The vegetative phase change (VPC) is precisely controlled by microRNA156 (miR156) in flowering plants. We previously showed that mature miR156 is mainly produced from MdMIR156a5 in apple (Malus domestica Borkh.) and that MdMIR156a5 expression and miR156 abundance were positively correlated with glutathione (GSH) contents during the VPC. In this study, we identified three transcription factor genes co-expressed with MdMIR156a5: the REVEILLE member MdRVE1-1, PHYTOCHROME-INTERACTING FACTOR 4 (MdPIF4), and BES1/BZR1 HOMOLOG 4 (MdBEH4). MdRVE1-1 activated MdMIR156a5 transcription by directly binding to its promoter, whereas MdBEH4 and MdPIF4 bound to the MdRVE1-1 promoter to indirectly promote MdMIR156a5 expression. MdBEH4 also directly induced MdPIF4 expression. Application of the brassinosteroid (BR) epibrassinolide or the GSH precursor 2-oxothiazolidine-4-carboxylate elevated BR and GSH contents, increased expression of MdBEH4, MdPIF4, MdRVE1-1, MdMIR156a5, and BR and GSH biosynthesis genes, and increased miR156 abundance, indicative of reciprocal promotion of GSH and BR biosynthesis and MdMIR156a5 expression. Overexpression of MdMIR156a6 in apple plants resulted in higher BR and GSH contents, higher expression of MdBEH4, MdPIF4, MdRVE1-1, MdMIR156a5, and BR and GSH biosynthesis genes, and higher miR156 abundance, defining a GSH-BR-miR156-positive feedback loop that becomes gradually attenuated during the VPC. These results establish that the MdBEH4-MdPIF4-MdRVE1-1-MdMIR156a5 module regulates miR156 abundance by integrating GSH and BR signaling pathways during the VPC in apple.

Gene therapy is hampered by low delivery efficiency and poor biosafety. Although polyethylenimine (PEI) exhibits excellent DNA condensation capability as a non-viral vector, its inherent cytotoxicity restricts clinical application. To...

The Maillard reaction is fundamental to food flavor and color, with the Amadori rearrangement as a critical branching point. Using density functional theory, this study investigated the Amadori rearrangement mechanisms between glucose and 20 amino acids, and between leucine and 10 sugars. Leucine exhibited the lowest energy barrier (93.55 kJ/mol) in the rate-determining condensation step with glucose, significantly lower than other amino acids (133.73-221.22 kJ/mol). For subsequent dicarbonyl formation, leucine maintained the lowest energy barriers across all pH conditions. Among sugars, glucose showed the lowest condensation barrier (93.55 kJ/mol) versus others (128.77-162.98 kJ/mol). Reactivity order with leucine was: glucose > lactose > xylose > erythrose > arabinose > galactose > maltose > fructose > sucrose > mannose. Based on a comparison of DFT-calculated energy barriers, this study identifies leucine and glucose as the most reactive amino acid and sugar in the Maillard reaction, providing theoretical foundations for targeted product regulation and rational selection of sugar-amino acid pairs to control flavor, color, and safety in thermally processed foods.

High night-time temperature (HNT) poses a major challenge to tomato (Solanum lycopersicum L.) growth and productivity. To elucidate the molecular basis of HNT responses, this study systematically examined the morphological and transcriptomic changes in tomato seedlings under prolonged HNT stress. We observed that HNT suppressed plant growth and chlorophyll content while triggering H2O2 accumulation in new leaves; concurrently, it promoted thermomorphogenesis-related adaptations, such as reduced leaf angles and lower leaf trichome density; traits potentially facilitating heat dissipation. Transcriptome profiling identified 4551 differentially expressed genes (DEGs), comprising 2104 up-regulated and 2447 down-regulated genes. Functional enrichment analysis revealed that up-regulated DEGs were primarily involved in glycosyl transfer, flavonoid biosynthesis, mismatch repair, and protein processing, whereas down-regulated DEGs were enriched in photosynthesis, metabolic, and immune signaling. These changes suggest a strategic trade-off, with down-regulated photosynthetic and metabolic activities potentially enabling the reallocation of resources toward stress resilience mechanisms. As a central heat shock response mechanism, the SlHSPs-SlHSFs system responded to HNT, with 10-day stress inducing distinct expression patterns of SlHSP70/90 genes alongside concurrent suppression of SlHSFs. Reverse transcription quantitative PCR (RT-qPCR) analysis unveiled a transcriptional shift in SlHSFs from an initial shock phase, marked by pronounced expression changes at 1-day HNT, to a sustained acclimation phase. Prolonged HNT also triggered gene-specific expression changes in the unfolded protein response pathway, as well as in genes involved in reactive oxygen species homeostasis and hormone signaling. In addition, it increased alternative splicing in genes associated with antioxidant defense, DNA repair, and protein processing. Collectively, these transcriptomic alterations reflect a systemic reprogramming that prioritizes energy conservation, redox homeostasis, and macromolecular stability to support nocturnal heat acclimation. Our findings provide novel insights into tomato adaptation to HNT and offer valuable genetic resources and a theoretical foundation for breeding HNT-resilient tomato varieties.

