Abscisic Acid (ABA ) Promotes the Induction and Maintenance of Pear (Pyrus pyrifolia White Pear Group) Flower Bud Endodormancy

AmDHN4, a winter accumulated SKn-type dehydrin from Ammopiptanthus mongolicus, and regulated by AmWRKY45, enhances the tolerance of Arabidopsis to low temperature and osmotic stress

Ammopiptanthus mongolicus, a rare temperate evergreen broadleaf shrub, exhibits remarkable tolerance to low temperature and drought stress in winter. Late embryogenesis abundant (LEA) proteins, a kind of hydrophilic protein with a protective function, play significant roles in enhancing plant tolerance to abiotic stress. In this present study, we analyzed the evolution and expression of LEA genes in A. mongolicus, and investigated the function and regulatory mechanism of dehydrin under abiotic stresses. Evolutionary analysis revealed that 14 AmLEA genes underwent tandem duplication events, and 36 AmLEA genes underwent segmental duplication events Notably, an expansion in SKn-type dehydrins was observed. Expression analysis showed that AmDHN4, a SKn-type dehydrin, was up-regulated in winter and under low temperature and osmotic stresses. Functional analysis showcased that the heterologous expression of the AmDHN4 enhanced the tolerance of yeast and tobacco to low temperature stress. Additionally, the overexpression of AmDHN4 significantly improved the tolerance of transgenic Arabidopsis to low temperature, drought, and osmotic stress. Further investigations identified AmWRKY45, a downstream transcription factor in the jasmonic acid signaling pathway, binding to the AmDHN4 promoter and positively regulating its expression. In summary, these findings contribute to a deeper understanding of the functional and regulatory mechanisms of dehydrin.

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

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

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

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

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

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

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

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

Interaction of Phytohormones and External Environmental Factors in the Regulation of the Bud Dormancy in Woody Plants

Bud dormancy and release are essential phenomena that greatly assist in adapting to adverse growing conditions and promoting the holistic growth and development of perennial plants. The dormancy and release process of buds in temperate perennial trees involves complex interactions between physiological and biochemical processes influenced by various environmental factors, representing a meticulously orchestrated life cycle. In this review, we summarize the role of phytohormones and their crosstalk in the establishment and release of bud dormancy. External environmental factors, such as light and temperature, play a crucial role in regulating bud germination. We also highlight the mechanisms of how light and temperature are involved in the regulation of bud dormancy by modulating phytohormones. Moreover, the role of nutrient factors, including sugar, in regulating bud dormancy is also discussed. This review provides a foundation for enhancing our understanding of plant growth and development patterns, fostering agricultural production, and exploring plant adaptive responses to adversity.

Hormonal Status of Transgenic Birch with a Pine Glutamine Synthetase Gene during Rooting In Vitro and Budburst Outdoors

Improving nitrogen use efficiency (NUE) is one of the main ways of increasing plant productivity through genetic engineering. The modification of nitrogen (N) metabolism can affect the hormonal content, but in transgenic plants, this aspect has not been sufficiently studied. Transgenic birch (Betula pubescens) plants with the pine glutamine synthetase gene GS1 were evaluated for hormone levels during rooting in vitro and budburst under outdoor conditions. In the shoots of the transgenic lines, the content of indoleacetic acid (IAA) was 1.5-3 times higher than in the wild type. The addition of phosphinothricin (PPT), a glutamine synthetase (GS) inhibitor, to the medium reduced the IAA content in transgenic plants, but it did not change in the control. In the roots of birch plants, PPT had the opposite effect. PPT decreased the content of free amino acids in the leaves of nontransgenic birch, but their content increased in GS-overexpressing plants. A three-year pot experiment with different N availability showed that the productivity of the transgenic birch line was significantly higher than in the control under N deficiency, but not excess, conditions. Nitrogen availability did not affect budburst in the spring of the fourth year; however, bud breaking in transgenic plants was delayed compared to the control. The IAA and abscisic acid (ABA) contents in the buds of birch plants at dormancy and budburst depended both on N availability and the transgenic status. These results enable a better understanding of the interaction between phytohormones and nutrients in woody plants.

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

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

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

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

The RING-H2 gene LdXERICO plays a negative role in dormancy release regulated by low temperature in Lilium davidii var. unicolor

Dormancy regulation is the basis of the sustainable development of the lily industry. Therefore, basic research on lily dormancy is crucial for innovation in lily cultivation and breeding. Previous studies revealed that dormancy release largely depends on abscisic acid (ABA) degradation. However, the key genes and potential regulatory network remain unclear. We used exogenous ABA and ABA inhibitors to elucidate the effect of ABA on lily dormancy. Based on the results of weighted gene coexpression network analysis (WGCNA), the hub gene LdXERICO was identified in modules highly related to endogenous ABA, and a large number of coexpressed genes were identified. LdXERICO was induced by exogenous ABA and expressed at higher levels in tissues with vigorous physiological activity. Silencing LdXERICO increased the low-temperature sensitivity of bulblets and accelerated bulblet sprouting. LdXERICO rescued the ABA insensitivity of xerico mutants during seed germination in Arabidopsis, suggesting that it promotes seed dormancy and supporting overexpression studies on lily bulblets. The significant increase in ABA levels in transgenic Arabidopsis expressing LdXERICO indicated that LdXERICO played a role by promoting ABA synthesis. We generated three transgenic lines by overexpressing LdICE1 in Arabidopsis thaliana and showed that, in contrast to LdXERICO, LdICE1 positively regulated dormancy release. Finally, qRT-PCR confirmed that LdXERICO was epistatic to LdICE1 for dormancy release. We propose that LdXERICO, an essential gene in dormancy regulation through the ABA-related pathway, has a complex regulatory network involving temperature signals. This study provides a theoretical basis for further exploring the mechanism of bulb dormancy release.

Integrated transcriptome, metabolome and phytohormone analysis reveals developmental differences between the first and secondary flowering in Castanea mollissima

INTRODUCTION

Chestnut (Castanea mollissima BL.) is an important woody grain, and its flower formation has a significant impact on fruit yield and quality. Some chestnut species in northern China re-flower in the late summer. On the one hand, the second flowering consumes a lot of nutrients in the tree, weakening the tree and thus affecting flowering in the following year. On the other hand, the number of female flowers on a single bearing branch during the second flowering is significantly higher than that of the first flowering, which can bear fruit in bunches. Therefore, these can be used to study the sex differentiation of chestnut.

METHODS

In this study, the transcriptomes, metabolomes, and phytohormones of male and female chestnut flowers were determined during spring and late summer. We aimed to understand the developmental differences between the first and secondary flowering stages in chestnuts. We analysed the reasons why the number of female flowers is higher in the secondary flowering than in the first flowering and found ways to increase the number of female flowers or decrease the number of male flowers in chestnuts.

RESULTS

Transcriptome analysis of male and female flowers in different developmental seasons revealed that EREBP-like mainly affected the development of secondary female flowers and HSP20 mainly affected the development of secondary male flowers. KEGG enrichment analysis showed that 147 common differentially-regulated genes were mainly enriched from circadian rhythm-plant, carotenoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways. Metabolome analysis showed that the main differentially accumulated metabolites in female flowers were flavonoids and phenolic acids, whereas the main differentially accumulated metabolites in male flowers were lipids, flavonoids, and phenolic acids. These genes and their metabolites are positively correlated with secondary flower formation. Phytohormone analysis showed that abscisic and salicylic acids were negatively correlated with secondary flower formation. MYB305, a candidate gene for sex differentiation in chestnuts, promoted the synthesis of flavonoid substances and thus increased the number of female flowers.

DISCUSSION

We constructed a regulatory network for secondary flower development in chestnuts, which provides a theoretical basis for the reproductive development mechanism of chestnuts. This study has important practical implications for improving chestnut yield and quality.

Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology

BACKGROUND

Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations.

RESULTS

In the present study, we used an elevation gradient in the Pyrenees Mountains to explore the gene expression network underlying dormancy regulation in natural populations of sessile oak stands sampled along an elevation cline and potentially adapted to different climatic conditions mainly driven by temperature. By performing analyses of gene expression in terminal buds we identified genes displaying significant dormancy, elevation or dormancy-by-elevation interaction effects. Our Results highlighted that low- and high-altitude populations have evolved different molecular strategies for minimizing late frost damage and maximizing the growth period, thereby increasing potentially their respective fitness in these contrasting environmental conditions. More particularly, population from high elevation overexpressed genes involved in the inhibition of cell elongation and delaying flowering time while genes involved in cell division and flowering, enabling buds to flush earlier were identified in population from low elevation.

CONCLUSION

Our study made it possible to identify key dormancy-by-elevation responsive genes revealing that the stands analyzed in this study have evolved distinct molecular strategies to adapt their bud phenology in response to temperature.

Small RNA and Degradome Sequencing in Floral Bud Reveal Roles of miRNAs in Dormancy Release of Chimonanthus praecox

Chimonanthus praecox (wintersweet) is highly valued ornamentally and economically. Floral bud dormancy is an important biological characteristic in the life cycle of wintersweet, and a certain period of chilling accumulation is necessary for breaking floral bud dormancy. Understanding the mechanism of floral bud dormancy release is essential for developing measures against the effects of global warming. miRNAs play important roles in low-temperature regulation of flower bud dormancy through mechanisms that are unclear. In this study, small RNA and degradome sequencing were performed for wintersweet floral buds in dormancy and break stages for the first time. Small RNA sequencing identified 862 known and 402 novel miRNAs; 23 differentially expressed miRNAs (10 known and 13 novel) were screened via comparative analysis of breaking and other dormant floral bud samples. Degradome sequencing identified 1707 target genes of 21 differentially expressed miRNAs. The annotations of the predicted target genes showed that these miRNAs were mainly involved in the regulation of phytohormone metabolism and signal transduction, epigenetic modification, transcription factors, amino acid metabolism, and stress response, etc., during the dormancy release of wintersweet floral buds. These data provide an important foundation for further research on the mechanism of floral bud dormancy in wintersweet.

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

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

Transcriptomics and metabolomics changes triggered by exogenous 6-benzylaminopurine in relieving epicotyl dormancy of Polygonatum cyrtonema Hua seeds

Polygonatum cyrtonema Hua is one of the most useful herbs in traditional Chinese medicine and widely used in medicinal and edible perennial plant. However, the seeds have the characteristics of epicotyl dormancy. In this study, the molecular basis for relieving epicotyl dormancy of P. cyrtonema seeds under exogenous 6-benzylaminopurine (6-BA) treatment was revealed for the first time through transcriptome and metabolomics analysis. We determined the elongation of epicotyl buds as a critical period for dormancy release and found that the content of trans-zeatin, proline, auxin and gibberellin was higher, while flavonoids and arginine were lower in the treatment group. Transcriptome analysis showed that there were significant differences in gene expression in related pathways, and the expression patterns were highly consistent with the change of metabolites in corresponding pathways. Co-expression analysis showed that cytokinin dehydrogenase of P. cyrtonema (PcCKXs) and pelargonidin in flavonoid biosynthesis, as well as L-proline, L-ornithine, and L-citrulline in arginine and proline metabolism form network modules, indicating that they have related regulatory roles. Above all, our findings provide new insight into the exogenous 6-BA relieving epicotyl dormancy of P. cyrtonema seeds.

Genome-Wide Identification and Expression Analysis of SnRK2 Gene Family in Dormant Vegetative Buds of Liriodendron chinense in Response to Abscisic Acid, Chilling, and Photoperiod

Protein kinases play an essential role in plants’ responses to environmental stress signals. SnRK2 (sucrose non-fermenting 1-related protein kinase 2) is a plant-specific protein kinase that plays a crucial role in abscisic acid and abiotic stress responses in some model plant species. In apple, corn, rice, pepper, grapevine, Arabidopsis thaliana, potato, and tomato, a genome-wide study of the SnRK2 protein family was performed earlier. The genome-wide comprehensive investigation was first revealed to categorize the SnRK2 genes in the Liriodendron chinense (L. chinense). The five SnRK2 genes found in the L. chinense genome were highlighted in this study. The structural gene variants, 3D structure, chromosomal distributions, motif analysis, phylogeny, subcellular localization, cis-regulatory elements, expression profiles in dormant buds, and photoperiod and chilling responses were all investigated in this research. The five SnRK2 genes from L. chinense were grouped into groups (I–IV) based on phylogeny analysis, with three being closely related to other species. Five hormones-, six stress-, two growths and biological process-, and two metabolic-related responsive elements were discovered by studying the cis-elements in the promoters. According to the expression analyses, all five genes were up- and down-regulated in response to abscisic acid (ABA), photoperiod, chilling, and chilling, as well as photoperiod treatments. Our findings gave insight into the SnRK2 family genes in L. chinense and opened up new study options.

Genome-Wide Identification of MAPKK and MAPKKK Gene Family Members and Transcriptional Profiling Analysis during Bud Dormancy in Pear (Pyrus x bretschneideri)

The mitogen-activated protein kinase (MAPK) cascade consisting of three types of reversibly major signal transduction module (MAPKKK, MAPKK, and MAPK) is distributed in eukaryotes. MAPK cascades participate in various aspects of plant development, including hormone responses, cell division and plant dormancy. Pear is one of the most economically important species worldwide, and its yield is directly affected by dormancy. In this study, genome-wide identification of MAPKK and MAPKKK gene family members in Pyrus x bretschneideri and transcriptional expression analysis of MAPK cascades during pear dormancy were performed. We identified 8 MAPKKs (PbrMKKs) and 100 MAPKKKs (PbrMAPKKKs) in Pyrus using recent genomic information. PbrMAPKKs were classified into four subgroups based on phylogenetic analysis, whereas PbrMAPKKKs were grouped into 3 subfamilies (MEKK, Raf, and ZIK). Most PbrMAPKKKs and PbrMAPKKs in the same subfamily had similar gene structures and conserved motifs. The genes were found on all 17 chromosomes. The comprehensive transcriptome analysis and quantitative real-time polymerase chain reaction (qRT–PCR) results showed that numerous MAPK cascade genes participated in pear bud dormancy. The interaction network and co-expression analyses indicated the crucial roles of the MAPK member-mediated network in pear bud dormancy. Overall, this study advances our understanding of the intricate transcriptional control of MAPKKK-MAPKK-MAPK genes and provides useful information on the functions of dormancy in perennial fruit trees.

Evaluation and Comparison of Pear Flower Aroma Characteristics of Seven Cultivars

Due to its ornamental and medicinal value, pear flower has been historically loved and used in China. However, the current understanding of their odor-active compounds and aroma profiles is rather limited. This work aimed to evaluate and compare the overall aroma profile of pear flowers; the volatiles in flowers of seven pear cultivars (Anli, Bayuesu, Golden, Brown peel, KorlaXiangli, Lyubaoshi, Xizilü) were analyzed using solid-phase microextraction–gas chromatography-mass spectrometry (SPME-GC-MS). A total of 93 volatile compounds were identified and quantified within the amount of volatiles in the range of 62.7–691.8 μg kg−1 (FW) and showed high and significant variability in different cultivars. Anli and Brown peel flowers showed a relatively higher volatile abundance, while KorlaXiangli flowers were significantly lower than other cultivars. Although the composition of volatiles depended on the existence of different chemical classes, the odor activity values (OAVs) and odor descriptions showed some aldehydes were part of their main peculiarities and were considered as the basic active odorants that presented strong intensity of citrus and floral odor. Moreover, multivariate analysis showed the pear flower of different cultivars could be arranged in different clusters by the identified odorants. This study provides first-hand knowledge regarding pear flower aroma profiles, and that the cultivar differences were critical for the overall pattern.

