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In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. Each species and/or cultivar requires exposure to low winter temperature followed by warm temperatures, quantified as chilling and heat requirements, to remove the physiological blocks that inhibit budburst. A comprehensive meta-analysis of transcriptomic studies on flower buds of sweet cherry, apricot and peach was conducted, by investigating the gene expression profiles during bud endo- to ecodormancy transition in genotypes differing in chilling requirements. Conserved and distinctive expression patterns were observed, allowing the identification of gene specifically associated with endodormancy or ecodormancy. In addition to the MADS-box transcription factor family, hormone-related genes, chromatin modifiers, macro- and micro-gametogenesis related genes and environmental integrators, were identified as novel biomarker candidates for flower bud development during winter in stone fruits. In parallel, flower bud differentiation processes were associated to dormancy progression and termination and to environmental factors triggering dormancy phase-specific gene expression.

Background Leaves require the coordinated regulation of multiple types of cells to accumulate energy for plants. Transcriptome analysis at the tissue level cannot analyze the heterogeneity of cells or reveal the molecular regulatory mechanisms of different cell types. Recently, single-cell sequencing technology has become an important tool for analyzing cell heterogeneity, identifying rare cell populations, and drawing dynamic development tracks at a single-cell resolution. However, single-cell sequencing has not been conducted in Prunus leaf, limiting our understanding of key regulatory factors and the establishment of peach leaf cell lineages. Results In this study, we performed single-cell RNA sequencing on young leaves in two varieties of rootstock almond and cultivated red leaf winter peach. A total of 11,132 high-quality leaf cells from both varieties were divided into seven cell clusters based on reported marker genes in Arabidopsis. Potentially useful and representative markers were obtained in each cell cluster. Reconstructing the developmental trajectory of procambial cells showed that PpAPL , expressed in phloem cells, was a good candidate gene involved in phloem development. In the epidermis cell cluster, PpCER1 was found to increase the leaf wax content, thereby enhancing drought resistance in almond leaves. Conclusions Our findings reveal the heterogeneity of leaf cells and identify key regulators in peach and almond, providing a theoretical basis for peach molecular breeding to enhance drought resistance.

Leaf senescence and abscission in autumn are critical phenological events in deciduous woody perennials. After leaf fall, dormant buds remain on deciduous woody perennials, which then enter a winter dormancy phase. Thus, leaf fall is widely believed to be linked to the onset of dormancy. In Rosaceae fruit trees, DORMANCY-ASSOCIATED MADS-box (DAM) transcription factors control bud dormancy. However, apart from their regulatory effects on bud dormancy, the biological functions of DAMs have not been thoroughly characterized. In this study, we revealed a novel DAM function influencing leaf senescence and abscission in autumn. In Prunus mume, PmDAM6 expression was gradually up-regulated in leaves during autumn toward leaf fall. Our comparative transcriptome analysis using two RNA-seq datasets for the leaves of transgenic plants overexpressing PmDAM6 and peach (Prunus persica) DAM6 (PpeDAM6) indicated Prunus DAM6 may up-regulate the expression of genes involved in ethylene biosynthesis and signaling as well as leaf abscission. Significant increases in 1-aminocyclopropane-1-carboxylate accumulation and ethylene emission in DEX-treated 35S:PmDAM6-GR leaves reflect the inductive effect of PmDAM6 on ethylene biosynthesis. Additionally, ethephon treatments promoted autumn leaf senescence and abscission in apple and P. mume, mirroring the changes due to PmDAM6 overexpression. Collectively, these findings suggest that PmDAM6 may induce ethylene emission from leaves, thereby promoting leaf senescence and abscission. This study clarified the effects of Prunus DAM6 on autumn leaf fall, which is associated with bud dormancy onset. Accordingly, in Rosaceae, DAMs may play multiple important roles affecting whole plant growth during the tree dormancy induction phase.