The wheat tribe Triticeae, widely known for its economic importance, is a species-diverse and polyploid-rich group in Poaceae. However, despite decades of intensive efforts, the phylogenetic relationships, genome origins, and diversification dynamics of Triticeae species remain uncertain. Here, we infer the phylogenetic and diversification patterns of Triticeae using 1,546 nuclear genes from 164 transcriptomes/genomes that represent ∼83% of the recognized genera. Our phylogeny provides robust and well-supported estimates of the relationships among diploids and polyploids, which will be indispensable for studying biodiversity and breeding innovative germplasms. Diversification dynamic analysis suggests that Triticeae has undergone continuous evolutionary diversification to varying degrees since its origin during the Miocene, with acceleration in the St-ortholog lineages, indicating asymmetric diversification patterns among the homoeologous lineages in the St-genome-containing polyploid radiation. Multiple factors, including extinct donors and nonreciprocal recombination, complicated the origin of the B and G genomes of wheat and the Y and Xm genomes of wheatgrass. Asymmetric polyploidization and mixed-ploidy introgression might have constituted an evolutionary impetus driving rapid radiation and hyperdiversity of the St-genome-containing polyploid species in Triticeae. Our results provide new insights into the evolutionary origins of Triticeae that could promote the study of other rapidly radiated lineages in terms of polyploid origin and diversification processes.

Iron (Fe) deficiency is a major limitation to apple (Malus domestica) growth in calcareous soils. Understanding the molecular mechanisms underlying Fe deficiency responses is crucial for improving Fe use efficiency in fruit trees. In this study, we identified the ETHYLENE RESPONSE FACTOR 4 (MxERF4) as a negative regulator of the Fe deficiency response in apple. Transgenic analysis revealed that overexpression of MxERF4 exacerbated leaf chlorosis and reduced root Fe content under Fe-deficient conditions, whereas RNA interference (RNAi) lines exhibited enhanced tolerance. We further identified the MITOGEN-ACTIVATED PROTEIN KINASE (MxMPK6-2) as an interactor of MxERF4. MxMPK6-2 phosphorylates MxERF4, reducing its protein stability and promoting its degradation. MxERF4 interacted with the key Fe uptake regulator FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (MxFIT) and co-localized with it in root tissues. Phosphorylation weakened the MxERF4–MxFIT interaction, thereby relieving the inhibition of MxFIT–basic Helix-Loop-Helix 38/39 (MxbHLH38/39) complex formation. This in turn restored the activation of Fe uptake genes IRON TRANSPORTER1 (MxIRT1) and FERRIC REDUCTASE OXIDASE 2 (MxFRO2), enhanced ferric chelate reductase (FCR) activity, and promoted active Fe accumulation. Together, these findings reveal a previously uncharacterized MPK6-2–ERF4 signaling module that regulates Fe deficiency responses in apple by modulating ERF4 stability and its interaction with FIT, providing insights into the molecular basis of Fe efficiency and offering potential strategies for breeding Fe-efficient rootstocks.

