Frontiers In Plant Science[JOURNAL]
Sun
200 papers
Machine-learning-assisted comparative analysis of rice growth and yield formation in field and plant factory systems.
Yang Y, Yang J, Lu J … +5 more , Tao Y, Xie J, Zhang T, Wang S, Yang Q
Front Plant Sci · 2026 · PMID 42394673 · Full text
INTRODUCTION: Plant factories provide a controlled platform for rice cultivation and rapid breeding, yet the effects of controlled environments on rice growth and yield formation remain poorly understood relative to fiel...
INTRODUCTION: Plant factories provide a controlled platform for rice cultivation and rapid breeding, yet the effects of controlled environments on rice growth and yield formation remain poorly understood relative to field conditions. METHODS: This study systematically compared growth duration, plant architecture, root and leaf traits, biomass accumulation, yield components, and environmental dynamics of three representative rice cultivars grown under field and plant factory conditions. Logistic model fitting was used to characterize plant height growth dynamics, and five machine learning models were further applied to predict plant height and assess the relative importance of growth- and environment-related variables. RESULTS: The results showed that a plant factory shortened the average growth duration from 138 to 95 days compared with field cultivation and promoted early vegetative development, including stronger tillering, larger total leaf area, longer roots, and greater fresh biomass accumulation. It also increased the total panicles per unit area and the grain number per panicle, whereas seed-setting rate, 1000-grain weight, and final grain yield were not significantly increased. The machine learning models achieved high predictive accuracy for plant height (R>0.9), with growth duration as the dominant predictor in both systems, followed by CO concentration in the plant factory and cultivar in the field. DISCUSSION: These findings reveal that controlled-environment cultivation reshapes rice developmental rhythm and vegetative-reproductive allocation, providing a physiological basis for understanding rice plasticity and optimizing plant factory-based rice production.
TomatoweedDet: a real-field multi-class weed detection dataset and YOLO benchmark for tomato production systems.
Sevinç AM, Yıldırım ÇV, Ağırman AK
Front Plant Sci · 2026 · PMID 42394672 · Full text
This study presents an approach for the object detection of multiple weeds in tomato production systems based on deep learning. A comprehensive dataset has been collected in three provinces of Türkiye (Balıkesir, Ankara,...
This study presents an approach for the object detection of multiple weeds in tomato production systems based on deep learning. A comprehensive dataset has been collected in three provinces of Türkiye (Balıkesir, Ankara, and Aksaray) under real-world field conditions. The data set has 32,607 images and 44,165 bounding boxes annotations. The two weed species included in the dataset are, to our knowledge, underrepresented in the current deep learning-based agricultural object detection literature. Drone and smartphone cameras took pictures at different times of the day (morning, noon, and afternoon) of different soil textures, light levels, and weather conditions, such as rain, mud, and shadows. The dataset reflects agricultural diversity as it exists in the real world, unlike previous studies that relied on controlled experimental environments. The model was trained using YOLO-based deep learning algorithms within the PyTorch framework. The metrics Precision, Recall, mAP@0.5, and mAP@[0.5:0.95] were used to evaluate the performance of the models. In this study, seven different YOLO architectures were comparatively evaluated on the TomatoWeedDet dataset created under real field conditions. The results show that the YOLOv8l model demonstrates high performance in the multi-class weed detection task and has significant potential for precision weed management applications. The model that was created could be used in mobile or embedded systems to monitor weeds in real time with drones. The proposed system enables targeted herbicide application and less use of chemicals. This study advances research on weed detection using deep learning. It also helps to make precision and sustainable farming systems a reality.
Genomic advances in orphan and underutilized Brassicaceae crops and their wild relatives.
Amas J, Natarajan RK, Thomas WJW … +3 more , Edwards D, Batley J, Dolatabadian A
Front Plant Sci · 2026 · PMID 42394671 · Full text
Orphan Brassicaceae crops, alongside other underutilized species and their wild relatives, represent an important but underexploited reservoir of genetic diversity with potential to enhance crop resilience, nutritional q...
Orphan Brassicaceae crops, alongside other underutilized species and their wild relatives, represent an important but underexploited reservoir of genetic diversity with potential to enhance crop resilience, nutritional quality, and sustainable agriculture. These taxa include emerging oilseed, leafy vegetable, industrial, medicinal and stress-adapted species that harbor valuable traits such as tolerance to abiotic stresses, resistance to pests and diseases, improved seed and oil quality, and specialized bioactive compounds. Despite their potential, many of these species have received limited investment in breeding and genetic improvement compared to major Brassica crops. Recent advances in genomics and high-throughput sequencing have accelerated the development of genomic resources across Brassicaceae species, including chromosome-level genome assemblies, pan-genomes, and transcriptomic atlases. These resources have provided insights into genome evolution, gene family expansions, sub-genome dominance, and regulatory networks underlying key adaptive and agronomic traits. The increasing availability of genomic datasets has enabled molecular breeding approaches such as marker-assisted selection, genome-wide association studies, genomic selection, and genome editing. The close evolutionary relationships among Brassicaceae species further facilitate the transfer of knowledge and introgression of beneficial alleles from orphan and underutilized crops, as well as wild relatives, into cultivated Brassica species. Integration of genomic, transcriptomic, and multi-omics datasets enables the identification of candidate genes and regulatory pathways, guiding targeted breeding and accelerating the development of climate-resilient, nutrient-dense crops. This review highlights recent progress, challenges, and prospects for genomics-enabled breeding in orphan and underutilized Brassicaceae crops and their wild relatives.
