Extreme low temperature tolerance in woody plants

Functions and Regulatory Mechanisms of bHLH Transcription Factors during the Responses to Biotic and Abiotic Stresses in Woody Plants

Environmental stresses, including abiotic and biotic stresses, have complex and diverse effects on the growth and development of woody plants, which have become a matter of contention due to concerns about the outcomes of climate change on plant resources, genetic diversity, and world food safety. Plant basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in a variety of physiological processes and play an important role in biotic and abiotic stress responses of woody plants. In recent years, an increasing body of studies have been conducted on the bHLH TFs in woody plants, and the roles of bHLH TFs in response to various stresses are increasingly clear and precise. Therefore, it is necessary to conduct a systematic and comprehensive review of the progress of the research of woody plants. In this review, the structural characteristics, research history and roles in the plant growth process of bHLH TFs are summarized, the gene families of bHLH TFs in woody plants are summarized, and the roles of bHLH TFs in biotic and abiotic stresses in woody plants are highlighted. Numerous studies mentioned in this review have shown that bHLH transcription factors play a crucial role in the response of woody plants to biotic and abiotic stresses. This review serves as a reference for further studies about enhancing the stress resistance and breeding of woody plants. Also, the future possible research directions of bHLH TFs in response to various stresses in woody plants will be discussed.

Epigenetic stress memory in gymnosperms

Gymnosperms are long-lived, cone-bearing seed plants that include some of the most ancient extant plant species. These relict land plants have evolved to survive in habitats marked by chronic or episodic stress. Their ability to thrive in these environments is partly due to their phenotypic flexibility, and epigenetic regulation likely plays a crucial part in this plasticity. We review the current knowledge on abiotic and biotic stress memory in gymnosperms and the possible epigenetic mechanisms underlying long-term phenotypic adaptations. We also discuss recent technological improvements and new experimental possibilities that likely will advance our understanding of epigenetic regulation in these ancient and hard-to-study plants.

Freeze dehydration vs supercooling in tree stems: physical and physiological modelling

Frost resistance is the major factor affecting the distribution of plant species at high latitude and elevation. The main effects of freeze-thaw cycles are damage to living cells and formation of gas embolism in tree xylem vessels. Lethal intracellular freezing can be prevented in living cells by two mechanisms, such as dehydration and deep supercooling. We developed a multiphysics numerical model coupling water flow, heat transfer and phase change, considering different cell types in plant tissues, to study the dynamics and extent of cell dehydration, xylem pressure changes and stem diameter changes in response to freezing and thawing. Results were validated using experimental data for stem diameter changes of walnut trees (Juglans regia). The effect of cell mechanical properties was found to be negligible as long as the intracellular tension developed during dehydration was sufficiently low compared with the ice-induced cryostatic suction. The model was finally used to explore the coupled effects of relevant physiological parameters (initial water and sugar content) and environmental conditions (air temperature variations) on the dynamics and extent of dehydration. It revealed configurations where cell dehydration could be sufficient to protect cells from intracellular freezing, and situations where supercooling was necessary. This model, freely available with this paper, could easily be extended to explore different anatomical structures, different species and more complex physical processes.

Spring wood phenology responds more strongly to chilling temperatures than bud phenology in European conifers

A comparative assessment of bud and wood phenology could aid a better understanding of tree growth dynamics. However, the reason for asynchronism or synchronism in leaf and cambial phenology remains unclear. To test the assumption that the temporal relationship between the budburst date and the onset date of wood formation is due to their common or different responses to environmental factors, we constructed a wood phenology dataset from previous literature, and compared it with an existing bud phenology dataset in Europe. We selected three common conifers (Larix decidua Mill., Picea abies (L.) H. Karst. and Pinus sylvestris L.) in both datasets and analyzed 909 records of the onset of wood formation at 47 sites and 238,720 records of budburst date at 3051 sites. We quantified chilling accumulation (CA) and forcing requirement (FR) of budburst and onset of wood formation based on common measures of CA and FR. We then constructed negative exponential CA-FR curves for bud and wood phenology separately. The results showed that the median, variance and probability distribution of CA-FR curves varied significantly between bud and wood phenology for three conifers. The different FR under the same chilling condition caused asynchronous bud and wood phenology. Furthermore, the CA-FR curves manifested that wood phenology was more sensitive to chilling than bud phenology. Thus, the FR of the onset of wood formation increases more than that of budburst under the same warming scenarios, explaining the stronger earlier trends in the budburst date than the onset date of woody formation simulated by the process-based model. Our work not only provides a possible explanation for asynchronous bud and wood phenology from the perspective of organ-specific responses to chilling and forcing, but also develops a phenological model for predicting both bud and wood phenology with acceptable uncertainties.

Physiochemical Responses and Ecological Adaptations of Peach to Low-Temperature Stress: Assessing the Cold Resistance of Local Peach Varieties from Gansu, China

In recent years, extreme weather events have become increasingly frequent, and low winter temperatures have had a significant impact on peach cultivation. The selection of cold-resistant peach varieties is an effective solution to mitigate freezing damage. To comprehensively and accurately evaluate the cold resistance of peaches and screen for high cold resistance among Gansu local resources, nine different types of peach were selected as test resources to assess physiological, biochemical, and anatomical indices. Subsequently, 28 peach germplasms were evaluated using relevant indices. The semi-lethal temperature (LT50) was calculated by fitting the change curve of the electrolyte leakage index (ELI) with the Logistic equation; this can be used as an important index for identifying and evaluating the cold resistance of peach trees. The LT50 values ranged from -28.22 °C to -17.22 °C among the 28 tested resources; Dingjiaba Liguang Tao exhibited the lowest LT50 value at -28.22 °C, indicating its high level of cold resistance. The LT50 was positively correlated with the ELI and malondialdehyde (MDA) content with correlation coefficients of 0.894 and 0.863, respectively, while it was negatively correlated with the soluble sugar (SS), soluble protein (SP), and free proline (Pro) contents with correlation coefficients of -0.894, -0.721, and -0.863, respectively. The thicknesses of the xylem, cork layer, cork layer ratio (CLR) and thickness/cortex thickness (X/C) showed negative correlations (-0.694, -0.741, -0.822, -0.814, respectively). Finally, the membership function method was used to evaluate cold resistance based on the ELI, MDA, Pro, SP, SS, CLR, and xylem thickness/cortex thickness (X/C) indices. The average membership degree among all tested resources ranged from 0.17 to 0.61. Dingjiaba Liguang Tao emerged prominently in terms of high-cold-resistance (HR) membership value (0.61).

Genome-wide identification of late embryogenesis abundant protein family and their key regulatory network in Pinus tabuliformis cold acclimation

Cold acclimation is a crucial biological process that enables conifers to overwinter safely. The late embryogenesis abundant (LEA) protein family plays a pivotal role in enhancing freezing tolerance during this process. Despite its importance, the identification, molecular functions and regulatory networks of the LEA protein family have not been extensively studied in conifers or gymnosperms. Pinus tabuliformis, a conifer with high ecological and economic values and with high-quality genome sequence, is an ideal candidate for such studies. Here, a total of 104 LEA genes were identified from P. tabuliformis, and we renamed them according to their subfamily group: PtLEA1-PtLEA92 (group LEA1-LEA6), PtSMP1-PtSMP6 (group seed maturation protein) and PtDHN1-PtDHN6 (group Dehydrin). While the sequence structure of P. tabuliformis  LEA genes are conserved, their physicochemical properties exhibit unique characteristics within different subfamily groupings. Notably, the abundance of low-temperature responsive elements in PtLEA genes was observed. Using annual rhythm and temperature gradient transcriptome data, PtLEA22 was identified as a key gene that responds to low-temperature induction while conforming to the annual cycle of cold acclimation. Overexpression of PtLEA22 enhanced Arabidopsis freezing tolerance. Furthermore, several transcription factors potentially co-expressed with PtLEA22 were validated using yeast one-hybrid and dual-luciferase assays, revealing that PtDREB1 could directly bind PtLEA22 promoter to positively regulate its expression. These findings reveal the genome-wide characterization of P. tabuliformis  LEA genes and their importance in the cold acclimation, while providing a theoretical basis for studying the molecular mechanisms of cold acclimation in conifers.