Abstract Arbuscular mycorrhizal (AM) fungi redistribute plant‐derived photosynthetic carbon (C) into the hyphosphere, where it mediates complex microbial interactions. This review synthesizes evidence suggesting that the hyphosphere may function as a dynamic micro‐marketplace, with fungal‐exuded C serving as a resource currency whose value is modulated by C form, lability and accessibility to different microbial guilds. We aim to integrate the surplus C hypothesis and biological market principles to propose how C acts as a resource currency and nutrient availability as its price regulator, potentially governing trade outcomes between AM fungi and soil microbes. Critically, we distinguish the hyphosphere micro‐market from classic biological market models by emphasizing that fungal C exudation is not necessarily under tight reciprocal control but rather emerges from plant source‐sink dynamics, creating a ‘capital pool’ that then enables conditional microbial transactions. Under nutrient limitation, conditional cooperative exchanges (e.g. C‐for‐P trades) can emerge though we note that such cooperation is conditional and may be less common than competitive interactions in undisturbed soils. Under C scarcity or nutrient surplus, cooperation collapses, shifting the system toward multi‐scale competition, from antagonistic interactions to network‐mediated allocation conflicts. This framework positions AM fungi as ecosystem engineers that allocate 10%–30% of host C to structure microbial communities and drive nutrient cycling, with implications for symbiotic stability and ecosystem functioning. Synthesis . Viewing the hyphosphere as a micro‐market unifies mechanisms of cooperation and competition when we explicitly recognize the market as a heuristic framework rather than assuming strict economic rationality. Future research should quantify real‐time C flows using coupled isotope tracing and microbial services to guide management of soil carbon economies for sustainable ecosystem outcomes.

As an essential regulator of abiotic stress signaling, protein phosphatase 2C (PP2C) plays a critical role in plant stress responses. However, a systematic investigation of the PP2C gene family in kiwifruit (Actinidia chinensis) remains lacking. In this study, we identified 114 AcPP2C genes from the kiwifruit genome and analyzed their physicochemical properties, chromosomal locations, evolutionary relationships, and conserved motifs. The results showed that the AcPP2C genes were non-uniformly distributed and formed clusters on 28 chromosomes. They were phylogenetically grouped into six subfamilies, with genes in each subfamily exhibiting pronounced conservation in both structure and motif composition. Analysis of cis-acting elements in the promoter regions revealed that most genes were enriched with various stress-responsive elements, suggesting the important potential function of the AcPP2C family in stress response. Transcriptome analysis and qRT-PCR indicated that AcPP2Cs responded to heat stress to varying degrees, and AcPP2C40 was significantly down-regulated. Comprehensive analysis of phenotypes and physiological indicators demonstrated that AcPP2C40 silenced plants were more heat-tolerant, which maintained significantly higher chlorophyll content and chlorophyll fluorescence parameters, while showing substantially lower accumulation of malondialdehyde (MDA) and hydrogen peroxide (H2O2), coupled with significantly enhanced activities of peroxidase (POD) and superoxide dismutase (SOD). Conversely, plants with transient overexpression of AcPP2C40 displayed increased sensitivity to heat stress, suffering more severe damage to their photosynthetic system. These results indicate that AcPP2C40 negatively regulates kiwifruit's response to heat stress. This study provides important clues for deciphering the biological functions of the PP2C gene family in kiwifruit and provides a theoretical foundation for the molecular breeding of heat-tolerant kiwifruit cultivars.