Influence of Climate Change on Metabolism and Biological Characteristics in Perennial Woody Fruit Crops in the Mediterranean Environment

The changes in the state of the climate have a high impact on perennial fruit crops thus threatening food availability. Indeed, climatic factors affect several plant aspects, such as phenological stages, physiological processes, disease-pest frequency, yield, and qualitative composition of the plant tissues and derived products. To mitigate the effects of climatic parameters variability, plants implement several strategies of defense, by changing phenological trends, altering physiology, increasing carbon sequestration, and metabolites synthesis. This review was divided into two sections. The first provides data on climate change in the last years and a general consideration on their impact, mitigation, and resilience in the production of food crops. The second section reviews the consequences of climate change on the industry of two woody fruit crops models (evergreen and deciduous trees). The research focused on, citrus, olive, and loquat as evergreen trees examples; while grape, apple, pear, cherry, apricot, almond, peach, kiwi, fig, and persimmon as deciduous species. Perennial fruit crops originated by a complex of decisions valuable in a long period and involving economic and technical problems that farmers may quickly change in the case of annual crops. However, the low flexibility of woody crops is balanced by resilience in the long-life cycle.

Metabolites in Cherry Buds to Detect Winter Dormancy

Winter dormancy is still a “black box” in phenological models, because it evades simple observation. This study presents the first step in the identification of suitable metabolites which could indicate the timing and length of dormancy phases for the sweet cherry cultivar ‘Summit’. Global metabolite profiling detected 445 named metabolites in flower buds, which can be assigned to different substance groups such as amino acids, carbohydrates, phytohormones, lipids, nucleotides, peptides and some secondary metabolites. During the phases of endo- and ecodormancy, the energy metabolism in the form of glycolysis and the tricarboxylic acid (TCA) cycle was shut down to a minimum. However, the beginning of ontogenetic development was closely related to the up-regulation of the carbohydrate metabolism and thus to the generation of energy for the growth and development of the sweet cherry buds. From the 445 metabolites found in cherry buds, seven were selected which could be suitable markers for the ecodormancy phase, whose duration is limited by the date of endodormancy release (t₁) and the beginning of ontogenetic development (t₁*). With the exception of abscisic acid (ABA), which has been proven to control bud dormancy, all of these metabolites show nearly constant intensity during this phase.

Comparative Transcriptomic Analysis Provides Insight into the Key Regulatory Pathways and Differentially Expressed Genes in Blueberry Flower Bud Endo- and Ecodormancy Release

Endodormancy is the stage that perennial plants must go through to prepare for the next seasonal cycle, and it is also an adaptation that allows plants to survive harsh winters. Blueberries (Vaccinium spp.) are known to have high nutritional and commercial value. To better understand the molecular mechanisms of bud dormancy release, the transcriptomes of flower buds from the southern highbush blueberry variety “O’Neal” were analyzed at seven time points of the endo- and ecodormancy release processes. Pairwise comparisons were conducted between adjacent time points; five kinds of phytohormone were identified via these processes. A total of 12,350 differentially expressed genes (DEGs) were obtained from six comparisons. Gene Ontology analysis indicated that these DEGs were significantly involved in metabolic processes and catalytic activity. KEGG pathway analysis showed that these DEGs were predominantly mapped to metabolic pathways and the biosynthesis of secondary metabolites in endodormancy release, but these DEGs were significantly enriched in RNA transport, plant hormone signal transduction, and circadian rhythm pathways in the process of ecodormancy release. The contents of abscisic acid (ABA), salicylic acid (SA), and 1-aminocyclopropane-1-carboxylate (ACC) decreased in endo- and ecodormancy release, and the jasmonic acid (JA) level first decreased in endodormancy release and then increased in ecodormancy release. Weighted correlation network analysis (WGCNA) of transcriptomic data associated with hormone contents generated 25 modules, 9 of which were significantly related to the change in hormone content. The results of this study have important reference value for elucidating the molecular mechanism of flower bud dormancy release.

Abscisic Acid: Role in Fruit Development and Ripening

Abscisic acid (ABA) is a plant growth regulator known for its functions, especially in seed maturation, seed dormancy, adaptive responses to biotic and abiotic stresses, and leaf and bud abscission. ABA activity is governed by multiple regulatory pathways that control ABA biosynthesis, signal transduction, and transport. The transport of the ABA signaling molecule occurs from the shoot (site of synthesis) to the fruit (site of action), where ABA receptors decode information as fruit maturation begins and is significantly promoted. The maximum amount of ABA is exported by the phloem from developing fruits during seed formation and initiation of fruit expansion. In the later stages of fruit ripening, ABA export from the phloem decreases significantly, leading to an accumulation of ABA in ripening fruit. Fruit growth, ripening, and senescence are under the control of ABA, and the mechanisms governing these processes are still unfolding. During the fruit ripening phase, interactions between ABA and ethylene are found in both climacteric and non-climacteric fruits. It is clear that ABA regulates ethylene biosynthesis and signaling during fruit ripening, but the molecular mechanism controlling the interaction between ABA and ethylene has not yet been discovered. The effects of ABA and ethylene on fruit ripening are synergistic, and the interaction of ABA with other plant hormones is an essential determinant of fruit growth and ripening. Reaction and biosynthetic mechanisms, signal transduction, and recognition of ABA receptors in fruits need to be elucidated by a more thorough study to understand the role of ABA in fruit ripening. Genetic modifications of ABA signaling can be used in commercial applications to increase fruit yield and quality. This review discusses the mechanism of ABA biosynthesis, its translocation, and signaling pathways, as well as the recent findings on ABA function in fruit development and ripening.

The Identification of Small RNAs Differentially Expressed in Apple Buds Reveals a Potential Role of the Mir159-MYB Regulatory Module during Dormancy

Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warmer temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of 17 micro RNAs (miRNAs) that change their pattern of expression in apple buds during dormancy. Furthermore, the functional analysis of their predicted target genes suggests a main role of the 17 miRNAs in phenylpropanoid biosynthesis, gene regulation, plant development and growth, and response to stimulus. Finally, we studied the conservation of the Arabidopsis thaliana regulatory miR159-MYB module in apple in the context of the plant hormone abscisic acid homeostasis.

Cold induced genes (CIGs) regulate flower development and dormancy in Prunus avium L

The flower buds continue to develop during the whole winter in tree fruit species, which is affected by environmental factors and hormones. However, little is known about the molecular mechanism of flower development during dormancy phase of sweet cherry in response to light, temperature and ABA. Therefore, we identified two cold induced gene (CIG) PavCIG1 and PavCIG2 from sweet cherry, which were closely to PpCBF and PyDREB from Prunus persica and Prunus yedoensis by using phylogenetic analysis, suggesting conserved functions with these evolutionarily closer DREB subfamily genes. Subcellular localization analysis indicated that, PavCIG1 and PavCIG2 were both localized in the nucleus. The seasonal expression levels of PavCIG1 and PavCIG2 were higher at the stage of endodormancy in winter, and induced by low temperature. Ectopic expression of PavCIG1 and PavCIG2 resulted in a delayed flowering in Arabidopsis. Furthermore, PavCIG2 increased light-responsive gene PavHY5 transcriptional activity by binding to its promoter, meanwhile, PavHY5-mediated positive feedback regulated PavCIG2. Moreover, ABA-responsive protein PavABI5-like could also increase transcriptional activity of PavCIG and PavCIG2. In addition, PavCIG and PavCIG2 target gene PavCAL-like was involved in floral initiation, demonstrated by ectopic expression in Arabidopsis. These findings provide evidences to better understand the molecular mechanism of CIG-mediated flower development and dormancy in fruit species, including sweet cherry.

