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

Transcriptome analysis reveals the key network of axillary bud outgrowth modulated by topping in citrus

Topping, an important tree shaping and pruning technique, can promote the outgrowth of citrus axillary buds. However, the underlying molecular mechanism is still unclear. In this study, spring shoots of Citrus reticulata 'Huagan No.2' were topped and transcriptome was compared between axillary buds of topped and untopped shoots at 6 and 11 days after topping (DAT). 1944 and 2394 differentially expressed genes (DEGs) were found at 6 and 11 DAT, respectively. KEGG analysis revealed that many DEGs were related to starch and sucrose metabolism, signal transduction of auxin, cytokinin and abscisic acid. Specially, transcript levels of auxin synthesis, transport, and signaling-related genes (SAURs and ARF5), cytokinin signal transduction related genes (CRE1, AHP and Type-A ARRs), ABA signal responsive genes (PYL and ABF) were up-regulated by topping; while transcript levels of auxin receptor TIR1, auxin responsive genes AUX/IAAs, ABA signal transduction related gene PP2Cs and synthesis related genes NCED3 were down-regulated. On the other hand, the contents of sucrose and fructose in axillary buds of topped shoots were significantly higher than those in untopped shoots; transcript levels of 16 genes related to sucrose synthase, hexokinase, sucrose phosphate synthase, endoglucanase and glucosidase, were up-regulated in axillary buds after topping. In addition, transcript levels of genes related to trehalose 6-phosphate metabolism and glycolysis/tricarboxylic acid (TCA) cycle, as well to some transcription factors including Pkinase, Pkinase_Tyr, Kinesin, AP2/ERF, P450, MYB, NAC and Cyclin_c, significantly responded to topping. Taken together, the present results suggested that topping promoted citrus axillary bud outgrowth through comprehensively regulating plant hormone and carbohydrate metabolism, as well as signal transduction. These results deepened our understanding of citrus axillary bud outgrowth by topping and laid a foundation for further research on the molecular mechanisms of citrus axillary bud outgrowth.

ABA exerts a promotive effect on the early process of somatic embryogenesis in Quercus aliena Bl

Quercus aliena, a native Chinese tree species, is significant in industry and landscaping. However, it is traditionally propagated by seeds with many limitations, such as pest infestations, seed yield and quality. Thus, this study firstly introduces a somatic embryogenesis (SE) system for Q. aliena, enhancing its cultivation prospects. Thereinto, the development stage of zygotic embryo had a significant effect on SE, only immature embryos in 10-11 weeks after full bloom (WAF), rich in endogenous abscisic acid (ABA), could induce SE. Exogenous application ABA had positive roles in the early development process of both primary and secondary SE, while its antagonist had opposite roles. Transcriptome analysis showed that transcription regulation occupied the major position. Mfuzz cluster and WGCNA co-expression analysis showed that 24 candidate genes were involved in the SE process. The expression of the 24 genes were also affected by exogenous ABA signals, among which QaLEC2, QaCALS11 and QaSSRP1 occupied the important roles. Additionally, the callose content were also affected by exogenous ABA signals, which had significantly positive correlations with the expression of QaLEC2 and QaCALS11. This study not only established an efficient reproduction system for Q. aliena, but also revealed the difference in embryogenic ability of zygotic embryos from the aspects of transcriptome and endogenous hormone content, and lay a foundation for clarifying the molecular mechanism of SE, and provided a reference for exploring the vital roles of ABA in SE.

PbGBF3 enhances salt response in pear by upregulating PbAPL2 and PbSDH1 and reducing ABA-mediated salt sensitivity

Pear is a widely cultivated fruit crop, but its distribution and sustainable production are significantly limited by salt stress. This study used RNA-Seq time-course analysis, WGCNA, and functional enrichment analysis to uncover the molecular mechanisms underlying salt stress tolerance in Pyrus ussuriensis. We identified an ABA-related regulatory module, PbGBF3-PbAPL2-PbSDH1, as crucial in this response. PbGBF3, a bZIP transcription factor, enhances salt tolerance by upregulating PbAPL2 and PbSDH1. Overexpression of PbGBF3 improved salt tolerance in Pyrus communis calli and Arabidopsis, while silencing it reduced tolerance in Pyrus betulifolia. Functional assays showed that PbGBF3 binds to the promoters of PbAPL2 and PbSDH1, increasing their expression. PbAPL2 and PbSDH1, key enzymes in starch synthesis and the sorbitol pathway, respectively, enhance salt tolerance by increasing AGPase activity, soluble sugar content, and SDH activity, improving ROS scavenging and ion balance. Our findings suggest that the PbGBF3-PbAPL2 and PbGBF3-PbSDH1 modules positively regulate salt tolerance by enhancing ABA signaling and reducing ABA-mediated growth inhibition. These insights provide a foundation for developing salt-tolerant pear cultivars.

Genetic factors acting prior to dormancy in sour cherry influence bloom time the following spring

Understanding the process of Prunus species floral development is crucial for developing strategies to manipulate bloom time and prevent crop loss due to climate change. Here, we present a detailed examination of flower development from initiation until bloom for early- and late-blooming sour cherries (Prunus cerasus) from a population segregating for a major bloom time QTL on chromosome 4. Using a new staging system, we show floral buds from early-blooming trees were persistently more advanced than those from late-blooming siblings. A genomic DNA coverage analysis revealed the late-blooming haplotype of this QTL, k, is located on a subgenome originating from the late-blooming P. fruticosa progenitor. Transcriptome analyses identified many genes within this QTL as differentially expressed between early- and late-blooming trees during the vegetative-to-floral transition. From these, we identified candidate genes for the late bloom phenotype, including multiple transcription factors homologous to Reproductive Meristem B3 domain-containing proteins. Additionally, we determined that the basis of k in sour cherry is likely separate from candidate genes found in sweet cherry-suggesting several major regulators of bloom time are located on Prunus chromosome 4.

