A total of 178 AP2/ERF genes (CsAP2/ERFs) were identified in the genome of tea plant. Based on the phylogenetic analysis, these genes could be classified into five subfamilies. The analysis of gene duplication events demonstrated that whole genome duplication (WGD) or segmental duplication was the primary way of CsAP2/ERFs amplification. According to the result of the Ka/Ks value calculation, purification selection dominated the evolution of CsAP2/ERFs. Furthermore, gene composition and structure analyses of CsAP2/ERFs indicated that different subfamilies contained a variety of gene structures and conserved motifs, potentially resulting in functional differences among five subfamilies. The promoters of CsAP2/ERFs also contained various signal-sensing elements, such as abscisic acid responsive elements, light responsive elements and low temperature responsive elements. The evidence presented here offers a theoretical foundation for the diverse functions of CsAP2/ERFs. Additionally, the expressions of CsAP2/ERFs during spring bud break of tea plant were analyzed by RNA-seq and grouped into clusters A-F according to their expression patterns. The gene expression changes in clusters A and B were more synchronized with the spring bud break of tea plant. Moreover, several potential correlation genes, such as D-type cyclin genes, were screened out through weighted correlation network analysis (WGCNA). Temperature and light treatment experiments individually identified nine candidate CsAP2/ERFs that may be related to the spring bud break of tea plant.

CONCLUSIONS

This study provides new evidence for role of the CsAP2/ERFs in the spring bud break of tea plant, establishes a theoretical foundation for analyzing the molecular mechanism of the spring bud break of tea plant, and contributes to the improvement of tea cultivars.

A high-confidence Physcomitrium patens plasmodesmata proteome by iterative scoring and validation reveals diversification of cell wall proteins during evolution

Plasmodesmata (PD) facilitate movement of molecules between plant cells. Regulation of this movement is still not understood. Plasmodesmata are hard to study, being deeply embedded within cell walls and incorporating several membrane types. Thus, structure and protein composition of PD remain enigmatic. Previous studies of PD protein composition identified protein lists with few validations, making functional conclusions difficult. We developed a PD scoring approach in iteration with large-scale systematic localization, defining a high-confidence PD proteome of Physcomitrium patens (HC300). HC300, together with bona fide PD proteins from literature, were placed in Pddb. About 65% of proteins in HC300 were not previously PD-localized. Callose-degrading glycolyl hydrolase family 17 (GHL17) is an abundant protein family with representatives across evolutionary scale. Among GHL17s, we exclusively found members of one phylogenetic clade with PD localization and orthologs occur only in species with developed PD. Phylogenetic comparison was expanded to xyloglucan endotransglucosylases/hydrolases and Exordium-like proteins, which also diversified into PD-localized and non-PD-localized members on distinct phylogenetic clades. Our high-confidence PD proteome HC300 provides insights into diversification of large protein families. Iterative and systematic large-scale localization across plant species strengthens the reliability of HC300 as basis for exploring structure, function, and evolution of this important organelle.

Is a seasonally reduced growth potential a convergent strategy to survive drought and frost in plants?

BACKGROUND

Plants have adapted to survive seasonal life-threatening frost and drought. However, the timing and frequency of such events are impacted by climate change, jeopardizing plant survival. Understanding better the strategies of survival to dehydration stress is therefore timely and can be enhanced by the cross-fertilization of research between disciplines (ecology, physiology), models (woody, herbaceous species) and types of stress (drought, frost).

SCOPE

We build upon the 'growth-stress survival' trade-off, which underpins the identification of global plant strategies across environments along a 'fast-slow' economics spectrum. Although phenological adaptations such as dormancy are crucial to survive stress, plant global strategies along the fast-slow economic spectrum rarely integrate growth variations across seasons. We argue that the growth-stress survival trade-off can be a useful framework to identify convergent plant ecophysiological strategies to survive both frost and drought. We review evidence that reduced physiological activity, embolism resistance and dehydration tolerance of meristematic tissues are interdependent strategies that determine thresholds of mortality among plants under severe frost and drought. We show that complete dormancy, i.e. programmed growth cessation, before stress occurrence, minimizes water flows and maximizes dehydration tolerance during seasonal life-threatening stresses. We propose that incomplete dormancy, i.e. the programmed reduction of growth potential during the harshest seasons, could be an overlooked but major adaptation across plants. Quantifying stress survival in a range of non-dormant versus winter- or summer-dormant plants, should reveal to what extent incomplete to complete dormancy could represent a proxy for dehydration tolerance and stress survival.