Delayed sowing limits grain number per spike in wheat by restricting young spike differentiation through reduced photothermal resources.
Tian W, Wang J, Yu S … +6 more , Akesumu A, Zhang Z, Dong R, Wang J, Shi S, Zhang J
Front Plant Sci · 2026 · PMID 42394670 · Full text
Delayed sowing has become increasingly common in wheat production, yet the key developmental processes underlying the reduction in grain number per spike remain poorly understood, particularly the relationships among pho...
Delayed sowing has become increasingly common in wheat production, yet the key developmental processes underlying the reduction in grain number per spike remain poorly understood, particularly the relationships among photothermal resources, young spike differentiation, and spike formation. In this study, a two-year field experiment was conducted with five delayed sowing-date treatments at 15-day intervals, and accumulated temperature, actual sunshine duration, and total solar radiation during young spike differentiation were integrated with the overall morphology of young spikes, spikelet/floret primordium differentiation, mature spike structure, and grain number per spike for analysis. The results showed that, as sowing was delayed, young spike differentiation was generally postponed and its duration was markedly shortened, while accumulated temperature, actual sunshine duration, and total solar radiation continuously declined. These changes were accompanied by restricted development of young spike morphology (length, width, and lateral width), reduced differentiation of spikelet and floret primordia, impaired formation of mature spike structure (length, width, and lateral width), and decreases in grain number per spike, including spikelet number, floret number, and fertility, as well as grain weight per spike. These stress effects became stronger with further delays in sowing. Further integrated analysis showed that the decline in grain number per spike under delayed sowing was consistent with a continuous association pathway of "reduced photothermal resources → restricted young spike development → impaired spike formation → decreased grain number per spike." Among these processes, young spike development was the key link connecting environmental changes with grain number per spike formation, and the decrease in actual sunshine duration showed the strongest statistical association with the reduction in grain number per spike. These findings indicate that the restricted formation of grain number per spike under delayed sowing is closely associated with changes in young spike development and mature spike formation, and they provide a basis for stabilizing wheat yield management under delayed sowing conditions.
Deterministic assembly and centralized networks define the rhizosphere mycobiota.
Wang H, Zhang M, Chen L … +4 more , Lin J, Li S, Zhao L, Dou P
Front Plant Sci · 2026 · PMID 42394669 · Full text
INTRODUCTION: The rhizosphere serves as the most active interface for plant-soil microbial interactions. Resource inputs and micro-environmental gradients within this zone are expected to drive the selective recruitment...
INTRODUCTION: The rhizosphere serves as the most active interface for plant-soil microbial interactions. Resource inputs and micro-environmental gradients within this zone are expected to drive the selective recruitment and structural reorganization of fungal communities. However, systematic evidence regarding the divergence patterns and assembly mechanisms between rhizosphere and bulk soil fungal communities in coniferous forests in subtropical area remains limited. METHODS: In this study, we collected 44 soil samples (rhizosphere and bulk soil) from plantations. Fungal amplicon sequencing was conducted, integrated with indicator taxa analysis, -diversity comparisons, null model frameworks (Normalized Stochasticity Ratio, NST), and co-occurrence network topological analysis to resolve the fungal communities "composition-assembly-structure" variations across these two microhabitats. RESULTS: A total of 2,398 fungal ASVs were identified. While the majority of taxa were shared between habitats, the community composition exhibited significant differentiation: the rhizosphere was relatively enriched with Ascomycota and Mortierellomycota, whereas Basidiomycota predominated in the bulk soil. Multiple potential bioindicators were identified for each niche. Although α-diversity indices showed no significant differences between microhabitats, -diversity revealed a distinct separation in community structure, and with higher inter-sample heterogeneity observed in the rhizosphere. NST analysis indicated that fungal assembly in the rhizosphere was predominantly governed by deterministic processes, while stochastic processes played a more dominant role in the bulk soil. Co-occurrence networks further demonstrated that both microhabitats possessed highly modular structures. However, the bulk soil network was more complex and highly connected, whereas the rhizosphere network was more centralized with a more uneven distribution of nodal connections. DISCUSSION: These findings provide comparative evidence for the divergence in fungal community assembly and network organization in subtropical coniferous forests, offering valuable insights for the assessment and management of forest soil health from a microbial perspective.