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

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

BnaC06.WIP2-BnaA09.STM transcriptional regulatory module promotes leaf lobe formation in Brassica napus

The lobed leaves of rapeseed (Brassica napus L.) offer significant advantages in dense planting, leading to increased yield. Although AtWIP2, a C2H2 zinc finger transcription factor, acts as a regulator of leaf development in Arabidopsis thaliana, the function and regulatory mechanisms of BnaWIP2 in B. napus remain unclear. Here, constitutive expression of the BnaC06.WIP2 paralog, predominantly expressed in leaf serrations, produced lobed leaves in both A. thaliana and B. napus. We demonstrated that BnaC06.WIP2 directly repressed the expression of BnaA01.TCP4, BnaA03.TCP4, and BnaC03.TCP4 and indirectly inhibited the expression of BnaA05.BOP1 and BnaC02.AS2 to promote leaf lobe formation. On the other hand, we discovered that BnaC06.WIP2 modulated the levels of endogenous gibberellin, cytokinin, and auxin, and controlled the auxin distribution in B. napus leaves, thus accelerating leaf lobe formation. Meanwhile, we revealed that BnaA09.STM physically interacted with BnaC06.WIP2, and ectopic expression of BnaA09.STM generated smaller and lobed leaves in B. napus. Furthermore, we found that BnaC06.WIP2 and BnaA09.STM synergistically promoted leaf lobe formation through forming transcriptional regulatory module. Collectively, our findings not only facilitate in-depth understanding of the regulatory mechanisms underlying lobed leaf formation, but also are helpful for guiding high-density breeding practices through improving leaf morphology in B. napus.

Genomic basis of the distinct biosynthesis of β-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species

Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.

FLOWERING LOCUS T1 and TERMINAL FLOWER1 regulatory networks mediate flowering initiation in apple

Flower bud formation is a critical process that directly determines yield and fruit quality in fruit crops. Floral induction is modulated by the balance between 2 flowering-related proteins, FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1); however, the mechanisms underlying the establishment and maintenance of this dynamic balance remain largely elusive. Here, we showed that in apple (Malus × domestica Borkh.), MdFT1 is predominantly expressed in spur buds and exhibits an increase in expression coinciding with flower induction; in contrast, MdTFL1 exhibited downregulation in apices during flower induction, suggesting that MdTFL1 has a role in floral repression. Interestingly, both the MdFT1 and MdTFL1 transcripts are directly regulated by transcription factor basic HELIX-LOOP-HELIX48 (MdbHLH48), and overexpression of MdbHLH48 in Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum) results in accelerated flowering. Binding and activation analyses revealed that MdbHLH48 functions as a positive regulator of MdFT1 and a negative regulator of MdTFL1. Further studies established that both MdFT1 and MdTFL1 interact competitively with MdWRKY6 protein to facilitate and inhibit, respectively, MdWRKY6-mediated transcriptional activation of target gene APPLE FLORICAULA/LFY (AFL1, an apple LEAFY-like gene), ultimately regulating apple flower bud formation. These findings illustrate the fine-tuned regulation of flowering by the MdbHLH48-MdFT1/MdTFL1-MdWRKY6 module and provide insights into flower bud formation in apples.

Genome-Wide Identification of GAST Family Members and Their Potential Roles in Epicotyl Dormancy in Chinese Cork Oak (Quercus variabilis)

Chinese cork oak (Quercus variabilis Blume) is a widespread tree species with high economic and ecological values. Chinese cork oak exhibits epicotyl dormancy, causing emergence heterogeneity and affecting the quality of seedling cultivation. Gibberellic acid-stimulated transcript (GAST) is a plant-specific protein family that plays a crucial regulatory role in plant growth, development, and seed germination. However, their evolution in Chinese cork oak and roles in epicotyl dormancy are still unclear. Here, a genome-wide identification of the GAST gene family was conducted in Chinese cork oak. Ten QvGAST genes were identified, and nine of them were expressed in seed. The physicochemical properties and promoter cis-acting elements of the selected Chinese cork oak GAST family genes indicated that the cis-acting elements in the GAST promoter are involved in plant development, hormone response, and stress response. Germinated seeds were subjected to gibberellins (GAs), abscisic acid (ABA), and fluridone treatments to show their response during epicotyl dormancy release. Significant changes in the expression of certain QvGAST genes were observed under different hormone treatments. QvGAST1, QvGAST2, QvGAST3, and QvGAST6 exhibited upregulation in response to gibberellin. QvGAST2 was markedly upregulated during the release of epicotyl dormancy in response to GA. These findings suggested that QvGAST2 might play an important role in epicotyl dormancy release. This study provides a basis for further analysis of the mechanisms underlying the alleviation of epicotyl dormancy in Chinese cork oak by QvGASTs genes.

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.

Molecular Mechanisms of Seasonal Gene Expression in Trees

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

Antagonistic MADS-box transcription factors SEEDSTICK and SEPALLATA3 form a transcriptional regulatory network that regulates seed oil accumulation

Transcriptional regulation is essential for balancing multiple metabolic pathways that influence oil accumulation in seeds. Thus far, the transcriptional regulatory mechanisms that govern seed oil accumulation remain largely unknown. Here, we identified the transcriptional regulatory network composed of MADS-box transcription factors SEEDSTICK (STK) and SEPALLATA3 (SEP3), which bridges several key genes to regulate oil accumulation in seeds. We found that STK, highly expressed in the developing embryo, positively regulates seed oil accumulation in Arabidopsis (Arabidopsis thaliana). Furthermore, we discovered that SEP3 physically interacts with STK in vivo and in vitro. Seed oil content is increased by the SEP3 mutation, while it is decreased by SEP3 overexpression. The chromatin immunoprecipitation, electrophoretic mobility shift assay, and transient dual-luciferase reporter assays showed that STK positively regulates seed oil accumulation by directly repressing the expression of MYB5, SEP3, and SEED FATTY ACID REDUCER 4 (SFAR4). Moreover, genetic and molecular analyses demonstrated that STK and SEP3 antagonistically regulate seed oil production and that SEP3 weakens the binding ability of STK to MYB5, SEP3, and SFAR4. Additionally, we demonstrated that TRANSPARENT TESTA 8 (TT8) and ACYL-ACYL CARRIER PROTEIN DESATURASE 3 (AAD3) are direct targets of MYB5 during seed oil accumulation in Arabidopsis. Together, our findings provide the transcriptional regulatory network antagonistically orchestrated by STK and SEP3, which fine tunes oil accumulation in seeds.

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.

