Apples exhibit S-RNase-mediated self-incompatibility and typically require cross-pollination in nature. ‘Hanfu’ is a cultivar that produces abundant fruit after self-pollination, although it also shows a high rate of seed abortion afterwards, which greatly reduces fruit quality. In this study, we investigated the ovule development process and the mechanism of ovule abortion in apples after self-pollination. Using a DIC microscope and biomicroscope, we found that the abortion of apple ovules occurs before embryo formation and results from the failure of sperm–egg fusion. Further, we used laser-assisted microdissection (LAM) cutting and sperm and egg cell sequencing at different periods after pollination to obtain the genes related to ovule abortion. The top 40 differentially expressed genes (DEGs) were further verified, and the results were consistent with switching the mechanism at the 5′ end of the RNA transcript (SMART-seq). Through this study, we can preliminarily clarify the mechanism of ovule abortion in self-pollinated apple fruits and provide a gene reserve for further study and improvement of ‘Hanfu’ apple fruit quality.

Grafting is widely used as a breeding method to enhance productivity and resilience. However, the mechanisms of graft healing remain poorly understood. In this study, we performed Malus domestica (‘Hanfu’) homograft and observed morphological and anatomical changes during the healing process in the graft junction within 40 days after grafting (DAG). The results showed that the healing process was divided into two phases: 0–20 days (callus proliferation phase) and 20–40 days (vascular bundle reconnection phase). During the early stage (20 DAG), gene expression exhibited asymmetry between the scion and rootstock, whereas synchronization occurred in the late stage (40 DAG). Transcriptomic and metabolomic analyses of the scion and rootstock during these two critical phases identified that differentially expressed genes (DEGs) were enriched in “Carbon fixation by Calvin cycle” and “photosynthesis-related pathways”, while differentially expressed metabolites (DEMs) were clustered in “Galactose metabolism”, implying a critical role of carbohydrates in grafting. Genes encoding enzymes involved in sugar biosynthesis, such as amylase (MdAMY), invertase (MdINV), galactinol synthase (MdGS), raffinose synthase (MdRS), and stachyose synthase (MdSS), were generally more highly expressed during Phase I than Phase II. In contrast, genes encoding enzymes related to sugar consumption, such as fructose kinases (MdSUS), cellulose synthases (MdCESA), and galacturonosyltransferase (MdGAUT), showed weak expression in Phase I but were strongly activated in Phase II. Glucose, sucrose, galactose, and melibiose levels increased significantly at 20 DAG compared with 0 DAG and subsequently decreased by 40 DAG. Exogenous application of 0.5% sucrose, raffinose, or melibiose significantly enhanced vascular bundle reconnection rates at 7 DAG compared with the control group (p < 0.01), confirming the pivotal role of sugar metabolism in graft healing.

Distant hybridization, such as between apple (Malus domestica Borkh.) and pear (Pyrus communis L.), can introduce unique genetic traits that aren’t possible through traditional hybridization methods. However, these hybrids often display maternal traits, making it difficult to visually identify hybrid offspring in the early stages. Thus, identifying these hybrids has been a longstanding challenge. To address this challenge, this study performed whole-genome resequencing of apple ‘Golden Delicious’ and pear ‘Yan Zhuang’, along with 62 of their hybrid offspring, to develop effective molecular markers. Genomic variation analysis revealed significant genetic diversity between apple and pear. By selecting markers based on notable parental differences and high polymorphism among offspring, 51 effective markers were identified from 340 apple-specific InDel markers. These markers could reliably identify the 62 offspring as distant hybrids with genetic material from both apple and pear. Among them, InDel1-7, InDel2-3, InDel3-1, and InDel4-3 proved to be the most efficient, achieving a 100% identification rate for hybrid offspring when used in combination in the ‘Golden Delicious’ × ‘Yan Zhuang’ population. Furthermore, marker universality tests showed that 88.2%, 76.5%, and 70.6% of the 51 markers were transferable to the ‘Golden Delicious’ × ‘Jin Zhui’, ‘Fuji’ × ‘Yan Zhuang’, and ‘Fuji’ × ‘Jin Zhui’ hybrid populations, respectively. The identification efficiencies in these three validation populations were 82.6%, 80.3%, and 85.0%, with the four highly efficient markers exceeding a 70% identification rate. This study developed an efficient molecular marker system for identifying apple and pear distant hybrid offspring based on InDel variation, providing a valuable tool for breeding new varieties of Rosaceae fruit trees.