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.

Sub-arctic mosses and lichens show idiosyncratic responses to combinations of winter heatwaves, freezing and nitrogen deposition

Arctic ecosystems are increasingly exposed to extreme climatic events throughout the year, which can affect species performance. Cryptogams (bryophytes and lichens) provide important ecosystem services in polar ecosystems but may be physiologically affected or killed by extreme events. Through field and laboratory manipulations, we compared physiological responses of seven dominant sub-Arctic cryptogams (three bryophytes, four lichens) to single events and factorial combinations of mid-winter heatwave (6°C for 7 days), re-freezing, snow removal and summer nitrogen addition. We aimed to identify which mosses and lichens are vulnerable to these abiotic extremes and if combinations would exacerbate physiological responses. Combinations of extremes resulted in stronger species responses but included idiosyncratic species-specific responses. Species that remained dormant during winter (March), irrespective of extremes, showed little physiological response during summer (August). However, winter physiological activity, and response to winter extremes, was not consistently associated with summer physiological impacts. Winter extremes affect cryptogam physiology, but summer responses appear mild, and lichens affect the photobiont more than the mycobiont. Accounting for Arctic cryptogam response to multiple climatic extremes in ecosystem functioning and modelling will require a better understanding of their winter eco-physiology and repair capabilities.

Field plus lab experiments help identify freezing tolerance and associated genes in subtropical evergreen broadleaf trees: A case study of Camellia oleifera

The molecular mechanisms of freezing tolerance are unresolved in the perennial trees that can survive under much lower freezing temperatures than annual herbs. Since natural conditions involve many factors and temperature usually cannot be controlled, field experiments alone cannot directly identify the effects of freezing stress. Lab experiments are insufficient for trees to complete cold acclimation and cannot reflect natural freezing-stress responses. In this study, a new method was proposed using field plus lab experiments to identify freezing tolerance and associated genes in subtropical evergreen broadleaf trees using Camellia oleifera as a case. Cultivated C. oleifera is the dominant woody oil crop in China. Wild C. oleifera at the high-elevation site in Lu Mountain could survive below -30°C, providing a valuable genetic resource for the breeding of freezing tolerance. In the field experiment, air temperature was monitored from autumn to winter on wild C. oleifera at the high-elevation site in Lu Mountain. Leave samples were taken from wild C. oleifera before cold acclimation, during cold acclimation and under freezing temperature. Leaf transcriptome analyses indicated that the gene functions and expression patterns were very different during cold acclimation and under freezing temperature. In the lab experiments, leaves samples from wild C. oleifera after cold acclimation were placed under -10°C in climate chambers. A cultivated C. oleifera variety "Ganwu 1" was used as a control. According to relative conductivity changes of leaves, wild C. oleifera showed more freezing-tolerant than cultivated C. oleifera. Leaf transcriptome analyses showed that the gene expression patterns were very different between wild and cultivated C. oleifera in the lab experiment. Combing transcriptome results in both of the field and lab experiments, the common genes associated with freezing-stress responses were identified. Key genes of the flg22, Ca²⁺ and gibberellin signal transduction pathways and the lignin biosynthesis pathway may be involved in the freezing-stress responses. Most of the genes had the highest expression levels under freezing temperature in the field experiment and showed higher expression in wild C. oleifera with stronger freezing tolerance in the lab experiment. Our study may help identify freezing tolerance and underlying molecular mechanisms in trees.

The genome of Magnolia hypoleuca provides a new insight into cold tolerance and the evolutionary position of magnoliids

Magnolia hypoleuca Sieb. & Zucc, a member of the Magnoliaceae of magnoliids, is one of the most economically valuable, phylogenetic and ornamental tree species in Eastern China. Here, the 1.64 Gb chromosome-level assembly covers 96.64% of the genome which is anchored to 19 chromosomes, with a contig N50 value of 1.71 Mb and 33,873 protein-coding genes was predicted. Phylogenetic analyses between M. hypoleuca and other 10 representative angiosperms suggested that magnoliids were placed as a sister group to the eudicots, rather than sister to monocots or both monocots and eudicots. In addition, the relative timing of the whole-genome duplication (WGD) events about 115.32 Mya for magnoliid plants. M. hypoleuca was found to have a common ancestor with M. officinalis approximately 23.4 MYA, and the climate change of OMT (Oligocene-Miocene transition) is the main reason for the divergence of M. hypoleuca and M. officinalis, which was along with the division of Japanese islands. Moreover, the TPS gene expansion observed in M. hypoleuca might contribute to the enhancement of flower fragrance. Tandem and proximal duplicates of younger age that have been preserved have experienced more rapid sequence divergence and a more clustered distribution on chromosomes contributing to fragrance accumulation, especially phenylpropanoid, monoterpenes and sesquiterpenes and cold tolerance. The stronger selective pressure drived the evolution of tandem and proximal duplicates toward plant self-defense and adaptation. The reference M. hypoleuca genome will provide insights into the evolutionary process of M. hypoleuca and the relationships between the magnoliids with monocots and eudicots, and enable us to delve into the fragrance and cold tolerance produced by M. hypoleuca and provide more robust and deep insight of how the Magnoliales evolved and diversified.

At least it is a dry cold: the global distribution of freeze-thaw and drought stress and the traits that may impart poly-tolerance in conifers

Conifers inhabit some of the most challenging landscapes where multiple abiotic stressors (e.g., aridity, freezing temperatures) often co-occur. Physiological tolerance to multiple stressors ('poly-tolerance') is thought to be rare because exposure to one stress generally limits responses to another through functional trade-offs. However, the capacity to exhibit poly-tolerance may be greater when combined abiotic stressors have similar physiological impacts, such as the disruption of hydraulic function imposed by drought or freezing. Here, we reviewed empirical data in light of theoretical expectations for conifer adaptations to drought and freeze-thaw cycles with particular attention to hydraulic traits of the stem and leaf. Additionally, we examined the commonality and spatial distribution of poly-stress along indices of these combined stressors. We found that locations with the highest values of our poly-stress index (PSi) are characterized by moderate drought and moderate freeze-thaw, and most of the global conifer distribution occupies areas of moderate poly-stress. Among traits examined, we found diverse responses to the stressors. Turgor loss point did not correlate with freeze-thaw or drought stress individually, but did with the PSi, albeit inverse to what was hypothesized. Leaf mass per area was more strongly linked with drought stress than the poly-stress and not at all with freeze-thaw stress. In stems, the water potential causing 50% loss of hydraulic conductivity became more negative with increasing drought stress and poly-stress but did not correlate with freeze-thaw stress. For these traits, we identified a striking lack of coverage for substantial portions of species ranges, particularly at the upper boundaries of their respective PSis, demonstrating a critical gap in our understanding of trait prevalence and plasticity along these stress gradients. Future research should investigate traits that confer tolerance to both freeze-thaw and drought stress in a wide range of species across broad geographic scales.

