2026-10-23 · Original Research
Jiangchen Zan, Jinfeng Peng, Ruijun Gao, Xiangyu Ma, Bowen Xue, Xiaoying Zhang
Accurate sowing-quality assessment of maize seedling trays requires both reliable seed localisation and correct correspondence between detected seeds and physical tray cells. This study presents a semi-automated machine-vision framework combining heatmap-based seed-centre localisation, sliding-window inference, global non-maximum suppression (NMS), and four-corner-calibrated adaptive grid assignment. Each assessable cell was classified as empty, single-seeded, or multi-seeded according to the number of assigned seed centres. On source-image-independent subsets, the framework achieved an accuracy of 0.9821 and a macro F1-score of 0.9040 for 27 complete-tray images (3,456 cells), and 0.9798 and 0.9344, respectively, for 9 visible-cell images (1,140 assessable cells). Separately, the larger evaluation sets yielded accuracy/macro F1 values of 0.9783/0.9145 for 44 complete trays and 0.9782/0.9368 for 30 visible-cell images. These results support cell-level sowing-quality assessment under the evaluated acquisition conditions and within manually assessable regions. The source-image-independent subsets control direct source overlap but remain within the same acquisition domain; external generalisation across production sites, imaging devices, tray specifications, and acquisition conditions has not yet been established.
DOI: 10.3389/fpls.2026.19814932026-10-23 · Original Research
Shubham Roy, Shakir Khan, Neha Gupta, Achin Jain, Arvind Panwar, Fahad Omar Alomary, Abeer Aljohani, Saqib Qamar
Plant diseases pose a critical challenge to agricultural productivity, underscoring the need for rapid and reliable automated detection methods. Manual disease identification is labor-intensive and error-prone, whereas deep learning techniques offer scalable alternatives. This study evaluates five convolutional neural network (CNN) architectures—XceptionNet, DenseNet121, a baseline five-layer CNN, a six-layer CNN, and a proposed custom architecture, TomaNet-6H—for classifying tomato leaf conditions using the PlantVillage dataset. Image preprocessing combines color space transformations and Contrast Limited Adaptive Histogram Equalization (CLAHE), alongside targeted data augmentation to mitigate class imbalance. Experimental results demonstrate that TomaNet-6H achieves a test accuracy of 97.42% and a macro F1-score of 96.60%, while maintaining moderate computational complexity (∼7M parameters) and an inference latency of 68.4 ms per image. Furthermore, Grad-CAM visualizations qualitatively indicate that the network predominantly focuses on symptomatic leaf areas rather than background artifacts. These findings highlight TomaNet-6H as an effective, resource-conscious framework for precision agriculture deployment.
DOI: 10.3389/fpls.2026.19701112026-10-23 · Opinion
Shailja Singh, Christina Dixelius
DOI: 10.3389/fpls.2026.19724092026-10-23 · Original Research
Hui Sun, Zhijun Zhang, Jun Liu, Delong Zhang, Minghan Feng
Detecting fruit diseases and pests in complex agricultural scenes remains challenging due to large target-scale variation, weak lesion features, leaf and branch occlusion, and severe background interference. To address these problems, this study focuses on eggplant fruit disease and pest detection and proposes FSF-RTDETR, a frequency–spatial fusion model. The proposed model builds a dual-branch frequency–spatial enhanced backbone to improve disease and pest feature representation from both frequency details and spatial structures. In the frequency branch, AFDC and MFFWBlock enhance high-frequency responses such as fruit borer edges, rot lesion textures, and thrips bite marks through attention-guided frequency-domain convolution and multiscale wavelet feature modeling. This design improves the perception of small targets with weak boundaries and fine textures. In the spatial branch, VisionClueMerge and G6MambaLayer preserve local spatial cues and introduce six directional scanning paths covering horizontal, vertical, and diagonal interactions. This helps the model better describe occluded targets, complex backgrounds, and irregular lesion distributions. Furthermore, EGMuF adaptively integrates edge-texture information from the frequency branch and structural semantic information from the spatial branch through channel, spatial, and pixel-level gated attention. Experimental results show that FSF-RTDETR achieves Precision, Recall, mAP50, and mAP50:95 of 81.5%, 71.3%, 78.8%, and 50.7% on the Eggplant dataset, respectively, outperforming the RT-DETR-R18 baseline by 1.7, 2.0, 4.2, and 4.7 percentage points. The model achieves an inference speed of 104.07 FPS. Results on the PlantDoc Dataset further verify the effectiveness and generalization ability of the proposed method in plant leaf disease detection scenarios.
DOI: 10.3389/fpls.2026.19569532026-10-23 · Original Research
Yajiao Wang, Sen Han, Xuetong Liu, Hongkai Dang, Chunlian Zheng, Yudong Zheng, Caiyun Cao, Yuxing Wu
Soil salinization threatens global agricultural sustainability and may elevate soil-borne disease risk through coordinated changes in soil conditions and the rhizosphere microbiome, yet long-term field evidence remains limited. Here, a 19-year controlled field experiment with an artificial salinity gradient (non-saline, moderate, and severe) was conducted to characterise salinity-associated responses of soil physicochemical properties, wheat crown rot (WCR), and the rhizosphere microbiome. A 3-year field remediation demonstration was implemented to test whether replacing saline irrigation with non-saline water could reverse soil deterioration and reduce disease severity. The results showed that severe salinity increased soil pH from 7.64 to 8.38 and reduced available phosphorus, total nitrogen, and available potassium by 54.11%, 14.63%, and 37.69%, respectively, while the WCR disease index increased from 10.51 to 32.88. It also reduced microbial richness and diversity, altered rhizosphere community composition, with taxon-specific abundance shifts among halophilic taxa, and redistributed community functional potential, with greater representation of genes associated with compatible-solute metabolism and ion homeostasis alongside changes in carbon, nitrogen, and sulfur metabolism. Remediation reduced soil salinity and pH, improved nutrient availability, and decreased the WCR disease index by 49.17%. Together, our results show that long-term salinization is associated with coordinated deterioration of soil conditions, restructuring of the rhizosphere microbiome, redistribution of microbial functional potential, and increased WCR severity. The remediation experiment showed that reducing salinity improved soil conditions and reduced disease severity. Re-establishing favourable soil abiotic conditions may be a prerequisite for alleviating disease risk in salinized agroecosystems.