CONCLUSIONS

Our review of the strategies involved in dehydration stress survival suggests that winter and summer dormancy are insufficiently acknowledged as plant ecological strategies. Incorporating a seasonal fast-slow economics spectrum into global plant strategies improves our understanding of plant resilience to seasonal stress and refines our prevision of plant adaptation to extreme climatic events.

Phenological response to climate variation in a northern red oak plantation: Links to survival and productivity

In a changing climate, the future survival and productivity of species rely on individual populations to respond to shifting environmental conditions. Many tree species, including northern red oak (Quercus rubra), exhibit phenotypic plasticity, the ability to respond to changes in environmental conditions at within-generation time scales, through varying traits such as leaf phenology. Phenotypic plasticity of phenology may vary among populations within a species' range, and it is unclear if the range of plasticity is adequate to promote fitness. Here, we used a 58-year-old common garden to test whether northern red oak populations differed in phenological sensitivity to changes in temperature and whether differences in phenological sensitivity were associated with differences in productivity and survival (proxies of fitness). We recorded 8 years of spring leaf emergence and autumn leaf coloration and loss in 28 distinct populations from across the species' full range. Across the 28 populations, spring leaf out consistently advanced in warmer years, but fall phenology was less responsive to changes in temperature. Southern, warm-adapted populations had larger shifts in phenology in response to springtime warming but had lower long-term survival. Moreover, higher phenological sensitivity to spring warming was not strongly linked to increased productivity. Instead, fitness was more closely linked to latitudinal gradients. Although springtime phenological sensitivity to climate change is common across northern red oak populations, responses of productivity and survival, which could determine longer-term trajectories of species abundance, are more variable across the species' range.

Phenological physiology: seasonal patterns of plant stress tolerance in a changing climate

The physiological challenges posed by climate change for seasonal, perennial plants include increased risk of heat waves, postbudbreak freezing ('false springs'), and droughts. Although considerable physiological work has shown that the traits conferring tolerance to these stressors - thermotolerance, cold hardiness, and water deficit stress, respectively - are not static in time, they are frequently treated as such. In this review, I synthesize the recent literature on predictable seasonal - and therefore, phenological - patterns of acclimation and deacclimation to heat, cold, and water-deficit stress in perennials, focusing on woody plants native to temperate climates. I highlight promising, high-throughput techniques for quantifying thermotolerance, cold hardiness, and drought tolerance. For each of these forms of stress tolerance, I summarize the current balance of evidence regarding temporal patterns over the course of a year and suggest a characteristic temporal scale in these responses to environmental stress. In doing so, I offer a synthetic framework of 'phenological physiology', in which understanding and leveraging seasonally recurring (phenological) patterns of physiological stress acclimation can facilitate climate change adaptation and mitigation.

Cold stress induces malformed tomato fruits by breaking the feedback loops of stem cell regulation in floral meristem

Fruit malformation is a major constrain in fruit production worldwide resulting in substantial economic losses. The farmers for decades noticed that the chilling temperature before blooming often caused malformed fruits. However, the molecular mechanism underlying this phenomenon is unclear. Here we examined the fruit development in response to cold stress in tomato, and demonstrated that short-term cold stress increased the callose accumulation in both shoot apical and floral meristems, resulting in the symplastic isolation and altered intercellular movement of WUS. In contrast to the rapidly restored SlWUS transcription during the recovery from cold stress, the callose removal was delayed due to obstructed plasmodesmata. The delayed reinstatement of cell-to-cell transport of SlWUS prevented the activation of SlCLV3 and TAG1, causing the interrupted feedback inhibition of SlWUS expression, leading to the expanded stem cell population and malformed fruits. We further showed that the callose dynamics in response to short-term cold stress presumably exploits the mechanism of bud dormancy during the seasonal growth, involving two antagonistic hormones, abscisic acid and gibberellin. Our results provide a novel insight into the cold stress regulated malformation of fruit.

