Differences in cold hardiness, carbohydrates, dehydrins and related gene expressions under an experimental deacclimation and reacclimation in Prunus persica

Analyzing cold hardiness (Based on DTA) of one-year-old branches of peaches

In this study, we conducted a low-temperature exothermic (LTE) investigation on 1-year-old (1a) branches of sixteen peach cultivars through a differential thermal analysis (DTA) procedure. We used a three-point approach to determine the lethal injury temperature (LT-I) of the xylem, the LTE correlation indexes, and the subordinate function value method were applied to compare cold hardiness of sixteen peach varieties. The results showed that the slope of the LT-I for the xylem of sixteen peach cultivars was different, and the LTE indexes were significantly different. Among all the studied varieties, the cold hardiness was strongest in Donghe No.1, followed by Wangjiazhuangmaotao No.2 and Hunchun. Qiuyan and Yanhong are second, and belong to the cold-resistant type; Qiuyi, Okubo, Zhongnongjinhui, and Chunmei, exhibited medium cold hardiness. Zhongtaohongyu, Spring snow, Yufei, and Zhongyou No.8 varieties exhibited low hardiness; while the 21st century, Golden Honey No. 1 and Zhonghuashoutao have the worst cold hardiness and are the weakest cold-hardiness types. In addition, the injury degrees of xylem from LT-I analysis were significantly related to the browning rates (BR) and electrolytic leakage (EI) from traditional low temperature freezing analysis. It is demonstrated that the LTE analysis is a simple, accurate, and practical method for identifying the cold hardiness of 1a branches of peach.

Transcriptomic analysis of Asparagus officinalis cultivars with varying levels of freezing tolerance over fall acclimation and spring deacclimation periods

Asparagus (Asparagus officinalis L.) is an important vegetable crop in southern Ontario, Canada, where winter air and soil temperatures below 0°C are common. Consequently, cultivars growing in this area must possess winterhardiness and freezing tolerance for survival. Asparagus acquires freezing tolerance in the fall through cold acclimation and loses freezing tolerance in the spring through deacclimation. To understand the molecular bases of these processes, transcriptomic analysis (RNA-Seq) was conducted on two cultivars, one adapted, 'Guelph Millennium' (GM), and one unadapted, 'UC157' (UC), to the winter conditions of southern Ontario. RNA extracted from bud and rhizome tissues, sampled on three dates during early spring and late fall, was subjected to sequencing. In the fall, the numbers of differentially expressed (DE) genes at the second and third harvests increased, relative to the first harvest, in dormant buds and rhizomes as freezing tolerance of cultivars increased, and the majority of DE genes were downregulated. In spring, freezing tolerance decreased as plants deacclimated and most genes DE at second and third harvests were upregulated in both cultivars. GM had lower LT50 (lethal temperature at which 50% of plants die) values and hence higher freezing tolerance than UC on specific sampling dates during both spring and fall, and expression patterns of specific genes were correlated with LT50 differences. Functional analysis revealed that these genes were involved in carbohydrate metabolic process, plant hormone signal transduction (auxin and gibberellin), proline metabolism, biosynthesis of secondary metabolites, circadian rhythm, and late embryogenesis abundant proteins and could be associated with cold acclimation and deacclimation processes. These findings will help researchers understand the molecular mechanisms of freezing tolerance in asparagus, leading to breeding and genetic strategies to improve the trait.

Comprehensive Identification of the β-Amylase (BAM) Gene Family in Response to Cold Stress in White Clover

White clover (Trifolium repens L.) is an allopolyploid plant and an excellent perennial legume forage. However, white clover is subjected to various stresses during its growth, with cold stress being one of the major limiting factors affecting its growth and development. Beta-amylase (BAM) is an important starch-hydrolyzing enzyme that plays a significant role in starch degradation and responses to environmental stress. In this study, 21 members of the BAM gene family were identified in the white clover genome. A phylogenetic analysis using BAMs from Arabidopsis divided TrBAMs into four groups based on sequence similarity. Through analysis of conserved motifs, gene duplication, synteny analysis, and cis-acting elements, a deeper understanding of the structure and evolution of TrBAMs in white clover was gained. Additionally, a gene regulatory network (GRN) containing TrBAMs was constructed; gene ontology (GO) annotation analysis revealed close interactions between TrBAMs and AMY (α-amylase) and DPE (4-alpha-glucanotransferase). To determine the function of TrBAMs under various tissues and stresses, RNA-seq datasets were analyzed, showing that most TrBAMs were significantly upregulated in response to biotic and abiotic stresses and the highest expression in leaves. These results were validated through qRT-PCR experiments, indicating their involvement in multiple gene regulatory pathways responding to cold stress. This study provides new insights into the structure, evolution, and function of the white clover BAM gene family, laying the foundation for further exploration of the functional mechanisms through which TrBAMs respond to cold stress.