DOI: 10.3389/fpls.2026.19928822026-10-23 · Original Research
Esma Yigider, Melek Ekinci, Sadia Hakeem, Selda Ors, Murat Aydin, Metin Turan, Ertan Yildirim
IntroductionCucumber is a heat- and salt-stress-sensitive vegetable crop, whose productivity and marketability are endangered by increasing temperatures and soil salinization driven by climate change. Combined stresses are becoming frequent, yet their interactive effects remain poorly understood.MethodologyThe current study evaluated the negative impacts of high temperature (HT, 40 °C) and salinity (75 and 150 mM NaCl) alone and in combination on cucumber seedlings, under a triplicated completely randomized design. Standard plant growth parameters, micro- and macronutrients, phytohormones, photosynthetic pigment concentrations, oxidative stress biomarkers, osmo-protectants, and antioxidant enzymes were recorded.ResultsCombined HT and 150 mM salt stress caused greater damage to photosynthetic pigments (49-68%), and >98% reduction in growth-promoting hormones, resulting in reduced plant growth (67-93%). Combined stress drastically depleted essential nutrients (94-99.6%) despite lower Na+ and Cl- ion concentrations compared to 150 mM NaCl stress alone. Reduced plant growth under combined heat–salinity stress was associated with pronounced disturbances in mineral nutrition and ion homeostasis, although the relative contributions of nutrient imbalance and ionic toxicity could not be distinguished based on tissue mineral concentrations alone. Moreover, plant growth reprogramming toward survival rather than growth was observed with a 206-fold increase in abscisic acid (ABA) and ~99% decline in indole acetic acid, gibberellic acid, and zeatin. Intensified oxidative stress stimulated coordinated activation of ROS (reactive oxygen species) scavenging enzymes, and glutathione-dependent redox metabolism (glucose-6-phosphate dehydrogenase, glutathione reductase, 6-phosphogluconate dehydrogenase, and glutathione-S-transferase increased by 36-, 38-, 41- and 54-fold, respectively), but these remained insufficient to prevent oxidative damage. However, HT and salinity stress triggered distinct pathways: HT preferentially promoted hydrogen peroxide accumulation and activated antioxidant defenses, while salt stress caused greater damage through membrane lipid peroxidation along with ionic imbalance.ConclusionThese findings suggest that salinity primarily caused physiological impairment, whereas HT amplified oxidative signaling and antioxidant metabolism, providing new insights and potential targets for developing cucumber cultivars with enhanced tolerance to combined stresses. Future research should integrate multi-omics technologies with functional genomics to study the molecular networks regulating nutrient homeostasis, antioxidant metabolism, and ABA signaling under combined stress.
DOI: 10.3389/fpls.2026.19639622026-10-22 · Original Research
Hexin Chen, Wenting Li, Junwei Guo, Hongbo Wang, Song Yang, Ran Wan, Yanling Liu, Zhenyu Liu, Guoxin Qin, Cong Wang, Zeli Wang, Haiyue Su, Xianyue Zhu, Zhen Wang, Zhicai Wang, Cong Nie, Le Zhao, Shan Li, Xufeng Wang
IntroductionTo address the need for the value-added utilization of tobacco leaves with low sensory quality, this study proposed a targeted chemical composition regulation method based on counterfactual explanations and preliminarily evaluated the resulting chemical adjustment strategies using samples processed by a rotary-drum tobacco high-temperature (THT) drying process.MethodsBased on 70 chemical indicators and sensory smoking evaluation data from 354 tobacco leaf samples, binary shrinkage linear discriminant analysis (shrinkage LDA) models were developed to distinguish between the high- and low-sensory-quality groups in terms of aroma quality, aroma intensity, and offensive odor. Incremental feature selection (IFS) was employed to identify key chemical indicators, after which indicators with low adjustability under THT conditions were further excluded. The decision models for counterfactual explanations were then reconstructed using the remaining indicators. Sequential least squares programming (SLSQP) was applied to generate chemical-indicator adjustment pathways for improving sensory quality, and the resulting pathways were validated through a THT experiment conducted at 215 °C.ResultsThe results showed that: (1) following incremental feature selection and further screening based on the adjustability of chemical indicators under THT conditions, 11, 9, and 10 key chemical indicators were ultimately retained in the decision models for aroma quality, aroma intensity, and offensive odor, respectively; (2) all the developed models achieved classification accuracies above 84% on the test sets, indicating good mapping relationships between the key chemical indicators and sensory quality; (3) the directional agreement between the theoretically predicted adjustments and the experimentally measured changes ranged from 66.7% to 72.7%. Moreover, indicators showing directional agreement contributed significantly more to improvements in discriminant scores than those showing opposite directions, confirming their dominant role in sensory quality improvement.DiscussionThese findings demonstrate that counterfactual explanations can effectively predict optimization pathways in complex chemical systems, thereby providing theoretical support and methodological guidance for the targeted improvement of tobacco leaves with low sensory quality.