Changes in annual transcriptome dynamics of a clone of Japanese cedar (Cryptomeria japonica D. Don) planted under different climate conditions

Environmental responses are critical for plant growth and survival under different climate conditions. To elucidate the underlying biological mechanisms of environmental responses in Japanese cedar (Cryptomeria japonica D. Don), the annual transcriptome dynamics of common clonal trees (Godai1) planted at three different climate sites (Yamagata, Ibaraki, and Kumamoto Prefectures) were analyzed using microarrays. Both principal component analysis (PCA) and hierarchical clustering of the microarray data indicated the transition to dormant transcriptome status occurred earlier and the transition to active growth status later in the colder region. Interestingly, PCA also indicated that the transcriptomes of trees grown under three different conditions were similar during the growth period (June to September), whereas the transcriptomes differed between sites during the dormant period (January to March). In between-site comparisons, analyses of the annual expression profiles of genes for sites 'Yamagata vs. Kumamoto', 'Yamagata vs. Ibaraki', and 'Ibaraki vs. Kumamoto' identified 1,473, 1,137, and 925 targets exhibiting significantly different expression patterns, respectively. The total of 2,505 targets that exhibited significantly different expression patterns in all three comparisons may play important roles in enabling cuttings to adapt to local environmental conditions. Partial least-squares regression analysis and Pearson correlation coefficient analysis revealed that air temperature and day length were the dominant factors controlling the expression levels of these targets. GO and Pfam enrichment analyses indicated that these targets include genes that may contribute to environmental adaptation, such as genes related to stress and abiotic stimulus responses. This study provided fundamental information regarding transcripts that may play an important role in adaptation to environmental conditions at different planting sites.

Chromosome-Level Assembly of Flowering Cherry (Prunus campanulata) Provides Insight into Anthocyanin Accumulation

The flowering cherries (genus Prunus, subgenus Cerasus) are popular ornamental trees in China, Japan, Korea, and elsewhere. Prunus campanulata Maxim. is an important species of flowering cherry native to Southern China, which is also distributed in Taiwan, the Ryukyu Islands of Japan, and Vietnam. It produces bell-shaped flowers with colors ranging from bright pink to crimson during the Chinese Spring Festival from January to March each year. We selected the P. campanulata cultivar "Lianmeiren", with only 0.54% of heterozygosity, as the focus of this study, and generated a high-quality chromosome-scale genome assembly of P. campanulata by combining Pacific Biosciences (PacBio) single-molecule sequencing, 10× Genomics sequencing, and high-throughput chromosome conformation capture (Hi-C) technology. We first assembled a 300.48 Mb genome assembly with a contig N50 length of 2.02 Mb. In total, 28,319 protein-coding genes were predicted from the genome, 95.8% of which were functionally annotated. Phylogenetic analyses indicated that P. campanulata diverged from a common ancestor of cherry approximately 15.1 million years ago. Comparative genomic analyses showed that the expanded gene families were significantly involved in ribosome biogenesis, diterpenoid biosynthesis, flavonoid biosynthesis, and circadian rhythm. Furthermore, we identified 171 MYB genes from the P. campanulata genome. Based on the RNA-seq of five organs at three flowering stages, expression analyses revealed that the majority of the MYB genes exhibited tissue-specific expression patterns, and some genes were identified as being associated with anthocyanin accumulation. This reference sequence is an important resource for further studies of floral morphology and phenology, and comparative genomics of the subgenera Cerasus and Prunus.