Background Peach ( Prunus persica ) and almond (P. dulcis ) are closely related species within the Prunus genus that exhibit strikingly different fruit characteristics, particularly in mesocarp expansion and ripening behaviour. To investigate the biological processes driving these differences, we performed a comprehensive transcriptomic analysis of fruit development in the peach cultivar ‘Earlygold’, the almond cultivar ‘Texas’, and their interspecific F1 hybrid. Fruit samples were collected at three developmental stages that are key in the different ripening behaviour of peach and almond: initial phase of rapid growth (T1), cell expansion and lignification (T2), and ripening (T3). Results Global transcriptome profiling revealed almost identical expression patterns irrespective of the reference genome used for the RNA-seq analysis. We found 4,241, 3,862 and 2,922 DEGs between T1 and T2 in ‘Earlygold’, ‘Texas’ and F1 hybrid respectively, with most specific changes (55%, 76.6% and 51.3%) occurring during the first half of fruit development. Between T2 and T3, peach-type fruits continued active transcriptional regulation (2,665 DEGs in ‘Earlygold’, 2,199 in F1 hybrid), whereas almond showed limited late-stage changes (1,032 DEGs), reflecting its non-ripening phenotype. Enrichment analysis showed conserved cell division and photosynthesis-related genes enriched at T1 at both species. Peach displayed unique enrichment in pathways related to auxin signaling, DNA replication, and cyanogenic compound metabolism whereas almond for abscisic acid- and ethylene-related stress pathways. Allele-specific expression (ASE) analysis in the F1 hybrid revealed 79, 99 and 119 peach-biased ASE genes, and 27, 51 and 77 almond-biased ASE genes at T1, T2 and T3, respectively. Conclusions These findings reveal that peach and almond share conserved early developmental programs but diverge markedly from mid-development. Our data highlight auxin signaling, DNA replication, and ethylene-mediated ripening as central processes driving these developmental differences. The limited number of ASE genes and their parental bias patterns further illuminate cis-regulatory divergence between both species. This study provides new insights into the genetic regulation of fruit development in Prunus species and demonstrates a robust pipeline for cross-species transcriptomic analysis.

In plants, fruit ripening is a coordinated developmental process that requires the change in expression of hundreds to thousands of genes to modify many biochemical and physiological signal cascades such as carbohydrate and organic acid metabolism, cell wall restructuring, ethylene production, stress response, and organoleptic compound formation. In Prunus species (including peaches, apricots, plums, and cherries), fruit ripening leads to the breakdown of complex carbohydrates into sugars, fruit firmness reductions (softening by cell wall degradation and cuticle properties alteration), color changes (loss of green color by chlorophylls degradation and increase in non-photosynthetic pigments like anthocyanins and carotenoids), acidity decreases, and aroma increases (the production and release of organic volatile compounds). Actually, the level of information of molecular events at the transcriptional, biochemical, hormonal, and metabolite levels underlying ripening in Prunus fruits has increased considerably. However, we still poorly understand the molecular switch that occurs during the transition from unripe to ripe fruits. The objective of this review was to analyze of the molecular bases of fruit quality in Prunus species through an integrated metabolic, genomic, transcriptomic, and epigenetic approach to better understand the molecular switch involved in the ripening process with important consequences from a breeding point of view.

Fruit from rosaceous species collectively display a great variety of flavors and textures as well as a generally high content of nutritionally beneficial metabolites. However, relatively little analysis of metabolic networks in rosaceous fruit has been reported. Among rosaceous species, peach (Prunus persica) has stone fruits composed of a juicy mesocarp and lignified endocarp. Here, peach mesocarp metabolic networks were studied across development using metabolomics and analysis of key regulatory enzymes. Principal component analysis of peach metabolic composition revealed clear metabolic shifts from early through late development stages and subsequently during postharvest ripening. Early developmental stages were characterized by a substantial decrease in protein abundance and high levels of bioactive polyphenols and amino acids, which are substrates for the phenylpropanoid and lignin pathways during stone hardening. Sucrose levels showed a large increase during development, reflecting translocation from the leaf, while the importance of galactinol and raffinose is also inferred. Our study further suggests that posttranscriptional mechanisms are key for metabolic regulation at early stages. In contrast to early developmental stages, a decrease in amino acid levels is coupled to an induction of transcripts encoding amino acid and organic acid catabolic enzymes during ripening. These data are consistent with the mobilization of amino acids to support respiration. In addition, sucrose cycling, suggested by the parallel increase of transcripts encoding sucrose degradative and synthetic enzymes, appears to operate during postharvest ripening. When taken together, these data highlight singular metabolic programs for peach development and may allow the identification of key factors related to agronomic traits of this important crop species.

The success of vegetative propagation in woody ornamentals is strongly influenced by the physiological age and positional origin of donor shoots, yet the underlying mechanisms linking topophytic origin, hormonal dynamics, and root system quality remain unclear. This study examined adventitious rooting, root system morphology, and endogenous phytohormone profiles in basal (inner/lower crown) and terminal (outer/upper crown) leafy cuttings of Prunus subhirtella ‘Autumnalis’ from a mature 60-year-old tree. Despite similar rooting success between cutting types (66.7%), basal cuttings produced more extensive root systems, with greater total length, surface area, and numbers of tips and forks, whereas terminal cuttings formed thicker roots and a higher proportion of coarse roots (> 2 mm). Free indole-3-acetic acid (IAA) peaked at 4 hours post-severance in both types. However, terminal cuttings exhibited elevated levels of IAA conjugates and oxidative metabolites, as well as transiently higher jasmonic acid immediately after excision indicating that they exhibited stronger stress after wounding compared with basal cuttings. In contrast, the basal cuttings maintained higher indole-3-butyric acid (IBA) and distinct 4-chloro-indole-acetic acid (4-Cl-IAA) dynamics. These results suggest that differences in auxin metabolism and jasmonate dynamics shape root system morphology and quality. Integrating topophytic origin and hormonal profiling provides valuable insights for optimizing clonal propagation and improving root system performance in woody ornamentals.