Transcriptomic Analysis Reveals the Positive Role of Abscisic Acid in Endodormancy Maintenance of Leaf Buds of Magnolia wufengensis

Magnolia wufengensis (Magnoliaceae) is a deciduous landscape species, known for its ornamental value with uniquely shaped and coloured tepals. The species has been introduced to many cities in south China, but low temperatures limit the expansion of this species in cold regions. Bud dormancy is critical for plants to survive in cold environments during the winter. In this study, we performed transcriptomic analysis of leaf buds using RNA sequencing and compared their gene expression during endodormancy, endodormancy release, and ecodormancy. A total of 187,406 unigenes were generated with an average length of 621.82 bp (N50 = 895 bp). In the transcriptomic analysis, differentially expressed genes involved in metabolism and signal transduction of hormones especially abscisic acid (ABA) were substantially annotated during dormancy transition. Our results showed that ABA at a concentration of 100 μM promoted dormancy maintenance in buds of M. wufengensis. Furthermore, the expression of genes related to ABA biosynthesis, catabolism, and signalling pathway was analysed by qPCR. We found that the expression of MwCYP707A-1-2 was consistent with ABA content and the dormancy transition phase, indicating that MwCYP707A-1-2 played a role in endodormancy release. In addition, the upregulation of MwCBF1 during dormancy release highlighted the enhancement of cold resistance. This study provides new insights into the cold tolerance of M. wufengensis in the winter from bud dormancy based on RNA-sequencing and offers fundamental data for further research on breeding improvement of M. wufengensis.

Downregulation of lncRNA PpL-T31511 and Pp-miRn182 Promotes Hydrogen Cyanamide-Induced Endodormancy Release through the PP2C-H2O2 Pathway in Pear (Pyrus pyrifolia)

Bud endodormancy is an important, complex process subject to both genetic and epigenetic control, the mechanism of which is still unclear. The endogenous hormone abscisic acid (ABA) and its signaling pathway play important roles in the endodormancy process, in which the type 2C protein phosphatases (PP2Cs) is key to the ABA signal pathway. Due to its excellent effect on endodormancy release, hydrogen cyanamide (HC) treatment is considered an effective measure to study the mechanism of endodormancy release. In this study, RNA-Seq analysis was conducted on endodormant floral buds of pear (Pyrus pyrifolia) with HC treatment, and the HC-induced PP2C gene PpPP2C1 was identified. Next, software prediction, expression tests and transient assays revealed that lncRNA PpL-T31511-derived Pp-miRn182 targets PpPP2C1. The expression analysis showed that HC treatment upregulated the expression of PpPP2C1 and downregulated the expression of PpL-T31511 and Pp-miRn182. Moreover, HC treatment inhibited the accumulation of ABA signaling pathway-related genes and hydrogen peroxide (H₂O₂). Furthermore, overexpression of Pp-miRn182 reduced the inhibitory effect of PpPP2C1 on the H₂O₂ content. In summary, our study suggests that downregulation of PpL-T31511-derived Pp-miRn182 promotes HC-induced endodormancy release in pear plants through the PP2C-H₂O₂ pathway.

Alternative splicing of the dormancy-associated MADS-box transcription factor gene PpDAM1 is associated with flower bud dormancy in 'Dangshansu' pear (Pyrus pyrifolia white pear group)

Alternative splicing (AS) plays a crucial role in plant growth, development and response to various environmental changes. However, whether alternative splicing of MADS-box transcription factors contributes to the flower bud dormancy process in fruit trees still remains unknown. In this work, the AS profile of genes in the dormant flower buds of 'Dangshansu' pear tree were examined. A total number of 3661 alternatively spliced genes were identified, and three mRNA isoforms of the dormancy associated MADS box (DAM) gene, PpDAM1, derived by alternative splicing, designated as PpDAM1.1, PpDAM1.2 and PpDAM1.3, were characterized. Bimolecular fluorescence complementation (BiFC) analysis indicated that AS of PpDAM1 didn't affect the nucleus localization and homo-/heterodimerization of PpDAM1.1, PpDAM1.2 and PpDAM1.3 proteins, but disturbed the translocation of PpDAM1.1/PpDAM1.1, PpDAM1.3/PpDAM1.3, PpDAM1.1/PpDAM1.3, and PpDAM1.2/PpDAM1.3 dimers to the nucleus. Constitutive expression of PpDAM1.2, but not PpDAM1.1 and PpDAM1.3, in Arabidopsis retarded the growth and development of transgenic plants. Further comparative expression analyses of PpDAM1.1, PpDAM1.2 and PpDAM1.3 in the flower buds of 'Dangshansu' and a less dormant pear cultivar, 'Cuiguan', exhibited that the expression of all the three isoforms in 'Dangshansu' were significantly higher than in 'Cuiguan', especially PpDAM1.2, which showed a predominantly higher expression than PpDAM1.1 and PpDAM1.3 in both cultivars. Our results suggest that alternative splicing of PpDAM1 could play a crucial role in pear flower bud dormancy process.

High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy

Dormancy-associated MADS-box (DAM) genes serve as crucial regulators of the endodormancy cycle in rosaceous plants. Although pear DAM genes have been identified previously, the lack of a high-quality reference genome and techniques to study gene function have prevented accurate genome-wide analysis and functional verification of such genes. Additionally, the contribution of other genes to the regulation of endodormancy release remains poorly understood. In this study, a high-quality genome assembly for 'Cuiguan' pear (Pyrus pyrifolia), which is a leading cultivar with a low chilling requirement cultivated in China, was constructed using PacBio and Hi-C technologies. Using this genome sequence, we revealed that pear DAM genes were tandemly clustered on Chr8 and Chr15 and were differentially expressed in the buds between 'Cuiguan' and the high-chilling-requirement cultivar 'Suli' during the dormancy cycle. Using a virus-induced gene silencing system, we determined the repressive effects of DAM genes on bud break. Several novel genes potentially involved in the regulation of endodormancy release were identified by RNA sequencing and H3K4me3 chromatin immunoprecipitation sequencing analyses of 'Suli' buds during artificial chilling using the new reference genome. Our findings enrich the knowledge of the regulatory mechanism underlying endodormancy release and chilling requirements and provide a foundation for the practical regulation of dormancy release in fruit trees as an adaptation to climate change.

BTB-TAZ Domain Protein PpBT3 modulates peach bud endodormancy by interacting with PpDAM5

The dormancy-associated MADS-box (DAM) gene DAM5 has crucial roles in bud endodormancy; however, the molecular regulatory mechanism of PpDAM5 in peach (Prunus persica) has not been elucidated. In this study, using yeast two-hybrid screening, we isolated a BTB-TAZ Domain Protein PpBT3, which interacts with PpDAM5 protein, in the peach cultivar 'Chun xue'. As expected, we found that abscisic acid (ABA) maintained bud endodormancy and induced expression of the PpDAM5 gene, and that over-expressing PpDAM5 in Arabidopsis thaliana repressed seed germination. In contrast, over-expressing PpBT3 in A. thaliana promoted seed germination, and conferred resistance to ABA-mediated germination inhibition. Additionally, a qRT-PCR (quantitative real-time polymerase chain reaction) experiment suggested that the transcript level of PpBT3 gradually increased towards the endodormancy release period, which is the opposite trend of the expression pattern of PpDAM5. Our results suggest that PpBT3 modulates peach bud endodormancy by interacting with PpDAM5, thus revealing a new mechanism for regulating bud dormancy of perennial deciduous trees.