Summer dormancy of Myricaria laxiflora to escape flooding stress: Changes in phytohormones and enzymes induced by environmental factors

Dormancy is an adaptation mechanism of plants to environmental stress. Myricaria laxiflora undergoes a long period of flooding stress every year. In order to determine whether this species escapes flooding stress through dormancy, young branches and leaves were collected at different time points before the onset of flooding, and changes in the content/activity of hormones/enzymes that are closely involved in plant growth were monitored. The inducing environmental factors of summer dormancy were identified. The branches and leaves of M. laxiflora showed the following trends as summer flooding approached: (1) gradual increase in the abscisic acid content; (2) gradual decrease in the gibberellin and cytokinin contents; and (3) a continuous decrease in the activities of malate dehydrogenase (MDH), ribulose diphosphate carboxylase (RuBisCo), and glycolate oxidase (GLO). Pearson correlation analysis revealed (1) daylight duration was highly correlated with the hormone content and enzyme activity; (2) the daily mean air temperature (DMAT) was significantly correlated with the cytokinin content. These findings suggest that daylight duration was the main environmental factor leading to changes in the phytohormone content and enzyme activity as well as leading to summer dormancy. M. laxiflora undergoes dormancy before the onset of summer flooding to escape summer flooding stress. Our data indicate that summer flooding does not impede the survival and growth of M. laxiflora.

Changing winter climate and snow conditions induce various transcriptional stress responses in Scots pine seedlings

In northern boreal forests the warming winter climate leads to more frequent snowmelt, rain-on-snow events and freeze-thaw cycles. This may be harmful or even lethal for tree seedlings that spend even a half of the year under snow. We conducted a snow cover manipulation experiment in a natural forest to find out how changing snow conditions affect young Scots pine (Pinus sylvestris L.) seedlings. The ice encasement (IE), absence of snow (NoSNOW) and snow compaction (COMP) treatments affected ground level temperature, ground frost and subnivean gas concentrations compared to the ambient snow cover (AMB) and led to the increased physical damage and mortality of seedlings. The expression responses of 28 genes related to circadian clock, aerobic and anaerobic energy metabolism, carbohydrate metabolism and stress protection revealed that seedlings were exposed to different stresses in a complex way depending on the thickness and quality of the snow cover. The IE treatment caused hypoxic stress and probably affected roots which resulted in reduced water uptake in the beginning of the growing season. Without protective snowpack in NoSNOW seedlings suffered from cold and drought stresses. The combination of hypoxic and cold stresses in COMP evoked unique transcriptional responses including oxidative stress. Snow cover manipulation induced changes in the expression of several circadian clock related genes suggested that photoreceptors and the circadian clock system play an essential role in the adaptation of Scots pine seedlings to stresses under different snow conditions. Our findings show that warming winter climate alters snow conditions and consequently causes Scots pine seedlings various abiotic stresses, whose effects extend from overwintering to the following growing season.

Effect of the photoperiod on bud dormancy in Liriodendron chinense

Bud dormancy and its release are complex physiological phenomena in plants. The molecular mechanisms of bud dormancy in Liriodendron chinense are mainly unknown. Here, we studied bud dormancy and the related physiological and molecular phenomena in Liriodendron under long-day (LD) and short-day (SD). Bud burst was released faster under LD than under SD. Abscisic acid (ABA), superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GR) activities were increased significantly under LD in Liriodendron buds. In contrast, the contents of gibberellic acid (GA3), ascorbic acid (AsA), glutathione (GSH), malondialdehyde (MDA), and ascorbate peroxidase (APX) activity decreased under LD but increased under SD. Differentially expressed genes (DEGs) were up-regulated under LD and down-regulated under SD and these changes correspondingly promoted (LD) or repressed (SD) cell division and the number and/or size of cells in the bud. Transcriptomic analysis of Liriodendron buds under different photoperiods identified 187 DEGs enriched in several pathways such as flavonoid biosynthesis and phenylpropanoid biosynthesis, plant hormone and signal transduction, etc. that are associated with antioxidant enzymes, non-enzymatic antioxidants, and subsequently promote the growth of the buds. Our findings provide novel insights into regulating bud dormancy via flavonoid and phenylpropanoid biosynthesis, plant hormone and signal transduction pathways, and ABA content. These physiological and biochemical traits would help detect bud dormancy in plants.