DOI: 10.3389/fpls.2026.19916482026-10-22 · Original Research
Yaxin Wang, Lingxiang Li, Xuzhe Xiong, Shuangwen Wang, Hang Ni, Feng He, Bo Zhu, Jiaxin Xiao
IntroductionGrafting can be used in blueberry cultivation to improve soil adaptability and scion fruit quality. However, the underlying molecular mechanisms remain poorly understood.MethodsWe investigated the effects of rabbiteye blueberry (Vaccinium virgatum) ‘Climax’ and ‘Brightwell’ rootstocks on fruit quality, biochemical characteristics, and related gene expression in ‘Misty’ blueberry (Vaccinium corymbosum).ResultsThe fruit quality of ‘Climax’-grafted ‘Misty’ (CM) was superior to that of ‘Brightwell’-grafted ‘Misty’ (BM). CM showed greater scion stem diameter and fruit size, as well as the net photosynthetic rate, and chlorophyll contents in leaves. Notably, LC-MS/MS analysis detected significant increases in specific sugars and flavonoids in CM fruit, with glucose and fructose contents 10.2% and 11.4% higher than BM, respectively. Twenty-four out of the 31 quantified flavonoids were more abundant in CM. In contrast, 26 of the 28 detected amino acids accumulated at higher levels in BM, as did most organic acids. A total of 1,411 differentially expressed genes, including 830 upregulated and 581 downregulated genes, were detected between CM and BM fruit, in which the genes associated with sugar (VcSWEET12 and VcINV1) and flavonoids (VcF3′H and VcUFGT) were upregulated in CM fruit. An integrated analysis pinpointed nine transcription factors, including VcWRKY75 and VcWRKY24, as potential modulators of sugar metabolism and flavonoid biosynthesis.DiscussionThese findings indicate that different rabbiteye blueberry rootstocks are associated with distinct physiological and metabolic responses in southern highbush blueberry. Compared with ‘Brightwell’, the ‘Climax’ rootstock was more conducive to improving the comprehensive quality of ‘Misty’ blueberry fruit. The results provide candidate molecular targets for dissecting the process of fruit quality formation mediated by rootstock–scion interactions, and they form a basis for high-quality blueberry cultivation.
DOI: 10.3389/fpls.2026.19959042026-10-22 · Original Research
DanDan Rong, Min Song, Yongjia Han, Changzhi Yang, Wenjun Wei, Yan Lin, Duoqiang Zhai
IntroductionOil-well retirement ends production but may leave physical, chemical and ecological legacies in coastal wetlands. MethodsWe assessed soil conditions, heavy-metal risk and vegetation across retirement stages in the Yellow River Delta, China, in 2021, using 15 oilfield-associated sites and six natural reference wetlands. Sites were classified as Active, Abandoned, Restored (infrastructure removed and restoration implemented) or Reference, with retired sites assigned to <3, 3–5 and 5–10 year classes. ResultsOilfield sites had lower mean vegetation cover than reference wetlands in June (50.29% versus 69.00%) and December (38.00% versus 56.23%), together with higher pH and generally lower salinity. Cd accounted for 54.3-65.7% of potential ecological risk, and its single-factor index exceeded one at three sites. Mean cover and richness at Restored sites increased across age classes, from 15.8% and 1.5 species at <3 years to 64.2% and 7.0 species at 5–10 years, whereas diversity peaked in the intermediate class. Cd index, pollution load index (PLI) and potential ecological risk index (RI) did not decline monotonically with retirement age. Restored sites had lower mean metal-risk indices than Abandoned sites at 5–10 years but higher means at 3–5 years. Soil pH was positively associated with cover and richness; Cd index and PLI showed no significant associations with vegetation metrics. DiscussionThese descriptive chronosequence patterns indicate that vegetation reorganisation and chemical-risk attenuation do not follow a common trajectory, and that recovery cannot be inferred from retirement age alone. Wetland retirement management should combine site-specific contamination assessment with vegetation and habitat evaluation.
DOI: 10.3389/fpls.2026.19895172026-10-22 · Original Research
Xiaocui Chen, Xiaowei Zhang, Shichao Sun, Hong Yang, Cheng Qin, Dan Zhou, Di Peng, Qingqing Li, Xiaosong Gou, Ao Wang
Fruit morphology and yield are major determinants of pepper market value and productivity, but the genetic basis of these traits remains incompletely resolved. In this study, we evaluated 195 Capsicum annuum accessions for six fruit morphology and yield-related traits in two environments. The traits showed substantial variation, with coefficients of variation of 40.43-57.09% and broad-sense heritability of 0.59-0.97. Reduced-representation sequencing generated 76,418 high-quality single nucleotide polymorphisms, and population analyses resolved eight genetic subgroups. Genome-wide association analysis detected 23 significant loci, comprising 12 loci for fruit morphology and 11 loci for yield-related traits. These loci contained 318 unique genes. Notably, the major fruit-length loci qFL2 and qFL5 contained gibberellin 20 oxidase 1 (GA20ox1) and an OVATE family protein gene corresponding to the functionally characterized pepper fruit-elongation regulator CaOFP20, respectively. These loci, allele-trait associations, and putative candidate genes provide a basis for further validation and marker development in pepper breeding.
DOI: 10.3389/fpls.2026.19269542026-10-22 · Original Research
Honglang Luo, Lixin Huang, Song Guo, Xiuhua Zhang, Yuan Wang, Deming Lu, Qian Lu, Zailiu Li
Dendrocalamus brandisii is a high-value horticultural vegetable crop prized for its sweet and tender shoots, yet its stage- and tissue-specific nutrient dynamics remain unclear, limiting standardized harvesting for the fresh-market industry. Here, we combined morphological observation, anatomical analysis, nutrient quantification, and TOPSIS comprehensive evaluation to elucidate the growth pattern, anatomical characteristics, and distribution of quality-related components in young shoots. The edible period lasted 25 days from emergence to the point of inedibility, and height growth followed a slow-then-fast pattern that was divided into four stages (I–IV). Anatomically, cell division dominated in Stages I–II, whereas cell elongation dominated in Stages III–IV. Nutrient contents exhibited significant spatiotemporal heterogeneity: moisture, vitamin C, and flavonoids were highest in the upper part at Stage I; starch and protein peaked in the lower part at Stages II and III, respectively; soluble sugars, fats, cellulose, and lignin accumulated continuously during Stages III–IV; and total free amino acids as well as sweet amino acids reached their maximum in the upper part at Stage III. Ca, Mg, Fe, Zn, Mn, and Cu contents peaked at Stage I and then declined, whereas K peaked at Stage II and Na showed no clear directional change. Oxalic acid was highest in the middle part at Stage IV, whereas tannin content peaked in the upper part at Stage I and then declined. TOPSIS comprehensive ranking confirmed Stage III (19–22 d) as the optimal harvest window, with the upper and middle segments as premium raw materials for fresh consumption. This study reveals the anatomical-metabolic basis of shoot quality and provides a scientific basis for both large-scale D. brandisii cultivation and precision harvesting in bamboo vegetable production. These findings offer practical guidance for timing the harvest and selecting the premium edible portions of D. brandisii shoots, thereby enhancing the commercial value and economic returns of fresh bamboo shoots.