Cover cropping enhances fruit quality in protected citrus cultivation by modulating rhizosphere microbiome and iron availability.
Deng L, Pan Y, Li H … +7 more , Wu L, Wang C, Liu D, Zhang J, Cheng J, Song F, Pan Z
Front Plant Sci · 2026 · PMID 42394668 · Full text
INTRODUCTION: Citrus is one of the most widely cultivated fruit trees worldwide, and protected cultivation has become increasingly prevalent in recent years. Cover cropping improves orchard soil health, yet its mechanism...
INTRODUCTION: Citrus is one of the most widely cultivated fruit trees worldwide, and protected cultivation has become increasingly prevalent in recent years. Cover cropping improves orchard soil health, yet its mechanisms in protected citrus cultivation remain unclear. This study investigated how white clover ( L.) and ryegrass ( L.) affect soil properties, rhizosphere microbiota, and fruit quality in greenhouse-grown 'Kanpei' citrus through integrated analyses of soil physicochemical properties, high-throughput amplicon sequencing, and microbial isolation. RESULTS: Both cover crops significantly increased total soluble solids (TSS) and vitamin C levels in mature fruits. Ryegrass enhanced the availability of nitrogen, phosphorus, calcium, magnesium, and manganese, whereas white clover more effectively acidified the soil and increased iron (Fe) availability. Each cover crop distinctively altered the rhizosphere microbial community. Notably, white clover specifically enriched Pseudomonas, which strongly correlated with elevated soil available Fe, TSS, and vitamin C. Screening with Chrome Azurol S (CAS) agar identified Pseudomonas as the dominant siderophore-producing genus. Inoculation with a representative strain, sp. PA9, significantly enhanced Fe uptake, chlorophyll content, and fruit quality, offering insights into its potential role in promoting fruit quality under protected cultivation. CONCLUSIONS: This work provides a comprehensive understanding of how white clover promotes fruit quality via fostering siderophore-producing Pseudomonas that enhance Fe mobilization, suggesting new avenues for developing microbiome-based management strategies in protected citrus cultivation. These findings underscore the potential of cover crop-mediated microbial recruitment in advancing sustainable citrus production and soil health improvement.
MSDF-Net: a cross-version lightweight detection framework based on deformable convolution and high-resolution feature enhancement for pine wilt disease.
Xiao X, Lin Y, Wang S … +2 more , Lin H, Wang F
Front Plant Sci · 2026 · PMID 42394667 · Full text
INTRODUCTION: Early and precise identification of pine wilt disease is critical for effective control. However, early-stage lesions are extremely small, sparse, and scattered, making them highly susceptible to being obsc...
INTRODUCTION: Early and precise identification of pine wilt disease is critical for effective control. However, early-stage lesions are extremely small, sparse, and scattered, making them highly susceptible to being obscured by noise in complex forest backgrounds. Moreover, feature simplification in lightweight deployment further leads to the loss of critical pathological information. METHODS: We propose MSDF-Net, a lightweight object detection framework that integrates a high-resolution P2 detection layer for enhanced small-target sensitivity, DCNv4-based deformable convolution for adaptive modeling of irregular spatial patterns, an EMA attention mechanism for background suppression, and a dual-branch C2f DualConv module for efficient multi-scale feature fusion. The model was evaluated on a cross-regional dataset spanning three provinces and two pine species. RESULTS: MSDF-Net achieves an mAP@0.5 of 80.1%, outperforming the YOLOv8n baseline by 5.1 percentage points while maintaining 2.67M parameters and 11.7 GFLOPs. The most substantial improvement occurs in early-stage disease detection (PWD-E), with an AP gain of 20.2 percentage points. Cross-version validation on YOLOv11n, YOLOv12n, and YOLOv13n yields consistent improvements of 6.1, 4.3, and 5.1 percentage points in mAP@0.5, respectively. DISCUSSION: Given its effectiveness across multiple YOLO versions and ecological conditions, MSDF-Net provides a generalizable solution with low parameter count and moderate computational complexity, making it a promising candidate for future UAV edge deployment pending on-device validation.
Autophagy in plants: molecular mechanisms and roles in abiotic stress responses.
Lv Q, Soltani A, Lei M … +1 more , Ma G
Front Plant Sci · 2026 · PMID 42394666 · Full text
Autophagy is an evolutionarily conserved catabolic pathway that maintains cellular homeostasis by degrading and recycling cytoplasmic components in the vacuole or lysosome. In plants, this process is indispensable for nu...
