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

Multi-omics analysis of the regulatory network in winter buds of 'Cabernet Sauvignon' grapevine from dormancy to bud break

Winter dormancy and bud break are crucial to the viability, adaptability and yield of fruit trees, but not all metabolic activities or regulatory factors involved in maintaining and breaking dormancy are known. Here, winter buds, spanning from natural dormancy to bud break, were collected from 'Cabernet Sauvignon' grapevines maintained outdoors or forced indoors. The transcriptomes, proteomes and plant hormone contents were analysed across several bud stages. The winter buds presented three main stages, dormancy, dormancy release and bud development, whether grown in or outdoors. Weighted Correlation Network Analysis (WGCNA) and Gene Ontology (GO) analysis of the omics data revealed that the different stages were enriched for different biological processes. Analysis of the differentially expressed genes (DEGs) identified seven candidate genes that may affect grape dormancy and bud break. Transient transformation of these seven genes showed that VvDOGL4, VvAGL65 and VvMARD could promote maintenance of winter bud dormancy in grapevine. Subcellular localization showed that these three proteins all located to the nucleus, and yeast two-hybrid screening showed that they may interact with proteins related to plant hormone signal transduction, respiration, energy metabolism and transcription regulation to affect winter bud break in grapevine. Overall, these findings contribute to a better understanding of the regulatory dynamics of bud dormancy in a perennial fruit crop and lay a foundation for exploring key genes and regulatory mechanisms that can be manipulated to improve fruit quality and yields as the global climate shifts growing regions.

Spatiotemporally transcriptomic analyses of floral buds reveal the high-resolution landscape of flower development and dormancy regulation in peach

The spatiotemporal transcriptome dataset reported here provides the peach flower bud's gene expression atlas at spatiotemporal resolution level using the 10x Genomics Visium platform. This dataset can be used to define transcript accumulation for any interesting genes across several flower bud cells. It was generated using three peach flower bud samples during the activity-dormancy period, providing valuable insight into gene expression profiling and developmental stages under different environmental contexts or conditions. Importantly, we found that different cell types are related to specific regulatory programs, including signal transduction, environment and stress responses, and flower development. Our research provides insight into the transcriptomic landscape of the key cell types for flower buds and opens new avenues to study cell-type specification, function, and differentiation in Rosaceae fruit trees. A series of pivotal genes (e.g. AMS, MS188, MS1) for flower bud development were identified. These results provide a valuable reference for the activity-dormancy transition in perennial deciduous fruit trees.

MIKC-Type MADS-Box Gene Analysis Reveals the Role of PlSOC1 in Bud Dormancy Transition in Herbaceous Peony

The MIKC-type MADS-box (MIKC) gene family is essential for controlling various plant developmental processes, including flowering time and dormancy transitions. Although the MIKC gene family has been widely studied across different plants, its characterization and functional study in herbaceous peony remain limited. In this study, 19 Paeonia lactiflora Pall. MIKC-type (PlMIKC) genes were identified from the transcriptome of a low-chilling requirement Paeonia lactiflora Pall. cultivar 'Hang Baishao'. These MIKC genes were categorized into seven clades: six were classified as MIKCC-type, including FUL/AP1, DAM, PI, AGL18, AGL12, AG, and SOC1, and one, AGL30, was classified as MIKC*-type. Notably, the FLC clade genes were absent in Paeonia lactiflora Pall. The PlMIKC genes were predominantly localized to the nucleus, and their sequences contained highly conserved MADS and K-domains. Phylogenetic analysis demonstrated that PlMIKC genes share a strong evolutionary affinity with the MIKC genes from grapevine (Vitis vinifera) and poplar (Populus trichocarpa). A low-temperature-induced bud dormancy transition (BDT) experiment revealed that PlMIKC genes, such as PlFUL and PlDAM, were highly expressed during dormancy maintenance, while PlSOC1, PlAGL12, and PlAGL30 were upregulated during BDT. Additionally, the transient overexpression of PlSOC1 in 'Hang Baishao' significantly accelerated BDT and promoted bud break, suggesting that SOC1, traditionally linked to flowering regulation, also plays a key role in dormancy transition. Since limited literature on the MIKC gene family is currently available in herbaceous peony, this study expands the knowledge of the MIKC genes in Paeonia lactiflora Pall. and offers valuable insights into the molecular regulation of bud dormancy in response to low temperatures.