DOI: 10.3389/fpls.2026.19827272026-10-22 · Review
Julia Morales, Belén Martínez-Alcántara, Ana Pérez-Piqueres, Isabel Rodríguez-Carretero, Ana Quiñones
Citrus production across growing regions is increasingly exposed to rising atmospheric CO2, higher temperatures, and greater variability in water availability, with Mediterranean orchards facing particularly pronounced climatic pressures. These climatic drivers affect citrus performance through interconnected changes in photosynthesis, root functioning, flowering, salinity responses, redox regulation, and source–sink relationships, with consequences for productivity and fruit quality. This review synthesises current knowledge on how climate change modifies citrus physiology and mineral nutrition, with particular attention to carbon–nitrogen coordination, carbohydrate partitioning, and nutrient allocation, and examines strategies to strengthen soil–plant functioning and nutritional resilience under increasing climatic variability. Temperature effects depend on exposure conditions: warmer soils may sustain root activity and prolong seasonal N uptake, whereas excessive temperatures can impair root functioning and nutrient acquisition, potentially altering coordination between vegetative and reproductive demand. Elevated CO2 may initially enhance carbon assimilation and water-use efficiency, but acclimation and changes in nitrogen allocation can limit this response. These alterations can affect fruit growth, ripening, composition, and susceptibility to physiological disorders, although their expression depends on stress intensity and timing, genotype, and developmental stage. The management discussion focuses on selected soil-management practices, biostimulants, and exogenous signalling compounds that may improve soil fertility and soil–root functioning or support physiological adaptation within established citrus orchards. This emphasis addresses opportunities to sustain existing plantings, including traditional cultivars, particularly where orchard renewal is economically constrained. Future progress will require multi-year field studies integrating soil, plant, climatic, and fruit-quality responses to assess the effectiveness and feasibility of these approaches under site-specific conditions.
DOI: 10.3389/fpls.2026.20096582026-10-22 · Original Research
Renjie Zhao, Zexin Qi, Lihua Zhang, Fei Li, Ning Sun, Weiping Yan, Mo Zhu, Qian Li, Hongxiang Zhao, Chen Xu, Zhian Zhang
IntroductionDrought is a major constraint on the early growth and photosynthetic productivity of maize (Zea mays L.), yet whether the physiological benefits of straw mulching depend on drought severity remains unclear.MethodsA two-year experiment was conducted in 2025 and 2026 using straw removal and straw mulching under three irrigation levels (135, 105, and 75 mm), representing well-watered, moderate-drought, and severe-drought conditions, respectively. Plant growth, photosynthetic performance, carbon-assimilation enzyme activities, osmotic adjustment, and antioxidant responses were evaluated.ResultsIncreasing drought severity generally reduced leaf area index (LAI), plant height (PH), dry matter accumulation (DW), photosynthetic performance, and carbon-assimilation capacity, while increasing the accumulation of proline, soluble sugars, betaine, malondialdehyde (MDA), and hydrogen peroxide (H2O2), together with antioxidant responses. The physiological effects of straw mulching varied markedly with drought severity. Under moderate drought, mulching more consistently maintained plant growth and photosynthetic performance, preserved carbon-assimilation enzyme activities, and reduced MDA and H₂O₂ accumulation. In contrast, these beneficial responses were substantially weaker and less consistent under severe drought. Across physiological traits, better growth and carbon-assimilation performance were generally associated with lower osmotic and oxidative stress. Multivariate patterns further showed that mulched plants under moderate drought exhibited a physiological profile closer to that under well-watered conditions, whereas plants under severe drought remained distinctly separated despite straw mulching.DiscussionOverall, straw mulching provided more consistent physiological protection against moderate drought than severe drought during early maize growth, indicating that drought severity strongly constrains the effectiveness of straw mulching.
DOI: 10.3389/fpls.2026.19836682026-10-22 · Correction
Frontiers Production Office
DOI: 10.3389/fpls.2026.20191722026-10-22 · Original Research
Deyi Lei, Zhibo Zhong, Ping Zhang, Jianling Guo, Liang Tang, Yu Yu, Xiuqing Fu
By precisely quantifying the growth changes of seed radicles and cotyledons over continuous time periods, the impact of saline stress environments on early crop growth can be assessed. However, traditional manual measurements struggle to accurately quantify these indicators continuously. Therefore, we developed a Full-Time Series Crop Growth Vigor Monitoring System. This system captured images of the hydroponic germination process and the soil-based seedling growth process of Xinjiang cotton seeds. We constructed a labeled dataset for identifying the germination process and calculating cotyledon growth. Using the SDI-YOLO11-seg model, we achieved the extraction and quantification of germination rate, emergence rate, radicle length, and cotyledon area over continuous time, validating the feasibility of a rapid, batch-assessment method for early cotton seed growth vigor based on the full-time series monitoring system and deep learning. Building on this, we conducted experiments involving four Xinjiang cotton varieties under hydroponic (germination stage) and soil-based (seedling stage) conditions with six different concentrations of NaCl solution stress. Germination rate, emergence rate, radicle length, and cotyledon area for each variety were measured continuously over time. The results show that the proposed SDI-YOLO11-seg model achieved a mean average precision for bounding boxes at IoU 0.5 (mAPbox50) of 0.961 and for masks (mAPmask50) of 0.937, representing improvements of 0.9% and 6.0% over the baseline YOLO11-seg, respectively. Validation against manual ImageJ measurements yielded coefficients of determination (R²) of 0.970 for radicle length and 0.993 for cotyledon area, confirming high measurement accuracy. Under salt stress concentrations ranging from 0 to 250 mmol/L, Jinken 1565 exhibited the fastest germination rate, the highest final germination rate, and the longest average radicle length, indicating strong salt tolerance during the bud stage. In contrast, Jinken 1775 demonstrated a higher seedling emergence rate, the fastest cotyledon growth rate, and the largest cotyledon area, suggesting excellent salt tolerance during the seedling stage. The Tahe 2 variety exhibited weaker salt tolerance during both the bud and seedling stages compared to the other three varieties. Coefficient of variation analysis further revealed that Jinken 1565 exhibited the most uniform radicle growth under high salt stress during the germination stage, while Jinken 1775 and Xinluzao 64 demonstrated superior uniformity in seedling growth, complementing the mean-based vigor assessment.