Grafting is widely used as a breeding method to enhance productivity and resilience. However, the mechanisms of graft healing remain poorly understood. In this study, we performed Malus domestica (‘Hanfu’) homograft and observed morphological and anatomical changes during the healing process in the graft junction within 40 days after grafting (DAG) with focus on vascular connection between the stock and the scion traced with acid fuchsin dye. The observation showed different phases in the healing process. Phase I, from 0 to 20 DAG, involved formation and proliferation of callus, while phase II, from 20 to 40 DAG, involved reestablishment of vascular connection between the stock and the scion. In order to obtain an in-depth understanding of graft healing processes, transcriptomic and metabolomic changes were analyzed in the stock and the scion tissues at the graft junction in different phases. The transcriptomic data showed different gene expression profiles in the scion and stock in phase I, while gene expression profiles were similar between the scion and the stock during phase II, when differentially expressed genes (DGEs) (20 DAG vs 40 DAG) were highly enriched in pathway of sugar metabolism. In agreement with the transcriptomic result, there was significant difference in metabolite profile between the stock and the scion at 20 DAG, while their metabolomic difference reduced at 40 DAG. Metabolomic analysis highlighted increase in many sugars such as sucrose, glucose, raffinose and melibiose before vascular reconnection (phase I) while decrease in these sugars after vascular reconnection (phase II). Exogenous application of glucose, sucrose, raffinose and melibiose promoted vascular reconnection. The results suggest a shift from asymmetry to relative symmetry in gene expression and metabolism between the stock and the scion during the process of graft junction formation, which involves changes in sugar metabolism. Sugar accumulation is important for the healing process between the stock and the scions.

Rape is one of the most widely cultivated and highest-yielding fruit crops in the world. However, research on its precise nutrient diagnosis and fertilization theory is severely lacking, significantly restricting the development of the grape industry. In this study, an L₁₆(4⁵) orthogonal experimental design was applied to determine the effects of varying ratios of nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) on the fruit quality of ‘87-1’ grape (Vitis vinifera L.) cultivated in a facility, aiming to optimize nutrient application rates and improve fruit quality. Among the treatments T5 (N2P1K2Ca3Mg4), T14 (N4P2K3Ca1Mg4), and T9 (N3P1K3Ca4Mg2), treatment T9 had the most significant effect on single fruit weight, total soluble solids (TSS) content, fruit firmness (FF), and fruit quality index (FQI) and was conducive to the positive accumulation of the above quality indicators. Based on a comprehensive multi-factor analysis of variance, the optimal fertilization combination for achieving a high FQI was N3P1K2Ca1Mg2, corresponding to application rates of 375.0, 0, 168.8, 0, and 70.5 kg·hm⁻² for N, P₂O₅, K₂O, CaO, and MgO, respectively. Furthermore, to establish standards for multivariate compositional nutrient diagnosis (CND) and define the nutrient sufficiency range for ‘87-1’ grape fruit cultivated in a facility, the nutrient concentrations in various plant tissues and the soil and the FQI were measured across 80 treatments over five consecutive years. The nutritional status of the grapes cultivated under these treatments was calculated using the Technique for Order Preference by Similarity to Ideal Solution and the CND method. Based on the optimal nutrient ranges for high FQI sub-populations, a precise fertilization model was developed to facilitate economic fertilizer savings, quality improvement, and standardized grape cultivation in a facility.