Jujube witches' broom phytoplasmas inhibit ZjBRC1-mediated abscisic acid metabolism to induce shoot proliferation

Jujube witches' broom (JWB) phytoplasmas parasitize the sieve tubes of diseased phloem and cause an excessive proliferation of axillary shoots from dormant lateral buds to favour their transmission. In previous research, two JWB effectors, SJP1 and SJP2, were identified to induce lateral bud outgrowth by disrupting ZjBRC1-mediated auxin flux. However, the pathogenesis of JWB disease remains largely unknown. Here, tissue-specific transcriptional reprogramming was examined to gain insight into the genetic mechanisms acting inside jujube lateral buds under JWB phytoplasma infection. JWB phytoplasmas modulated a series of plant signalling networks involved in lateral bud development and defence, including auxin, abscisic acid (ABA), ethylene, jasmonic acid, and salicylic acid. JWB-induced bud outgrowth was accompanied by downregulation of ABA synthesis within lateral buds. ABA application rescued the bushy appearances of transgenic Arabidopsis overexpressing SJP1 and SJP2 in Col-0 and ZjBRC1 in the brc1-2 mutant. Furthermore, the expression of ZjBRC1 and ABA-related genes ZjHB40 and ZjNCED3 was negatively correlated with lateral main bud outgrowth in decapitated healthy jujube. Molecular evidence showed that ZjBRC1 interacted with ZjBRC2 via its N-terminus to activate ZjHB40 and ZjNCED3 expression and ABA accumulation in transgenic jujube calli. In addition, ZjBRC1 widely regulated differentially expressed genes related to ABA homeostasis and ABA signalling, especially by binding to and suppressing ABA receptors. Therefore, these results suggest that JWB phytoplasmas hijack the ZjBRC1-mediated ABA pathways to stimulate lateral bud outgrowth and expansion, providing a strategy to engineer plants resistant to JWB phytoplasma disease and regulate woody plant architecture to promote crop yield and quality.

MADS-box protein PpDAM6 regulates chilling requirement-mediated dormancy and bud break in peach

Bud dormancy is crucial for winter survival and is characterized by the inability of the bud meristem to respond to growth-promotive signals before the chilling requirement (CR) is met. However, our understanding of the genetic mechanism regulating CR and bud dormancy remains limited. This study identified PpDAM6 (DORMANCY-ASSOCIATED MADS-box) as a key gene for CR using a genome-wide association study analysis based on structural variations in 345 peach (Prunus persica (L.) Batsch) accessions. The function of PpDAM6 in CR regulation was demonstrated by transiently silencing the gene in peach buds and stably overexpressing the gene in transgenic apple (Malus × domestica) plants. The results showed an evolutionarily conserved function of PpDAM6 in regulating bud dormancy release, followed by vegetative growth and flowering, in peach and apple. The 30-bp deletion in the PpDAM6 promoter was substantially associated with reducing PpDAM6 expression in low-CR accessions. A PCR marker based on the 30-bp indel was developed to distinguish peach plants with non-low and low CR. Modification of the H3K27me3 marker at the PpDAM6 locus showed no apparent change across the dormancy process in low- and non-low- CR cultivars. Additionally, H3K27me3 modification occurred earlier in low-CR cultivars on a genome-wide scale. PpDAM6 could mediate cell-cell communication by inducing the expression of the downstream genes PpNCED1 (9-cis-epoxycarotenoid dioxygenase 1), encoding a key enzyme for ABA biosynthesis, and CALS (CALLOSE SYNTHASE), encoding callose synthase. We shed light on a gene regulatory network formed by PpDAM6-containing complexes that mediate CR underlying dormancy and bud break in peach. A better understanding of the genetic basis for natural variations of CR can help breeders develop cultivars with different CR for growing in different geographical regions.

ABRE-BINDING FACTOR3-WRKY DNA-BINDING PROTEIN44 module promotes salinity-induced malate accumulation in pear

Malate impacts fruit acidity and plays a vital role in stress tolerance. Malate accumulation is induced by salinity in various plants as a metabolite in coping with this stress. However, the exact molecular mechanism responsible for salinity-induced malate accumulation remains unclear. Here, we determined that salinity treatment induces malate accumulation in pear (Pyrus spp.) fruit, calli, and plantlets compared to the control. Genetic and biochemical analyses established the key roles of PpWRKY44 and ABRE-BINDING FACTOR3 (PpABF3) transcription factors in promoting malate accumulation in response to salinity. We found that PpWRKY44 is involved in salinity-induced malate accumulation by directly binding to a W-box on the promoter of the malate-associated gene aluminum-activated malate transporter 9 (PpALMT9) to activate its expression. A series of in-vivo and in-vitro assays revealed that the G-box cis-element in the promoter of PpWRKY44 was targeted by PpABF3, which further enhanced salinity-induced malate accumulation. Taken together, these findings suggest that PpWRKY44 and PpABF3 play positive roles in salinity-induced malate accumulation in pears. This research provides insights into the molecular mechanism by which salinity affects malate accumulation and fruit quality.

Twenty years of mining salt tolerance genes in soybean

Current combined challenges of rising food demand, climate change and farmland degradation exert enormous pressure on agricultural production. Worldwide soil salinization, in particular, necessitates the development of salt-tolerant crops. Soybean, being a globally important produce, has its genetic resources increasingly examined to facilitate crop improvement based on functional genomics. In response to the multifaceted physiological challenge that salt stress imposes, soybean has evolved an array of defences against salinity. These include maintaining cell homeostasis by ion transportation, osmoregulation, and restoring oxidative balance. Other adaptations include cell wall alterations, transcriptomic reprogramming, and efficient signal transduction for detecting and responding to salt stress. Here, we reviewed functionally verified genes that underly different salt tolerance mechanisms employed by soybean in the past two decades, and discussed the strategy in selecting salt tolerance genes for crop improvement. Future studies could adopt an integrated multi-omic approach in characterizing soybean salt tolerance adaptations and put our existing knowledge into practice via omic-assisted breeding and gene editing. This review serves as a guide and inspiration for crop developers in enhancing soybean tolerance against abiotic stresses, thereby fulfilling the role of science in solving real-life problems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01383-3.

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.