DOI: 10.3389/fpls.2026.19055932026-10-21 · Original Research
Yousry A. El-Kassaby, Eduardo P. Cappa
Accurate estimation of quantitative genetic parameters is critical for genomic selection in forest tree breeding. Compared with pedigree-based relationship matrices (A-matrices), genomic relationship matrices (G-matrices) better capture realized genetic relationships, including Mendelian sampling and cryptic relatedness. This study evaluated a genome-wide association study (GWAS)-based SNP selection strategy to improve G-matrix construction and estimates of additive genetic variance, heritability, and breeding values in white spruce (Picea glauca) and Eucalyptus (Eucalyptus grandis), two species with contrasting genome sizes and genotyping platforms. Progeny trials were analyzed using both pedigree-based best linear unbiased prediction (ABLUP) and genomic BLUP (GBLUP). Genomic relationship matrices were constructed from complete SNP datasets and compared with pedigree-based relationship matrices. To evaluate the impact of marker selection, SNPs were ranked according to the absolute magnitude of their GWAS-estimated effects, and sequential subsets of informative markers were used to reconstruct G-matrices. Parameter estimates and theoretical accuracy from reduced SNP panels were compared with those from the complete datasets. Genomic relationship matrices generated connected family networks, revealing hidden relatedness and overcoming limitations of pedigree-based relationships. GBLUP yielded consistently higher heritability estimates for all traits in white spruce but only for tree volume in Eucalyptus. GWAS-informed SNP selection showed that marker informativeness was more important than marker number; in white spruce, ~50,000 informative SNPs performed comparably to the full 467K SNP panel for some traits, although marker requirements varied among traits. In contrast, gains in Eucalyptus were limited, likely due to reduced representation of trait-associated variation. The results demonstrate that integrating realized genomic relationship matrices with biologically informed SNP selection can provide genetic parameter estimates and theoretical accuracies comparable to those obtained with much larger marker sets while substantially reducing genotyping requirements for genomic evaluation. Responses were species- and trait-dependent. Reduced gains in Eucalyptus may reflect SNP ascertainment bias and other factors limiting the representation of causal genetic variation. Overall, biologically relevant and genomically representative markers were more important than marker density alone, and optimized SNP selection may reduce genotyping requirements while maintaining effective genomic evaluation in forest tree breeding.
DOI: 10.3389/fpls.2026.19746942026-10-21 · Original Research
Mikhail G. Divashuk, Aleksey S. Yanovsky, Varvara A. Gorskaia, Alexandra A. Mudrova, Maria S. Esina, Ludmila A. Bespalova, Viktoria S. Voronezhskaya, Mikhail G. Monakhos, Anastasiya D. Voropaeva, Anastasiya G. Chernook, Andrey V. Arkhipov, Daniil S. Ulyanov, Gennady I. Karlov
Frost tolerance limits the expansion of winter durum wheat (Triticum durum) into continental zones. Its control is attributed mainly to chromosome 5A loci, Fr-A2 [the CBF cluster: CBF-A14 copy number variation (CNV) and a non-CNV component], and Fr-A1/VRN-A1. We assessed candidate KASP (kompetitive allele-specific polymerase chain reaction) markers in the Russian winter durum wheat gene pool (161 accessions) and in a segregating F2 panel from crosses with foreign frost-susceptible lines. Frost tolerance was measured as the percentage of plants surviving a controlled freezing test. In the collection, the favorable Fr-A2 class is nearly fixed at all four markers of the CBF-A14 copy-number haplotype [minor allele frequency (MAF), 0.04 to 0.08]. Minor-class lines survive at 7.3% to 13.5% against 43.7% to 45.4%, but only 2 of the 15 come from the Krasnodar program, a contrast confounded with origin. The frequency of the favorable class rose from 0.60 to 0.87 among accessions entered into State Variety Trials before 2000 to 0.95 to 1.00 after 2010. The non-CNV component S1051014 is polymorphic and not associated with the trait (p = 0.442). In the F2 panel, the dose of the adapted-parent allele among survivors rose from 1.510 to 1.750 at S2269949 (within-family randomization test, one-sided p = 0.005, two-sided p = 0.010) and from 1.752 to 1.958 at S1077313 (p = 0.038 and 0.076). Of three polymorphic independent non-Fr loci, 7B (Mor866) showed no effect, whereas 1B (Mor587, allele T) and 5B (Mor534, allele G) showed a nominal effect of the same direction, approximately 7 to 8 percentage points (p = 0.048 and 0.052); the long-vernalization VRN-A1 allele was associated with higher survival (p = 0.019). These markers, untested in segregating material, are presented as candidates. Later heading accompanied higher survival (+0.0142 per day on the angular scale, p = 0.0004, n = 155), largely a between-program contrast. The Fr-A2 markers are the most valuable when external frost-susceptible material is used. With Fr-A2 fixed, the choice of marker follows from the crossing plan rather than from the published effect size.
DOI: 10.3389/fpls.2026.19594652026-10-21 · Original Research
Fabio Pietrolucci, Vittoria Valesi, Elena Sgaravatti, Flavia Guzzo, Stefano Negri, Linda Avesani
Artemisinin, a sesquiterpene lactone produced in glandular trichomes of Artemisia annua, remains a key compound for artemisinin-based combination therapies against malaria. Although stable transformation has been widely used to enhance artemisinin production, rapid in planta systems for testing metabolic engineering strategies in A. annua remain limited. In this study, we developed a transient expression system based on vacuum agroinfiltration of whole A. annua plants, providing a fast and flexible tool to explore the engineering potential of the artemisinin pathway. Using GFP as a reporter, we established experimental conditions that support reproducible transient expression, identifying in vitro-grown plants as the most suitable material. We then assembled five key genes of the artemisinin biosynthetic pathway into a single multigene construct and tested its ability to redirect metabolism in both Nicotiana benthamiana and A. annua. While heterologous expression in N. benthamiana did not lead to detectable artemisinin-related metabolites, transient expression in A. annua produced a measurable, although temporary, shift in the specialized metabolome. At 2 dpi, targeted LC–HRMS analysis showed that artemisinin content increased from 0.086 ± 0.015 to 0.123 ± 0.012 mg/g fresh weight, while deoxyartemisinin and several putative sesquiterpenoid compounds also increased in relative abundance, suggesting that the introduced pathway genes influenced metabolic flux. These effects faded over time, revealing the strong endogenous regulatory constraints that shape artemisinin accumulation in its native plant host. Overall, this work establishes a rapid in planta platform for probing and modulating specialized metabolism in A. annua. Beyond artemisinin, it highlights the value of transient expression as a bridge between molecular design and plant-based production, supporting the broader vision of plants as dynamic biofactories for health-relevant natural products.