A Pan-Transcriptome Analysis Indicates Efficient Downregulation of the FIB Genes Plays a Critical Role in the Response of Alfalfa to Cold Stress

Alfalfa (Medicago sativa L.) is a perennial forage legume that is widely distributed throughout the world, and cold stress is an important environmental factor limiting the growth and production of alfalfa in cold regions. However, little is known of the molecular mechanisms regarding cold tolerance in alfalfa. Here, we conducted physiological metabolism assays and pan-transcriptome sequencing on eight cultivars of alfalfa under cold stress conditions. The results of the RNA-seq analysis showed that the genes are "oxidoreductase activity" and "transcription regulator activity", suggesting that genes with such functions are more likely to play important roles in the response to cold stress by alfalfa. In addition, to identify specific gene modules and hub genes in response to alfalfa cold stress, we applied weighted gene co-expression network (WGCNA) analyses to the RNA-seq data. Our results indicate that the modules of genes that focus on the ATPase complex, ribosome biogenesis, are more likely to be involved in the alfalfa response to cold stress. It is important to note that we identified two fibronectin (FIB) genes as hub genes in alfalfa in response to cold stress and that they negatively regulate alfalfa response to chilling stress, and it is possible that dormant alfalfa is more effective at down-regulating FIB expression and therefore more resistant to cold stress.

Low temperature and short daylength interact to affect the leaf senescence of two temperate tree species

Temperature and photoperiod are two major environmental cues shaping the leaf senescence of temperate tree species. However, how the control of leaf senescence is split between photoperiod and temperature is unknown for many ecologically important species. Here, we conducted a growth chamber experiment to test the effects of temperature (6, 9, 18 and 21°C) and photoperiod (8 and 16 h daylength) on leaf senescence of two temperate tree species (Quercus mongolica Fisch. and Larix principis-rupprechtii Mayr.) distributed in montane forest of China. The results showed that low temperature (LT) alone could induce leaf senescence of both species under long daylength (LD) conditions, but the leaf senescence of L. principis-rupprechtii was more sensitive to the decrease in temperature than that of Q. mongolica under the LD condition. Short daylength (SD) alone could only induce the leaf senescence of L. principis-rupprechtii, suggesting that the photoperiod sensitivity varies between species. SD could accelerate the LT-induced senescence, but the effect of SD reduced with the decrease in temperature. Based on these findings, we developed a new autumn phenology model by incorporating interspecific differences in the photoperiod sensitivity of leaf senescence. Compared with the three existing process-based autumn phenology models, the new model was more robust in simulating the experimental data. When employing these models to available long-term phenological data, our new model also performed best in reproducing the observed leaf senescence date of two closely related species (Quercus robur L. and Larix decidua Mill.). These results enhance our understanding of how LT and SD control leaf senescence. The prediction of the climate change impacts on forest carbon uptake could be improved by incorporating this new autumn phenological model into the terrestrial biosphere models.

Sucrose accumulation and endodormancy are synchronized events induced by the short-day photoperiod in grapevine buds

At the end of the summer season, grapevine buds (Vitis vinifera L) grown in temperate climates enter a state of winter recess or endodormancy (ED), which is induced by the shortening of the photoperiod, and during this period, the buds accumulate sucrose. In this study, we investigated whether the shortening of the photoperiod regulates the accumulation of sucrose in the buds in the same way as it regulates its entry into the ED. Because sucrose accumulation is regulated by genes that control its transport and degradation, the effect of the SD photoperiod and the transition of buds from paradormancy (PD) to ED on the expression of sucrose transporter (VvSUTs) and invertase genes (VvINVs) was studied. To analyze the possible role of sucrose during ED development, its effect on bud swelling and sprouting was studied on dormant and nondormant buds under forced growth conditions. The results showed that the SD photoperiod upregulates the expression of the VvSUT genes and downregulates that of the VvINV genes in grapevine buds. Additionally, during the transition of buds from PD to ED, the sucrose content increased, the expression of the VvINV genes decreased, and the expression of the VvSUT genes did not change significantly. Sucrose delayed bud swelling and sprouting when applied to dormant buds but had no effect when applied to nondormant buds. Therefore, we concluded that ED development and sucrose accumulation were synchronized events induced by the SD photoperiod and that a sucrose peak marks the end of ED development in grapevine buds.