ABA-responsive AREB1/ABI3-1/ABI5 cascade regulates IAA oxidase gene SlDAO2 to inhibit hypocotyl elongation in tomato

Hypocotyl elongation is dramatically influenced by environmental factors and phytohormones. Indole-3-acetic acid (IAA) plays a prominent role in hypocotyl elongation, whereas abscisic acid (ABA) is regarded as an inhibitor through repressing IAA synthesis and signalling. However, the regulatory role of ABA in local IAA deactivation remains largely uncharacterized. In this study, we confirmed the antagonistic interplay of ABA and IAA during the hypocotyl elongation of tomato (Solanum lycopersicum) seedlings. We identified an IAA oxidase enzyme DIOXYGENASE FOR AUXIN OXIDATION2 (SlDAO2), and its expression was induced by both external and internal ABA signals in tomato hypocotyls. Moreover, the overexpression of SlDAO2 led to a reduced sensitivity to IAA, and the knockout of SlDAO2 alleviated the inhibitory effect of ABA on hypocotyl elongation. Furthermore, an ABA-responsive regulatory SlAREB1/SlABI3-1/SlABI5 cascade was identified to act upstream of SlDAO2 and to precisely control its expression. SlAREB1 directly bound to the ABRE present in the SlDAO2 promoter to activate SlDAO2 expression, and SlABI3-1 enhanced while SlABI5 inhibited the activation ability of SlAREB1 by directly interacting with SlAREB1. Our findings revealed that ABA might induce local IAA oxidation and deactivation via SlDAO2 to modulate IAA homoeostasis and thereby repress hypocotyl elongation in tomato.

Brassica napus Transcription Factor Bna.A07.WRKY70 Negatively Regulates Leaf Senescence in Arabidopsis thaliana

Leaf senescence is the final stage of leaf development and is essential for storage properties and crop productivity. WRKY transcription factors have been revealed to play crucial roles in several biological processes during plant growth and development, especially in leaf senescence. However, the functions of Brassica napus WRKY transcription factors in leaf senescence remain unclear. In the present study, Bna.A07.WRKY70, one paralogue of Brassica napus WRKY70, was cloned from the B. napus cultivar "Zhongshuang11 (ZS11)". We found that Bna.A07.WRKY70 contains a highly conserved WRKY domain and is most closely related to Arabidopsis thaliana WRKY70. The subcellular localization and transcriptional self-activation assays indicated that Bna.A07.WRKY70 functions as a transcription factor. Meanwhile, RT-qPCR and promoter-GUS analysis showed that Bna.A07.WRKY70 is predominantly expressed in the leaves of B. napus and rosette leaves of A. thaliana. In addition, our results demonstrated that ectopic expression of Bna.A07.WRKY70 in A. thaliana wrky70 mutants could restore the senescence phenotypes to wild-type levels. Consistently, the expression levels of three senescence-related marker genes of wrky70 mutants were restored to wild-type levels by ectopic expression of Bna.A07.WRKY70. These findings improve our understanding of the function of Bna.A07.WRKY70 in B. napus and provide a novel strategy for breeding the new stay-green cultivars in rapeseed through genetic manipulation.

PpyABF3 recruits the COMPASS-like complex to regulate bud dormancy maintenance via integrating ABA signaling and GA catabolism

Bud dormancy is essential for perennial trees that survive the cold winters and to flower on time in the following spring. Histone modifications have been reported to be involved in the control of the dormancy cycle and DAM/SVPs are considered targets. However, how the histone modification marks are added to the specific gene loci during bud dormancy cycle is still unknown. Using yeast-two hybrid library screening and co-immunoprecipitation assays, we found that PpyABF3, a key protein regulating bud dormancy, recruits Complex of Proteins Associated with Set1-like complex via interacting with PpyWDR5a, which increases the H3K4me3 deposition at DAM4 locus. Chromatin immunoprecipitation-quantitative polymerase chain reaction showed that PpyGA2OX1 was downstream gene of PpyABF3 and it was also activated by H3K4me3 deposition. Silencing of GA2OX1 in pear calli and pear buds resulted in a similar phenotype with silencing of ABF3. Furthermore, overexpression of PpyWDR5a increased H3K4me3 levels at DAM4 and GA2OX1 loci and inhibited the growth of pear calli, whereas silencing of PpyWDR5a in pear buds resulted in a higher bud-break percentage. Our findings provide new insights into how H3K4me3 marks are added to dormancy-related genes in perennial woody plants and reveal a novel mechanism by which ABF3 integrates abscisic acid signaling and gibberellic acid catabolism during bud dormancy maintenance.

Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family

Background

Alternative splicing (AS) is an important channel for gene expression regulation and protein diversification, in addition to a major reason for the considerable differences in the number of genes and proteins in eukaryotes. In plants, U2 small nuclear ribonucleoprotein B″ (U2B″), a component of splicing complex U2 snRNP, plays an important role in AS. Currently, few studies have investigated plant U2B″, and its mechanism remains unclear.

Result

Phylogenetic analysis, including gene and protein structures, revealed that U2B″ is highly conserved in plants and typically contains two RNA recognition motifs. Subcellular localisation showed that OsU2B″ is located in the nucleus and cytoplasm, indicating that it has broad functions throughout the cell. Elemental analysis of the promoter region showed that it responded to numerous external stimuli, including hormones, stress, and light. Subsequent qPCR experiments examining response to stress (cold, salt, drought, and heavy metal cadmium) corroborated the findings. The prediction results of protein–protein interactions showed that its function is largely through a single pathway, mainly through interaction with snRNP proteins.

Conclusion

U2B″ is highly conserved in the plant kingdom, functions in the nucleus and cytoplasm, and participates in a wide range of processes in plant growth and development.