The aim was to explore the alterations in growth traits, physiological and biochemical characteristics of Prunus sibirica seedlings raised from spaceflight seeds. The seedlings cultivated by the “Shenzhou XII” spacecraft carrying the seeds of superior clones of P. sibirica were used to observe their growth traits and determine physiological indicators. The results showed that plant height of Prunus sibirica seedlings raised from spaceflight seeds increased by 18–34% and internode length increased by 8–26%, but the number of primary branches, secondary branches, and leaves showed no significant change compared to the ground control. Leaf length and width of Prunus sibirica seedlings raised from spaceflight seeds were significantly higher than those of the ground control, with leaf length, width, and area increasing to 1.21–1.80 times higher than that of the ground control. Furthermore, the antioxidant and osmoregulatory capacities of P. sibirica seedlings raised from spaceflight seeds were altered. The peroxidase (POD) activity and Malondialdehyde (MDA) content were increased in ST28, ST207, and ST507, while they were reduced in ST1 and ST453. Compared with the ground control, the content of soluble sugar(SS), starch (St), and free proline (Pro) were significantly or highly significantly increased in all lines. The content of soluble protein (SP) was significantly increased in ST1, ST28, ST207, and ST507, while there was no significant change in ST453. P. sibirica seedlings raised from spaceflight seeds exhibited increased leaf pigment content, the interstitial CO 2 concentration (Ci), net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr). In conclusion, compared with the ground control, the growth indexes and physiological characteristics of Prunus sibirica seedlings raised from spaceflight seeds were changed, and the direction of change was different for different lines. This provided a foundation for subsequent germplasm improvement and variety selection.

Background Prunus sibirica L. is one of the most pivotal eco-economic tree species in China’s arid and semi-arid areas. The phenomenon of physiological fruit drop in P. sibirica L. is severe, and understanding fruit growth patterns and drop characteristics is crucial for high-quality cultivar production. However, there are few reports on P. sibirica fruit development and physiological fruit drop. Results In this study, we investigated the characteristics of fruit development, vegetative bud outgrowth, and fruit abscission, and explored the dynamic features of sugar metabolism in different tissues during physiological fruit drop and its relationship with fruit drop. The results showed that the fruit and vegetative bud outgrowth of the “Shanxing No. 1” variety exhibited an S-shaped growth pattern with three physiological stages. The flower and fruit drop of “Shanxing No. 1” lasted for about 70 days with an 89.73% total drop rate and three abscission peaks, which could be divided into the flower abscission stage mainly caused by pistil abortion, rapid fruitlet abscission stage, mainly caused by carbohydrate competition between the fruit and vegetative bud outgrowth; and slow fruit abscission stage mostly related to seed abortion. The perspective of the vegetative buds removal experiment further proved the competition between fruitlet and vegetative bud outgrowth simultaneously. During physiological fruit drop, the sugar contents and activities of sucrose metabolism enzymes in different tissues showed regular changes, corresponding to the dynamic law of fruit drop. Sucrose metabolism was mainly dominated by decomposition, and the enzymes involved in sucrose decomposition played a significant role. Acid invertase and sucrose synthase (decomposition direction) were the key enzymes regulating fruit abscission in P. sibirica L. Conclusions These results laid a foundation for revealing the physiological characteristics and physiological mechanism of P. sibirica L. fruit development, and also provided a theoretical basis for high-quality and high-yield cultivation of P. sibirica L.

Hormones are closely associated with dormancy in deciduous fruit trees, and gibberellins (GAs) are known to be particularly important. In this study, we observed that GA4 treatment led to earlier bud break in Japanese apricot. To understand better the promoting effect of GA4 on the dormancy release of Japanese apricot flower buds, proteomic and transcriptomic approaches were used to analyse the mechanisms of dormancy release following GA4 treatment, based on two-dimensional gel electrophoresis (2-DE) and digital gene expression (DGE) profiling, respectively. More than 600 highly reproducible protein spots (P<0.05) were detected and, following GA4 treatment, 38 protein spots showed more than a 2-fold difference in expression, and 32 protein spots were confidently identified according to the databases. Compared with water treatment, many proteins that were associated with energy metabolism and oxidation–reduction showed significant changes after GA4 treatment, which might promote dormancy release. We observed that genes at the mRNA level associated with energy metabolism and oxidation–reduction also played an important role in this process. Analysis of the functions of the identified proteins and genes and the related metabolic pathways would provide a comprehensive proteomic and transcriptomic view of the coordination of dormancy release after GA4 treatment in Japanese apricot flower buds.