Chilling Requirement Validation and Physiological and Molecular Responses of the Bud Endodormancy Release in Paeonia lactiflora 'Meiju'

The introduction of herbaceous peony (Paeonia lactiflora Pall.) in low-latitude areas is of great significance to expand the landscape application of this world-famous ornamental. With the hazards of climate warming, warm winters occurs frequently, which makes many excellent northern herbaceous peony cultivars unable to meet their chilling requirements (CR) and leads to their poor growth and flowering in southern China. Exploring the endodormancy release mechanism of underground buds is crucial for improving low-CR cultivar screening and breeding. A systematic study was conducted on P. lactiflora 'Meiju', a screened cultivar with a typical low-CR trait introduced from northern China, at the morphological, physiological and molecular levels. The CR value of 'Meiju' was further verified as 677.5 CUs based on the UT model and morphological observation. As a kind of signal transducer, reactive oxygen species (ROS) released a signal to enter dormancy, which led to corresponding changes in carbohydrate and hormone metabolism in buds, thus promoting underground buds to acquire strong cold resistance and enter endodormancy. The expression of important genes related to ABA metabolism, such as NCED3, PP2C, CBF4 and ABF2, reached peaks at the critical stage of endodormancy release (9 January) and then decreased rapidly; the expression of the GA2ox8 gene related to GA synthesis increased significantly in the early stage of endodormancy release and decreased rapidly after the release of ecodormancy (23 January). Cytological observation showed that the period when the sugar and starch contents decreased and the ABA/GA ratio decreased was when 'Meiju' bud endodormancy was released. This study reveals the endodormancy regulation mechanism of 'Meiju' buds with the low-CR trait, which lays a theoretical foundation for breeding new herbaceous peony cultivars with the low-CR trait.

Integrative Identification of Crucial Genes Associated With Plant Hormone-Mediated Bud Dormancy in Prunus mume

Prunus mume is an important ornamental woody plant with winter-flowering property, which is closely related to bud dormancy. Despite recent scientific headway in deciphering the mechanism of bud dormancy in P. mume, the overall picture of gene co-expression regulating P. mume bud dormancy is still unclear. Here a total of 23 modules were screened by weighted gene co-expression network analysis (WGCNA), of which 12 modules were significantly associated with heteroauxin, abscisic acid (ABA), and gibberellin (GA), including GA1, GA3, and GA4. The yellow module, which was positively correlated with the content of ABA and negatively correlated with the content of GA, was composed of 1,426 genes, among which 156 transcription factors (TFs) were annotated with transcriptional regulation function. An enrichment analysis revealed that these genes are related to the dormancy process and plant hormone signal transduction. Interestingly, the expression trends of PmABF2 and PmABF4 genes, the core members of ABA signal transduction, were positively correlated with P. mume bud dormancy. Additionally, the PmSVP gene had attracted lots of attention because of its co-expression, function enrichment, and expression level. PmABF2, PmABF4, and PmSVP were the genes with a high degree of expression in the co-expression network, which was upregulated by ABA treatment. Our results provide insights into the underlying molecular mechanism of plant hormone-regulated dormancy and screen the hub genes involved in bud dormancy in P. mume.

Ethylene-Mediated Modulation of Bud Phenology, Cold Hardiness, and Hormone Biosynthesis in Peach (Prunus persica)

Spring frosts exacerbated by global climate change have become a constant threat to temperate fruit production. Delaying the bloom date by plant growth regulators (PGRs) has been proposed as a practical frost avoidance strategy. Ethephon is an ethylene-releasing PGR found to delay bloom in several fruit species, yet its use is often coupled with harmful effects, limiting its applicability in commercial tree fruit production. Little information is available regarding the mechanisms by which ethephon influences blooming and bud dormancy. This study investigated the effects of fall-applied ethephon on bud phenology, cold hardiness, and hormonal balance throughout the bud dormancy cycle in peach. Our findings concluded that ethephon could alter several significant aspects of peach bud physiology, including accelerated leaf fall, extended chilling accumulation period, increased heat requirements, improved cold hardiness, and delayed bloom date. Ethephon effects on these traits were primarily dependent on its concentration and application timing, with a high concentration (500 ppm) and an early application timing (10% leaf fall) being the most effective. Endogenous ethylene levels were induced significantly in the buds when ethephon was applied at 10% versus 90% leaf fall, indicating that leaves are essential for ethephon uptake. The hormonal analysis of buds at regular intervals of chilling hours (CH) and growing degree hours (GDH) also indicated that ethephon might exert its effects through an abscisic acid (ABA)-independent way in dormant buds. Instead, our data signifies the role of jasmonic acid (JA) in mediating budburst and bloom in peach, which also appears to be influenced by ethephon treatment. Overall, this research presents a new perspective in interpreting horticultural traits in the light of biochemical and molecular data and sheds light on the potential role of JA in bud dormancy, which deserves further attention in future studies that aim at mitigating spring frosts.

Bud endodormancy in deciduous fruit trees: advances and prospects

Bud endodormancy is a complex physiological process that is indispensable for the survival, growth, and development of deciduous perennial plants. The timely release of endodormancy is essential for flowering and fruit production of deciduous fruit trees. A better understanding of the mechanism of endodormancy will be of great help in the artificial regulation of endodormancy to cope with climate change and in creating new cultivars with different chilling requirements. Studies in poplar have clarified the mechanism of vegetative bud endodormancy, but the endodormancy of floral buds in fruit trees needs further study. In this review, we focus on the molecular regulation of endodormancy induction, maintenance and release in floral buds of deciduous fruit trees. We also describe recent advances in quantitative trait loci analysis of chilling requirements in fruit trees. We discuss phytohormones, epigenetic regulation, and the detailed molecular network controlling endodormancy, centered on SHORT VEGETATIVE PHASE (SVP) and Dormancy-associated MADS-box (DAM) genes during endodormancy maintenance and release. Combining previous studies and our observations, we propose a regulatory model for bud endodormancy and offer some perspectives for the future.

Growing in time: exploring the molecular mechanisms of tree growth

Trees cover vast areas of the Earth's landmasses. They mitigate erosion, capture carbon dioxide, produce oxygen and support biodiversity, and also are a source of food, raw materials and energy for human populations. Understanding the growth cycles of trees is fundamental for many areas of research. Trees, like most other organisms, have evolved a circadian clock to synchronize their growth and development with the daily and seasonal cycles of the environment. These regular changes in light, daylength and temperature are perceived via a range of dedicated receptors and cause resetting of the circadian clock to local time. This allows anticipation of daily and seasonal fluctuations and enables trees to co-ordinate their metabolism and physiology to ensure vital processes occur at the optimal times. In this review, we explore the current state of knowledge concerning the regulation of growth and seasonal dormancy in trees, using information drawn from model systems such as Populus spp.

Identification of early and late flowering time candidate genes in endodormant and ecodormant almond flower buds

Flower bud dormancy in temperate fruit tree species, such as almond [Prunus dulcis (Mill.) D.A. Webb], is a survival mechanism that ensures that flowering will occur under suitable weather conditions for successful flower development, pollination and fruit set. Dormancy is divided into three sequential phases: paradormancy, endodormancy and ecodormancy. During the winter, buds need cultivar-specific chilling requirements (CRs) to overcome endodormancy and heat requirements to activate the machinery to flower in the ecodormancy phase. One of the main factors that enables the transition from endodormancy to ecodormancy is transcriptome reprogramming. In this work, we therefore monitored three almond cultivars with different CRs and flowering times by RNA sequencing during the endodormancy release of flower buds and validated the data by quantitative real-time PCR in two consecutive seasons. We were thus able to identify early and late flowering time candidate genes in endodormant and ecodormant almond flower buds associated with metabolic switches, transmembrane transport, cell wall remodeling, phytohormone signaling and pollen development. These candidate genes were indeed involved in the overcoming of the endodormancy in almond. This information may be used for the development of dormancy molecular markers, increasing the efficiency of temperate fruit tree breeding programs in a climate-change context.