Thinopyrum elongatum (2n = 4x = 28) harbors multiple valuable resistance genes and serves as a valuable genetic resource for wheat improvement. Yr1EL was primarily identified on chromosome arm 1EL of tetraploid Th. elongatum, conferring adult-plant resistance to stripe rust. To further map and utilize Yr1EL, we introduced chromosomal rearrangements by crossing the wheat–tetraploid Th. elongatum 1E(1D) substitution line and the T1BS·1EL translocation line with the common wheat Chinese Spring ph1b mutant. In total, eight wheat–Th. elongatum chromosome 1E structural variants were identified by in situ hybridization, the GenoBaits®WheatplusEE panel, and molecular markers. These variants include one large segment translocation, one terminal fragment deletion, one chromosome 1E insertion translocation, and five chromosome 1EL terminal small fragment translocations. Based on phenotyping and genotyping of these variant lines, Yr1EL was mapped to an approximately 20.91 Mb physical interval (532.45 to 553.35 Mb) on the distal long arm of chromosome 1E corresponding to the diploid Th. elongatum reference genome. Genetic analysis confirmed that stripe rust resistance was conferred by the Yr1EL locus with incomplete dominance. Five codominant molecular markers co-segregated with the Yr1EL locus and will facilitate marker-assisted selection. Furthermore, collinearity analysis showed that this interval is structurally conserved among Triticeae species, and 29 candidate genes potentially related to disease resistance were annotated. Those candidates included receptor-like proteins, kinases, nucleotide-binding and leucine-rich repeat receptors, and other disease resistance proteins. The adult-plant resistance gene Yr1EL expands the wheat disease-resistance gene pool and provides valuable germplasm for breeding durable stripe rust-resistant cultivars.

Soil waterlogging threatens global wheat production by inducing root hypoxia. While stress priming can enhance plant resilience, the specific mechanisms underlying this pre-adaptation remain poorly understood. Here, we demonstrate that a single day of mild waterlogging priming (MP) induces a robust primed state in wheat, conferring superior recovery and tolerance to subsequent hypoxic stress. Crucially, we identify the post-priming recovery phase as a decisive window for physiological reprogramming, rather than a mere period of passive repair. During this window, MP plants developmentally reconstruct their adventitious roots (ARs) system, transitioning from transient, short ARs to a persistent architecture dominated by long ARs. This reprogrammed root system exhibits functionally superior through the synergistic co-optimization of root hydraulic conductivity (Lpr) and radial oxygen loss (ROL). Physiological and molecular analyses reveal that enhanced Lpr is accompanied by the sustained upregulation of aquaporin genes (TaTIP2-1, TaTIP2-2, and TaPIP2-6), while improved ROL facilitates superior root rhizosphere aeration. Structural equation modeling statistically validates that the formation of long ARs during recovery is the pivotal trait causally driving the optimization of Lpr and ROL. In contrast, severe priming causes irreversible damage and confers no adaptive benefit. Our findings propose a model of “anticipatory root priming”, wherein mild stress leverages the recovery window to pre-construct an energetically efficient root system. This fundamentally shifts the plant’s strategy from a reactive emergency response to proactive, regulated resilience, providing a physiological framework for priming-based crop improvement.

Strigolactones (SLs) are a class of plant hormones essential for tiller development and yield under diverse environmental conditions. Drought is a major limiting factor for rice yields. Although SLs contribute to drought resistance, mechanisms and practical applications of SL pathway in drought acclimation of rice remain poorly understood. Our study shows that short-term dehydration represses SL biosynthesis in rice roots. Genetic assays indicate that disruption of SL biosynthesis or signaling elevates rice drought resistance, whereas SL signaling activation or supplementation with the SL analog GR244DO impairs drought resistance. SLs negatively regulate drought acclimation by promoting degradation of the repressor protein DWARF53 (D53). D53 interacts with the transcription factor OsWRKY31 via its N-terminal domain and suppresses the protein level of OsWRKY31, which binds to and represses transcription of the ZFP36 promoter. ZFP36 encodes a zinc-finger transcription factor that promotes H2O2 scavenging to sustain reactive oxygen species (ROS) homeostasis during drought stress. Notably, the drought-resistant upland rice variety IRAT109 exhibits lower SL levels in root exudates than the lowland rice variety Nipponbare (NP). Genome editing of key components in SL pathway enhances drought resistance in NP, Huazhan (HZ), and IRAT109. The agronomic potential of tuning SL biosynthesis is further supported by the elite D17/HTD1 allele, which weakens SL biosynthesis and improves drought resistance and grain yield in Nekken 2 (NK2) under field conditions. These findings uncover a key mechanism underlying SL-repressed drought acclimation in rice and provide an effective strategy to improve drought resistance in diverse rice varieties amid ongoing climate change.