Autophagy is an evolutionarily conserved catabolic pathway that maintains cellular homeostasis by degrading and recycling cytoplasmic components in the vacuole or lysosome. In plants, this process is indispensable for nutrient remobilization and stress acclimation, clearing dysfunctional organelles, protein aggregates, and other cytoplasmic material. This review covers current knowledge of plant autophagy, beginning with the core ATG (autophagy-related) machinery and the mechanisms of selective cargo recognition mediated by receptors such as NBR1 and the ATG8 protein family, then extending to organelle-specific degradation pathways including chlorophagy, mitophagy, and ER (endoplasmic reticulum)-phagy. We examine how autophagy supports plant survival under adverse conditions with attention to the regulatory networks governing autophagic activity, including the antagonistic TOR (Target of Rapamycin) and SnRK1 (Sucrose Non-Fermenting Related Kinase 1) kinase pathways that act as central nutrient and energy sensors. Collectively, these findings establish autophagy not merely as a cellular housekeeping mechanism, but as a central regulatory hub that coordinates plant growth with environmental adaptation, with important implications for engineering stress-resilient crops.
Nanoparticle-modified fishpond sediments improve metal immobilization, redox homeostasis, and stress tolerance in under multi-metal exposure.
Zhu Y, Ahmed W, Mahmood M … +5 more , Bundschuh J, Akmal M, Tan L, Mehmood S, Li W
Front Plant Sci · 2026 · PMID 42394665 · Full text
Roots represent the primary interface for sensing and responding to complex soil environments, where cytoskeletal networks play a central role in coordinating stress perception, ion transport, and detoxification processe...
Roots represent the primary interface for sensing and responding to complex soil environments, where cytoskeletal networks play a central role in coordinating stress perception, ion transport, and detoxification processes. However, the contribution of cytoskeleton-mediated mechanisms to root adaptation under combined metal stress and sediment-based remediation strategies remains poorly understood. In this study, we investigated the cytoskeleton-associated physiological and molecular responses of L. grown in chromium (Cr), copper (Cu), and zinc (Zn) co-contaminated soils amended with fishpond sediments (FPS) and nanoparticle-modified sediments (FPS+ZnONPs and FPS+SiNPs). By integrating soil chemical properties with root and whole-plant responses, we evaluated metal immobilization, stress mitigation, and putative cytoskeleton-associated uptake regulation inferred indirectly from physiological, biochemical, and redox-related indicators rather than direct cytological evidence under multifactorial environmental constraints. Both FPS and nanoparticle-treated FPS significantly reduced the bioavailable fractions of Cr, Cu, and Zn, with FPS+ZnONPs exhibiting the highest immobilization efficiency. These changes were associated with decreased metal accumulation in roots and shoots, which may reflect altered ion transport and cellular detoxification responses potentially associated with cytoskeleton-related processes. Improved rhizosphere conditions enhanced photosynthetic performance, chlorophyll content, and biomass production. Notably, FPS+ZnONPs markedly increased antioxidant enzyme activities and soluble sugar levels, while reducing proline, malondialdehyde, and hydrogen peroxide concentrations, indicating restoration of redox homeostasis and possible stabilization of stress-related cellular functions. Expression patterns of stress-responsive genes further supported the activation of coordinated detoxification networks, which may indirectly interact with cytoskeleton-associated and reactive oxygen species (ROS)-related signaling pathways, although direct cytoskeletal analyses were not performed in this study. Importantly, FPS+ZnONPs substantially reduced the estimated dietary intake of Cr, Cu, and Zn through spinach consumption, demonstrating the downstream benefits of improved root detoxification for food safety. Collectively, our findings suggest that nanoparticle-modified fishpond sediments enhance plant tolerance to multifactorial metal stress by coupling soil metal immobilization with physiological and molecular stress responses, while indirectly supporting the potential involvement of cytoskeleton-associated adaptive mechanisms in complex soil systems.
Enhancing the pectolinarigenin production in L. f. cell suspension cultures and machine learning-based predictive modeling.
Kumar RP, Kumar SR
Front Plant Sci · 2026 · PMID 42394664 · Full text
L. f. is known for its valuable secondary metabolites and their pharmacological importance. Pectolinarigenin (PEC), a natural flavonoid recognized for its promising and diverse biological properties, particularly its pot...
L. f. is known for its valuable secondary metabolites and their pharmacological importance. Pectolinarigenin (PEC), a natural flavonoid recognized for its promising and diverse biological properties, particularly its potent anticancer effects, faces a significant translational challenge due to its inherent scarcity and low abundance in natural sources. In this study, the first-ever development of cell suspension cultures in the genus Clerodendrum using was reported. The study subsequently investigated the effect of salicylic acid (SA), a potent elicitor, at various concentrations on the PEC production. The UPLC quantification of elicited cultures showed that the PEC was produced maximum (343.94 ± 3.03 µg/g dry weight (DW) on 14 day in the cultures supplemented with 20.0 mg/L salicylic acid, followed by 20.0 mg/L salicylic acid yielding 337.84 ± 7.11 µg/g DW on 7 day. Among the three Machine Learning (ML) models employed (Logistic regression (LR), Random Forest (RF), Gradient Boosting Machine (GBM)), the R values of the best ML models, GBM and RF showed 0.953 and 0.991 for the settled cell volume and PEC yield in the elicited cultures, respectively. These novel findings successfully demonstrate the feasibility of establishing cell suspension cultures within the Clerodendrum genus and offer a practical and efficient strategy for the biosynthesis of PEC, a highly useful medicinal compound.