Changes in phytohormone content and associated gene expression throughout the stages of pear (Pyrus pyrifolia Nakai) dormancy

To elucidate the role of phytohormones during bud dormancy progression in the Japanese pear (Pyrus pyrifolia Nakai), we investigated changes in phytohormone levels of indole acetic acid (IAA), gibberellic acid (GA), abscisic acid (ABA) and trans-zeatin (tZ). Using ultra-performance liquid chromatography/mass spectrometry/mass spectrometry, we monitored phytohormone levels in the buds of field-grown and potted trees that were artificially heated to modify the timing of dormancy and flowering (spring flush) progression. We also analyzed the expression of GA- and ABA-metabolic genes during dormancy. Indole acetic acid and tZ levels were low during dormancy and increased toward the flowering stage. Gibberellic acid levels were maintained at relatively high concentrations during the dormancy induction stage, then decreased before slightly increasing prior to flowering. The low GA concentration in potted trees compared with field-grown trees indicated that GA functions in regulating tree vigor. Abscisic acid levels increased from the dormancy induction stage, peaked near endodormancy release and steadily decreased before increasing again before the flowering stage. The ABA peak levels did not always coincide with endodormancy release, but peak height correlated with flowering uniformity, suggesting that a decline in ABA concentration was not necessary for resumption of growth but the abundance of ABA might be associated with dormancy depth. From monitoring the expression of genes related to GA and ABA metabolism, we inferred that phytohormone metabolism changed significantly during dormancy, even though the levels of bioactive molecules were consistently low. Phytohormones regulate dormancy progression not only upon the reception of internal signals but also upon sensing ambient conditions.

Interplay among Antioxidant System, Hormone Profile and Carbohydrate Metabolism during Bud Dormancy Breaking in a High-Chill Peach Variety

(1) Background: Prunus species have the ability to suspend (induce dormancy) and restart growth, in an intricate process in which environmental and physiological factors interact. (2) Methods: In this work, we studied the evolution of sugars, antioxidant metabolism, and abscisic acid (ABA) and gibberellins (GAs) levels during bud dormancy evolution in a high-chill peach variety, grown for two seasons in two different geographical areas with different annual media temperature, a cold (CA) and a temperate area (TA). (3) Results: In both areas, starch content reached a peak at ecodormancy, and then decreased at dormancy release (DR). Sorbitol and sucrose declined at DR, mainly in the CA. In contrast, glucose and fructose levels progressively rose until DR. A decline in ascorbate peroxidase, dehydroascorbate reductase, superoxide dismutase and catalase activities occurred in both seasons at DR. Moreover, the H2O2-sensitive SOD isoenzymes, Fe-SOD and Cu,Zn-SOD, and two novel peroxidase isoenzymes, were detected. Overall, these results suggest the occurrence of a controlled oxidative stress during DR. GA7 was the major bioactive GA in both areas, the evolution of its levels being different between seasons and areas. In contrast, ABA content decreased during the dormancy period in both areas, resulting in a reduction in the ABA/total GAs ratio, being more evident in the CA. (4) Conclusion: A possible interaction sugars-hormones-ROS could take place in high-chill peach buds, favoring the DR process, suggesting that, in addition to sugar metabolism, redox interactions can govern bud DR, regardless of chilling requirements.

Genome-wide identification, characterisation, and evolution of ABF/AREB subfamily in nine Rosaceae species and expression analysis in mei (Prunus mume)

Rosaceae is an important family containing some of the highly evolved fruit and ornamental plants. Abiotic stress responses play key roles in the seasonal growth and development of plants. However, the molecular basis of stress responses remains largely unknown in Rosaceae. Abscisic acid (ABA) is a stress hormone involving abiotic stress response pathways. The ABRE-binding factor/ABA-responsive element-binding protein (ABF/AREB) is a subfamily of the basic domain/leucine zipper (bZIP) transcription factor family. It plays an important role in the ABA-mediated signaling pathway. Here, we analyzed the ABF/AREB subfamily genes in nine Rosaceae species. A total of 64 ABF/AREB genes were identified, including 18, 28, and 18 genes in the Rosoideae, Amygdaloideae, and Maloideae traditional subfamilies, respectively. The evolutionary relationship of the ABF/AREB subfamily genes was studied through the phylogenetic analysis, the gene structure and conserved motif composition, Ka/Ks values, and interspecies colinearity. These gene sets were clustered into four groups. In the Prunus ABF/AREB (PmABF) promoters, several cis-elements related to light, hormone, and abiotic stress response were predicted. PmABFs expressed in five different tissues, except PmABF5, which expressed only in buds. In the dormancy stages, PmABF1, 2, 5 and 7 showed differential expression. The expression of PmABF3, 4 and 6 was positively correlated with the ABA concentration. Except for PmABF5, all the PmABFs were sensitive to ABA. Several ABRE elements were contained in the promoters of PmABF1, 3, 6, 7. Based on the findings of our study, we speculate that PmABFs may play a role in flower bud dormancy in P. mume.

Endodormancy Release Can Be Modulated by the GA4-GID1c-DELLA2 Module in Peach Leaf Buds

Gibberellin (GA) plays a key role in the release of bud dormancy and the GA receptor GID1 (GIBBERELLIN INSENSITIVE DWARF1) and DELLA protein are the GA signaling parts, but the molecular mechanism of GA-GID1-DELLA module regulating leaf bud dormancy in peach (Prunus persica) is still not very clear. In this study, we isolated and characterized the GID1 gene PpGID1c from the peach cultivar "Zhong you No.4." Overexpressing PpGID1c in Arabidopsis promoted seed germination, which indicated that PpGID1c has an important function in dormancy. The expression level of PpGID1c in peach leaf buds during endodormancy release was higher than that during ecodormancy and was positively correlated with GA₄ levels. Our study also found that GA₄ had the most obvious effect on promoting the bud break, indicating that GA₄ may be the key gibberellin to promoting peach leaf bud endodormancy release. Moreover, a quantitative real-time PCR (qRT-PCR) found that GA₄ could increase the expression of the gibberellin signaling gene PpDELLA2. A yeast two-hybrid (Y2H) assay suggested that the PpGID1c interaction with the PpDELLA1 protein was not dependent on gibberellin, while the PpGID1c interaction with PpDELLA2 required GA₄ or another gibberellin. These findings suggested that the GA₄-GID1c-DELLA2 module regulates peach leaf bud endodormancy release, with this finding significantly enhancing our comprehensive understanding of bud endodormancy release and revealing a new mechanism for regulating leaf bud endodormancy release in peach.

Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume

Prunus mume is one of the most important woody perennials for edible and ornamental use. Despite a substantial variation in the flowering phenology among the P. mume germplasm resources, the genetic control for flowering time remains to be elucidated. In this study, we examined five blooming time-related traits of 235 P. mume landraces for 2 years. Based on the phenotypic data, we performed genome-wide association studies, which included a combination of marker- and gene-based association tests, and identified 1,445 candidate genes that are consistently linked with flowering time across multiple years. Furthermore, we assessed the global transcriptome change of floral buds from the two P. mume cultivars exhibiting contrasting bloom dates and detected 617 associated genes that were differentially expressed during the flowering process. By integrating a co-expression network analysis, we screened out 191 gene candidates of conserved transcriptional pattern during blooming across cultivars. Finally, we validated the temporal expression profiles of these candidates and highlighted their putative roles in regulating floral bud break and blooming time in P. mume. Our findings are important to expand the understanding of flowering time control in woody perennials and will boost the molecular breeding of novel varieties in P. mume.