Background: The Camellia genus is widely recognized for its remarkable diversity in floral morphology and coloration, with Camellia petelotii (Merr.) Sealy being particularly notable for its rare golden-yellow flowers, which possess exceptional ornamental value. Despite its horticultural significance, the molecular mechanisms governing its flowering process remain poorly elucidated, presenting a substantial barrier to effective conservation and breeding initiatives. Methods: To address this knowledge gap, we conducted a comprehensive transcriptomic analysis, focusing on three distinct developmental stages of C. petelotii floral organs: the alabastrum stage (S1), the half-opened flower stage (S2), and the full bloom stage (S3). These samples were subjected to high-throughput sequencing using the Illumina platform. Following rigorous quality control and alignment with the reference genome, we performed transcript assembly and integrated comprehensive gene annotation data with quantitative gene expression profiles. Results: Our analysis identified 18,732 differentially expressed genes (DEGs) showing significant expression changes across developmental stages. Notably, we identified 134 DEGs as potential flowering-related genes, which were functionally associated with key pathways involved in floral regulation, including plant hormone signal transduction (e.g., AUX/IAA, ARF, SAUR, GH3, JAR4, GID1 and SOC1), starch (SS, SUS, BAM) and sucrose metabolism (HK, FrK, and GH32), circadian rhythm regulation (e.g., PIF3, ELF3, LHY, and PRR), and the Autonomous pathway. Building upon these findings, we have proposed a comprehensive model illustrating the regulatory network underlying flowering transition in C. petelotii. The reliability of the transcriptomic data was demonstrated through the validation of 11 genes using quantitative real-time PCR (qRT-PCR). Conclusions: These insights not only enhance our understanding of the molecular basis of flowering in this species but also provide a valuable theoretical framework for future genetic improvement and breeding programs of C. petelotii.

Apple Glomerella leaf spot (GLS), a major fungal disease, severely threatens the sustainable development of the apple industry and causes significant yield and quality losses. Enhancing host resistance through grafting is a promising strategy against GLS (caused by Colletotrichum fructicola); however, the underlying molecular mechanisms remain unclear. In this study, detached-leaf inoculation, grafting, and RT-PCR assays were integrated to confirm that rootstock-derived mobile mRNAs can significantly enhance scion resistance to GLS. Using six apple genotypes (‘Gala’, ‘Royal Gala’, Malus xiaojinensis, Malus hupehensis Rehd. var. pingyiensis Jiang, G935, M9-T337), we evaluated detached-leaf resistance and constructed grafting combinations. Resistant rootstocks were found to elevate resistance in susceptible scions by modulating leaf enzyme activities (POD, CAT, SOD) and lignin content. Importantly, we identified the CC-NBS-LRR (CNL) gene MdNRG1.1 as a mobile mRNA that translocates from rootstock to scion in specific grafting combinations (GL/G935 and GL/Mh), providing a mechanistic explanation for the enhanced resistance. This study establishes a theoretical basis for breeding resistant rootstocks and developing sustainable disease control strategies.

Salt stress imposes osmotic imbalance and ion toxicity, severely impairing crop growth and development. Na⁺/H⁺ antiporters (NHXs) play a central role in salt tolerance by mediating sodium transport across cellular membranes. We conducted a genome-wide characterization of the NHX gene family in four hexaploid oat cultivars, identifying 126 NHX genes. These were grouped into 33 orthologous gene groups (OGGs), comprising 10 core and 23 dispensable OGGs. The naked oat cultivar ‘Sanfensan (SFS)’ contained the largest number of both total and core NHX genes. Phylogenetic analysis classified AsNHX genes into three classes: vacuolar (Vac-class), endosomal (Endo-class), and plasma membrane (PM-class). Ka/Ks analysis indicated strong purifying selection across most members. Cis-regulatory element analysis revealed abundant stress-related motifs, including abscisic acid (ABA) and methyl jasmonate (MeJA) response elements, suggesting roles in abiotic stress adaptation. Transcriptome and qRT-PCR data confirmed that AsNHX1/3/7/9/14/23/24/25/32 were up-regulated under salt stress, highlighting their importance in salinity tolerance. This study provides the first comprehensive characterization of the AsNHX gene family, detailing their evolutionary, structural, and functional features. The findings offer critical insights into salt adaptation mechanisms in oat and identify promising targets for genetic improvement of salinity tolerance.