Revisiting volatile organic compounds' role in plant communication using real-time bioimaging.
Kinoshita N, Hirakawa MS, Uehara T … +1 more , Lustig B
Front Plant Sci · 2026 · PMID 42394663 · Full text
Plants release Volatile Organic Compounds (VOCs) in response to insect attacks. VOC facilitates communication with neighboring, undamaged plants. In response to VOC from insect damaged plants, neighboring undamaged plant...
Plants release Volatile Organic Compounds (VOCs) in response to insect attacks. VOC facilitates communication with neighboring, undamaged plants. In response to VOC from insect damaged plants, neighboring undamaged plants upregulate their own defenses as if they were being attacked themselves. To date, Green Leaf Volatiles (GLVs) within VOC have been widely considered a primary mediator for plant communication. GLV is a six-carbon compound which all land plants emit immediately and in large quantities after wounding. We hypothesized that GLVs' lack of specificity and abundance is unlikely to account for key aspects of plant communication like increased sensitivity between closely related plants. To test our hypothesis, we used an Arabidopsis accession which does not produce GLVs. We also developed a non-invasive imaging technique to visualize plant communication utilizing expressions of insect stress marker gene . Our analysis confirmed that plant communication occurs even without GLVs. Cytosolic calcium ion concentration increased before this timing, and moved towards the tip of the leaf in undamaged plants. Additionally, when plants were damaged by insects, acetophenone and alkanes accumulated the experiment's enclosed space. This suggests that plants communicate independently of GLV using alkanes and acetophenone, which are known to attract natural enemies of herbivore insects like parasitoid wasps.
enhances drought tolerance in maize inbred lines through root transcriptomic reprogramming.
Virág E, Zombori Z, Hóvári M … +5 more , Hegedűs G, Sass L, Ferenc G, Dudits D, Posta K
Front Plant Sci · 2026 · PMID 42394662 · Full text
Drought is a major constraint on maize productivity, and its increasing frequency due to climate change necessitates improved stress adaptation strategies. Arbuscular mycorrhizal fungi (AMF) can enhance plant drought tol...
Drought is a major constraint on maize productivity, and its increasing frequency due to climate change necessitates improved stress adaptation strategies. Arbuscular mycorrhizal fungi (AMF) can enhance plant drought tolerance; however, the integrated mechanisms linking root development, host transcriptional regulation, and microbiome activity remain poorly understood. Here, we investigated these interactions in maize using an integrated phenotyping-transcriptomic-metatranscriptomic approach under controlled greenhouse conditions. Two inbred lines with contrasting drought tolerance (K1, tolerant; K2, sensitive) and their hybrid (KH) were grown under well-watered (60% soil moisture) and drought (30%) conditions, with or without inoculation. Mycorrhizal colonization reached 51.3-62.5% under drought, confirming effective symbiosis. RNA-seq analysis (FDR ≤ 0.05, |log;FC| ≥ 1) revealed strong genotype-dependent transcriptional responses, with the drought-sensitive genotype showing the largest number of differentially expressed genes. Principal component analysis identified genotype as the primary driver of variation (PC1: 13%), followed by mycorrhizal status (PC2: 8%). AMF induced distinct, genotype-specific functional reprogramming. The drought-tolerant genotype showed moderated stress responses and maintained metabolic activity, whereas the drought-sensitive genotype exhibited sustained stress signaling and compensatory metabolic activation. The hybrid displayed a non-additive response associated with enhanced root remodeling and symbiosis-related functions. Metatranscriptomic analysis of the non-host root-associated transcript pool further revealed genotype-specific microbial functional activity patterns, ranging from activation to repression. These results demonstrate that AMF-mediated drought tolerance emerges from coordinated, genotype-dependent interactions among root development, host regulatory networks, and microbiome activity. This study provides a holobiont-level framework for understanding crop stress adaptation.
Identification of genomic regions and candidate genes associated with soybean seed sugars in a RIL population.
Bellaloui N, Smith JR, Ray JD … +4 more , Kumar N, Abdelraheem A, Feng C, Mengistu A
Front Plant Sci · 2026 · PMID 42394661 · Full text
Soybean seed sugar profiling determines the quality of soymeal for humans and livestock nutrition. Seed sucrose is desirable for taste and flavor, whereas raffinose and stachyose are indigestible, and therefore undesirab...