Integrated transcriptome and proteome analysis provides insight into chilling-induced dormancy breaking in Chimonanthus praecox

Chilling has a critical role in the growth and development of perennial plants. The chilling requirement (CR) for dormancy breaking largely depends on the species. However, global warming is expected to negatively affect chilling accumulation and dormancy release in a wide range of perennial plants. Here, we used Chimonanthus praecox as a model to investigate the CR for dormancy breaking under natural and artificial conditions. We determined the minimum CR (570 chill units, CU) needed for chilling-induced dormancy breaking and analyzed the transcriptomes and proteomes of flowering and non-flowering flower buds (FBs, anther and ovary differentiation completed) with different CRs. The concentrations of ABA and GA3 in the FBs were also determined using HPLC. The results indicate that chilling induced an upregulation of ABA levels and significant downregulation of SHORT VEGETATIVE PHASE (SVP) and FLOWERING LOCUS T (FT) homologs at the transcript level in FBs when the accumulated CR reached 570 CU (IB570) compared to FBs in November (FB.Nov, CK) and nF16 (non-flowering FBs after treatment at 16 °C for -300 CU), which suggested that dormancy breaking of FBs could be regulated by the ABA-mediated SVP-FT module. Overexpression in Arabidopsis was used to confirm the function of candidate genes, and early flowering was induced in 35S::CpFT1 transgenic lines. Our data provide insight into the minimum CR (570 CU) needed for chilling-induced dormancy breaking and its underlying regulatory mechanism in C. praecox, which provides a new tool for the artificial regulation of flowering time and a rich gene resource for controlling chilling-induced blooming.

Revisiting the Complex Pathosystem of Huanglongbing: Deciphering the Role of Citrus Metabolites in Symptom Development

Huanglongbing (HLB), formerly known as citrus greening disease, is one of the most devastating bacterial diseases in citrus worldwide. HLB is caused by 'Candidatus Liberibacter asiaticus' bacterium and transmitted by Diaphorina citri. Both 'Ca. L. asiaticus' and its vector manipulate the host metabolism to fulfill their nutritional needs and/or to neutralize the host defense responses. Herein, we discuss the history of HLB and the complexity of its pathosystem as well as the geographical distribution of its pathogens and vectors. Recently, our recognition of physiological events associated with 'Ca. L. asiaticus' infection and/or D. citri-infestation has greatly improved. However, the roles of citrus metabolites in the development of HLB symptoms are still unclear. We believe that symptom development of HLB disease is a complicated process and relies on a multilayered metabolic network which is mainly regulated by phytohormones. Citrus metabolites play vital roles in the development of HLB symptoms through the modulation of carbohydrate metabolism, phytohormone homeostasis, antioxidant pathways, or via the interaction with other metabolic pathways, particularly involving amino acids, leaf pigments, and polyamines. Understanding how 'Ca. L. asiaticus' and its vector, D. citri, affect the metabolic pathways of their host is critical for developing novel, sustainable strategies for HLB management.

ABA-responsive ABRE-BINDING FACTOR3 activates DAM3 expression to promote bud dormancy in Asian pear

Bud dormancy is indispensable for the survival of perennial plants in cold winters. Abscisic acid (ABA) has essential functions influencing the endo-dormancy status. Dormancy-associated MADS-box/SHORT VEGETATIVE PHASE-like genes function downstream of the ABA signalling pathway to regulate bud dormancy. However, the regulation of DAM/SVP expression remains largely uncharacterized. In this study, we confirmed that endo-dormancy maintenance and PpyDAM3 expression are controlled by the ABA content in pear (Pyrus pyrifolia) buds. The expression of pear ABRE-BINDING FACTOR3 (PpyABF3) was positively correlated with PpyDAM3 expression. Furthermore, PpyABF3 directly bound to the second ABRE in the PpyDAM3 promoter to activate its expression. Interestingly, both PpyABF3 and PpyDAM3 repressed the cell division and growth of transgenic pear calli. Another ABA-induced ABF protein, PpyABF2, physically interacted with PpyABF3 and disrupted the activation of the PpyDAM3 promoter by PpyABF3, indicating DAM expression was precisely controlled. Additionally, our results suggested that the differences in the PpyDAM3 promoter in two pear cultivars might be responsible for the diversity in the chilling requirements. In summary, our data clarify the finely tuned regulatory mechanism underlying the effect of ABA on DAM gene expression and provide new insights into ABA-related bud dormancy regulation.

Relationships Among the Rootstock, Crop Load, and Sugar Hormone Signaling of Apple Tree, and Their Effects on Biennial Bearing

Adjustable crop load primarily involves bud manipulation, and usually switches from vegetative to reproductive buds. While this switch is not fully understood, it is still controlled by the ratio of hormones, which promote or inhibit bud formation. To determine the reasons for biennial bearing, the effect of apple rootstock, scion cultivar, crop load, as well as metabolic changes of endogenous phytohormones [zeatin, jasmonic acid, indole-3 acetic acid (IAA), abscisic acid (ABA), and gibberellins 1, 3, and 7 (GAs)], and soluble sugars (glucose, fructose, and sorbitol) were evaluated, and their connections with return bloom and yield of apple tree buds were analyzed. Cultivars "Ligol" and "Auksis" were tested on five rootstocks contrasting in induced vigor: semi-dwarfing M.26; dwarfing M.9, B.396, and P 67; and super-dwarfing P 22. Crop load levels were adjusted before flowering, leaving 75, 113, and 150 fruits per tree. Principal component analysis (PCA) scatter plot of the metabolic response of phytohormones and sugars indicated that the effect of the semi-dwarfing M.26 rootstock was significantly different from that of the dwarfing M.9 and P 67, as well as the super-dwarfing P 22 rootstocks in both varieties. The most intensive crop load (150 fruits per tree) produced a significantly different response compared to less intensive crop loads (113 and 75) in both varieties. In contrast to soluble sugar accumulation, increased crop load resulted in an increased accumulation of phytohormones, except for ABA. Dwarfing rootstocks M.9, B.396, and P 67, as well as super-dwarf P 22 produced an altered accumulation of promoter phytohormones, while the more vigorous semi-dwarfing M.26 rootstock induced a higher content of glucose and inhibitory phytohormones, by increasing content of IAA, ABA, and GAs. The most significant decrease in return bloom resulted from the highest crop load in "Auksis" grafted on M.9 and P 22 rootstocks. Average difference in flower number between crop loads of 75 and 150 fruits per tree in "Ligol" was 68%, while this difference reached ~ 90% for P 22, and ~ 75% for M.9 and M.26 rootstocks. Return bloom was dependent on the previous year's crop load, cultivar, and rootstock.

Identification and characterization of the GmRD26 soybean promoter in response to abiotic stresses: potential tool for biotechnological application

BACKGROUND

Drought is one of the most harmful abiotic stresses for plants, leading to reduced productivity of several economically important crops and, consequently, considerable losses in the agricultural sector. When plants are exposed to stressful conditions, such as drought and high salinity, they modulate the expression of genes that lead to developmental, biochemical, and physiological changes, which help to overcome the deleterious effects of adverse circumstances. Thus, the search for new specific gene promoter sequences has proved to be a powerful biotechnological strategy to control the expression of key genes involved in water deprivation or multiple stress responses.