The colored calla lily, a member of the genus Zantedeschia in the Araceae family native to South Africa, is a valuable ornamental plant. However, the lack of a high-quality genome has hindered genetic analysis and the identification of key trait-related genes. We successfully assembled a haplotype-resolved genome of the colored calla lily, revealing extensive heterozygosity between homologous chromosomes. Comparative genomics analyses demonstrated that transposon insertions have led to significant differences in genome size among Araceae species. Notably, Araceae species experienced two closely-spaced whole-genome duplication (WGD) events before species divergence. Further analysis revealed that in terrestrial True Araceae species, genes associated with lignin synthase, cellulose synthase, expansin, and sugar transport proteins have undergone expansion, likely contributing to environmental adaptation and tuber starch accumulation. Additionally, we identified a key MIKCC gene that may play a crucial role in spathe development. This study not only elucidates the evolutionary history of Araceae species but also provides valuable data to support functional genomics research and breeding efforts for the colored calla lily.

Sweet cherry (Prunus avium) contains abundant nutrients and is highly favored by consumers. However, cold stress severely limits its growth and development. Transcription factor AP2/ERF plays a crucial role in plant responses to abiotic stress. In this study, a total of 126 PavERF genes were identified in sweet cherry, and their gene structures, conserved motifs were analyzed using TBtools-II software. 23 collinearity events occurred within the PavERF gene members of sweet cherry, and 102 collinearity events were found between sweet cherry and Arabidopsis. Cis-element analysis indicated that AP2/ERF contained a variety of hormone- and stress-responsive elements. qRT-PCR analysis showed that PavERF responded to low-temperature stress to varying degrees, with PavERF45 being the most significantly upregulated. Transient overexpression of PavERF45 was achieved in transgenic tobacco via Agrobacterium-mediated genetic transformation, and its function was verified under cold stress. Under cold stress, tobacco plants overexpressing PavERF45 had lower relative conductivity (REC) than wild type (WT), while chlorophyll (Chl) content and SPAD value were higher than those of WT. Lower reactive oxygen (ROS) accumulation and higher ROS scavenger enzyme activities were noticed in OE-PavERF45 plants. This study provides insights into the functional roles of AP2/ERF in the cold stress response of sweet cherry.

Cadmium (Cd) contamination in farmland soils severely threatens wheat productivity and human health via food chain transmission. Although ATP-binding cassette (ABC) transporters are known to participate in heavy metal uptake and detoxification in plants, the genetic mechanisms coordinating Cd uptake, root retention and long-distance translocation in wheat remain poorly understood. In this study, we identified the wheat ABC transporter ABCG42 as a key regulator of Cd bioaccumulation and partitioning by regulating cell wall sequestration and interacting with ABA-, stress- and ripening-induced protein 1 (ASR1). Knockout of ABCG42 reduced Cd retention in root cell walls, thereby decreasing root Cd uptake and root-to-shoot translocation. Conversely, ABCG42 overexpression enhanced Cd sequestration in root cell walls and reduced Cd translocation to shoots, revealing a dual role of ABCG42 in promoting root Cd uptake and limiting long-distance Cd transport. Unlike previously reported plasma‑membrane‑localized ABCG homologs that extrude Cd out of plant cells, this ER‑resident transporter facilitates root cell‑wall Cd sequestration. ABCG42 physically interacted with ASR1, and both proteins were co-localized to the endoplasmic reticulum (ER). ABCG42 overexpression upregulated ASR1 expression and increased abscisic acid (ABA), salicylic acid (SA), and gibberellic acid (GA) levels under Cd stress. Transcriptomic and proteomic analyses revealed that the ABCG42-ASR1 module modulates Cd tolerance by regulating hormone signaling, mitogen-activated protein kinase (MAPK) cascades, and antioxidant enzyme activity. Our findings elucidate a novel molecular module that integrates Cd transport and ABA signaling to coordinate wheat Cd tolerance and accumulation. Collectively, these findings establish ABCG42 as a key genetic determinant of wheat Cd uptake and partitioning, providing a mechanistic basis for developing genetic strategies to mitigate Cd accumulation and reduce Cd entry into the food chain.