Soybean seed sugar profiling determines the quality of soymeal for humans and livestock nutrition. Seed sucrose is desirable for taste and flavor, whereas raffinose and stachyose are indigestible, and therefore undesirable for humans and monogastric animals. Thus, identifying the genomic regions and genes controlling sugar type and level in the seed is desirable for developing optimal levels of each sugar. The objective of this research was to locate the genomic regions for seed sugars content and further identify potential candidate genes involved in sugar metabolism. A segregating mapping population (recombinant inbred lines, RILs) for heat tolerance was developed from a cross between DS25-1 (heat-tolerant parent) and DT97-4290. Both DS25-1 and DT97-4290 are maturity group IV. 201 RILs, parents, and checks were planted in field experiments conducted in 2018 and 2019 without irrigation at Stoneville, MS. Composite interval mapping (CIM) was performed to identify QTLs using a high-density linkage map with 8,445 polymorphic SNP markers. A logarithm of odds (LOD) value of ≥ 2.5 was used as the QTL significance level. Results showed that a total of 19 QTL for seed sugars, among which 12 were novel, were identified. A total of 8 QTL was identified for sugars in 2018. Four QTL (-2018, -2018, -2018, and -2018) were identified for sucrose on chromosomes (chrs) 3, 5, 11, and 19, respectively. Two QTL (Gm06-2018 and -2018) were detected for raffinose on chrs 6 and 20, respectively, and two QTL were identified for stachyose (2018 and -2018) on chrs 6 and 19, respectively. In 2019, four QTL on chrs 5, 9, 17, 19; four QTL on chrs 6, 14, 19, and 20; and three QTL on chrs 3, 13, 19, were identified for sucrose, raffinose and stachyose, respectively. More than 50 candidate genes within each QTL interval were identified that are involved in sugar metabolic pathways. The SNP markers, QTLs, and candidate genes identified in this study provide new information that was previously unknown. The molecular markers will potentially assist breeders to select higher sucrose and lower stachyose that will increase soymeal nutritional qualities, enhancing farmer economic profit and minimizing production cost.
A condition-aware retrieval-augmented decision support framework for tomato cultivation management.
Wang Y, Zhao K, Li H … +2 more , Wang R, Chen W
Front Plant Sci · 2026 · PMID 42394660 · Full text
Tomato cultivation management requires decisions that depend on growth stage, environment, and production scenarios. Retrieval-augmented generation (RAG) can ground large language model (LLM) outputs in external knowledg...
Tomato cultivation management requires decisions that depend on growth stage, environment, and production scenarios. Retrieval-augmented generation (RAG) can ground large language model (LLM) outputs in external knowledge, but conventional retrieval often ignores such conditional constraints, leading to evidence that is topically relevant yet condition-inapplicable. This study develops TSCA-RAG, a condition-aware RAG framework for tomato cultivation question answering. TSCA-RAG extracts temporal, environmental, and contextual conditions from user queries using a structured label set and employs TSCAF-Retrieval, which combines semantic retrieval, BM25 keyword retrieval, and metadata-based condition retrieval through adaptive fusion and a cross-strategy consistency reward. A tomato cultivation knowledge base was constructed as fine-grained knowledge units with condition annotations and used to evaluate both retrieval and end-to-end generation. Retrieval performance was assessed using Recall@K, MRR, and NDCG@5, and answer quality was evaluated using similarity-based and rubric-based metrics under matched generation settings. On retrieval benchmarks, TSCA-RAG improves over Fine-tuned BGE-M3 with relative gains of 5.70% in Recall@1, 4.31% in Recall@5, and 4.76% in NDCG@5. In end-to-end evaluation, TSCA-RAG achieves higher Faithfulness, Correctness, and Utility, with an 11.29% increase in Utility compared with the strongest baseline RAG system. The condition extraction module attains an overall F1 of 81.8%, and a built-in confidence attenuation mechanism recovers approximately 53% of performance loss from single-dimension extraction errors. These results indicate that explicitly modeling cultivation conditions, combined with robust extraction and adaptive error mitigation, can improve evidence applicability and response usefulness for AI-assisted tomato cultivation decision support.
Robust retrieval of biophysical traits under shade gradients in young using visible and near-infrared hyperspectral hybrid modeling.
Chen L, Yang X, Dong X … +7 more , Lin L, Shi M, Chen F, Huang C, Yu H, Yuan Y, Han M
Front Plant Sci · 2026 · PMID 42394659 · Full text
INTRODUCTION: Shading regulation is crucial for cultivating and restoring endangered saplings. However, the high variability in light conditions introduced by shading gradients can increase noise in visible and near-inf...