Later Growth Cessation and Increased Freezing Tolerance Potentially Result in Later Dormancy in Evergreen Iris Compared with Deciduous Iris

Winter dormancy is a protective survival strategy for plants to resist harsh natural environments. In the context of global warming, the progression of dormancy has been significantly affected in perennials, which requires further research. Here, a systematic study was performed to compare the induction of dormancy in two closely related iris species with an ecodormancy-only process, the evergreen Iris japonica Thunb. and the deciduous Iris tectorum Maxim. under artificial conditions. Firstly, morphological and physiological observations were evaluated to ensure the developmental status of the two iris species. Furthermore, the expression patterns of the genes involved in key pathways related to plant winter dormancy were determined, and correlation analyses with dormancy marker genes were conducted. We found that deciduous iris entered dormancy earlier than evergreen iris under artificial dormancy induction conditions. Phytohormones and carbohydrates play roles in coordinating growth and stress responses during dormancy induction in both iris species. Moreover, dormancy-related MADS-box genes and SnRKs (Snf1-related protein kinase) might represent a bridge between carbohydrate and phytohormone interaction during iris dormancy. These findings provide a hypothetical model explaining the later dormancy in evergreen iris compared with deciduous iris under artificial dormancy induction conditions and reveal some candidate genes. The findings of this study could provide new insights into the research of dormancy in perennial plants with an ecodormancy-only process and contribute to effectively managing iris production, postharvest storage, and shipping.

Light-responsive transcription factor PpWRKY44 induces anthocyanin accumulation by regulating PpMYB10 expression in pear

Anthocyanins are a valuable source of antioxidants in the human diet and contribute to fruit coloration. In red-skinned pears, anthocyanin biosynthesis can be induced by light, in which the MYB-bHLH-WDR complex plays a critically important role in transcriptional regulation. However, knowledge of WRKY-mediated transcriptional regulation of light-induced anthocyanin biosynthesis is scarce in red pears. This work identified and functionally characterized a light-inducing WRKY transcription factor, PpWRKY44, in pear. Functional analysis based on overexpressed pear calli showed that PpWRKY44 promoted anthocyanin accumulation. Also, transiently overexpressed PpWRKY44 in pear leaves and fruit peels significantly enhanced the accumulation of anthocyanin, whereas silencing PpWRKY44 in pear fruit peels impaired induction of the accumulation of anthocyanin by light. By chromatin immunoprecipitation and electrophoretic mobility shift assay coupled to a quantitative polymerase chain reaction, we found that PpWRKY44 bound in vivo and in vitro to the PpMYB10 promoter, revealing it as a direct downstream target gene. Moreover, PpWRKY44 was activated by PpBBX18, a light signal transduction pathway component. Our results explained the mechanism mediating the impacts of PpWRKY44 on the transcriptional regulation of anthocyanin accumulation, with potential implications for fine-tuning the fruit peel coloration triggered by light in red pears.

H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple

Bud dormancy helps woody perennials survive winter and activate robust plant development in the spring. For apple (Malus × domestica), short-term chilling induces bud dormancy in autumn, then prolonged chilling leads to dormancy release and a shift to a quiescent state in winter, with subsequent warm periods promoting bud break in spring. Epigenetic regulation contributes to seasonal responses such as vernalization. However, how histone modifications integrate seasonal cues and internal signals during bud dormancy in woody perennials remains largely unknown. Here, we show that H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. The global changes in gene expression strongly correlated with changes in H3K4me3, but not H3K27me3. High expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes, key regulators of dormancy, in autumn was associated with high H3K4me3 levels. In addition, known DAM/SHORT VEGETATIVE PHASE (SVP) target genes significantly overlapped with H3K4me3-modified genes as bud dormancy progressed. These data suggest that H3K4me3 contributes to the central dormancy circuit, consisting of DAM/SVP and abscisic acid (ABA), in autumn. In winter, the lower expression and H3K4me3 levels at DAMs and gibberellin metabolism genes control chilling-induced release of dormancy. Warming conditions in spring facilitate the expression of genes related to phytohormones, the cell cycle, and cell wall modification by increasing H3K4me3 toward bud break. Our study also revealed that activation of auxin and repression of ABA sensitivity in spring are conditioned at least partly through temperature-mediated epigenetic regulation in winter.

The VvWRKY37 Regulates Bud Break in Grape Vine Through ABA-Mediated Signaling Pathways

Dormancy is a common survival strategy in plants to temporarily suspend visible growth under unsuitable conditions. The elaborate mechanism underlying bud break in perennial woody plants is gradually illustrated. Here, we identified a grape vine WRKY transcription factor, VvWRKY37, which was highly expressed in dormant buds. It was particularly induced by the application of exogenous abscisic acid, and depressed on exposure to gibberellin and low temperature (4°C) stress at the transcript level. The yeast one-hybrid assay confirmed that VvWRKY37 had a transcriptional activity. Ectopic over-expression of VvWRKY37 significantly delayed bud break of transgenic poplar plants. As an ABA-inducible gene, VvWRKY37 also depressed the expression of ABA catabolic gene CYP707As and enhanced the accumulation of endogenous ABA in transgenic poplar plants. The molecular pieces of evidence showed that VvWRKY37 preferentially recognized and bound W-box 5'-G/CATTGACT/C/G-3' cis-element in vitro. Additionally, VvABI5 and VvABF2 acted as the upstream transcriptional activators of VvWRKY37 via protein-DNA interactions. Taken together, our findings provided valuable insights into a new regulatory mechanism of WRKY TF by which it modulates bud break through ABA-mediated signaling pathways.

Whole-Transcriptome Analysis Reveals Long Noncoding RNAs Involved in Female Floral Development of Hickory (Carya cathayensis Sarg.)

Hickory, an endemic woody oil and fruit tree species in China, is of great economic value. However, hickory has a long juvenile period and an inconsistent flowering of males and females, thus influencing the bearing rates and further limiting fruits yield. Currently, it is reported that long noncoding RNAs (lncRNAs) play critical regulatory roles in biological processes. However, the role of lncRNAs in the development of hickory female flowers remains unclear. In this study, a total of 6,862 putative lncRNAs were identified from the female flower transcriptomes in three different growth stages of hickory. We proposed that lncRNAs might play an important role in phytohormone signaling processes for flower formation, especially in the abscisic acid and jasmonic acid pathways, according to the results of our Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Moreover, we predicted the interactions among four microRNAs (miRNAs), three lncRNAs, and four genes. We proposed that facing the changing environment, LNC_002115 competes with PHOSPHATE2 (PHO2) for the binding sites on cca-miR399f, and protects PHO2 from suppression. In addition, cis-acting LNC_002115 regulates the expression of the SHORT VEGETATIVE PHASE (SVP) by influencing ABRE-binding factor (ABF). In brief, LNC_002115 regulates hickory female floral development by impacting both PHO2 and SVP. This study was the first to identify lncRNAs involved in hickory female floral development, and provided new insight to elucidate how lncRNAs and their targets play a role in female floral development in hickory, thus unfolding the opportunities for functional characterization of blossom-related lncRNAs in further studies.