Cold acclimation threshold induction temperatures of switchgrass ecotypes grown under a long and short photoperiod

Plants can cold acclimate to enhance their freezing tolerance by sensing declining temperature and photoperiod cues. However, the factors influencing genotypic variation in the induction of cold acclimation are poorly understood among perennial grasses. We hypothesized that the more northern upland switchgrass (Panicum virgatum L.) ecotype develops a higher degree of freezing tolerance by initiating cold acclimation at higher temperatures as compared with the coastal and southern lowland ecotypes. First, we determined the optimal method for assessing freezing tolerance and the length of exposure to 8/4°C required to induce the maximum level of freezing tolerance in the most northern upland and most southern lowland genotypes. We characterized the maximum freezing tolerance of eight uplands, three coastal and five lowland genotypes grown for 21 days at 8/4°C and a 10 or 16 h photoperiod. Next, we identified the temperature required to induce cold acclimation by exposing the 16 genotypes for 7 days at 20-6°C constant temperatures under a 10 or 16 h photoperiod. Cold acclimation initiated at temperatures 5 and 7°C higher in upland than in coastal and lowland genotypes. Among upland genotypes the shorter photoperiod induced cold acclimation at a 1°C higher temperature. Genotypes originating from a more northern latitude initiate cold acclimation at higher temperatures and develop higher maximum freezing tolerances. An earlier response to declining temperatures may provide the upland ecotype with additional time to prepare for winter and provide an advantage when plants are subjected to the rapid changes in fall temperature associated with injurious frosts.

Assisted migration is plausible for a boreal tree species under climate change: A quantitative and population genetics study of trembling aspen (Populus tremuloides Michx.) in western Canada

A novel method was tested for improving tree breeding strategies that integrate quantitative and population genetics based on range‐wide reciprocal transplant experiments. Five reciprocal common garden tests of Populus tremuloides were investigated including 6450 trees across western Canada focusing on adaptation traits and growth. Both genetic parameters and home‐site transplant models were evaluated. We found a genetic trade‐off between growth and early spring leaf flush and late fall senescence. Coefficients of phenotypic variation (CVp) of cell lysis (CL), a measure of freezing injury, shrank from 0.28 to 0.10 during acclimation in the fall, and the CVp slope versus the freezing temperature was significantly different from zero (R² = 0.33, p = .02). There was more between‐population genetic variation in fall phenology than in spring leaf phenology. We suggest that P. tremuloides demonstrated a discrepancy between the ecological optimum and the physiological optimum minimum winter temperature. The sub‐optimal growing condition of P. tremuloides is potentially caused by the warmer ecological optimum than the physiological optimum. Assisted migration and breeding of fast growers to reforest cooler plantation sites can improve productivity. Transferring the study populations to less than 4°C of extreme minimum temperature appears safe for reforestation aligning with the historical recolonization direction of the species. This is equivalent to a 5–10° latitudinal northward movement. Fall frost hardiness is an effective criterion for family selection in the range tested in this study.

Identification of Key Genes Related to Dormancy Control in Prunus Species by Meta-Analysis of RNAseq Data

Bud dormancy is a genotype-dependent mechanism observed in Prunus species in which bud growth is inhibited, and the accumulation of a specific amount of chilling (endodormancy) and heat (ecodormancy) is necessary to resume growth and reach flowering. We analyzed publicly available transcriptome data from fifteen cultivars of four Prunus species (almond, apricot, peach, and sweet cherry) sampled at endo- and ecodormancy points to identify conserved genes and pathways associated with dormancy control in the genus. A total of 13,018 genes were differentially expressed during dormancy transitions, of which 139 and 223 were of interest because their expression profiles correlated with endo- and ecodormancy, respectively, in at least one cultivar of each species. The endodormancy-related genes comprised transcripts mainly overexpressed during chilling accumulation and were associated with abiotic stresses, cell wall modifications, and hormone regulation. The ecodormancy-related genes, upregulated after chilling fulfillment, were primarily involved in the genetic control of carbohydrate regulation, hormone biosynthesis, and pollen development. Additionally, the integrated co-expression network of differentially expressed genes in the four species showed clusters of co-expressed genes correlated to dormancy stages and genes of breeding interest overlapping with quantitative trait loci for bloom time and chilling and heat requirements.