DOI: 10.3389/fpls.2026.18760672026-10-21 · Original Research
Bin Zhang, Jieyu Bao, Ze Zhang, Zixin Sun, Fusuo Zhang, Meijun Zhang
The interaction between arbuscular mycorrhizal fungi (AMF) and phosphorus (P) availability could enhance plant drought tolerance. Yet whether this interaction modulates nutrient uptake and grain yield in oat by reshaping rhizosphere metabolite and microbial networks remains unresolved. A pot experiment was conducted across three relative water contents (75%, 55%, and 35% relative water content, designated WW, MDS, and SDS), two AMF treatments, and three P levels (0, 40, and 80 mg kg−¹ soil, designated P0, P1, and P2). Untargeted metabolomics and metagenomics were applied to characterize rhizosphere metabolite profiles and bacterial community structure, and to assess their relationships with nitrogen (N) and P status in the plant–soil system, grain yield and β-glucan. Drought significantly reduced grain yield, whereas moderate drought increased β-glucan accumulation; the beneficial effects of AMF on both traits were strongly modulated by soil P level. Under drought, AMF inoculation and P addition synergistically promoted N and P accumulation across oat organs; relative to P0AMF, P2AMF significantly elevated total N and P concentrations in roots, stems, leaves, panicles, and grains. Water availability was the dominant driver of rhizosphere metabolome and bacterial community variation. Under drought, AMF–P interaction further enriched rhizosphere metabolites, including amino acids and derivatives, organic acids, and benzene and substituted derivatives, while shifting the signature bacterial taxa toward Pseudomonadota (P1AMF) and Myxococcota and Gemmatimonadota (P2AMF). Network analysis identified isopentenyl pyrophosphate (IPP) as a highly connected hub metabolite, exhibiting the strongest associations with N and P nutrition, grain yield, β-glucan, and bacterial community composition. Exogenous IPP application significantly increased oat plant height, stem dry weight, and average root diameter under drought and markedly elevated the relative abundances of several rhizosphere bacterial taxa. Collectively, these findings indicate that AMF inoculation combined with P addition is associated with restructuring of the rhizosphere metabolite–microbe network under drought, and that IPP represents a candidate metabolite that warrants further investigation in these plant–microbe–soil interactions. This study provides a correlative framework linking this dual strategy to shifts in rhizosphere microbial communities and crop yield and functional quality under water-limited conditions, although mechanistic validation will require future experimental work.
DOI: 10.3389/fpls.2026.19849432026-10-21 · Original Research
Florent Weiller, Jonatan U. Fangel, William G.T. Willats, Azeddine Driouich, Melané A. Vivier, John P. Moore
IntroductionGrapevine PGIP1 (polygalacturonase inhibiting protein 1) expressed in tobacco produces plants with enhanced resistance against B. cinerea infection. Grapevine PGIP1 has been shown to remodel leaf cell walls in transgenic tobacco in the absence of fungal infection. The associated dynamic cell wall changes linked to the mechanism of resistance have not been investigated in the context of fungal infection. MethodsScanning electron microscopy was used to evaluate infection progression. Monosaccharide composition analysis was used to evaluate cell wall changes as infection progressed. Comprehensive microarray polymer profiling tracked polysaccharide and glycoprotein changes. ResultsNo difference was observed for lesions between wild-type and transgenic PGIP1 during the first 72 hpi. Rhamnogalacturonan I (RG-I) levels increased at the infection site. The cell wall glycoproteins, arabinogalactan proteins and extensin proteins, show higher signals in the lesion and adjacent tissue in response to Botrytis cinerea infection. DiscussionRG-I and cell wall protein reorganisation in grapevine PGIP1-expressing tobacco lines upon infection with Botrytis cinerea suggest cell wall remodelling enhances fungal resistance.
DOI: 10.3389/fpls.2026.19357362026-04-02
Prerana Upretee, Manjula S. Bandara, Randy W. Purves, Yongfeng Ai, Lawrence V. Gusta, Karen K. Tanino
Late fall seeding (aka dormant seeding) can offer significant benefits over spring seeding, including earlier crop maturity, increased grain yield, and reduced risk of frost damage. However, this practice in Western Canada has not yet been adopted due to failures of canola crop establishment the following spring. A series of experiments was conducted on lentil (Lens culinaris Medik.) seeds to identify which characteristics are associated with winter survival and freezing tolerance. The lentil crop was used as a model system due to its variation in seed characteristics. We evaluated 38 genotypes for water uptake at +2 °C and freezing tolerance (LT50, LD50). Seed characteristics, including thousand-seed weight (TSW), surface area, volume, coat thickness, starch, protein and phenolic content, were quantified to determine their impact on water uptake and freezing tolerance. The total water uptake amount was positively and linearly correlated with TSW, seed surface area, volume and starch content, whereas it was negatively correlated with protein and phenolic content. Seeds that were frozen after imbibition exhibited lower germination percentages than seeds frozen without prior imbibition, indicating increased hydration is a key factor contributing to the loss of freezing tolerance. These findings suggest that seed morphological traits and biochemical composition modulate freezing tolerance primarily through their influence on water uptake dynamics. This research may help improve winter survival of fall-seeded spring crops, such as lentils, enabling a shift from conventional spring planting to late-fall seeding, potentially transforming crop establishment practice on the semi-arid Canadian prairies.
