The Defective in Induced Resistance 1 (DIR1) gene, a member of the lipid transferase proteins (LTPs), plays a crucial role in plant defense against pathogens. While previous transcriptomic studies have highlighted the significant expression of citrus LTPs during biotic stress, functional annotations of LTPs in the Citrus genera remain limited. In this study, we cloned the Murraya paniculata DIR1 (MpDIR1(t)) gene and overexpressed it in Arabidopsis thaliana to evaluate its stress response mechanisms against biotic stress. The transgenic Arabidopsis lines showed fewer disease symptoms in response to Pseudomonas syringae (Pst DC3000) compared to wild-type Arabidopsis. Defense and pathogenesis-responsive genes such as PR1, PR4, PR5, and WRKY12 were significantly induced, showing a 2- to 12-fold increase in all transgenic lines compared to the wild type. In addition, the Pst DC3000-infected transgenic Arabidopsis lines demonstrated elevated levels of flavonoids and salicylic acid (SA), along with higher expression of SA-related genes, compared to the wild type. Moreover, all transgenic lines possessed lower reactive oxygen species levels and higher activity of antioxidant defense enzymes such as superoxide dismutase, peroxidase, and catalase under Pst DC3000 stress compared to the wild type. The up-regulation of defense genes, activation of the SA pathway, accumulation of flavonoids, and reinforcement of antioxidant defense mechanisms in transgenic Arabidopsis lines in response to Pst DC3000 underscore the critical role of MpDIR1(t) in fortifying plant immunity. Thus, MpDIR1(t) constitutes a promising candidate gene for improving bacterial disease resistance in commercial citrus cultivars.

Strawberry fruit quality is linked to its phytochemical composition, yet the diversity of non-volatile terpenoids remains largely unexplored. Therefore, a comparative LC-MS/MS-based metabolomic analysis of terpenoid profiles was conducted using three commercial cultivars (Fragaria × ananassa) and a wild accession of Fragaria nilgerrensis (HM). Results from this study showed that the HM cultivar had a total terpenoid abundance 5–6 times higher than the commercial cultivars. The HM cultivar was uniquely enriched in specific triterpenoids, such as 3β,6β,19α,24-Tetrahydroxyurs-12-en-28-oic acid and 13,27-Cyclo-2,3-Dihydroxy-11,19(29)-Ursadien-28-Oic Acid, which was over 450 times higher than the ‘Danxue’ and ‘Fenyu’ commercial strawberry cultivars. Conversely, sesquiterpenoids like Alismol and Pterocarpol were 100 times lower in HM than in the commercial cultivars. This enhanced triterpenoid accumulation strongly correlated with a superior capacity to scavenge free radicals in vitro, with HM showing maximum capacity, as measured by the DPPH assay. These findings highlight the value of wild strawberry germplasm as a reservoir of biochemical diversity for breeding strawberries with enhanced functional quality.

Phenolic compounds are vital bioactive constituents in fruits, yet modern strawberry breeding has often reduced their diversity. Here, we employed a multi-omics approach integrating UPLC-MS/MS-based metabolomics and RNA-seq transcriptomics to investigate the divergence in phenolic profiles and their transcriptional regulation between a wild strawberry (Fragaria nilgerrensis, HM) and three cultivated varieties (white ‘Danxue’ (DX), pink ‘Fenyu’ (FY), and red ‘Red Face 99’ (RF)). The wild HM genotype exhibited higher antioxidant activity and a significantly more complex phenolic profile, dominated by high-abundance galloylated and benzoylated glucosides (e.g., digallic acid methyl ester, salicylic acid-2-O-glucoside) that were largely absent or depleted in cultivated fruits. In contrast, the cultivated varieties displayed specialized yet simplified profiles: DX accumulated hydroxycinnamoyl galactonic acids, FY was enriched in feruloylated glucosides, and RF was characterized by coumaroyl-glucose derivatives. Transcriptomic analysis identified a set of MYB transcription factors (e.g., FxaYL_531g0581170, FxaYL_642g0175720) significantly upregulated in wild HM, with strong correlations to key bioactive phenolics such as 4-hydroxybenzoate and salicylic acid derivatives. These findings illustrate how selective breeding has reshaped phenolic composition through alterations in MYB regulatory networks. The wild strawberry germplasm thus represents a valuable natural reservoir for biofortification strategies aimed at restoring the nutritional and functional quality of modern strawberry cultivars.

Armillaria mellea (A. mellea) serves as a crucial nutritional source for Gastrodia elata (GE) growth, and its origin directly influences the GE quality and yield. This study analyzed GE symbiotic with A. mellea from different sources using metabolomics and transcriptomics. Results demonstrated that Group A exhibited significant differences in metabolites and gene expression compared to other groups. Group A showed significantly higher accumulation of active components like gastrodin and p-hydroxybenzyl alcohol than others, but its yield was lower than Group B. Metabolomic analysis identified 2418 metabolites, while transcriptomic sequencing produced 964,110,904 clean reads, with 14,637 annotated transcripts. KEGG analysis revealed that Group A’s DEGs and DEMs were co-enriched in three key pathways, including flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant hormone signal transduction, such as the positive regulatory roles of key genes (CHS, 4CL, MYC2) on metabolites such as hesperetin, ferulate, and jasmonic acid, respectively. The coordinated upregulation of gene–metabolite interactions in Group A GE may be closely related to the accumulation of major active components, indirectly suggesting the influence of the A. mellea source on metabolic and transcriptional response differences in GE. This study, centered on the host GE, indirectly deduces the association between A. mellea and GE, providing a theoretical basis for screening high-quality “fungus-GE” combinations. Further in-depth research and validation experiments will be conducted in conjunction with fungal omics.