Overexpression of BnaAGL11, a MADS-Box Transcription Factor, Regulates Leaf Morphogenesis and Senescence in Brassica napus

Previous studies have reported that SEEDSTICK/AGAMOUS-LIKE 11 (AtSTK/AtAGL11), a MADS-box transcription factor, plays important roles in many biological processes in Arabidopsis thaliana. However, the function of BnaAGL11, an AtAGL11 homologous gene from Brassica napus, in leaf development remains unknown. Here, we found that the ectopic expression of any copy of Bna.C09.AGL11, Bna.A03.AGL11, and Bna.A09.AGL11 in A. thaliana led to smaller and curly leaves and promoted leaf senescence. Consistently, the overexpression of Bna.C09.AGL11 in B. napus also caused smaller and curly leaves and accelerated leaf senescence. Furthermore, we demonstrated that Bna.C09.AGL11 controlled leaf morphogenesis by indirectly downregulating the genes of Bna.A01.DWF4 and Bna.C07.PGX3 and promoted leaf senescence by indirectly upregulating the genes of Bna.A04.ABI5, Bna.A05.ABI5, Bna.C04.ABI5-1, and Bna.C01.SEN4 and directly activating the transcription of Bna.C04.ABI5-2 and Bna.C03.SEN4 genes. Our results provide new insights into the underlying regulatory mechanism of BnaAGL11 during leaf development in B. napus.

MADS-box transcription factors determine the duration of temporary winter dormancy in closely related evergreen and deciduous Iris spp

Winter dormancy (WD) is a crucial strategy for plants coping with potentially deadly environments. In recent decades, this process has been extensively studied in economically important perennial eudicots due to changing climate. However, in evergreen monocots with no chilling requirements, dormancy processes are so far a mystery. In this study, we compared the WD process in closely related evergreen (Iris japonica) and deciduous (I. tectorum) iris species across crucial developmental time points. Both iris species exhibit a 'temporary' WD process with distinct durations, and could easily resume growth under warm conditions. To decipher transcriptional changes, full-length sequencing for evergreen iris and short read RNA sequencing for deciduous iris were applied to generate respective reference transcriptomes. Combining results from a multipronged approach, SHORT VEGETATIVE PHASE and FRUITFULL (FUL) from MADS-box was associated with a dormancy- and a growth-related module, respectively. They were co-expressed with genes involved in phytohormone signaling, carbohydrate metabolism, and environmental adaptation. Also, gene expression patterns and physiological changes in the above pathways highlighted potential abscisic acid and jasmonic acid antagonism in coordinating growth and stress responses, whereas differences in carbohydrate metabolism and reactive oxygen species scavenging might lead to species-specific WD durations. Moreover, a detailed analysis of MIKCCMADS-box in irises revealed common features described in eudicots as well as possible new roles for monocots during temporary WD, such as FLOWERING LOCUS C and FUL. In essence, our results not only provide a portrait of temporary WD in perennial monocots but also offer new insights into the regulatory mechanism underlying WD in plants.

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.

The genome of low-chill Chinese plum 'Sanyueli' (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds

Chinese plum (Prunus salicina Lindl.) is a stone fruit that belongs to the Prunus genus and plays an important role in the global production of plum. In this study, we report the genome sequence of the Chinese plum 'Sanyueli', which is known to have a low-chill requirement for flower bud break. The assembled genome size was 282.38 Mb, with a contig N50 of 1.37 Mb. Over 99% of the assembly was anchored to eight pseudochromosomes, with a scaffold N50 of 34.46Mb. A total of 29,708 protein-coding genes were predicted from the genome and 46.85% (132.32 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in 'Sanyueli' revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of 'Sanyueli' was significantly lower than that in the dormant flower buds of the high chill requiring 'Furongli' plum. In addition, the expression of PsDAM6 was repressed by chilling treatment. The genome sequence of 'Sanyueli' plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and it is also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum.

MrTPS3 and MrTPS20 Are Responsible for β-Caryophyllene and α-Pinene Production, Respectively, in Red Bayberry (Morella rubra)

Red bayberry is a sweet, tart fruit native to China and grown widely in the south. The key organic compounds forming the distinctive aroma in red bayberry, are terpenoids, mainly β-caryophyllene and α-pinene. However, the key genes responsible for different terpenoids are still unknown. Here, transcriptome analysis on samples from four cultivars, during fruit development, with different terpenoid production, provided candidate genes for volatile organic compound (VOC) production. Terpene synthases (TPS) are key enzymes regulating terpenoid biosynthesis, and 34 TPS family members were identified in the red bayberry genome. MrTPS3 in chromosome 2 and MrTPS20 in chromosome 7 were identified as key genes regulating β-caryophyllene and α-pinene synthesis, respectively, by qRT-PCR. Subcellular localization and enzyme activity assay showed that MrTPS3 was responsible for β-caryophyllene (sesquiterpenes) production and MrTPS20 for α-pinene (monoterpenes). Notably, one amino acid substitution between dark color cultivars and light color cultivars resulted in the loss of function of MrTPS3, causing the different β-caryophyllene production. Our results lay the foundation to study volatile organic compounds (VOCs) in red bayberry and provide potential genes for molecular breeding.

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.