Regulatory Mechanisms of Bud Dormancy: Environmental, Hormonal, and Genetic Perspectives

Dormancy is a vital adaptive strategy in temperate and boreal plants, particularly fruit trees, enabling them to withstand harsh winter conditions and ensure survival and synchronized growth resumption in spring. This review comprehensively examines dormancy, focusing on its physiological, environmental, and molecular mechanisms. Dormancy is characterized by two distinct phases: endodormancy, which is regulated by internal plant signals and requires cold temperatures for release, and ecodormancy, which is influenced by external environmental factors. These stages are intricately linked to seasonal temperature fluctuations and the plant's ability to synchronize growth cycles, ensuring survival through harsh winters and optimal growth in warmer seasons. The review delves into the role of chilling requirements, temperature thresholds, and hormonal regulation in the dormancy process, highlighting how these factors influence critical growth events such as budbreak, flowering, and fruiting. Plant hormones, including abscisic acid, gibberellins, and cytokinins, regulate dormancy by modulating gene expression and growth activity. Additionally, we explore the historical development of dormancy research, from early observations of chilling requirements to the formulation of the chilling hours model. Considering ongoing climate change, the review examines how rising winter temperatures may disrupt dormancy cycles, potentially affecting the timing of flowering, fruiting, and overall crop productivity. This shift necessitates new strategies for managing dormancy, particularly in regions experiencing inconsistent or insufficient chilling. The review concludes by discussing practical approaches to enhance dormancy release and mitigate the impact of environmental stress on deciduous fruit tree growth, offering insights into improving agricultural practices amidst a changing climate.

Wake up: the regulation of dormancy release and bud break in perennial plants

In order to survive harsh winter conditions, perennial trees in the temperate and frigid regions enter a dormant state and cease growth in late summer after vigorous growth in spring and summer. After experiencing prolonged cold temperature and short days in winter, trees release their dormancy, and they resume growth to produce new buds in the following spring, a process known as bud break. The establishment/release of bud dormancy and bud break are crucial for the adaptations of woody plants and their survival in the natural environment. Photoperiod and temperature are key regulators in the bud dormancy and break cycle. In recent years, significant progress has been made in understanding the molecular mechanism for how photoperiod and temperature regulate seasonal growth and dormancy. Here, we summarized the regulatory network and mechanisms underlying the seasonal growth of perennial woody plants in the temperate and frigid regions, focusing on several molecular modules including the photoperiod, circadian clock, EARLY BUD BREAK 1 (EBB1) - SHORT VEGETATIVE PHASE Like (SVL) - EARLY BUD BREAK 3 (EBB3) module and hormone regulation. Through these modules, we will summarize how perennial trees release dormancy and bud break in order to better understand their differences and connections. By elucidating the interactions among these factors, we also point out the questions and challenges need to be addressed in understanding the bud dormancy and break cycle of perennial plants.

Transcriptome Analysis Provides Insights into the Safe Overwintering of Local Peach Flower Buds

During the dormant period of peach trees in winter, flower buds exhibit weak cold resistance and are susceptible to freezing at low temperatures. Understanding the physiological and molecular mechanisms underlying the response of local peach buds to low-temperature adversity is crucial for ensuring normal flowering, fruiting, and yield. In this study, the experimental materials included the conventional cultivar 'Xia cui' (XC) and the cold-resistant local resources 'Ding jiaba' (DJB) peach buds. The antioxidant enzyme activity, levels of malondialdehyde (MDA), proline (Pro), and hydrogen peroxide content (H2O2) were determined in peach buds at different dormancy periods. Transcriptome sequencing was performed at three dormancy stages: the dormancy entry stage (FD), deep dormancy release stage (MD), and dormancy release stage (RD). Additionally, transcriptome sequencing was conducted to analyze gene expression profiles during these stages. Our findings revealed that compared with XC cultivars, DJB peach buds exhibited decreased MDA and H2O2 contents but increased superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities as well as Pro content during the dormancy period. These findings suggest that cold-resistant cultivars possess significantly stronger antioxidant capacity than conventional cultivars under low-temperature stress. A total of 10,168 differential genes were annotated through transcriptome sequencing. Among them, 4975 were up-regulated while 5193 were down-regulated. The differentially expressed genes associated with low-temperature response in peach buds are primarily enriched in plant hormone signal transduction pathway and phenylpropane synthesis pathway. Key differentially expressed genes related to cold resistance include ARF2, GH3, and SAPK2, and differentially expressed transcription factors mainly belong to the AP2/ERF-ERF, bHLH, and C2H2 families. This study provides a theoretical foundation for understanding the key genes involved.