RESULTS

This study aimed to identify and characterize the GmRD26 promoter (pGmRD26), which is involved in the regulation of plant responses to drought stress. The expression profile of the GmRD26 gene was investigated by qRT-PCR under normal and stress conditions in Williams 82, BR16 and Embrapa48 soybean-cultivars. Our data confirm that GmRD26 is induced under water deficit with different induction folds between analyzed cultivars, which display different genetic background and physiological behaviour under drought. The characterization of the GmRD26 promoter was performed under simulated stress conditions with abscisic acid (ABA), polyethylene glycol (PEG) and drought (air dry) on A. thaliana plants containing the complete construct of pGmRD26::GUS (2.054 bp) and two promoter modules, pGmRD26A::GUS (909 pb) and pGmRD26B::GUS (435 bp), controlling the expression of the β-glucuronidase (uidA) gene. Analysis of GUS activity has demonstrated that pGmRD26 and pGmRD26A induce strong reporter gene expression, as the pAtRD29 positive control promoter under ABA and PEG treatment.

CONCLUSIONS

The full-length promoter pGmRD26 and the pGmRD26A module provides an improved uidA transcription capacity when compared with the other promoter module, especially in response to polyethylene glycol and drought treatments. These data indicate that pGmRD26A may become a promising biotechnological asset with potential use in the development of modified drought-tolerant plants or other plants designed for stress responses.

Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit development and ripening in red bayberry (Morella rubra)

The MADS-box gene family encodes transcription factors and plays an important role in plant growth and the development of flower and fruit. A perennial dioecious plant, the red bayberry genome has been published recently, providing the opportunity to analyze the MADS-box gene family and its role in fruit development and ripening. Here, we identified 54 MADS-box genes in the red bayberry genome, and classified them into two types based on phylogenetic analysis. Thirteen Type I MADS-box genes were subdivided into three subfamilies and 41 Type II MADS-box genes into 13 subfamilies. A total of 46 MADS-box genes were distributed across eight red bayberry chromosomes, and the other eight genes were located on the unmapped scaffolds. Transcriptome analysis suggested that the expression of most Type II genes was higher than Type I in five female tissues. Moreover, 26 MADS-box genes were expressed during red bayberry fruit development and ten of them showed high expression. qRT-PCR showed that the expression of MrMADS01 (SEP, MIKC^C), with differences between the pale pink and red varieties, increased significantly at the final ripening stage, suggesting it may participate in ripening as positive regulator and related to anthocyanin biosynthesis. These results provide some clues for future study of MADS-box genes in red bayberry, especially in ripening process.

Phylogenetic, Molecular, and Functional Characterization of PpyCBF Proteins in Asian Pears (Pyrus pyrifolia)

C-repeat binding factor/dehydration-responsive element (CBF/DRE) transcription factors (TFs) participate in a variety of adaptive mechanisms, and are involved in molecular signaling and abiotic stress tolerance in plants. In pear (Pyrus pyrifolia) and other rosaceous crops, the independent evolution of CBF subfamily members requires investigation to understand the possible divergent functions of these proteins. In this study, phylogenetic analysis divided six PpyCBFs from the Asian pear genome into three clades/subtypes, and collinearity and phylogenetic analyses suggested that PpyCBF3 was the mother CBF. All PpyCBFs were found to be highly expressed in response to low temperature, salt, drought, and abscisic acid (ABA) as well as bud endodormancy, similar to PpyCORs (PpyCOR47, PpyCOR15A, PpyRD29A, and PpyKIN). Transcript levels of clade II PpyCBFs during low temperature and ABA treatments were higher than those of clades I and III. Ectopic expression of PpyCBF2 and PpyCBF3 in Arabidopsis enhanced its tolerance against abiotic stresses, especially to low temperature in the first case and salt and drought stresses in the latter, and resulted in lower reactive oxygen species (ROS) and antioxidant gene activities compared with the wild type. The increased expression of endogenous ABA-dependent and -independent genes during normal conditions in PpyCBF2- and PpyCBF3-overexpressing Arabidopsis lines suggested that PpyCBFs were involved in both ABA-dependent and -independent pathways. All PpyCBFs, especially the mother CBF, had high transactivation activities with 6XCCGAC binding elements. Luciferase and Y1H assays revealed the existence of phylogenetically and promoter-dependent conserved CBF-COR cascades in the pear. The presence of a previously identified CCGA binding site, combined with the results of mutagenesis of the CGACA binding site of the PpyCOR15A promoter, indicated that CGA was a core binding element of PpyCBFs. In conclusion, PpyCBF TFs might operate redundantly via both ABA-dependent and -independent pathways, and are strongly linked to abiotic stress signaling and responses in the Asian pear.

PpCBFs selectively regulate PpDAMs and contribute to the pear bud endodormancy process

PpCBF2 directly binds to the promoters of PpCBF3 and PpCBF4 to activate their expressions and selectively regulates PpDAMs during the leaf bud endodormancy process of 'Wonhwang' pear (Pyrus pyrifolia). Endodormancy is critical for temperate plant survival under freezing winter conditions, and low temperature is a vital environmental factor in endodormancy regulation. A C-repeat binding factor (CBF) has been found to regulate important DAM transcription factors during endodormancy in pear (Pyrus pyrifolia). In this study, we analyzed the regulation of pear DAM genes by CBFs in further detail. Four CBF and three DAM genes were identified in the pear cultivar 'Wonhwang'. Under natural conditions, PpDAM1 expression decreased from the start of chilling accumulation, while the other two DAM and three CBF genes peaked during endodormancy release. Under chilling treatment, the expressions of PpDAM1, PpDAM2 and PpCBF1 genes were similar to those under natural conditions. Different biochemical methods revealed that PpCBF2/4 can bind to the promoter of PpDAM1 and activate its expression and that PpCBF1/4 can activate PpDAM3. Interestingly, we found that PpCBF2 can activate PpCBF3/4 transcription by directly binding to their promoters. The ICE-CBF regulon is conserved in some plants; three ICE genes were identified in pear, but their expressions did not obviously change under natural and artificial chilling conditions. On the contrary, the selective transcriptional induction of PpCBFs by PpICE1s was observed in a dual-luciferase assay. Considering all these results, we propose that the PpCBF1-PpDAM2 regulon mainly responds to low temperature during endodormancy regulation, with further post-translational regulation by PpICE3. Our results provide basic information on CBF genes functional redundancy and differentiation and demonstrate that the CBF-DAM signaling pathway is involved in the pear bud endodormancy process.

Transcriptome analysis and metabolic profiling reveal the key role of α-linolenic acid in dormancy regulation of European pear

Deciduous trees require sufficient chilling during winter dormancy to grow. To decipher the dormancy-regulating mechanism, we carried out RNA sequencing (RNA-Seq) analysis and metabolic profiling of European pear (Pyrus communis L.) vegetative buds during the dormancy phases. Samples were collected from two cultivars that differed greatly in their chilling requirements: 'Spadona' (SPD), a low chilling requirement cultivar; and Harrow Sweet (HS), a high chilling requirement cultivar. Comparative transcriptome analysis revealed >8500 differentially expressed transcripts; most were related to metabolic pathways. Out of 174 metabolites, 44 displayed differential levels in both cultivars, 38 were significantly changed only in SPD, and 15 only in HS. Phospholipids were mostly accumulated at the beginning of dormancy, sugars between before dormancy and mid-dormancy, and fatty acids, including α-linolenic acid, at dormancy break. Differentially expressed genes underlying previously identified major quantitative trait loci (QTLs) in linkage group 8 included genes related to the α-linolenic acid pathway, 12-oxophytodienoate reductase 2-like, and the DORMANCY-ASSOCIATED MADS-BOX (DAM) genes, PcDAM1 and PcDAM2, putative orthologs of PpDAM1 and PpDAM2, confirming their role for the first time in European pear. Additional new putative dormancy-related uncharacterized genes and genes related to metabolic pathways are suggested. These results suggest the crucial role of α-linolenic acid and DAM genes in pear bud dormancy phase transitions.