DOI: 10.3389/fpls.2026.18025662026-04-02
Chongqin Luo, Fusen Yang, Yuhong Pu, Yanxia Kang, Yanlin Ma, Guangping Qi, Chungang Jing, Huile Lv, Haiyan Li, Yuanbo Jiang, Mingzhu Wang
AbstractGoji berry planting in arid saline-alkali areas faces the challenges of soil micro-ecological imbalance and excessive application of nitrogen fertilizer. ObjectivesTo clarify the interactive effects of different planting patterns and nitrogen application levels on the structure, diversity and function of soil microbial communities in the root zone of goji berry in arid saline-alkali areas, which is of great significance for optimizing the planting system of goji berry in this area and reducing nitrogen application rates and improving nitrogen use efficiency. MethodsBased on field experiments, this study set up two planting patterns: goji berry monoculture and goji–alfalfa intercropping, four nitrogen application gradients: 0 kg·hm-² (N0), 150 kg·hm-² (N1), 300 kg·hm-² (N2), and 450 kg·hm-² (N3). The culturable microbial counts, community structure, diversity and functional genes of bacteria and fungi were analyzed by dilution coating plate method, high-throughput sequencing and functional prediction. Results: Compared with monoculture, the abundances of culturable soil bacteria and actinomycetes were significantly increased under the goji–alfalfa intercropping pattern, while the abundance of culturable fungi and the relative abundance of potential pathogens were inhibited, and the bacterial community structure was optimized. For example, the relative abundance of Proteobacteria decreased, and the proportion of Gemmatimonadota, Actinomycetota and Thermomicrobiota, increased. Diversity analysis showed that N1 treatment was beneficial to maintain the diversity and stability of bacterial and fungal communities in the goji-alfalfa pattern, while N3 treatment significantly inhibited microbial diversity in the goji berry monoculture pattern. The functional prediction showed that the function of bacteria was mainly amino acid metabolism and carbohydrate metabolism. The ILN1 treatment appeared to facilitate the transformation of fungi to mixed trophic strategies such as endophyte-plant pathogens, while the goji berry monoculture pattern tended to rely more heavily on saprophytic nutrition.ConclusionsIn the arid saline-alkali area, the nitrogen reduction management mode of goji-alfalfa intercropping with 150 kg·hm-² could effectively reconstruct the microbial community in the root zone of goji berry. It is a suitable cultivation and nitrogen application management mode for the green and sustainable development of goji berry industry in this area.
DOI: 10.3389/fpls.2026.17936322026-04-02
Guoji Wang, Duo Zhao, Xiaoyu Hu, Haowei Zheng, Wei Wang, Pengyu Bai, Long Miao, Huihui Gao, Longlong Wang, Hongye Sun, Jiajia Li
100-seed weight (100-SW) is a critical determinant of soybean yield. The identification and functional characterization of its underlying genes are therefore essential for the genetic improvement of seed and yield-related traits. A residual heterozygous line (RHL) segregating for 100-SW was derived from a recombinant inbred line (RIL) population generated by crossing small-seed (19.75 ± 1.93 g) and large-seed (26.20 ± 0.82 g) soybean parents. Phenotypic segregation of 100-SW was analyzed, and Chi-square test was used to verify the segregation ratio. Bulked segregant analysis combined with whole-genome sequencing (BSA-seq) was performed using both Euclidean distance and index algorithms to map the target gene. Functional annotation, molecular marker validation, and germplasm resequencing were conducted to identify the key candidate gene and its haplotypes. Phenotypic analysis showed significant segregation and normal distribution of 100-SW in the RHL, with a Chi-square-verified 1:2:1 segregation ratio, indicating control by a single nuclear gene. BSA-seq mapped the gene to a 5.46 Mb region on chromosome 19, where 74 non-synonymous SNPs in coding sequences were identified (including one causing initiation codon loss), distributed across 36 genes. GmDt1 (Glycine max Determinant stem 1) was confirmed as the key candidate gene, with a G-to-T non-synonymous mutation in its first exon as the functional locus (validated in the original RIL population). Resequencing of diverse germplasm classified GmDt1 into five haplotypes; the large-seed haplotype GmDt1-H2 was absent in wild soybeans, present in 9.07% of landraces, and 15.83% of cultivated soybeans. The gradual increase in the frequency of GmDt1-H2 from wild to cultivated soybeans suggests that this haplotype has been positively selected during soybean breeding. Identification of GmDt1 and its functional mutation provides a valuable molecular target for the genetic improvement of soybean seed traits and yield.
DOI: 10.3389/fpls.2026.18019202026-04-02
Natalie J Graham, Gancho Slavov, Steve A. Wakelin, Jaroslav Klápště, Nicola J. Day
IntroductionBoth evolutionary history and recent breeding selections can influence plant microbiomes, with closely-related individuals often having more similar microbiomes. Pinus radiata D.Don is an emerging conifer model species for investigating tree-microbiome interactions. However, little is known about how the P. radiata microbiome covaries with host genotype, especially beyond the seedling stage. MethodsWe sampled the root microbiome of 528 individual P. radiata trees (age = 9 yrs), comprising four clonal copies each of 132 host genotypes from 28 full-sib families, from a clonal breeding trial in New Zealand. We determined whether variations in the bacterial and fungal root microbiomes were associated with host ancestry (i.e., provenance), family, and genotype.ResultsHost family was associated with fungal but not bacterial root microbiome composition, whereas broader ancestry and individual genotype within families had no detectable effect on either bacterial or fungal microbiome composition. While core (in ≥80% samples) amplicon sequence variants (ASVs) typically had negligible heritability, the relative abundances of 83 bacterial and 13 fungal non-core ASVs had low to moderate broad-sense heritabilities (0.2 to 0.46). Host genetic effects associated with abundances of heritable ASVs were primarily non-additive and likely involve complex gene interactions. DiscussionOur study revealed subtle host family effects for the root fungal microbiome of P. radiata, with several heritable bacterial and fungal ASVs. This study broadens our understanding of host genetic influences on the composition of the root microbiome of P. radiata and indicates there are both opportunities and challenges for including microbiome-related traits in tree breeding programmes.