INTRODUCTION: Shading regulation is crucial for cultivating and restoring endangered saplings. However, the high variability in light conditions introduced by shading gradients can increase noise in visible and near-infrared (VNIR) canopy hyperspectral reflectance and exacerbate the domain shift between measured spectra and those simulated by radiative transfer models (RTMs). In addition, dry leaf density (DLD) retrieval from VNIR spectra remains challenging. These limitations restrict the robust nondestructive monitoring of physiological and structural responses of saplings to shading. METHODS: We developed an inversion framework that integrates multiple spectral scale-normalization methods with a hybrid RTM-deep learning modeling approach under controlled shading gradients. This framework was designed to improve cross-domain spectral consistency under shading-induced variability and to introduce a new carbon-based constituent index, DLD, as a VNIR-compatible proxy for DLD. RESULTS: Inter-group shading differences in original reflectance were easily obscured by noise, whereas scale normalization substantially enhanced the shading response in the green peak and red-edge regions and better-preserved physical consistency between RTM-simulated and field-measured data. The hybrid modeling achieved the highest accuracy for chlorophyll (R = 0.820; RMSE = 3.390 μg·cm), while nitrogen retrieval remained limited under VNIR (R = 0.404; RMSE = 0.207). DLD exhibited a consistent trend with measured DLD (r = 0.747; RMSE = 4.867 mg·cm). Both the inverted chlorophyll and DLD can effectively reproduce the directional response of measured traits along the shading gradient. DISCUSSION: This study provides a practical VNIR-based pathway for nondestructive and robust retrieval of key biophysical traits of saplings under highly variable shading conditions.
Editorial: Regulation of photosynthesis: redox dynamics and environmental adaptations.
Roach T, de Bont L, Liu H
Front Plant Sci · 2026 · PMID 42394658 · Full text
Abstract loading — click title to view on PubMed.
SbHsp70 overexpression enhances drought and salinity tolerance in wheat through improved cellular stability and stress-associated structural adaptations.
Augustine SM, Abdollahi Sisi N, Scheer L … +5 more , Heid A, Knoblauch B, Vukasovic S, Tzigos S, Snowdon RJ
Front Plant Sci · 2026 · PMID 42394657 · Full text
INTRODUCTION: Drought and salinity are major constraints to wheat productivity worldwide. Heat shock protein 70 () is a conserved molecular chaperone implicated in plant stress responses, but its role in cellular stabili...
INTRODUCTION: Drought and salinity are major constraints to wheat productivity worldwide. Heat shock protein 70 () is a conserved molecular chaperone implicated in plant stress responses, but its role in cellular stability and structural adaptation in wheat remains poorly understood. METHODS: To investigate its function, the sorghum-derived gene was constitutively overexpressed in durum wheat (cv. Kofa) and bread wheat (cv. Bobwhite) via particle bombardment. Transgenic lines were evaluated under controlled drought and salinity stress conditions using physiological, cellular, molecular, and agronomic analyses. RESULTS: overexpression enhanced drought and salinity tolerance in both wheat backgrounds. Transgenic plants maintained higher membrane stability, relative water content, and photosynthetic activity under stress. Enhanced interlocking marginal lobe formation, altered actin organization, and modulation of stress-responsive gene expression were also observed. Importantly, transgenic lines maintained agronomic performance under drought without yield penalties under well-watered conditions. DISCUSSION: These findings suggest that contributes to abiotic stress tolerance through improved cellular stability and stress-associated structural adaptations. While the observed cytoskeletal and transcriptional changes indicate a coordinated stress response, further studies are required to elucidate the underlying molecular mechanisms.
Soil-free bioassays for testing novel control agents against root rot.
Pame LJ, Pegg KG, Mitter N … +3 more , Carroll BJ, Shuey LS, Sawyer A
Front Plant Sci · 2026 · PMID 42389140 · Full text
is considered as one of the world's worst plant pathogens, infecting about 5,000 plant species including those of agricultural and environmental significance. Disease management is largely dependent on chemical control,...
is considered as one of the world's worst plant pathogens, infecting about 5,000 plant species including those of agricultural and environmental significance. Disease management is largely dependent on chemical control, particularly synthetic fungicides such as phosphonic acid-based fungicides, e.g., phosphite/potassium phosphonate. While phosphonic-acid-based fungicides have been highly effective for more than 40 years, their prolonged use has led to the development of tolerance and decreased sensitivity in . Novel control agents that are effective but environmentally sustainable are therefore urgently needed. RNA-based biopesticides, which use exogenously applied double-stranded RNA (dsRNA) specific to the target pest or pathogen to avoid off-target effects on other organisms in the environment including beneficials, have emerged as a potential novel disease management strategy against . Due to the limited availability of bioassays to study the efficacy of this novel control agent against , we developed water-based lupin and pineapple bioassays using readily available plastic cups and glassware with mycelial plugs as inoculum. Infection rate was assessed 3 to 7 days post-inoculation (dpi) for lupin and 7 to 14 dpi for pineapple by measuring root lesion length and rating root rot. Potassium phosphonate (Agri Fos 600) and dsRNA were tested as example control agents, with dsRNA uptake tested via northern blotting. The bioassays were found suitable for pathogenicity assays, with one mycelial plug an effective inoculum; fungicide sensitivity testing, with doses as low as 0.45 g L Agri Fos® 600 providing protection; and exogenous dsRNA studies targeting root pathogens, with dsRNA able to be taken up by germinating lupin seeds. Overall, the assays are soil-free and thus overcome dsRNA stability issues in the soil and enable the collection of intact clean roots for molecular analyses. Furthermore, the bioassays are non-destructive, allowing root lesion symptoms to be visually monitored and repeatedly measured across different timepoints.