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.

Temperature-phase transcriptomics reveals that hormones and sugars in the phloem of grape participate in tolerance during cold acclimation

Most of the upregulated genes contributed to the accumulation of soluble sugars and ABA in the phloem of 'Vitis amurensis' compared to 'Merlot' during cold acclimation. Extreme cold is one of the dominant abiotic factors affecting grape yield and quality. However, the changes in sugars, phytohormones, and gene expression in the branch phloem of different tolerant grape varieties during cold acclimation remain elusive. The data supported that with decreasing temperature, the contents of fructose, sucrose, and ABA in the phloem of Vitis amurensis (cold-tolerant, T) and 'Merlot' (cold-sensitive, S) increased during cold acclimation, and these indicators were higher in T than in S. Furthermore, the activities of sucrose synthetase, sucrose phosphate synthetase, and acid invertase peaked in the early phase of cold acclimation (approximately 5 °C) compared to other phases (approximately 28 °C, 0 °C, - 5 °C and - 10 °C). Moreover, the RNA sequencing results helped identify a total of 11,343 differentially expressed genes in the phloem of T and S, among which 4912 were upregulated and 6431 were downregulated. In the abscisic acid pathway, CRTISO, PSPY1-1, CYCP707A4-2, PYL4-1, PYL4-2, P2C08, SAPK2, TARAB1, and DBF3 were more highly expressed in T than in S. In the starch and sucrose metabolism pathway, HXK1, PGMP, GLGL1, SUS6, VCINV, BGL11, SSY1, GPS, BAM1 and BAM3 were also more highly expressed in T than in S. Moreover, the genes related to oxidative phosphorylation, such as NDHF, ND4, ND1, NAD7, NAD2, ATPB, YMF19, ATP9, PMA1 and AHA8, were upregulated in T. These results will be beneficial for understanding the potential differences in tolerance across two different cold-tolerant grapes with respect to sugar metabolism and gene expression.

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.

Genome-Wide Identification and Expression Analysis of the β-Amylase Gene Family in Chenopodium quinoa

β-Amylase (BAM) is an important starch hydrolase, playing a role in a variety of plant growth and development processes. In this study, 22 BAM gene family members (GFMs) were identified in quinoa (Chenopodium quinoa), an ancient crop gaining modern consumer acceptance because of its nutritional qualities. The genetic structure, phylogenetic and evolutionary relationships, and expression patterns of CqBAM GFMs in different tissues, were analyzed. Phylogenetic analyses assigned the CqBAMs, AtBAMs, and OsBAMs into four clades. The CqBAM gene family had expanded due to segmental duplication. RNA-seq analysis revealed expression of the duplicated pairs to be similar, with the expression of CqBAM GFM pairs showing a degree of tissue specificity that was confirmed by reverse transcription quantitative PCR (RT-qPCR). Several CqBAM GFMs were also responsive to abiotic stresses in shoots and/or roots. In conclusion, the BAM gene family in quinoa was identified and systematically analyzed using bioinformatics and experimental methods. These results will help to elucidate the evolutionary relationship and biological functions of the BAM gene family in quinoa.

Cold Hardiness Dynamics and Spring Phenology: Climate-Driven Changes and New Molecular Insights Into Grapevine Adaptive Potential

Climate change has become a topic of increasing significance in viticulture, severely challenged by this issue. Average global temperatures are increasing, but frost events, with a large variability depending on geographical locations, have been predicted to be a potential risk for grapevine cultivation. Grape cold hardiness encompasses both midwinter and spring frost hardiness, whereas the avoidance of spring frost damage due to late budbreak is crucial in cold resilience. Cold hardiness kinetics and budbreak phenology are closely related and affected by bud's dormancy state. On the other hand, budbreak progress is also affected by temperatures during both winter and spring. Genetic control of bud phenology in grapevine is still largely undiscovered, but several studies have recently aimed at identifying the molecular drivers of cold hardiness loss and the mechanisms that control deacclimation and budbreak. A review of these related traits and their variability in different genotypes is proposed, possibly contributing to develop the sustainability of grapevine production as climate-related challenges rise.

Deacclimation after cold acclimation-a crucial, but widely neglected part of plant winter survival

Temperate and boreal plants show natural low temperature acclimation during autumn. This cold acclimation process results in increased freezing tolerance. Global climate change is leading to increasing spring and autumn temperatures that can trigger deacclimation and loss of freezing tolerance, making plants susceptible to both late-autumn and late-spring freezing events. In particular, spring frosts can have devastating effects on whole ecosystems and can significantly reduce the yield of crop plants. Although the timing and speed of deacclimation are clearly of crucial importance for plant winter survival, the molecular basis of this process is still largely unknown. The regulation of deacclimation is, however, not only related to freezing tolerance, but also to the termination of dormancy, and the initiation of growth and development. In this paper, we provide an overview of what is known about deacclimation in both woody and herbaceous plants. We use publicly available transcriptome data to identify a core set of deacclimation-related genes in Arabidopsis thaliana that highlight physiological determinants of deacclimation, and suggest important directions for future research in this area.

Cold deacclimation mechanisms and reacclimation potential in flower buds of blackcurrant (Ribes nigrum)

As a consequence of global climate change, cold acclimation and deacclimation cycles are becoming increasingly frequent during winter in temperate regions. However, little is known about plant deacclimation and in particular reacclimation mechanisms, although deacclimation resistance and the ability to reacclimate may have wide-ranging consequences regarding plant productivity in a changing climate. Here, we report time-dependent responses of freezing tolerance, respiration rates, metabolite contents (high-resolution magic angle spinning NMR) and fatty acid levels (gas chromatography) in flower buds of two ecodormant Ribes nigrum cultivars exposed to three different deacclimation temperatures followed by a reacclimation treatment at 4°C. The data reveal that despite differences in the progression of deacclimation, the capacity of blackcurrant flower buds to reharden in late winter is virtually non-existing, implying that increasingly irregular temperature patterns is critical for blackcurrant fruit yield. The early phase of deacclimation is associated with a transient increase in respiration and decreasing contents of amino acids, tricarboxylic acid (TCA) cycle intermediates and sugars, indicating an increased need for carbon sources and respiratory energy production for the activation of growth. Decreasing sugar levels may additionally cause loss of freezing tolerance. Deacclimation also involves desaturation of membrane lipids, which likely also contributes to decreased freezing tolerance but may also reflect biosynthesis of signaling molecules stimulating growth and floral organ differentiation. These data provide new insights into the under-researched deacclimation mechanisms and the ability of blackcurrant to reacclimate following different advancements of deacclimation and contribute to our understanding of plant responses to increasingly irregular temperature patterns.

Expression patterns of alpha-amylase and beta-amylase genes provide insights into the molecular mechanisms underlying the responses of tea plants (Camellia sinensis) to stress and postharvest processing treatments

The alpha-amylase and beta-amylase genes have been identified from tea plants, and their bioinformatic characteristics and expression patterns provide a foundation for further studies to elucidate their biological functions. Alpha-amylase (AMY)- and beta-amylase (BAM)-mediated starch degradation plays central roles in carbohydrate metabolism and participates extensively in the regulation of a wide range of biological processes, including growth, development and stress response. However, the AMY and BAM genes in tea plants (Camellia sinensis) are poorly understood, and the biological functions of these genes remain to be elucidated. In this study, three CsAMY and nine CsBAM genes from tea plants were identified based on genomic and transcriptomic database analyses, and the genes were subjected to comprehensive bioinformatic characterization. Phylogenetic analysis showed that the CsAMY proteins could be clustered into three different subfamilies, and nine CsBAM proteins could be classified into four groups. Putative catalytically active proteins were identified based on multiple sequence alignments, and the tertiary structures of these proteins were analyzed. Cis-element analysis indicated that CsAMY and CsBAM were extensively involved in tea plant growth, development and stress response. In addition, the CsAMY and CsBAM genes were differentially expressed in various tissues and were regulated by stress treatments (e.g., ABA, cold, drought and salt stress), and the expression patterns of these genes were associated with the postharvest withering and rotation processes. Taken together, our results will enhance the understanding of the roles of the CsAMY and CsBAM gene families in the growth, development and stress response of tea plants and of the potential functions of these genes in determining tea quality during the postharvest processing of tea leaves.