Protective Strategies of Haberlea rhodopensis for Acquisition of Freezing Tolerance: Interaction between Dehydration and Low Temperature

Resurrection plants are able to deal with complete dehydration of their leaves and then recover normal metabolic activity after rehydration. Only a few resurrection species are exposed to freezing temperatures in their natural environments, making them interesting models to study the key metabolic adjustments of freezing tolerances. Here, we investigate the effect of cold and freezing temperatures on physiological and biochemical changes in the leaves of Haberlea rhodopensis under natural and controlled environmental conditions. Our data shows that leaf water content affects its thermodynamical properties during vitrification under low temperatures. The changes in membrane lipid composition, accumulation of sugars, and synthesis of stress-induced proteins were significantly activated during the adaptation of H. rhodopensis to both cold and freezing temperatures. In particular, the freezing tolerance of H. rhodopensis relies on a sucrose/hexoses ratio in favor of hexoses during cold acclimation, while there is a shift in favor of sucrose upon exposure to freezing temperatures, especially evident when leaf desiccation is relevant. This pattern was paralleled by an elevated ratio of unsaturated/saturated fatty acids and significant quantitative and compositional changes in stress-induced proteins, namely dehydrins and early light-induced proteins (ELIPs). Taken together, our data indicate that common responses of H. rhodopensis plants to low temperature and desiccation involve the accumulation of sugars and upregulation of dehydrins/ELIP protein expression. Further studies on the molecular mechanisms underlying freezing tolerance (genes and genetic regulatory mechanisms) may help breeders to improve the resistance of crop plants.

Screening of cold hardiness-related indexes and establishment of a comprehensive evaluation method for grapevines (V. vinifera)

The goals of this work were to screen physiological and biochemical indexes to assess a set of V. vinifera germplasm resources, to compare evaluation methods for cold hardiness, and to establish a comprehensive method that can be used for more accurate screening for cold hardiness in V. vinifera. Four single methods were used to evaluate the cold hardiness of 20 germplasms resources and 18 physiological and biochemical indexes related to cold hardiness were determined. The LT₅₀ values determined by electrical conductivity (EL), 2,3,5-triphenyltetrazolium chloride staining (TTC), differential thermal analysis (DTA), and recovery growth (RG) methods showed extremely significant positive correlation. Bound water content (BW), proline content (Pro), total soluble sugar content (TSS), malondialdehyde content (MDA), catalase content (CAT), and ascorbic acid content (ASA) exhibited significant correlation with LT₅₀ values measured by different evaluation methods. The comprehensive cold hardiness index calculated by principal component analysis (PCA) combined with subordinate function (SF) was negatively correlated with LT₅₀ values measured by different evaluation methods. Meili and Ecolly exhibited the highest cold hardiness, indicating their potential for use as parents for cold hardiness breeding. EL, DTA, TTC, and RG methods successfully distinguished cold hardiness among different V. vinifera germplasm lines. Measurements of BW, Pro, TSS, MDA, CAT, and ASA in dormant shoots also can be used as main physiological and biochemical indexes related to cold hardiness of V. vinifera. Comprehensive evaluation by PCA combined with SF can accurately screen cold hardiness in V. vinifera. This study provides a reference and accurate identification method for the selection of cold hardiness parents and the evaluation of cold hardiness of germplasm of V. vinifera.

Morphological and physiological response of Chinese tallow (Triadica sebifera) to an extreme cold spell in subtropical, coastal forests of China

Acute and extreme weather events can cause considerable damage to the tissues of trees, including stem death and branch or leaf distortion, which may limit their survival and reproduction. In January 2016, a rare cold spell impacted the coastal forests of subtropical China. Using post-hoc assessments, we evaluated the morphological and physiological response of Chinese tallow (Triadica sebifera L.) to the extreme cold spell in two distinct ecoregions, one (Xiangshan, China) representing the cold spell impacted zone and the other (Taizhou, China) representing the non-affected zone. To determine if the extreme cold events impacted the vigor of Chinese tallow, we assessed differences in growth rate, leaf characteristics, and leaf gas exchange. As age may affect tree morphological and physiological response to stress, we grouped subject trees into three distinct cohorts, namely, seedlings (1–2 years old), young-aged (5–6 years old), and middle-aged (10–12 years old). Our results suggest that although tree height and diameter did not differ, leaf area expansion and leaf mass were reduced in the impacted zone. In seedling and young-aged trees, the cold spell significantly reduced leaf net photosynthetic (An), transpiration rates (Tr), stomatal conductance (Gs) and water use efficiency (WUE) while leaf intercellular CO2 concentration (Ci), vapor pressure deficit (Vpd), and intercellular CO2 pressure (Ci-Pa) increased. In contrast, the middle-aged group was less responsive to the cold spell. Across all cohorts, the event did not affect leaf temperature (Tleaf), but the activity of superoxide dismutase (SOD) and peroxidase (POD) decreased. We also detected increases of leaf malondialdehyde (MDA) and free proline (Pro) contents in young-aged and middle-aged groups. Hence, the extreme cold spell caused remarkable negative effects on the morphological and physiological traits of Chinese tallow. Redundancy analysis revealed that the cold spell also impacted the subsequent recovery process of damaged Chinese tallow by reducing the ability of leaf to utilize microenvironmental resources (radiation, air humidity, and CO2) for gas exchange. Results from this study are important to strengthen our understanding of Chinese tallow responding to extreme cold stress within its native range, also be helpful to predict the distributions of Chinese tallow in its invasive range where it has devastating impacts to coastal ecosystems in the southeast US.

The phenomenon of red and yellow autumn leaves: Hypotheses, agreements and disagreements

Yellow and red autumn leaves are typical of many temperate/boreal woody plants. Since the 19th century, it has been either considered the non-functional outcome of chlorophyll degradation that unmasks the pre-existing yellow and red pigments or that the de novo synthesis of red anthocyanins in autumn leaves indicated that it should have a physiological function, although it was commonly ignored. Defending free amino acids and various other resources released especially following the breakdown of the photosynthetic system, and mobilizing them for storage in other organs before leaf fall, is the cornerstone of both the physiological and anti-herbivory hypotheses about the functions of yellow and red autumn leaf colouration. The complicated phenomenon of conspicuous autumn leaf colouration has received significant attention since the year 2000, especially because ecologists started paying attention to its anti-herbivory potential. The obvious imperfection of the hypotheses put forth in several papers stimulated many other scientists. Hot debates among physiologists, among ecologists, and between physiologists and ecologists have been common since the year 2000, first because the various functions of yellow and red autumn leaf colouration are non-exclusive, and second because many scientists were trained to focus on a single subject. Here, I will review the debates, especially between the photoprotective and the anti-herbivory hypotheses, and describe both the progress in their understanding and the required progress.

Time-series RNA-Seq transcriptome profiling reveals novel insights about cold acclimation and de-acclimation processes in an evergreen shrub of high altitude

The high-altitude alpine regions are characterized by highly variable and harsh environmental conditions. However, relatively little is known about the diverse mechanisms adopted by alpine plants to adapt to these stressful conditions. Here, we studied variation in transcriptome and physiological adjustments occurring across the year at high elevation environments in the leaf tissue of Rhododendron anthopogon, an evergreen shrub of Himalaya. The samples were collected at 12 different time-points, from August until snowfall in November 2017, and then from June to September 2018. It was observed that with a drop in both ambient air temperature and photoperiod towards onset of winter, the freezing resistance of plants increased, resulting in 'cold acclimation'. Further, 'de-acclimation' was associated with a decrease in freezing resistance and increase in photosynthetic efficiency of leaves during spring. A considerable amount of variation was observed in the transcriptome in a time-dependent sequential manner, with a total of 9,881 differentially expressed genes. Based on gene expression profiles, the time-points could be segregated into four clusters directly correlating with the distinct phases of acclimation: non-acclimation (22-August-2017, 14-August-2018, 31-August-2018), early cold acclimation (12-September-2017, 29-September-2017), late cold acclimation (11-October-2017, 23-October-2017, 04-November-2017, 18-September-2018) and de-acclimation (15-June-2018, 28-June-2018, 14-July-2018). Cold acclimation was a gradual process, as indicated by presence of an intermediate stage (early acclimation). However, the plants can by-pass this stage when sudden decrease in temperature is encountered. The maximum variation in expression levels of genes occurred during the transition to de-acclimation, hence was 'transcriptionally' the most active phase. The similar or higher expression levels of genes during de-acclimation in comparison to non-acclimation suggested that molecular functionality is re-initiated after passing through the harsh winter conditions.