Genome-wide identification of Pistacia R2R3-MYB gene family and function characterization of PcMYB113 during autumn leaf coloration in Pistacia chinensis

Pistacia chinensis is known for its biodiesel production. Several varieties of this plant have leaves that produce anthocyanin, which is responsible for their reddish coloration in autumn. This reddish hue is what makes them useful as ornamental plants. However, the mechanism of anthocyanin accumulation during autumn leaf coloration remains unclear. R2R3-MYB proteins reportedly regulated anthocyanin biosynthesis in many plant species. Here, we performed a genome-wide analysis and expression profiles of R2R3-MYB transcription factor in Pistacia. A total of 158 R2R3-MYB proteins were identified and grouped into 32 clades. Combining the data from RNA-seq and qRT-PCR, one key gene, EVM0016534, was screened and identified to have the highest correlation with anthocyanin accumulation. It was named PcMYB113 due to its sequence similarity to AtMYB113 and it could bind to the promoter of PcF3H. Furthermore, ectopic expression of PcMYB113 in Arabidopsis promoted the accumulation of anthocyanin in the seed coat, cotyledon, and mature leaves, thus confirming the function of PcMYB113 in anthocyanin biosynthesis. In addition, PcMYB113 had a specifically higher expression in senesced red leaves than in mature green leaves and young red leaves in P. chinensis, thereby suggesting the potential role of PcMYB113 in promoting anthocyanin biosynthesis during autumn leaf coloration. These findings enrich our understanding of the function of R2R3-MYB genes in anthocyanin biosynthesis and autumn leaf coloration.

Regulatory circuits involving bud dormancy factor PpeDAM6

DORMANCY-ASSOCIATED MADS-BOX (DAM) genes have recently emerged as key potential regulators of the dormancy cycle and climate adaptation in perennial species. Particularly, PpeDAM6 has been proposed to act as a major repressor of bud dormancy release and bud break in peach (Prunus persica). PpeDAM6 expression is downregulated concomitantly with the perception of a given genotype-dependent accumulation of winter chilling time, and the coincident enrichment in H3K27me3 chromatin modification at a specific genomic region. We have identified three peach BASIC PENTACYSTEINE PROTEINs (PpeBPCs) interacting with two GA-repeat motifs present in this H3K27me3-enriched region. Moreover, PpeBPC1 represses PpeDAM6 promoter activity by transient expression experiments. On the other hand, the heterologous overexpression of PpeDAM6 in European plum (Prunus domestica) alters plant vegetative growth, resulting in dwarf plants tending toward shoot meristem collapse. These alterations in vegetative growth of transgenic lines associate with impaired hormone homeostasis due to the modulation of genes involved in jasmonic acid, cytokinin, abscisic acid, and gibberellin pathways, and the downregulation of shoot meristem factors, specifically in transgenic leaf and apical tissues. The expression of many of these genes is also modified in flower buds of peach concomitantly with PpeDAM6 downregulation, which suggests a role of hormone homeostasis mechanisms in PpeDAM6-dependent maintenance of floral bud dormancy and growth repression.

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.

ABA and Bud Dormancy in Perennials: Current Knowledge and Future Perspective

Bud dormancy is an evolved trait that confers adaptation to harsh environments, and affects flower differentiation, crop yield and vegetative growth in perennials. ABA is a stress hormone and a major regulator of dormancy. Although the physiology of bud dormancy is complex, several advancements have been achieved in this field recently by using genetics, omics and bioinformatics methods. Here, we review the current knowledge on the role of ABA and environmental signals, as well as the interplay of other hormones and sucrose, in the regulation of this process. We also discuss emerging potential mechanisms in this physiological process, including epigenetic regulation.

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.

Transcriptomics and targeted metabolomics reveal the regulatory network of Lilium davidii var. unicolor during bulb dormancy release

Through combined analysis of the transcriptome and targeted metabolome of lily bulbs, the possible molecular mechanism of dormancy release was revealed. Regulation of bulb dormancy is critical for ensuring annual production and high-quality cultivation. The application of low temperatures is the most effective method for breaking bulb dormancy, but the molecular mechanism underlying this response is unclear. Herein, targeted metabolome and transcriptome analyses were performed on Lilium davidii var. unicolor bulbs stored for 0, 50, and 100 days at 4 °C. Dormancy release mainly depended on the accumulation of gibberellins GA₄ and GA₇, which are synthesized by the non-13-hydroxylation pathway, rather than GA₃, and ABA was degraded in the process. The contents of nonbioactive GA₉, GA₁₅, and GA₂₄, the precursors of GA₄ synthesis, increased with bulb dormancy release. Altogether, 113,252 unique transcripts were de novo assembled through high-throughput transcriptome sequences, and 639 genes were continuously differentially expressed. Energy sources during carbohydrate metabolism mainly depend on glycolysis and the pentose phosphate pathway. Screening of transcription factor families involved in bulb dormancy release showed that MYB, WRKY, NAC, and TCP members were significantly correlated with the targeted metabolome. Coexpression analysis further confirmed that ABI5, PYL8, PYL4, and PP2C, which are vital ABA signaling elements, regulated GA3ox and GA20ox in the GA₄ biosynthesis pathway, and XERICO may be involved in the regulation of ABA and GA₄ signaling through the ubiquitination pathway. WRKY32, WRKY71, DAM14, NAC8, ICE1, bHLH93, and TCP15 also participated in the ABA/GA₄ regulatory network, and ICE1 may be the key factor linking temperature signals and hormone metabolism. These results will help to reveal the bulb dormancy molecular mechanism and develop new strategies for high-quality bulb production.

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.

Analysis of Evolution, Expression and Genetic Transformation of TCP Transcription Factors in Blueberry Reveal That VcTCP18 Negatively Regulates the Release of Flower Bud Dormancy

Plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) transcription factors have versatile functions in plant growth, development and response to environmental stress. Despite blueberry's value as an important fruit crop, the TCP gene family has not been systematically studied in this plant. The current study identified blueberry TCP genes (VcTCPs) using genomic data from the tetraploid blueberry variety 'Draper'; a total of 62 genes were obtained. Using multiple sequence alignment, conserved motif, and gene structure analyses, family members were divided into two subfamilies, of which class II was further divided into two subclasses, CIN and TB1. Synteny analysis showed that genome-wide or segment-based replication played an important role in the expansion of the blueberry TCP gene family. The expression patterns of VcTCP genes during fruit development, flower bud dormancy release, hormone treatment, and tissue-specific expression were analyzed using RNA-seq and qRT-PCR. The results showed that the TB1 subclass members exhibited a certain level of expression in the shoot, leaf, and bud; these genes were not expressed during fruit development, but transcript levels decreased uniformly during the release of flower bud dormancy by low-temperature accumulation. The further transgenic experiments showed the overexpression of VcTCP18 in Arabidopsis significantly decreased the seed germination rate in contrast to the wild type. The bud dormancy phenomena as late-flowering, fewer rosettes and main branches were also observed in transgenic plants. Overall, this study provides the first insight into the evolution, expression, and function of VcTCP genes, including the discovery that VcTCP18 negatively regulated bud dormancy release in blueberry. The results will deepen our understanding of the function of TCPs in plant growth and development.