Production, pomological and nutraceutical properties of apricot

Apricot (Prunus sp.) is an important fruit crop worldwide. Despite recent advances in apricot research, much is still to be done to improve its productivity and environmental adaptability. The availability of wild apricot germplasms with economically interesting traits is a strong incentive to increase research panels toward improving its economic, environmental and nutritional characteristics. New technologies and genomic studies have generated a large amount of raw data that the mining and exploitation can help decrypt the biology of apricot and enhance its agronomic values. Here, we outline recent findings in relation to apricot production, pomological and nutraceutical properties. In particular, we retrace its origin from central Asia and the path it took to attain Europe and other production areas around the Mediterranean basin while locating it in the rosaceae family and referring to its genetic diversities and new attempts of classification. The production, nutritional, and nutraceutical importance of apricot are recapped in an easy readable and comparable way. We also highlight and discuss the effects of late frost damages on apricot production over different growth stages, from swollen buds to green fruits formation. Issues related to the length of production season and biotic and abiotic environmental challenges are also discussed with future perspective on how to lengthen the production season without compromising the fruit quality and productivity.

Seasonal changes in cold hardiness and carbohydrate metabolism in four garden rose cultivars

We studied metabolic adaptations to cold stress in roses and identified genes in the carbohydrate pathway during acclimation and deacclimation. A field experiment with four rose cultivars belonging to different USDA plant hardiness zones was set up in Melle, Belgium (51° 0' N, 3° 48' E). The more cold-hardy cultivars ('Dagmar Hastrup' and 'John Cabot') reached their lowest LT₅₀ value in December, indicating a rapid acclimation after the first occurrence of frost. Less cold-hardy cultivars ('Abraham Darby' and 'Chandos Beauty') reached their lowest LT₅₀ in January/February when exposed to prolonged freezing temperatures. A cell dehydration pattern was found in the less cold-hardy cultivars 'Abraham Darby' and 'Chandos Beauty'. The expression of dehydrins (RhDHN5 and RhDNH6) was up-regulated during November-January. Carbohydrate metabolism is highly involved in cold acclimation in roses. Starch decreased from November towards January in all four cultivars and the hydrolysis of starch by the β-amylolytic pathway (BAM, DPE2) was identified in 'Dagmar Hastrup' from November to January. Oligosaccharides correlated with cold hardiness in three cultivars although no significant upregulation in RhMIPS and RhRS6, key genes in their biosynthesis, was found. Higher sucrose levels were found during acclimation in hardy cultivars, although transcript levels of RhINV2 was more prominent in 'Chandos Beauty'.

Bark cells and xylem cells in Japanese white birch twigs initiate deacclimation at different temperatures

Appropriate timing of cold deacclimation is an important component of winter survival of perennial plants, such as trees, in temperate and boreal zones. Recently, concerns about predicted global climate change disturbing deacclimation timing have been increasing. The relationship between ambient temperatures and the manner by which cells' freezing resistance changes is essential for forecasting the timing of deacclimation. In this study, Japanese white birch twigs that underwent deacclimation treatment at a constant temperature of -2, 0, 4, 10, or 20 °C were separated into bark in which cells adapted to subfreezing temperatures by extracellular freezing and xylem in which cells adapted to subfreezing temperatures by deep supercooling, and the freezing resistance of cells in each tissue type was investigated by measuring percentage electrolyte leakage. Birch cells deacclimated in a different manner according to tissue type. Within 7 days under deacclimation treatment, xylem cells decreased their freezing resistance significantly at a high subfreezing temperature (-2 °C). In contrast, bark cells required a temperature of 10 or 20 °C for a detectable decrease in freezing resistance to occur within the same period. At a temperature lower than 0 °C, bark cells did not decrease their freezing resistance, even after 28 days of treatment. The difference in freezing behavior of cells might involve the difference in how deacclimation occurred in bark and xylem cells.

Time-dependent deacclimation after cold acclimation in Arabidopsis thaliana accessions

During low temperature exposure, Arabidopsis thaliana and many other plants from temperate climates increase in freezing tolerance in a process termed cold acclimation. However, the correct timing and rate of deacclimation, resulting in loss of freezing tolerance and initiation of growth is equally important for plant fitness and survival. While the molecular basis of cold acclimation has been investigated in detail, much less information is available about deacclimation. We have characterized the responses of 10 natural accessions of Arabidopsis thaliana that vary widely in their freezing tolerance, to deacclimation conditions. Sugar, proline and transcript levels declined sharply over three days in all accessions after transfer of cold acclimated plants to ambient temperatures, while freezing tolerance only declined in tolerant accessions. Correlations between freezing tolerance and the expression levels of COR genes and the content of glucose, fructose and sucrose, as well as many correlations among transcript and solute levels, that were highly significant in cold acclimated plants, were lost during deacclimation. Other correlations persisted, indicating that after three days of deacclimation, plant metabolism had not completely reverted back to the non-acclimated state. These data provide the basis for further molecular and genetic studies to unravel the regulation of deacclimation.