Molecular Insights into Freezing Stress in Peach Based on Multi-Omics and Biotechnology: An Overview

In nature or field conditions, plants are frequently exposed to diverse environmental stressors. Among abiotic stresses, the low temperature of freezing conditions is a critical factor that influences plants, including horticultural crops, decreasing their growth, development, and eventually quality and productivity. Fortunately, plants have developed a mechanism to improve the tolerance to freezing during exposure to a range of low temperatures. In this present review, current findings on freezing stress physiology and genetics in peach (Prunus persica) were refined with an emphasis on adaptive mechanisms for cold acclimation, deacclimation, and reacclimation. In addition, advancements using multi-omics and genetic engineering approaches unravel the molecular physiological mechanisms, including hormonal regulations and their general perceptions of freezing tolerance in peach were comprehensively described. This review might pave the way for future research to the horticulturalists and research scientists to overcome the challenges of freezing temperature and improvement of crop management in these conditions.

Norway spruce deploys tissue-specific responses during acclimation to cold

Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover and lowering winter soil temperatures. To gain insight into the mechanisms that have enabled conifers to dominate extreme cold environments, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that the main transcriptional response of Norway spruce needles exposed to cold was delayed relative to Arabidopsis, and this delay was associated with slower development of freezing tolerance. Despite this difference in timing, Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as Arabidopsis, indicating broad evolutionary conservation of cold response networks. In keeping with their different metabolic and developmental states, needles and root of Norway spruce showed contrasting results. Regulatory network analysis identified both conserved TFs with known roles in cold acclimation (e.g. homologs of ICE1, AKS3, and of the NAC and AP2/ERF superfamilies), but also a root-specific bHLH101 homolog, providing functional insights into cold stress response strategies in Norway spruce.

Time-series eco-metabolomics reveals extensive reshuffling in metabolome during transition from cold acclimation to de-acclimation in an alpine shrub

Recording environmentally induced variations in the metabolome in plants can be a promising approach for understanding the complex patterns of metabolic regulation and their eco-physiological consequences. Here, we studied metabolome-wide changes and eco-physiological adjustments occurring across the year at high elevation environments in the leaf tissue of Rhododendron anthopogon, an alpine evergreen shrub of the Himalaya. New leaves of R. anthopogon appear after the snow-melt and remain intact even when the plants get covered under snow (November-June). During this whole period, they may undergo several physiological and biochemical adjustments in response to fluctuating temperatures and light conditions. To understand these changes, we analyzed eco-physiological traits, that is, freezing resistance, dry matter content and % of nitrogen and the overall metabolome across 10 different time-points, from August until the snowfall in November 2017, and then from June to August 2018. As anticipated, the freezing resistance increased toward the onset of winters. The leaf tissues exhibited a complete reshuffling of the metabolome during the growth cycle and time-points segregated into four clusters directly correlating with distinct phases of acclimation: non-acclimation (August 22, 2017; August 14, 2018), early cold acclimation (September 12, September 29, October 11, 2017), late cold acclimation (October 23, November 4, 2017), and de-acclimation (June 15, June 28, July 14, 2018). Cold acclimation involved metabolic progression (101 metabolites) with an increase of up to 19.4-fold (gentiobiose), whereas de-acclimation showed regression (120 metabolites) with a decrease of up to 30-fold (sucrose). The changes in the metabolome during de-acclimation were maximum and were not just a reversal of cold acclimation. Our results provided insights into the direction and magnitude of physiological changes in Rhododendron anthopogon that occurred across the year.

The physiological response of different tobacco varieties to chilling stress during the vigorous growing period

Tobacco is be sensitively affected by chilling injury in the vigorous growth period, which can easily lead to tobacco leaf browning during flue-curing and quality loss, however, the physiological response of tobacco in the prosperous period under low temperature stress is unclear. The physiological response parameters of two tobacco varieties to low temperature stress were determined. The main results were as follows: ① For tobacco in the vigorous growing period subjected to low-temperature stress at 4-16 °C, the tissue structure of chloroplast changed and photosynthetic pigments significantly decreased compared with each control with the increase of intensity of low-temperature stress. ② For tobacco in the vigorous growing period at 10-16 °C, antioxidant capacity of the protective enzyme system, osmotic adjustment capacity of the osmotic adjusting system and polyphenol metabolism in plants gradually increased due to induction of low temperature with the increase of intensity of low-temperature stress. ③ Under low-temperature stress at 4 °C, the protective enzyme system, osmotic adjusting system and polyphenol metabolism of the plants played an insignificant role in stress tolerance, which cannot be constantly enhanced based on low-temperature resistance at 10 °C. This study confirmed that under the temperature stress of 10-16 °C, the self-regulation ability of tobacco will be enhanced with the deepening of low temperature stress, but there is a critical temperature between 4 and 10 °C. The self-regulation ability of plants under low temperature stress will be inhibited.

The relationship of cold acclimation and extracellular ice formation to winter thermonasty in two Rhododendron species and their F1 hybrid

PREMISE

Thermonastic leaf movements in evergreen Rhododendron species have been used to study plant strategies for winter photoprotection. To add to the current fundamental understanding of this behavior, we addressed the following questions: (1) Is the cold-acclimated (CA) state necessary for thermonasty, and do cold-induced leaf movements also occur in non-acclimated (NA) plants? (2) Which of the two movements, leaf rolling versus curling, is more responsive to freezing, if any, in a non-thermonastic species? (3) What is the temporal relationship between extracellular freezing and thermonasty? (4) What genetic inferences can be drawn from leaf movement in an F₁ hybrid relative to its parents?

METHODS

A temperature-controlled, gradual cooling regime was used to quantify freeze-induced leaf movements. Infrared thermography was used to confirm extracellular ice-formation in leaves.

RESULTS

Both NA and CA plants of thermonastic species exhibited thermonasty, but leaf rolling/curling increased significantly in CA plants. In the cold-acclimated condition, a non-thermonastic species showed almost no rolling during freezing, while the thermonastic species and F₁ hybrid did, the latter exhibiting a response intermediate to the parents. Freezing-induced leaf curling in the non-thermonastic species and the F₁ hybrid was equivalent and significantly less than the degree of curling in the thermonastic species.

CONCLUSIONS

Milder thermonasty in NA than CA leaves could be associated with differential anisotropy in the rolling forces and/or response of aquaporins to freezing. Leaf movements in the hybrid suggest that leaf rolling and curling are additive and dominant genetic traits, respectively. Infrared thermography confirms that ice formation in tissues precedes cold-induced thermonasty in R. catawbiense.