A regulatory module mediating temperature control of cell-cell communication facilitates tree bud dormancy release

The control of cell-cell communication via plasmodesmata (PD) plays a key role in plant development. In tree buds, low-temperature conditions (LT) induce a switch in plasmodesmata from a closed to an open state, which restores cell-to-cell communication in the shoot apex and releases dormancy. Using genetic and cell-biological approaches, we have identified a previously uncharacterized transcription factor, Low-temperature-Induced MADS-box 1 (LIM1), as an LT-induced, direct upstream activator of the gibberellic acid (GA) pathway. The LIM1-GA module mediates low temperature-induced plasmodesmata opening, by negatively regulating callose accumulation to promote dormancy release. LIM1 also activates expression of FT1 (FLOWERING LOCUS T), another LT-induced factor, with LIM1-FT1 forming a coherent feedforward loop converging on low-temperature regulation of gibberellin signaling in dormancy release. Mathematical modeling and experimental validation suggest that negative feedback regulation of LIM1 by gibberellin could play a crucial role in maintaining the robust temporal regulation of bud responses to low temperature. These results reveal genetic factors linking temperature control of cell-cell communication with regulation of seasonally-aligned growth crucial for adaptation of trees.

Haplotype-resolved genome of a heterozygous wild peach reveals the PdaWRKY4-PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis

Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1-specific and 2,702 Pda_hap2-specific genes, and 1,118 allele-specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non-peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1-mediated anti-aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars.

Molecular advances in bud dormancy in trees

Seasonal bud dormancy in perennial woody plants is a crucial and intricate process that is vital for the survival and development of plants. Over the past few decades, significant advancements have been made in understanding many features of bud dormancy, particularly in model species, where certain molecular mechanisms underlying this process have been elucidated. We provide an overview of recent molecular progress in understanding bud dormancy in trees, with a specific emphasis on the integration of common signaling and molecular mechanisms identified across different tree species. Additionally, we address some challenges that have emerged from our current understanding of bud dormancy and offer insights for future studies.

Deciphering the genetic mechanisms of chilling requirement for bud endodormancy release in deciduous fruit trees

Bud endodormancy in deciduous fruit trees is an adaptive trait evolved by selection for the capacity to survive unfavorable environmental conditions. Deciduous trees require a certain amount of winter chill named chilling requirement (CR) to promote bud endodormancy release. In recent decades, global warming has endangered the chill accumulation in deciduous fruit trees. Developing low-CR cultivars is a practical way to neutralize the effect of climate changes on the cultivation and distribution of deciduous fruit trees. In this review, we focus on the effect of chilling accumulation on bud endodormancy release and the genetic mechanisms underlying the chilling requirement in deciduous fruit trees. Additionally, we put forth a regulatory model for bud endodormancy and provide prospective directions for future research in deciduous fruit trees.

PPGV: a comprehensive database of peach population genome variation

Peach tree is one of the most important fruit trees in the world, and it has been cultivated for more than 7,500 years. In recent years, the genome and population resequencing of peach trees have been published continuously, which has effectively promoted the research of peach tree genetics and breeding. In order to promote the further mining and utilization of these data, we integrated and constructed a comprehensive peach genome and variation database (PPGV, http://peachtree.work/home ). The PPGV contains 10 sets of published peach tree genome data, as well as genomic variation information for 1,378 peach tree samples (the resequencing data of 1,378 samples were aligned with the high-quality genomes of Lovell, CN14 and Chinesecling, respectively, for mutation detection). A variety of useful and flexible tools, such as BLAST, Gene ID Convert, KEGG/GO Enrichment, Primer Design and Gene function, were also specially designed for searching data and assisting in breeding.

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.

Advancing tree genomics to future proof next generation orchard production

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

Genome-Wide Identification of Callose Synthase Family Genes and Their Expression Analysis in Floral Bud Development and Hormonal Responses in Prunus mume

Callose is an important polysaccharide composed of beta-1,3-glucans and is widely implicated in plant development and defense responses. Callose synthesis is mainly catalyzed by a family of callose synthases, also known as glucan synthase-like (GSL) enzymes. Despite the fact that GSL family genes were studied in a few plant species, their functional roles have not been fully understood in woody perennials. In this study, we identified total of 84 GSL genes in seven plant species and classified them into six phylogenetic clades. An evolutionary analysis revealed different modes of duplication driving the expansion of GSL family genes in monocot and dicot species, with strong purifying selection constraining the protein evolution. We further examined the gene structure, protein sequences, and physiochemical properties of 11 GSL enzymes in Prunus mume and observed strong sequence conservation within the functional domain of PmGSL proteins. However, the exon-intron distribution and protein motif composition are less conservative among PmGSL genes. With a promoter analysis, we detected abundant hormonal responsive cis-acting elements and we inferred the putative transcription factors regulating PmGSLs. To further understand the function of GSL family genes, we analyzed their expression patterns across different tissues, and during the process of floral bud development, pathogen infection, and hormonal responses in Prunus species and identified multiple GSL gene members possibly implicated in the callose deposition associated with bud dormancy cycling, pathogen infection, and hormone signaling. In summary, our study provides a comprehensive understanding of GSL family genes in Prunus species and has laid the foundation for future functional research of callose synthase genes in perennial trees.

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.