GA3 is superior to GA4 in promoting bud endodormancy release in tree peony (Paeonia suffruticosa) and their potential working mechanism

BACKGROUND

Sufficient low temperature accumulation is the key strategy to break bud dormancy and promote subsequent flowering in tree peony anti-season culturing production. Exogenous gibberellins (GAs) could partially replace chilling to accelerate dormancy release, and different kinds of GAs showed inconsistent effects in various plants. To understand the effects of exogenous GA3 and GA4 on dormancy release and subsequent growth, the morphological changes were observed after exogenous GAs applications, the differentially expressed genes (DEGs) were identified, and the contents of endogenous phytohormones, starch and sugar were measured, respectively.

RESULTS

Morphological observation and photosynthesis measurements indicated that both GA3 and GA4 applications accelerated bud dormancy release, but GA3 feeding induced faster bud burst, higher shoot and more flowers per plant. Full-length transcriptome of dormant bud was used as the reference genome. Totally 124 110 459, 124 015 148 and 126 239 836 reads by illumina transcriptome sequencing were obtained in mock, GA3 and GA4 groups, respectively. Compared with the mock, there were 879 DEGs and 2 595 DEGs in GA3 and GA4 group, 1 179 DEGs in GA3 vs GA4, and 849 DEGs were common in these comparison groups. The significant enrichment KEGG pathways of 849 DEGs highlighted plant hormone signal transduction, starch and sucrose metabolism, cell cycle, DNA replication, etc. Interestingly, the contents of endogenous GA1, GA3, GA4, GA7 and IAA significantly increased, ABA decreased after GA3 and GA4 treatments by LC-MS/MS. Additionally, the soluble glucose, fructose and trehalose increased after exogenous GAs applications. Compared to GA4 treatment, GA3 induced higher GA1, GA3 and IAA level, more starch degradation to generate more monosaccharide for use, and promoted cell cycle and photosynthesis. Higher expression levels of dormancy-related genes, TFL, FT, EBB1, EBB3 and CYCD, and lower of SVP by GA3 treatment implied more efficiency of GA3.

CONCLUSIONS

Exogenous GA3 and GA4 significantly accelerated bud dormancy release and subsequent growth by increasing the contents of endogenous bioactive GAs, IAA, and soluble glucose such as fructose and trehalose, and accelerated cell cycle process, accompanied by decreasing ABA contents. GA3 was superior to GA4 in tree peony forcing culture, which might because tree peony was more sensitive to GA3 than GA4, and GA3 had a more effective ability to induce cell division and starch hydrolysis. These results provided the value data for understanding the mechanism of dormancy release in tree peony.

NAC Transcription Factor PwNAC11 Activates ERD1 by Interaction with ABF3 and DREB2A to Enhance Drought Tolerance in Transgenic Arabidopsis

NAC (NAM, ATAF1/2, and CUC2) transcription factors are ubiquitously distributed in eukaryotes and play significant roles in stress response. However, the functional verifications of NACs in Picea (P.) wilsonii remain largely uncharacterized. Here, we identified the NAC transcription factor PwNAC11 as a mediator of drought stress, which was significantly upregulated in P. wilsonii under drought and abscisic acid (ABA) treatments. Yeast two-hybrid assays showed that both the full length and C-terminal of PwNAC11 had transcriptional activation activity and PwNAC11 protein cannot form a homodimer by itself. Subcellular observation demonstrated that PwNAC11 protein was located in nucleus. The overexpression of PwNAC11 in Arabidopsis obviously improved the tolerance to drought stress but delayed flowering time under nonstress conditions. The steady-state level of antioxidant enzymes' activities and light energy conversion efficiency were significantly increased in PwNAC11 transgenic lines under dehydration compared to wild plants. PwNAC11 transgenic lines showed hypersensitivity to ABA and PwNAC11 activated the expression of the downstream gene ERD1 by binding to ABA-responsive elements (ABREs) instead of drought-responsive elements (DREs). Genetic evidence demonstrated that PwNAC11 physically interacted with an ABA-induced protein-ABRE Binding Factor3 (ABF3)-and promoted the activation of ERD1 promoter, which implied an ABA-dependent signaling cascade controlled by PwNAC11. In addition, qRT-PCR and yeast assays showed that an ABA-independent gene-DREB2A-was also probably involved in PwNAC11-mediated drought stress response. Taken together, our results provide the evidence that PwNAC11 plays a dominant role in plants positively responding to early drought stress and ABF3 and DREB2A synergistically regulate the expression of ERD1.

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.

Fine tuning of hormonal signaling is linked to dormancy status in sweet cherry flower buds

In temperate trees, optimal timing and quality of flowering directly depend on adequate winter dormancy progression, regulated by a combination of chilling and warm temperatures. Physiological, genetic and functional genomic studies have shown that hormones play a key role in bud dormancy establishment, maintenance and release. We combined physiological and transcriptional analyses, quantification of abscisic acid (ABA) and gibberellins (GAs), and modeling to further investigate how these signaling pathways are associated with dormancy progression in the flower buds of two sweet cherry cultivars. Our results demonstrated that GA-associated pathways have distinct functions and may be differentially related with dormancy. In addition, ABA levels rise at the onset of dormancy, associated with enhanced expression of ABA biosynthesis PavNCED genes, and decreased prior to dormancy release. Following the observations that ABA levels are correlated with dormancy depth, we identified PavUG71B6, a sweet cherry UDP-GLYCOSYLTRANSFERASE gene that up-regulates active catabolism of ABA to ABA glucosyl ester (ABA-GE) and may be associated with low ABA content in the early cultivar. Subsequently, we modeled ABA content and dormancy behavior in three cultivars based on the expression of a small set of genes regulating ABA levels. These results strongly suggest the central role of ABA pathway in the control of dormancy progression and open up new perspectives for the development of molecular-based phenological modeling.

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.