Wide variation of winter-induced sustained thermal energy dissipation in conifers: a common-garden study

Low temperature in winter depresses rates of photosynthesis, which, in evergreen plants, can exacerbate imbalances between light absorption and photochemical light use. Damage that could result from increased excess light absorption is minimized by the conversion of excitation energy to heat in a process known as energy dissipation, which involves the de-epoxidized carotenoids of the xanthophyll cycle. Overwintering evergreens employ sustained forms of energy dissipation observable even after lengthy periods of dark acclimation. Whereas most studies of photoprotective energy dissipation examine one or a small number of species; here, we measured the levels of sustained thermal energy dissipation of seventy conifer taxa growing outdoors under common-garden conditions at the Red Butte Garden in Salt Lake City, Utah, U.S.A. (forty nine taxa were also sampled for needle pigment content). We observed an extremely wide range of wintertime engagement of sustained energy dissipation; the percentage decrease in dark-acclimated photosystem II quantum efficiency from summer to winter ranged from 6 to 95%. Of the many pigment-based parameters measured, the magnitude of the seasonal decrease in quantum efficiency was most closely associated with the seasonal increase in zeaxanthin content expressed on a total chlorophyll basis, which explained only slightly more than one-third of the variation. We did not find evidence for a consistent wintertime decrease in needle chlorophyll content. Thus, the prevailing mechanism for winter decreases in solar-induced fluorescence emitted by evergreen forests may be decreases in fluorescence quantum yield, and wintertime deployment of sustained energy dissipation likely underlies this effect.

Advanced materials design based on waste wood and bark

Trees belong to the largest living organisms on Earth and plants in general are one of our main renewable resources. Wood as a material has been used since the beginning of humankind. Today, forestry still provides raw materials for a variety of applications, for example in the building industry, in paper manufacturing and for various wood products. However, many parts of the tree, such as reaction wood, branches and bark are often discarded as forestry residues and waste wood, used as additives in composite materials or burned for energy production. More advanced uses of bark include the extraction of chemical substances for glues, food additives or healthcare, as well as the transformation to advanced carbon materials. Here, we argue that a proper understanding of the internal fibrous structure and the resulting mechanical behaviour of these forest residues allows for the design of materials with greatly varying properties and applications. We show that simple and cheap treatments can give tree bark a leather-like appearance that can be used for the construction of shelters and even the fabrication of woven textiles. This article is part of the theme issue 'Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)'.

Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer

Temperate trees originating from warmer localities usually grow faster and acclimate to winter later than trees of the same species from colder localities. However, when trees are selected for faster growth, are climatically adaptive genes and traits affected? Our research demonstrates a simple, sensitive, broadly applicable, and elusive approach to integrating complex polygenic variation into applied environmental management. We show that selective breeding increases allele frequencies of many trait-associated genes, and that alleles that increase most display strong genetic linkage and potential trade-offs among traits. Increasing tree growth while maintaining adaptation is essential to reforestation in a changing climate, but this may be challenging because trait-associated genetic variation that underpins climate adaptation is responsive to selection for tree growth.

Locally adapted temperate tree populations exhibit genetic trade-offs among climate-related traits that can be exacerbated by selective breeding and are challenging to manage under climate change. To inform climatically adaptive forest management, we investigated the genetic architecture and impacts of selective breeding on four climate-related traits in 105 natural and 20 selectively bred lodgepole pine populations from western Canada. Growth, cold injury, growth initiation, and growth cessation phenotypes were tested for associations with 18,600 single-nucleotide polymorphisms (SNPs) in natural populations to identify “positive effect alleles” (PEAs). The effects of artificial selection for faster growth on the frequency of PEAs associated with each trait were quantified in breeding populations from different climates. Substantial shifts in PEA proportions and frequencies were observed across many loci after two generations of selective breeding for height, and responses of phenology-associated PEAs differed strongly among climatic regions. Extensive genetic overlap was evident among traits. Alleles most strongly associated with greater height were often associated with greater cold injury and delayed phenology, although it is unclear whether potential trade-offs arose directly from pleiotropy or indirectly via genetic linkage. Modest variation in multilocus PEA frequencies among populations was associated with large phenotypic differences and strong climatic gradients, providing support for assisted gene flow polices. Relationships among genotypes, phenotypes, and climate in natural populations were maintained or strengthened by selective breeding. However, future adaptive phenotypes and assisted gene flow may be compromised if selective breeding further increases the PEA frequencies of SNPs involved in adaptive trade-offs among climate-related traits.

Seasonal Metabolic Investigation in Pomegranate (Punica granatum L.) Highlights the Role of Amino Acids in Genotype- and Organ-Specific Adaptive Responses to Freezing Stress

Every winter, temperate woody plants have to cope with freezing stress. Winter hardiness is of crucial importance for pomegranate survival and productivity. A comparative morphological and metabolic study was conducted on the stems and buds of 15 field-grown mature pomegranate genotypes in seven time-points during two developmental cycles. Seasonal changes of frost hardiness, as determined by electrolyte leakage method, and metabolite analysis by HPLC and GC revealed the variability in frost hardiness and metabolic contents result from genetic background and organ, as well as seasonal condition. Morphological adaptations, as well as metabolic remodeling, are the distinct features of the hardy genotypes. Larger buds with a greater number of compressed scales and the higher number of protective leaves, together with the higher number and content of changed metabolites, especially amino acids, seem to provide a higher frost resistance for those trees. We recorded two-times the change in metabolites and several-times accumulation of amino acids in the stem compared with buds. A better potential of stem for metabolome adjustment during the hardening period and a higher level of tolerance to stress is therefore suggested. High levels of arginine, proline, glutamine, and asparagine, and particularly the accumulation of alanine, tryptophan, and histidine are responsible for excellent tolerance of the stem of tolerant genotypes. With regard to the protective roles of amino acids, a relation between stress tolerance and the level of amino acids is proposed. This points both to the importance of amino acids in the winter survival of pomegranate trees, and to the evaluation of frost tolerance in other plants, by these specific markers.

Standardization of electrolyte leakage data and a novel liquid nitrogen control improve measurements of cold hardiness in woody tissue

BACKGROUND

A variety of basic and applied research programs in plant biology require the accurate and reliable determination of plant tissue cold hardiness. Over the past 50 years, the electrolyte leakage method has emerged as a popular and practical method for quantifying the amount of damage inflicted on plant tissue by exposure to freezing temperatures. Numerous approaches for carrying out this method and analyzing the resultant data have emerged. These include multiple systems for standardizing and modeling raw electrolyte leakage data and multiple protocols for boiling or autoclaving samples in order to maximize leakage as a positive control. We compare four different routines for standardization of leakage data and assess a novel control method-immersion in liquid nitrogen in lieu of traditional autoclaving-and apply them to woody twigs collected from 12 maple (Acer) species in early spring. We compare leakage data from these samples using each of four previously published forms of data analysis and autoclaving vs. liquid nitrogen controls and validate each of these approaches against visual estimates of freezing damage and differential thermal analysis.

RESULTS

Through presentation of our own data and re-analysis of previously published findings, we show that standardization of raw data against estimates of both minimum and maximum attainable freezing damage allows for reliable estimation of cold hardiness at the species level and across studies in diverse systems. Furthermore, use of our novel liquid nitrogen control produces data commensurate across studies and enhances the consistency and realism of the electrolyte leakage method, especially for very cold hardy samples.

CONCLUSION

Future leakage studies that relativize data against minimum and maximum leakage and that employ our updated liquid nitrogen control will contribute generalizable, repeatable, and realistic data to the existing body of cold hardiness research in woody plants. Data from studies conducted using a liquid nitrogen (and not an autoclaving) control can still be compared to previously published data, especially when raw data are standardized using the best-performing approach among those we assessed. Electrolyte leakage of woody twigs emerges as a useful technique for quickly assessing the probability of tissue death in response to freezing in dormant plants. Differential thermal analysis may provide different and complementary information on cold hardiness.

Synergistic adaptations: freezing tolerance is associated with desiccation tolerance and activation of violaxanthin de-epoxidase in wintergreen ferns

This article comments on: Fernández-Marín B, Arzac MI, López-Pozo M, Laza JM, Roach T, Stegner M, Neuner G, García-Plazaola JI. 2021. Frozen in the dark: interplay of night-time activity of xanthophyll cycle, xylem attributes, and desiccation tolerance in fern resistance to winter. Journal of Experimental Botany 72, 3168–3184.

Brassinosteroids synthesised by CYP85A/A1 but not CYP85A2 function via a BRI1-like receptor but not via BRI1 in Picea abies

Brassinosteroids (BRs) are essential plant hormones. In angiosperms, brassinolide and castasterone, the first and second most active BRs, respectively, are synthesised by CYP85A2 and CYP85A/A1, respectively. BRs in angiosperms function through an essential receptor, BR Insensitive 1 (BRI1). In addition, some angiosperms also have non-essential BRI1-like 1/3 (BRL1/3). In conifers, BRs promote seed germination under drought stress; however, how BRs function in gymnosperms is unknown. In this study, we performed functional complementation of BR biosynthesis and receptor genes from Picea abies with respective Arabidopsis mutants. We found that P. abies possessed functional PaCYP85A and PaBRL1 but not PaCYP85A2 or PaBRI1, and this results in weak BR signaling, and both PaCYP85A and PaBRL1 were abundantly expressed. However, neither BR treatment of P. abies seedlings nor expression of PaBRL1 in the Arabidopsis Atbri1 mutant promoted plant height, despite the fact that BR-responsive genes were activated. Importantly, chimeric AtBRI1 replaced with the BR-binding domain of PaBRL1 complemented the Atbri1 phenotypes. Furthermore, PaBRL1 had less kinase activity than BRI1 in vitro. Overall, P. abies had weak but still active BR signaling, explaining aspects of its slow growth and high stress tolerance. Our study sheds light on the functional and evolutionary significance of distinct BR signaling that is independent of BRI1 and brassinolide.

Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers

Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.

Transcriptional regulation of bark freezing tolerance in apple (Malus domestica Borkh.)

Freezing tolerance is a significant trait in plants that grow in cold environments and survive through the winter. Apple (Malus domestica Borkh.) is a cold-tolerant fruit tree, and the cold tolerance of its bark is important for its survival at low temperatures. However, little is known about the gene activity related to its freezing tolerance. To better understand the gene expression and regulation properties of freezing tolerance in dormant apple trees, we analyzed the transcriptomic divergences in the bark from 1-year-old branches of two apple cultivars, "Golden Delicious" (G) and "Jinhong" (H), which have different levels of cold resistance, under chilling and freezing treatments. "H" can safely overwinter below -30 °C in extremely low-temperature regions, whereas "G" experiences severe freezing damage and death in similar environments. Based on 28 bark transcriptomes (from the epidermis, phloem, and cambium) from 1-year-old branches under seven temperature treatments (from 4 to -29 °C), we identified 4173 and 7734 differentially expressed genes (DEGs) in "G" and "H", respectively, between the chilling and freezing treatments. A gene coexpression network was constructed according to this expression information using weighted gene correlation network analysis (WGCNA), and seven biologically meaningful coexpression modules were identified from the network. The expression profiles of the genes from these modules suggested the gene regulatory pathways that are responsible for the chilling and freezing stress responses of "G" and/or "H." Module 7 was probably related to freezing acclimation and freezing damage in "H" at the lower temperatures. This module contained more interconnected hub transcription factors (TFs) and cold-responsive genes (CORs). Modules 6 and 7 contained C-repeat binding factor (CBF) TFs, and many CBF-dependent homologs were identified as hub genes. We also found that some hub TFs had higher intramodular connectivity (KME) and gene significance (GS) than CBFs. Specifically, most hub TFs in modules 6 and 7 were activated at the beginning of the early freezing stress phase and maintained upregulated expression during the whole freezing stress period in "G" and "H". The upregulation of DEGs related to methionine and carbohydrate biosynthetic processes in "H" under more severe freezing stress supported the maintenance of homeostasis in the cellular membrane. This study improves our understanding of the transcriptional regulation patterns underlying freezing tolerance in the bark of apple branches.

Climate change shapes the future evolution of plant metabolism

Planet Earth has experienced many dramatic atmospheric and climatic changes throughout its 4.5-billion-year history that have profoundly impacted the evolution of life as we know it. Photosynthetic organisms, and specifically plants, have played a paramount role in shaping the Earth's atmosphere through oxygen production and carbon sequestration. In turn, the diversity of plants has been shaped by historical atmospheric and climatic changes: plants rose to this challenge by evolving new developmental and metabolic traits. These adaptive traits help plants to thrive in diverse growth conditions, while benefiting humanity through the production of food, raw materials, and medicines. However, the current rapid rate of climate change caused by human activities presents unprecedented new challenges to the future of plants. Here, we discuss the potential effects of modern climate change on plants, with specific attention to plant specialized metabolism. We explore potential avenues of future scientific investigations, powered by cutting-edge methods such as synthetic biology and genome engineering, to better understand and mitigate the consequences of rapid climate change on plant fitness and plant usage by humans.

Screening of optimal reference genes for qRT-PCR and preliminary exploration of cold resistance mechanisms in Prunus mume and Prunus sibirica varieties

Prunus sibirica and Prunus mume are closely related plant species that differ in cold tolerance. Hybrids of P. sibirica and true mume, belonging to the apricot mei group, inherited strong cold resistance from P. sibirica. These materials are favourable for research on the molecular mechanisms of cold resistance. However, no suitable reference genes have been identified for analysing gene expression patterns between P. sibirica and P. mume. Ten candidate reference genes were assessed, namely, actins (ACT2-1, ACT2-2, ACT2-3, ACT2-4), protein phosphatase 2A-1 (PP2A-1), ubiquitins (UBQ2, UBQ3), ubiquitin extension protein (UBQ1) and tubulins (TUB1, TUB2), with four distinct algorithms (geNorm, NormFinder, BestKeeper and RefFinder). UBQ2 was recognized as the best reference gene in stems and buds across materials (P. sibirica; 'Xiaohong Zhusha', 'Beijing Yudie', and 'Xiao Lve' for true mume; and 'Dan Fenghou', 'Fenghou', and 'Yanxing' for apricot mei) under cold stress. In addition, the temporal and spatial expression patterns of PmCBF6 and PmLEA10 among seven varieties during winter periods were analysed using UBQ2 as a reference gene. The expression differed significantly among cultivars, which may contribute to their differences in cold tolerance. This paper confirmed the strong cold tolerance of apricot mei. And the best internal reference gene suitable for seven varieties was selected: UBQ2. Based on the above results, the expression of PmCBF6 and PmLEA10 genes during wintering in seven varieties was analysed. The molecular mechanisms of cold resistance were found to be possibly different in different varieties of P. sibirica and P. mume.

Photoperiod and temperature as dominant environmental drivers triggering secondary growth resumption in Northern Hemisphere conifers

Wood formation consumes around 15% of the anthropogenic CO₂ emissions per year and plays a critical role in long-term sequestration of carbon on Earth. However, the exogenous factors driving wood formation onset and the underlying cellular mechanisms are still poorly understood and quantified, and this hampers an effective assessment of terrestrial forest productivity and carbon budget under global warming. Here, we used an extensive collection of unique datasets of weekly xylem tissue formation (wood formation) from 21 coniferous species across the Northern Hemisphere (latitudes 23 to 67°N) to present a quantitative demonstration that the onset of wood formation in Northern Hemisphere conifers is primarily driven by photoperiod and mean annual temperature (MAT), and only secondarily by spring forcing, winter chilling, and moisture availability. Photoperiod interacts with MAT and plays the dominant role in regulating the onset of secondary meristem growth, contrary to its as-yet-unquantified role in affecting the springtime phenology of primary meristems. The unique relationships between exogenous factors and wood formation could help to predict how forest ecosystems respond and adapt to climate warming and could provide a better understanding of the feedback occurring between vegetation and climate that is mediated by phenology. Our study quantifies the role of major environmental drivers for incorporation into state-of-the-art Earth system models (ESMs), thereby providing an improved assessment of long-term and high-resolution observations of biogeochemical cycles across terrestrial biomes.

Important roles of glycinebetaine in stabilizing the structure and function of the photosystem II complex under abiotic stresses

The molecular and physiological mechanisms of glycinebetaine stabilizing photosystem II complex under abiotic stresses are discussed, helping to address food shortage problems threatening the survival of growing population. In the backdrop of climate change, the frequency, dimensions and duration of extreme events have increased sharply, which may have unintended consequences for agricultural. The acclimation of plants to a constantly changing environment involves the accumulation of compatible solutes. Various compatible solutes enable plants to tolerate abiotic stresses, and glycinebetaine (GB) is one of the most-studied. The biosynthesis and accumulation of GB appear in numerous plant species, especially under environmental stresses. The exogenous application of GB and GB-accumulating transgenic plants have been proven to further promote plant development under stresses. Early research on GB focused on the maintenance of osmotic potential in plants. Subsequent experimental evidence demonstrated that it also protects proteins including the photosystem II complex (PSII) from denaturation and deactivation. As reviewed here, multiple experimental evidences have indicated considerable progress in the roles of GB in stabilizing PSII under abiotic stresses. Based on these advances, we've concluded two effects of GB on PSII: (1) it stabilizes the structure of PSII by protecting extrinsic proteins from dissociation or by promoting protein synthesize; (2) it enhances the oxygen-evolving activity of PSII or promotes the repair of the photosynthetic damage of PSII.

Functional and morphological evolution in gymnosperms: A portrait of implicated gene families

Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.

The Roots of Plant Frost Hardiness and Tolerance

Frost stress severely affects agriculture and agroforestry worldwide. Although many studies about frost hardening and resistance have been published, most of them focused on the aboveground organs and only a minority specifically targets the roots. However, roots and aboveground tissues have different physiologies and stress response mechanisms. Climate models predict an increase in the magnitude and frequency of late-frost events, which, together with an observed loss of soil insulation, will greatly decrease plant primary production due to damage at the root level. Molecular and metabolic responses inducing root cold hardiness are complex. They involve a variety of processes related to modifications in cell wall composition, maintenance of the cellular homeostasis and the synthesis of primary and secondary metabolites. After a summary of the current climatic models, this review details the specificity of freezing stress at the root level and explores the strategies roots developed to cope with freezing stress. We then describe the level to which roots can be frost hardy, depending on their age, size category and species. After that, we compare the environmental signals inducing cold acclimation and frost hardening in the roots and aboveground organs. Subsequently, we discuss how roots sense cold at a cellular level and briefly describe the following signal transduction pathway, which leads to molecular and metabolic responses associated with frost hardening. Finally, the current options available to increase root frost tolerance are explored and promising lines of future research are discussed.

Cortical photosynthesis as a physiological marker for grape breeding: methods and approaches

Photosynthesis occurring in chlorenchymal tissues of lignified branches of perennial plants (cortical photosynthesis) has a significant impact on their productivity and resistance to adverse environmental conditions, such as water deficiency and low temperatures. Cortical photosynthesis occurring under the outer bark of a lignified grape vine can become a convenient marker for breeding freeze-tolerant varieties. The following approaches can be undertaken to assess the functional state of the cortical photosynthetic apparatus: (1) analysis of the variable chlorophyll fluorescence parameters and (2) biochemical analysis of photosynthetic membrane preparations. To evaluate these approaches, in this work we have carried out the comparative analysis of characteristics of the cortical photosynthetic apparatus in grape varieties differing in freeze tolerance.

This work was supported by grant №18-04-00079 from the Russian Foundation for Basic Research.

Parallels between natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize

Artificial selection has produced varieties of domesticated maize that thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and subtropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read Iso-Seq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation in other cold-adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes that were targets of artificial selection during the adaptation of maize to temperate climates and those that were targets of natural selection in temperate-adapted T. dactyloides. Genes related to growth, development, response to stimulus, signaling, and organelles were enriched in the set of genes identified as both targets of natural and artificial selection.

Rethinking false spring risk

Temperate plants are at risk of being exposed to late spring freezes. These freeze events-often called false springs-are one of the strongest factors determining temperate plants species range limits and can impose high ecological and economic damage. As climate change may alter the prevalence and severity of false springs, our ability to forecast such events has become more critical, and it has led to a growing body of research. Many false spring studies largely simplify the myriad complexities involved in assessing false spring risks and damage. While these studies have helped advance the field and may provide useful estimates at large scales, studies at the individual to community levels must integrate more complexity for accurate predictions of plant damage from late spring freezes. Here, we review current metrics of false spring, and how, when, and where plants are most at risk of freeze damage. We highlight how life stage, functional group, species differences in morphology and phenology, and regional climatic differences contribute to the damage potential of false springs. More studies aimed at understanding relationships among species tolerance and avoidance strategies, climatic regimes, and the environmental cues that underlie spring phenology would improve predictions at all biological levels. An integrated approach to assessing past and future spring freeze damage would provide novel insights into fundamental plant biology and offer more robust predictions as climate change progresses, which are essential for mitigating the adverse ecological and economic effects of false springs.

Chilling and forcing temperatures interact to predict the onset of wood formation in Northern Hemisphere conifers

The phenology of wood formation is a critical process to consider for predicting how trees from the temperate and boreal zones may react to climate change. Compared to leaf phenology, however, the determinism of wood phenology is still poorly known. Here, we compared for the first time three alternative ecophysiological model classes (threshold models, heat-sum models and chilling-influenced heat-sum models) and an empirical model in their ability to predict the starting date of xylem cell enlargement in spring, for four major Northern Hemisphere conifers (Larix decidua, Pinus sylvestris, Picea abies and Picea mariana). We fitted models with Bayesian inference to wood phenological data collected for 220 site-years over Europe and Canada. The chilling-influenced heat-sum model received most support for all the four studied species, predicting validation data with a 7.7-day error, which is within one day of the observed data resolution. We conclude that both chilling and forcing temperatures determine the onset of wood formation in Northern Hemisphere conifers. Importantly, the chilling-influenced heat-sum model showed virtually no spatial bias whichever the species, despite the large environmental gradients considered. This suggests that the spring onset of wood formation is far less affected by local adaptation than by environmentally driven plasticity. In a context of climate change, we therefore expect rising winter-spring temperature to exert ambivalent effects on the spring onset of wood formation, tending to hasten it through the accumulation of forcing temperature, but imposing a higher forcing temperature requirement through the lower accumulation of chilling.

Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume

NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. Prunus mume, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence PmNAC genes and characterized them by bioinformatics tools and expression profiles. These PmNACs were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of PmNACs were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (PmNAC59/66/73) and three miRNA-targeted genes (PmNAC40/41/83) were identified. Most PmNAC genes presented tissue-specific and time-specific expression patterns. Sixteen PmNACs (PmNAC11/19/20/23/41/48/58/74/75/76/78/79/85/86/103/111) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (PmNAC11/12/17/21/29/42/30/48/59/66/73/75/85/86/93/99/111) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative PmNACs was observed under 4 °C at different treatment times. The expression of 10 genes (PmNAC11/20/23/40/42/48/57/60/66/86) was upregulated, while 5 genes (PmNAC59/61/82/85/107) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the NAC gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.

Insights on the persistence of pines (Pinus species) in the Late Cretaceous and their increasing dominance in the Anthropocene

Although gymnosperms were nearly swept away by the rise of the angiosperms in the Late Cretaceous, conifers, and pines (Pinus species) in particular, survived and regained their dominance in some habitats. Diversification of pines into fire-avoiding (subgenus Haploxylon) and fire-adapted (subgenus Diploxylon) species occurred in response to abiotic and biotic factors in the Late Cretaceous such as competition with emerging angiosperms and changing fire regimes. Adaptations/traits that evolved in response to angiosperm-fuelled fire regimes and stressful environments in the Late Cretaceous were key to pine success and are also contributing to a new "pine rise" in some areas in the Anthropocene. Human-mediated activities exert both positive and negative impacts of range size and expansion and invasions of pines. Large-scale afforestation with pines, human-mediated changes to fire regimes, and other ecosystem processes are other contributing factors. We discuss traits that evolved in response to angiosperm-mediated fires and stressful environments in the Cretaceous and that continue to contribute to pine persistence and dominance and the numerous ways in which human activities favor pines.

Micromanaging freeze tolerance: the biogenesis and regulation of neuroprotective microRNAs in frozen brains

When temperatures plummet below 0 °C, wood frogs (Rana sylvatica) can endure the freezing of up to ~ 65% of their body water in extracellular ice masses, displaying no measurable brain activity, no breathing, no movement, and a flat-lined heart. To aid survival, frogs retreat into a state of suspended animation characterized by global suppression of metabolic functions and reprioritization of energy usage to essential survival processes that is elicited, in part, by the regulatory controls of microRNAs. The present study is the first to investigate miRNA biogenesis and regulation in the brain of a freeze tolerant vertebrate. Indeed, proper brain function and adaptations to environmental stimuli play a crucial role in coordinating stress responses. Immunoblotting of miRNA biogenesis factors illustrated an overall reduction in the majority of these processing proteins suggesting a potential suppression of miRNA maturation over the freeze-thaw cycle. This was coupled with a large-scale RT-qPCR analysis of relative expression levels of 113 microRNA species in the brains of control, 24 h frozen, and 8 h thawed R. sylvatica. Of the 41 microRNAs differentially regulated during freezing and thawing, only two were significantly upregulated. Bioinformatic target enrichment of the downregulated miRNAs, performed at the low temperatures experienced during freezing and thawing, predicted their involvement in the potential activation of various neuroprotective processes such as synaptic signaling, intracellular signal transduction, and anoxia/ischemia injury protection. The predominantly downregulated microRNA fingerprint identified herein suggests a microRNA-mediated cryoprotective mechanism responsible for maintaining neuronal functions and facilitating successful whole brain freezing and thawing.

Changes of soluble sugars and ATP content during DMSO droplet freezing and PVS3 droplet vitrification of potato shoot tips

The potato's great genetic diversity needs to be maintained for future agricultural applications and can be preserved at ultra-low temperatures. To decipher detailed physiological processes, the aim of the study was to analyze the regrowth in 28 gene bank accessions and to reveal metabolite changes in a subset of four accessions that showed pronounced differences after shoot tip cryopreservation using DMSO droplet freezing and PVS3 droplet vitrification. Regrowth varied in all 28 genotypes ranging from 5% ('Kagiri') to 100% ('Karakter') and was higher after PVS3 droplet vitrification (71 ± 19%) than after cryopreservation using DMSO (54 ± 17%). Sucrose, glucose, and fructose were analyzed and showed significant increases after pre-culture in combination with PVS3 or DMSO and liquid nitrogen treatment and were reduced during regeneration. In contrast, adenosine triphosphate (ATP) reached its minimum concentration after cryoprotection and liquid nitrogen treatment and recovered most quickly after PVS3 droplet vitrification. A shortening of the explant pre-culture period reduced dramatically the regrowth after PVS3 vitrification. However, correlations between the shoot tip regrowth and sugar concentration were absent and significant at a low extent with ATP (r = 0.4, P < 0.01). Interestingly, several sub-cultivations of the donor plants from the previous stock affected negatively the regrowth. In conclusion, the cryopreservation protocol, genotypes, pre-culture period and number of sub-cultures affect the regrowth ability of explants, which was best estimated by the ATP concentration after low-temperature treatment. Due to the superior performance of PVS3, the routine potato cryopreservation at the Gatersleben gene bank was changed to PVS3 droplet vitrification.

The Cold-Regulated Genes of Blueberry and Their Response to Overexpression of VcDDF1 in Several Tissues

Expression of blueberry cold-regulated genes (VcCORs) could play a role in the variable cold hardiness of blueberry tissues. In this study, transcriptome comparisons were conducted to reveal expression of VcCORs in non-acclimated leaves, flower buds, and flowers of both non-transgenic and transgenic blueberries containing an overexpressed blueberry DWARF AND DELAYED FLOWERING gene (VcDDF1) as well as in fully chilled flower buds of non-transgenic blueberry. In non-transgenic blueberries, 57.5% of VcCOR genes showed differential expression in at least one of the three pairwise comparisons between non-acclimated leaves, flower buds, and flowers, and six out of nine dehydration-responsive element-binding factors showed differential expression. In addition, expression of VcDDF1 was not cold-inducible in non-transgenic blueberries and had higher expression in flowers than in leaves or non-acclimated flower buds. In transgenic blueberries, overexpression of VcDDF1 resulted in higher VcDDF1 expression in leaves than in flower buds and flowers. VcDDF1 overexpression enhanced expression of blueberry CBF1 and CBF3 in leaves and repressed expression of CBF3 in both flower buds and flowers. Overall, the results revealed tissue-specific expression patterns of VcCORs. The responses of VcCORs to overexpression of VcDDF1 suggest that it is possible to increase plant cold hardiness through overexpression of a non-cold-inducible gene.

Mechanism of freeze-thaw injury and recovery: A cool retrospective and warming up to new ideas

Understanding cellular mechanism(s) of freeze-thaw injury (FTI) is key to the efforts for improving plant freeze-tolerance by cultural methods or molecular/genetic approaches. However, not much work has been done in the last 25+ years to advance our understanding of the nature and cellular loci of FTI. Currently, two FTI lesions are predominantly implicated: 1) structural and functional perturbations in plasma membrane; 2) ROS-induced oxidative damage. While both have stood the test of time, many questions remain unresolved and other potentially significant lesions need to be investigated. Additionally, molecular mechanism of post-thaw recovery (PTR), a critical component of frost-survival, has not been well investigated. Mechanistic understanding of repair after reversible injury could expand the options for strategies to improve frost-hardiness. In this review, without claiming to be exhaustive, I have attempted to synthesize major discoveries from last several decades on the mechanisms of FTI and the relatively little research conducted thus far on PTR mechanisms. It is followed by proposing of hypotheses for mechanism(s) for irreversible FTI or PTR involving cytosolic calcium and ROS signaling. Perspective is presented on some unresolved questions and research on new ideas to fill the knowledge gaps and advance the field.