DOI: 10.3389/fpls.2026.17933742026-04-01
Yuanqiao Li, Yunni Wang, Wenfang Xu, Jinkai Tan
IntroductionTree intrinsic water use efficiency (iWUE) is an important metric for carbon and water balance in forest ecosystems. Tree iWUE has widely increased due to rising atmospheric CO2 and intensified drought. However, the dominant effects of rising atmospheric CO22, vapor pressure deficit (VPD), and soil moisture on iWUE are not fully understood.MethodsWe developed tree-ring width, stable carbon and oxygen isotopic chronologies derived from Chinese pine (Pinus tabulaeformis) stands across northern China to quantify the ecophysiological responses of iWUE to atmospheric CO2 and drought. ResultsiWUE was significantly correlated with atmospheric CO2 and VPD at both dry and wet sites. Furthermore, increased assimilation rate led to increased iWUE at both dry and wet sites. Notably, the beneficial effect of atmospheric CO2 on iWUE outweighed that of VPD in Chinese pine. DiscussionOur findings highlight the dominant role of rising atmospheric CO2 in enhancing assimilation rate and increasing iWUE of Chinese pine and will aid in defining the performance of this tree species under climate change in northern China.
DOI: 10.3389/fpls.2026.17210572026-04-01
Yu Chen, Yuyuan Chai, Xi Chen, Jing Shi
IntroductionThe rhizosphere metabolome is a crucial mediator of plant-substrate interactions, yet how different cultivation substrates reprogram this metabolic interface and influence crop performance remains poorly understood.MethodsUsing tomato as a model, we employed non-targeted metabolomics based on solvent extraction followed by gas chromatography-mass spectrometry (GC-MS) to compare rhizosphere metabolic profiles under three substrates: conventional facility soil (SL), pinecone residue (PR), and peat substrate (PS).ResultsWe identified and annotated 276 metabolites, with lipids and lipid-like molecules being the most abundant class (24.28%). Substrate type fundamentally reshaped the metabolome, with PR inducing the most distinct profile and PS triggering the most extensive metabolic reprogramming (277 differential metabolites). Notably, over 91% of differential metabolites were up-regulated upon tomato cultivation. The superior physicochemical properties (e.g., lower bulk density, higher nutrient availability) of organic substrates (PR and PS) were linked to both the distinct metabolic signatures and significant enhancements in tomato growth and fruit quality, particularly in PS which showed an 80.08% yield increase and a 50.19% boost in fruit vitamin C content.DiscussionOur findings demonstrate that organic substrates, especially peat, enhance plant performance by activating a more diverse and functionally specialized rhizosphere metabolome, providing a mechanistic basis for optimizing substrate selection in facility agriculture.
DOI: 10.3389/fpls.2026.17837192026-04-01
Dashuang Cao, Dongliang Guo, Chunyan Gu, Wanwan Fu, Xin Zhang, Wenhong Ma, Jiacong Li, Haixia Jiang, Huixin Zhao
The GhABA2 gene encodes a short-chain dehydrogenase/reductase involved in abscisic acid (ABA) biosynthesis and plays a crucial role in plant salt stress responses. To explore its function in cotton salt tolerance, we performed bioinformatic analysis, heterologous overexpression in Arabidopsis, and virus-induced gene silencing (VIGS) in cotton. Bioinformatic prediction revealed that the promoter region of the GhABA2 contains multiple cis-acting elements associated with ABA, light, and stress responses. Subcellular localization analysis indicated that GhABA2 was predominantly localized in the cytoplasm. Overexpression of GhABA2 in Arabidopsis significantly enhanced salt tolerance, as manifested by increased germination rates and root elongation. This was accompanied by a reinforced antioxidant system, with elevated activities of catalase (CAT), peroxidase (POD), glutathione reductase (GR), and ascorbate peroxidase (APX), alongside reduced accumulation of malondialdehyde (MDA) and H2O2. Furthermore, the transgenic lines exhibited higher relative water content (RWC), proline accumulation, and increased endogenous abscisic acid (ABA) levels under salt stress. Consistently, the expression of stress-responsive genes and ABA biosynthesis genes (AtNCED3, AtAAO3) was upregulated. Conversely, virus-induced gene silencing (VIGS) of GhABA2 in cotton compromised salt tolerance, characterized by diminished antioxidant enzyme activities (superoxide dismutase SOD, POD, GR, APX), reduced ABA content, and lower RWC and proline levels, but higher MDA and H2O2 accumulation. Correspondingly, the transcript levels of ROS-related genes and cotton ABA biosynthesis genes (GhNCED3a, GhNCED3c, GhAAO3) were downregulated. These findings demonstrate that GhABA2 positively regulates salt tolerance by modulating ABA biosynthesis and the antioxidant defense system. These findings elucidate the role of GhABA2 in modulating cotton salt stress responses and highlight its potential as a genetic target for breeding salt-tolerant cotton varieties.
DOI: 10.3389/fpls.2026.18032312026-04-01
Sunil Kumaraswamy, Yinghua Huang
Plant resistance to insects and diseases is a cornerstone of sustainable agriculture, reducing dependence on chemical pesticides and enhancing long-term crop resilience. Plant resistance is a suite of constitutive and inducible defenses, including structural barriers, biochemical defenses, signaling pathways activated upon recognition of pest or pathogen derived cues. Understanding how plants perceive biotic stress and mobilize these defenses through secondary metabolite production, reinforcement of physical barriers, and coordinated regulation of defense genes, is essential for designing effective management strategies Host plant resistance to insect herbivores exemplifies how specific plant traits can deter feeding, limit pest survival, or reduce reproduction. Advances in biotechnology, such as CRISPR/Cas9-based gene editing, RNA interference (RNAi), and transgenic approaches, have accelerated the development of crops with enhanced and durable resistance. These technologies enable precise manipulation of key resistance genes and pathways. Likewise, the integration of traditional methods with marker-assisted selection and genomic selection is improving the efficiency and accuracy of developing resistant cultivars. This review highlights the importance of dissecting plant-insect and plant-pathogen interactions at the molecular, biochemical, physiological levels to inform robust resistance integration. Future research that leverages advanced technologies and integrates resistance traits with agronomic performance will be pivotal for advancing sustainable pest management and ensure global food security. Together, these insights underscore the essential role of plant resistance in integrated pest management and crop improvement programs.
DOI: 10.3389/fpls.2026.1789793