To investigate the effects of intercropping Morchella (morel mushrooms) between apple tree rows on fruit quality and orchard soil properties, a field experiment was conducted using a cultivation system combining plastic film mulching with small arched tunnels. Morchella was planted in the interrows of five-year-old apple trees, and after harvest, the spent mushroom substrate was returned to the soil via rotary tillage. Plots without Morchella cultivation served as the control. The experiment assessed the yield and quality of both apples and morels, as well as the overall impact on tree performance. In addition, soil physicochemical properties and enzyme activities were analyzed across the 0-40 cm soil profile at different depth intervals. The results demonstrated that: (1) Inter-cropping Morchella in apple interrows proved to be agronomically feasible, yielding a fresh mushroom production of 1333.737 g/m². Moreover, this cultivation system significantly enhanced the nutritional quality of the harvested morels, as evidenced by marked increases in crude fiber, total sugars, reducing sugars, and free amino acid contents. (2) In the 0-20 cm soil layer, the Morchella cultivated plots exhibited significantly higher natural water content compared to the control. The measured values for soil pH, alkali-hydrolyzable nitrogen, organic carbon, catalase activity, and sucrase activity were 5.46, 6.733 mg/kg, 38.303 g/kg, 411.859 μ mol/h/g, and 9.885 mg/d/g, respectively, all significantly greater than those in the control (p < 0.05). In the 20-40 cm layer, however, soil available potassium and organic carbon contents were 418.370 mg/kg and 28.453 g/kg, respectively, both significantly lower than the control (p < 0.05). Across both treatments, the values of soil pH, alkali -hydrolyzable nitrogen, organic carbon, available phosphorus, available potassium, and the activities of urease, amylase, catalase, and sucrase generally decreased with increasing soil depth. Notably, in the non-cultivated control plots, the contents of alkali-hydrolyzable nitrogen and organic carbon increased with depth. (3) Morchella intercropping significantly improved apple fruit quality, as reflected by marked increases in individual fresh weight, fruit shape index, reducing sugars, total sugars, and soluble solids content. (4) The treatment also substantially enhanced the photosynthetic performance of apple trees, with significant increases in transpiration rate, intercellular CO₂ concentration, and stomatal conductance. Collectively, our findings demonstrate that intercropping Morchella between apple tree rows confers substantial agronomic advantages. This practice not only elevates the productivity and quality of both the mushroom crop and the apples, but also ameliorates key soil physicochemical characteristics and boosts foliar photosynthesis. The cumulative positive effects highlight its considerable promise as a viable and scalable agroecological strategy.

To investigate the effects of interplanting Morchella (morel mushrooms) between rows of apple trees on orchard soil properties and apple tree performance, a field experiment was conducted using a cultivation system combining small-arch tunnels with plastic film covering. The Morchella was interplanted in a five-year-old apple orchard, with plots without Morchella cultivation serving as the control. Measurements included Morchella yield and quality, apple fruit quality, and leaf photosynthetic performance. Additionally, soil physicochemical properties and enzyme activities were analyzed across the 0–40 cm soil layer at different depths. The results demonstrated that: (1) Intercropping Morchella in apple interrows proved to be agronomically feasible, yielding a fresh mushroom production of 1333.74 g/m². Moreover, this cultivation system significantly enhanced the nutritional quality of the harvested morels, as evidenced by marked increases in crude fiber, total sugars, reducing sugars, and free amino acid contents. (2) In the 0–20 cm soil layer, the Morchella cultivated plots exhibited significantly higher natural water content compared to the control. The measured values for soil pH, alkali-hydrolyzable nitrogen, organic carbon, catalase activity, and sucrase activity were 5.46, 6.73 mg/kg, 38.30 g/kg, 411.86 μ mol/h/g, and 9.89 mg/d/g, respectively, all significantly greater than those in the control (p < 0.05). In the 20–40 cm layer, however, soil available potassium and organic carbon contents were 418.37 mg/kg and 28.45 g/kg, respectively, both significantly lower than the control (p < 0.05). Across both treatments, the values of soil pH, alkali -hydrolyzable nitrogen, organic carbon, available phosphorus, available potassium, and the activities of urease, amylase, catalase, and sucrase generally decreased with increasing soil depth. Notably, in the non-cultivated control plots, the contents of alkali-hydrolyzable nitrogen and organic carbon increased with depth. (3) Interplanting Morchella improved apple fruit quality to a certain extent, significantly increasing individual fruit fresh weight, fruit shape index, and the contents of reducing sugars, total sugars, and soluble solids. (4) Interplanting Morchella also enhanced the photosynthetic rate of apple trees to some degree, significantly increasing transpiration rate, intercellular CO₂ concentration, and stomatal conductance. Collectively, interplanting Morchella in apple orchards can produce a reasonably high yield of high-quality mushrooms, increase individual apple fruit fresh weight, improve the physicochemical properties of the 0–20 cm soil layer, and enhance the photosynthetic performance of the apple trees. These combined benefits demonstrate clear practical potential and support the promotion and application of this intercropping system in orchard production.