Acetylation as a dynamic regulatory interface between plant stress memory, cross-tolerance, and crop resilience design.
Ma R, Ruan X, Niu X … +4 more , Li Q, Wen J, Pan Y, Shang C
Front Plant Sci · 2026 · PMID 42389139 · Full text
Plants are increasingly exposed to recurrent, combined, and fluctuating environmental stresses, making it essential to understand how transient stress signals are converted into durable adaptive states. Stress memory and...
Plants are increasingly exposed to recurrent, combined, and fluctuating environmental stresses, making it essential to understand how transient stress signals are converted into durable adaptive states. Stress memory and cross-tolerance represent two interconnected strategies that enable plants to respond more rapidly or effectively to subsequent stresses, yet the regulatory mechanisms linking short-term responses with long-term adaptive potential remain incompletely understood. Acetylation has emerged as a dynamic regulatory interface in this process owing to its reversibility, rapid responsiveness, broad substrate range, and close coupling with cellular metabolic status. In this review, we summarize recent progress in acetylation-mediated plant stress adaptation, focusing on transcriptional bookmarking at the chromatin level, non-histone acetylation of signaling and metabolic proteins, acetyl-CoA-dependent and NAD-dependent metabolic coupling, and regulation in different subcellular compartments, including chloroplasts, mitochondria, and the cytoplasm. We further discuss the conservation, divergence, and evidence hierarchy of key HAT/HDAC regulatory nodes in model plants and crops, highlighting that their functional outputs depend on target identity, stress context, and crop background rather than on their enzymatic identity alone. Finally, we evaluate the potential and limitations of acetylation-based crop strategies for improving crop stress resilience, including priority target selection, small-molecule regulation, epigenome editing, synthetic regulatory modules, and molecular design breeding. Overall, acetylation should not be viewed simply as a transcriptional "on/off" switch, but as a multilayered regulatory hub linking environmental signals, metabolic states, chromatin plasticity, and adaptive phenotypes. Future advances will depend on causal validation of non-histone substrates, time-resolved acetylation maps, multi-stress network dissection, and validation in crop systems under complex field conditions.
Bioinformatic analysis, expression analysis, and subcellular localization of GeBP transcriptional regulator family in response to abiotic stress in .
Basharat S, Saeed W, Liu P … +1 more , Waseem M
Front Plant Sci · 2026 · PMID 42389138 · Full text
INTRODUCTION: The GLABROUS1 enhancer-binding protein (GeBP) gene family represents a plant-specific class of transcriptional regulators involved in plant growth, development, and adaptation to environmental stresses. Alt...
INTRODUCTION: The GLABROUS1 enhancer-binding protein (GeBP) gene family represents a plant-specific class of transcriptional regulators involved in plant growth, development, and adaptation to environmental stresses. Although GeBP proteins have been characterized in , systematic analysis of GeBP genes in and their responses to abiotic stresses remains limited. METHODS: In this study, we performed a genome-wide identification and characterization of GeBP genes in B. napus. Chromosomal distribution, phylogenetic relationships, gene duplication events, exonintron organization, conserved domains, promoter cis-regulatory elements, tissue-specific expression patterns, subcellular localization, and stress-responsive expression profiles under salt, drought, heat, and cold stresses were analyzed. RESULTS: A total of 35 BnaGeBP proteins were identified and found to be unevenly distributed across the B. napus chromosomes. Phylogenetic analysis classified the BnaGeBP proteins into three distinct groups together with GeBP homologs from selected monocot and dicot species. Duplication analysis indicated that the expansion of the BnaGeBP family was mainly driven by segmental duplication events, with 20 segmental duplication pairs and one tandem duplication pair identified. Gene structure and conserved domain analyses supported the phylogenetic conservation of BnaGeBP genes. Promoter analysis revealed diverse hormone- and stress-responsive cis-regulatory elements, including drought- and low-temperature-responsive motifs. Tissue expression profiling showed variable spatial expression patterns, while selected BnaGeBP genes displayed differential expression under salt, drought (PEG6000), heat, and cold stress treatments. DISCUSSION: This comprehensive analysis provides valuable insights into the evolution, structural conservation, and potential functions of the BnaGeBP gene family in . The stress-responsive expression patterns suggest that selected BnaGeBP genes may play important roles in abiotic stress adaptation, providing a foundation for future functional studies and genetic improvement of stress tolerance in .
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe