Abiotic stress represents a significant and increasing challenge to global crop productivity and food security. Calcium (Ca2+) signaling, initiated by specific “Ca2+ signatures” and interpreted by sensor proteins such as calcium-dependent protein kinases (CDPKs/CPKs) and the CBL-CIPK network, functions as a key regulator of plant adaptive responses. However, contemporary elite cultivars exhibit a reduced genetic base, having forfeited numerous resilient alleles present in wild relatives and landraces during intensive, yield-focused breeding. This review synthesizes evidence demonstrating that natural genetic variation within these calcium sensor genes significantly influences key agronomic traits, including ion homeostasis, stomatal regulation, and water-use efficiency. We then evaluate​ the effectiveness of integrated genomic approaches, such as pan-genomics, genome-wide association studies (GWAS), and CRISPR-Cas9 genome editing, for systematically identifying and validating these beneficial alleles. Finally, we propose a translational roadmap for the targeted introgression of enhanced calcium sensor variants into modern germplasm. This work provides a strategic framework for developing a new generation of climate-resilient crops, offering a pathway to safeguard global food systems against increasingly erratic environmental conditions.

A class of small RNAs, the phased small interfering RNAs (phasiRNAs), are specifically expressed in anthers and closely associated with male fertility in monocots. However, the specific 21-nt phasiRNAs involved in regulating male fertility remain unclear. Here, we identified a functional 5'-A phasiRNA (referred to as osphasiR1_1) that mediates the cleavage of OsARF7 transcripts to promote male fertility. CRISPR-Cas9 knockout and short tandem target-mimic knockdown of osphasiR1_1 led to significantly reduced male fertility and seed setting. Further mechanistic experiments revealed that osphasiR1_1 mediates OsARF7 cleavage and promotes male fertility in an OsAGO2-dependent but MEL1/OsAGO5c-independent manner. OsARF7 exhibits transcriptional activation activity, and its overexpression hyperactivates target genes such as the key fertility-related gene ubiquitin-fusion ribosomal protein L40 4 and heat shock protein 70-4. Identification of the osphasiR1_1-OsAGO2-OsARF7 regulatory module fills a critical gap in the phasiRNA pathway and expands our understanding of phasiRNA-mediated gene regulation, providing new insight into the molecular mechanisms that control male fertility in monocots.

High temperature disrupts chlorophyll synthesis and chloroplast stability, decreasing chlorophyll content. However, the mechanism of high temperature inhibition chlorophyll synthesis remains unknown in horticultural plants. Here, we investigated the impact of high temperatures on the precursors and key genes involved in chlorophyll synthesis in cucumber leaves, including glutamate (Glu) and 5-aminolevulinic acid (ALA), along with enzymes such as glutamyl-tRNA reductase (GluTR). High temperatures inhibited the conversion of Glu to ALA, a critical step in chlorophyll synthesis, with GluTR playing a key role in this inhibition. Manipulating the expression of CsGluTR1, a gene coding for GluTR, showed that overexpression enhanced ALA synthesis and chlorophyll content under high-temperature stress in tobacco, and silencing CsGluTR1 in cucumber plants had an opposite effect. The enhanced expression of CsGluTR1 improved the net photosynthetic rate. Furthermore, CsMYB44 bound to the promoter of CsGluTR1 and repressed its transcription under high temperatures to negatively regulate chlorophyll synthesis. In conclusion, high temperature induced the expression CsMYB44, which negatively affected CsGluTR1 expression, leading to blocked chlorophyll synthesis and decreased chlorophyll content in cucumber.

Coastal saline-alkali soils severely constrain agricultural production. Through field plot experiments, this study investigated the amelioration effects of co-applying of acid-modified biochar-based microbial inoculants with different exogenous amendments (chemical fertilizers, organic fertilizers, and organic acids) on coastal saline-alkali soils, as well as the underlying microbial-driven mechanisms. Compared with the CF treatment, the combined application of acid‑modified biochar‑based microbial inoculants with chemical fertilizers (BMF) and with organic acids (BMOA) both significantly decreased soil pH and EC, while concurrently raising soil nutrient levels and enzymatic activities. These treatments also led to marked improvements in wheat yield, with increases of 14.43% and 7.12% over the CF control, respectively. The BMF treatment enriched plant growth-promoting rhizobacteria (PGPR, e.g., Massilia), whereas the BMOA treatment shaped a highly diverse community dominated by generalist species (e.g., Pseudomonas).Both treatments significantly elevated the abundance of genes associated with C (e.g., cbbL, fhs), N (e.g., ureC, nosZ), and P (e.g., pky, phoR) cycling, thereby enhancing soil C, N, P cycling functions and soil multifunctionality, which represents an important pathway associated with crop productivity improvement under soil remediation treatments, as suggested by integrated statistical analyses. In conclusion, the combined application of biochar -based microbial inoculants with chemical fertilizers or organic acids can construct a synergistic improvement pathway of “soil improvement-microbial reorganization-function enhancement” by collaboratively optimizing the soil environment, directionally regulating the microbial community, and activating nutrient cycling functional genes. This offers a feasible technical scheme and theoretical basis for the green and sustainable remediation of coastal saline-alkali soils.

Root rot is a severe disease affecting cucumber production, and the use of high-quality rootstocks can enhance disease resistance. In this study, inoculation experiments with Fusarium were conducted on 30 pumpkin inbred lines, leading to the identification of an excellent pumpkin rootstock C53. This line exhibited significantly lower disease index and incidence rates compared to the susceptible line C70. Transcriptomic profiling via RNA-seq integrated with weighted gene co-expression network analysis elucidated the molecular basis of this differential resistance. The data demonstrated that C53 mounted a coordinated, multi-layered defense response. This includes metabolic reprogramming toward a root sugar profile less favorable to the pathogen, with sustained trehalose biosynthesis; enhanced immune perception and signaling characterized by resilient expression of key pattern recognition receptors (e.g., tuf, ERF, FLS2, EIX1/2, CERK1) and robust activation of both pattern-triggered and effector-triggered immunity; and enhanced defense signaling via a compensatory MAPK-WRKY network, where MPK4 activation counteracted upstream suppression. Structurally, C53 reinforced physical barriers through calcium-signaling-mediated enhancement of cell wall biosynthesis involving cellulose and lignin, alongside strengthening the casparian strip. In contrast, C70 displayed a dysregulated defense program, marked by accumulation of pathogen-favored carbohydrates, broad suppression of early immune signaling nodes, and inadequate cell wall reinforcement, culminating in heightened susceptibility. The resistance of C53 thus arose from the synergistic integration of metabolic, immunological, and structural adaptations, providing a comprehensive physiological framework for its enhanced tolerance. These findings not only identify a valuable germplasm but also delineate key molecular targets and pathways for breeding Fusarium-resistant cucurbit rootstocks.

The selection and breeding of salt-tolerant rice and the use of saline–alkali land for rice cultivation are crucial for food security. However, most studies have focused only on the seedling salt tolerance stage, with little research on the salt tolerance mechanisms during the reproductive growth period. This study selected the salt-tolerant rice line SR17, the salt-tolerant variety SR86, and the salt-sensitive variety IR29 as research subjects. Two salt stress gradients of 0% and 0.5% (7.8 dS m−1) were established. Salt stress was applied continuously from rice transplanting to the maturity stage, and the differences in response mechanisms during the young panicle stage under long-term salt stress were analyzed. The results showed that, under salt stress, SR17 exhibited the least lipid peroxidation and membrane damage, followed by SR86, while IR29 suffered the most severe damage. SR17 and SR86 could reduce oxidative damage and maintain membrane system integrity by activating the antioxidant enzyme system and accumulating soluble proteins. In contrast, the antioxidant system in IR29 was insufficiently activated; this indicates that the adaptability of this variety to salt-induced oxidative stress is relatively poor. The chlorophyll content and most photosynthetic parameters in SR17 showed no significant changes, and leaf gas exchange performance and chlorophyll status were the least affected, whereas IR29 suffered severe damage. Agronomic trait investigation revealed that, compared with the control, SR17 exhibited the smallest reductions in plant height, spikelets per panicle, 1000-grain weight, grain yield per plant, and main spikelet number under salt stress, and the decreases in key yield-related indicators—effective panicle number, grain yield per plant, and seed setting rate—were not significant. This study confirms that SR17 possesses superior salt tolerance and holds potential for further breeding and multi-environment trials, while also providing an important basis for elucidating the physiological mechanisms of salt tolerance during the reproductive stage of rice.

High temperature poses a serious threat to agriculture and plant growth. Ammonium (NH4 +) and nitrate (NO3 -) are the two main inorganic nitrogen sources used by plants. However, how ammonium shapes the plant response to heat stress remains a mystery. Here, we found that cucumber (Cucumis sativus L.) plants exhibited an increase in the NH4 +/NO3 - ratio in response to heat stress. Overexpression of Nitrate Transporter 1/Peptide Transporter Family 4.4 (CsNPF4.4) in cucumber compromised thermotolerance and reduced the NH4 +/NO3 - ratio, whereas CsNPF4.4-silenced plants exhibited enhanced thermotolerance and an increased NH4 +/NO3 - ratio. Using yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assay, we found that ERF/AP2 transcription factors 2-1 (CsRAP2-1), which was highly induced by high temperature, directly bound to the promoter of CsNPF4.4 to suppress its expression. Silencing CsRAP2-1 compromised thermotolerance, while overexpression CsRAP2-1 showed opposite effects. Meanwhile, we identified that Ammonium transporters 1 (CsAMT1) interacted with CsNPF4.4. Silencing CsAMT1 compromised thermotolerance and decreased the accumulation of NH4 +, while overexpression of CsAMT1 showed opposite effects. Importantly, CsNPF4.4 influenced the expression of CsAMT1 and inhibited activity of CsAMT1 to suppress NH4 + transport. Thus, heat stress induced the expression of CsRAP2-1, which repressed CsNPF4.4 transcription, leading to enhanced CsAMT1 expression and activity and ultimately increasing the ratio of NH4 +/NO3 - to enhance high-temperature stress tolerance. These findings not only uncover a regulatory module CsRAP2-1-CsNPF4.4-CsAMT1 that fine-tunes ammonium/nitrate homeostasis to enhance thermotolerance, but also provide actionable targets for molecular breeding or nutrient management strategies aimed at improving crop resilience under high-temperature stress.

Fragaria vesca L., a widely distributed model species, serves as a key resource for studying the evolution and genetics of the Fragaria genus. Research has shown that R2R3-MYB transcription factors are crucial for plant growth and development. However, their specific role in cold resistance in F. vesca is not well understood. In this study, we used the latest genome data for the strawberry (F. vesca v6.0). We performed a genome-wide identification of the R2R3-MYB gene family in F. vesca. We identified a total of 106 R2R3-FvMYBs. Based on their predicted functions in plants, we classified these genes into 25 distinct subfamilies. We then conducted a comprehensive bioinformatics analysis of this family. We performed a detailed examination of the R2R3-FvMYBs structures and physicochemical properties. This analysis provided five key parameters for each protein: molecular weight, the number of amino acids, theoretical isoelectric point, grand average of hydropathicity (GRAVY), and instability index. Gene duplication analysis suggested that segmental duplications were a primary driver of the proliferation of this gene family. Promoter cis-acting element prediction revealed that a large proportion of R2R3-FvMYBs possess elements predominantly associated with phytohormone responsiveness and biotic/abiotic stress responses. Quantitative real-time reverse transcription PCR (qRT-PCR) results confirmed that the expression levels of several R2R3-FvMYBs were upregulated under cold stress. Furthermore, compared to wild-type controls, the overexpression of FvMYB103 in Arabidopsis thaliana enhanced cold tolerance, accompanied by increases in the relevant physiological indices. Collectively, these findings support further investigation into R2R3-MYB gene family to directly assess their contribution to cold resistance.

Crataegus spp. plants are valuable horticultural crops because of their extensive use in Chinese herbal medications, cosmetics, food production, and other industries. However, the wide variety of species, similar morphological characteristics, inherent hybridization, apomixis, and polyploidy have led to confusion in terms of their taxonomic status. Herein, a total of 18 complete chloroplast genomes including 17 Crataegus species and 1 Mespilus species were newly sequenced and comprehensively analyzed for comparative genomics and phylogenetic relationships. The 18 chloroplast genomes possessed typical quadripartite structures with lengths from 159,638 to 159,973 bp in size. These chloroplast genomes encode 119–131 genes, including 37 transfer RNA (rRNA) genes, 8 ribosomal RNA (tRNA) genes, and 74–85 protein-coding genes (PCGs). In addition, 23–54 long repeat sequences and 74–87 simple sequence repeats (SSRs) were detected. The examination of Ka/Ks ratios for 18 chloroplast genomes revealed that the rpoC2 gene was significantly positively selected. Additionally, we identified nine distinct hotspot regions (infA, ndhC, pasl, rps19, ndhC~trnV-UAC, psbZ~trnG-UCC, rpl33~rps18, trnH-GUG~psbA, and trnR-UCU~atpA), and verified that ndhC~trnV-UAC might be used as a foundation for subsequent molecular marker studies aimed at identifying Crataegus species. Maximum likelihood and Bayesian phylogenetic trees using chloroplast genome sequences consistently revealed genetic relationships among Crataegus and Mespilus species, and confirmed the taxonomic status of Crataegus accessions (GSSZ, JRY, RR2H, RR3H, ZWSZ). The results of divergence time showed that the crown age of C. subg. Crataegus was about 33.487 Ma, and then started to diverge into the C. subg. Americanae and C. subg. Sanguineae around 27.059 Ma. Based on the results of molecular evidence, we speculate that genus Crataegus originated earliest from European-derived species within C. subg. Crataegus. Biogeographic and molecular dating analyses suggested that China represented a putative maternal origin of Crataegus species. The complete chloroplast genomes of Crataegus not only enable the resolution of phylogenetic relationships within the genus but also offer novel insights into chloroplast genome structure variation and evolution. Additionally, the identified divergent DNA regions hold significant utility for species identification and phylogenetic reconstruction in Crataegus.

Anthracnose caused by Colletotrichum gloeosporioides is a major threat to tea cultivation; however, the molecular mechanism underlying different resistance among tea cultivars remains unclear. We identified distinct expression patterns of CsMYB82 between anthracnose-resistant and susceptible varieties after infection with anthracnose from previous RNA-seq data. We further investigated the role of CsMYB82 within a lignin-associated regulatory network during anthracnose responses. We found that CsMYB1 negatively regulates CsMYB82 expression by Y1H screen. Additionally, we identified the interaction between CsMYB82 and CsbHLH48 both in vitro and in vivo. DNA-affinity purification sequencing (DAP-seq) revealed that CsMYB82 directly binds to the promoter of CsCAD4, and this binding activity is enhanced in the presence of CsbHLH48. Functional analyses indicated that overexpression of CsMYB82 or CsCAD4 in tobacco and tea leaves was associated with increased susceptibility to anthracnose, whereas transient silencing of CsMYB82 or CsCAD4 via virus-induced gene silencing (VIGS) in tea leaves resulted in reduced disease symptoms accompanied by elevated lignin accumulation. The functional analysis of CsMYB1 showed the opposite phenotype. Collectively, these results suggest that CsMYB82 participates in a transcriptional regulatory module involving CsMYB1, CsbHLH48, and CsCAD4, which modulates lignin biosynthesis and influences anthracnose responses in tea plants. This study provides mechanistic insights into the transcriptional regulation of lignin-associated defence responses and contributes to a better understanding of anthracnose resistance in tea.

Accurate and real-time diagnosis of nitrogen (N) status is critical for precision management in greenhouse tomato production. In this study, a robust and generalizable critical nitrogen concentration (Nc) dilution curve (Nc = 3.19 & times; AGB(-0.20)) was first established using a Bayesian approach based on above-ground biomass (AGB) across diverse genotype & times; environment & times; nitrogen management scenarios. The unified Nc curve reduced parameter uncertainty and enabled consistent estimation of the nitrogen nutrition index (NNI) across fruit types and growing seasons. Building on this physiological foundation, this study further developed a physiologically informed multimodal deep learning framework by integrating time-series RGB imagery, SPAD measurements, air temperature, and phenological stage information. Built on a CNN-Transformer architecture, the framework incorporates i) temporal modality alignment to synchronize heterogeneous data streams, ii) growth-stage-aware weighting to emphasize phenologically relevant inputs, and iii) semantic feature enhancement to better link visual information with crop physiological status. On an independent test dataset, the proposed model achieved an R-2 of 0.89 with an RMSE of 0.043, outperforming a single-frame CNN baseline (R-2 = 0.78, RMSE = 0.072). Modality contribution analysis indicated that RGB imagery, temperature, and SPAD measurements accounted for approximately 52.3%, 29.6%, and 18.1% of model performance, respectively, consistent with SHAP-based importance rankings. Temporal importance analysis further revealed dominant contributions of RGB features during early to mid-growth stages (t2 similar to t4), with increased relevance of temperature and SPAD at later phenological stages (t7 similar to t8). These results demonstrate the potential of physiology-informed deep learning for interpretable, stage-sensitive nitrogen monitoring in controlled-environment agriculture.

Autophagy, an evolutionarily conserved mechanism for cellular homeostasis, is essential for plant adaptation to abiotic stresses. DNA methylation is well-established as an epigenetic regulator of development and stress responses; however, its direct modulation of autophagy under salt stress remains unexplored. In this study, we found that a salt-sensitive cucumber (Cucumis sativus L.) cultivar exhibited higher accumulation of ubiquitinated proteins correlating with a lower level of autophagic activity compared to a salt-tolerant cucumber cultivar under salt stress. Whole-genome bisulfite sequencing analysis revealed that salt stress induced CG hypomethylation in the coding sequence (CDS) region of Autophagy-related gene 6 (CsATG6) in cucumber, coinciding with its upregulation and autophagy activation. The CDS hypomethylation of CsATG6 was induced by DNA methylation inhibitor 5-azacytidine (5-Aza), resulting in its transcriptional upregulation, which was accompanied by increased autophagic activity and decreased accumulation of ubiquitinated proteins. Silencing of CsATG6 decreased autophagic activity and salt tolerance, whereas its overexpression enhanced both. Loss of function of CsATG6 compromised 5-Aza-induced autophagic activity and salt tolerance. Furthermore, salt stress and 5-Aza co-induced Repressor of silencing 1b (CsROS1b) expression, which actively demethylated CsATG6 at CG sites and increased CsATG6 transcript abundance, enhancing autophagosome formation and reducing ubiquitinated protein accumulation. Our study reveals a mechanism by which CsROS1b-mediated CG hypomethylation of CsATG6 activates autophagy to enhance salt stress tolerance in cucumber.

Although salt acclimation is a recognized strategy for improving crop salt tolerance, its specific role in tomato (Solanum lycopersicum L.) remains unclear. This study investigated the effects of salt acclimation on enhancing salt tolerance in tomato seedlings through physiological and transcriptomic analyses. Here, we found that T3 acclimation treatment (irrigation with 14 mL of 7.5 g L−1 NaCl solution per plant) effectively conferred enhanced salt tolerance in tomato seedlings, with plant height, stem diameter, leaf area, chlorophyll content, net photosynthetic rate, and soluble protein content increasing by 4.52, 5.13, 3.16, 10.78, 11.85, and 25.96%, respectively, compared with the control. T3 treatment also reduced oxidative damage and ionic stress, as evidenced by reduced electrolyte leakage, lower malondialdehyde content, and a decreased root Na+/K+ ratio, while simultaneously boosting antioxidant enzyme activities. Membership function analysis confirmed T3 as the optimal treatment, with a 9 d duration consistently benefiting multiple cultivars. Transcriptomic analysis revealed that salt acclimation upregulated genes associated with phenylpropanoid biosynthesis, lignin catabolic process, and peroxidase activity, suggesting that these pathways might mediate acclimation-induced salt tolerance through promoting lignin biosynthesis to reduce Na+/K+ ratio and enhancing reactive oxygen species’ scavenging capacity to maintain cellular homeostasis. Our results indicate that tomato seedlings acclimated with 14 mL of 7.5 g L−1 NaCl solution per plant for 9 d significantly improves salt tolerance through coordinated physiological adjustments and transcriptional reprogramming.

Far-red light (FR, 700-800 nm) is a crucial environmental signal which regulates plant photosynthesis and salt stress tolerance, but its regulation mechanism is not well-addressed. In the present study, tomato seedlings under 0 mM NaCl or 150 mM NaCl salinity were treated with supplemental FR (R: FR = 0.8) or without supplemental FR (R: FR = 7.4). The growth components, leaf anatomical structure, photosynthetic capacity, and activities of key enzymes involved in carbon fixation were determined, along with the expression of related genes. Results showed that the increased dry mass with supplemental FR under normal conditions (non-salt stress, i.e., 0 mM NaCl) was due to the increase in net assimilation rate (NAR), while that under salt stress was attributed to the improvement in both NAR and leaf area ratio (LAR). FR supplementation elevated the palisade/spongy tissue ratio (P/S) by 10.92%, improving leaf anatomical traits and water retention capacity. In addition, FR addition improved the activities of PSII and PSI via increasing the actual quantum yields of PSII (ΦPSII) and PSI (ΦPSI) by 9.86% and 5.01%, respectively, and concomitantly decreasing the quantum yields of non-regulated non-photochemical quenching (ΦNO) and acceptor-side limitation in PSI (ΦNA) by 19.77% and 11.36%, respectively. Furthermore, FR supplementation not only increased the activities of Rubisco by 36.36% and Rubisco activase (RCA) by 40.65%, but also upregulated the expression of related genes, thereby resulting in higher CO2 fixation capacity. Synergistic improvements in morphological, anatomical, and photosynthetic properties induced by supplemental FR enhanced photosynthetic performance and further promoted carbon assimilation in salt-stressed tomato seedlings. These findings reveal the FR-mediated salt tolerance mechanism in tomato seedlings, thus providing guidance for alleviating secondary soil salinization in controlled agricultural systems.

Carbon-based nanomaterials exhibit promising potential in regulating plant growth and development, but their regulatory effects and molecular mechanisms on tomato remain to be systematically explored. This study used Solanum lycopersicum cv. Micro-Tom to investigate the regulatory mechanisms of root-applied graphene quantum dots (GQDs, 100 mg·L⁻¹) and graphene oxide (GO, 200 mg·L⁻¹) on tomato growth, development, and transcriptomic responses. Phenotypic analysis showed both nanomaterials significantly promoted growth, with increases in plant height (11.93%vs 12.93%), stem diameter (4.70%vs 6.44%), leaf area (3.86%vs 5.09%), canopy width (7.13%vs 5.15%), lateral branch number (4.17%vs 9.37%), root length (13.28%vs 13.46%), and root biomass (27.48%vs 81.36%) under GQDs and GO treatments, alongside an early flowering phenotype. Transcriptomic profiling revealed that GQDs induced 7881 differentially expressed genes (DEGs), far more than the 2628 DEGs induced by GO, and the two nanomaterials triggered distinct tissue-specific differential gene expression patterns: GQDs and GO differentially regulated root genes related to glycerolipid metabolism, phenylpropanoid biosynthesis, and transmembrane transport; both affected stem IAA/ABA signaling and substance transport with distinct patterns; GQDs activated leaf zeatin biosynthesis and light-harvesting complex genes, and upregulated flower genes for microtubule assembly, cell wall remodeling, and pectin metabolism. This study reveals tissue-specific transcriptomic responses to GQDs and GO in tomato, providing a theoretical basis for the rational application of carbon-based nanomaterials in sustainable agriculture.

The FAcilitates Chromatin Transcription (FACT) complex, comprising structure-specific recognition protein 1 (SSRP1) and suppressor of Ty 16 (SPT16), plays a key role in regulating gene transcription by facilitating ATP-independent nucleosome assembly. SSRP1 contains an HMG domain that binds to DNA and regulates cell proliferation, apoptosis, and DNA repair. However, its role in plant development remains poorly understood. In this study, we identified a mutant, small kernel 301 (smk301), characterized by reduced kernel size and semi-dwarfism. Map-based cloning revealed that the mutation affects ZmSSRP1 on chromosome 8, which is expressed throughout maize (Zea mays L.) tissues. ZmSSRP1 localizes to the nucleus and interacts with ZmSPT16 to form the FACT complex. Using RNA-seq and ATAC-seq analyses, we identified 3 candidate target genes involved in hormone pathways, all of which show a significant positive correlation with ZmSSRP1 expression. Notably, ZmSSRP1 was enriched in the chromatin open region of brassinosteroid-deficient dwarf 1 (ZmBRD1), which encodes a Brassinosteroid C-6 Oxidase. This indicates that ZmSSRP1 affects maize development by regulating the transcription of ZmBRD1, thereby influencing the brassinosteroid content in maize. Our findings shed light on how the FACT complex influences maize development by modulating the expression of brassinosteroid-related genes, offering insights into the molecular mechanisms underlying plant growth.

Excessive fertilization poses a major threat to sustainable agriculture, resulting in resource waste and environmental degradation. The ecological composite fertilizer (ECF) combined with fertilizer reduction represents a promising strategy to improve rhizosphere microbial diversity in wheat systems. A field experiment, containing six treatments, namely traditional compound fertilizer (TF, applied at the conventional rate) with a 10% reduction (TF90), TF90 plus ECF application (TF90+ECF), TF with a 15% reduction (TF85), TF85 plus ECF application (TF85+ECF), TF with a 20% reduction (TF80), and TF80 plus ECF application (TF80+ECF), was conducted to explore the influences of fertilizer reduction combined with ECF application on wheat yield and rhizosphere soil microbial diversity. Results showed that the TF85+ECF treatment achieved the highest wheat yield at 8,717.33 kg ha−1, which was significantly greater than all other treatments and represented a 30.63% increase over the TF85 treatment. The TF85+ECF group significantly enhanced the activities of the carbon and nitrogen cycling enzymes β-1, 4-glucosidase glucosidase (BG) and urease (UE), and increased the abundances of the functional genes cbbLR and amoA. In the +ECF treatment groups (TF90+ECF, TF85+ECF, and TF80+ECF), linear discriminant analysis effect size (LEfSe) and specialization-occupancy (SPEC-OCCU) analyses identified keystone microbial taxa, including positively correlated taxa with biocontrol and metabolic versatility (e.g., Trichoderma, Solicoccozyma) and negatively correlated potential pathogens (e.g., Alternaria). Co-occurrence network analysis revealed that the TF85+ECF group streamlined bacterial network architecture while enhanced fungal network complexity and connectivity. Mantel tests and correlation analyses indicated that soil organic carbon, BG activity, and cbbLR gene abundance were significantly linked to microbial community structure, and keystone taxa were strongly correlated with soil nutrient cycling functions. Our findings provide a microbiome-based strategy and a novel perspective for sustainable wheat production and targeted microbial management in agriculture.

Accurate estimation of leaf area index (LAI) is fundamental for understanding canopy dynamics and yield formation in greenhouse-grown tomato, yet remains hindered by severe occlusion and structural complexity. However, conventional approaches-such as extinction coefficient-based methods that rely on top–bottom measurements and threshold-based image segmentation with fixed cutoffs-struggle to delineate occluded regions and thus show poor generalization. To overcome these limitations, this study developed an interpretable deep learning framework that integrates porosity-based structural modeling with an enhanced segmentation network, NJ-Unet, for precise and scalable LAI estimation. NJ-Unet incorporates a Smooth Maximum Unit (SMU) activation function and a Spatial-Channel Self-Attention (SCSA) module into the Unet backbone, substantially improving segmentation accuracy and efficiency under complex canopy conditions. Based on segmented leaf masks, a concentric ring-based porosity analysis method was employed to estimate LAI, achieving high estimation efficiency and outperforming optical sensor and destructive sampling methods (R2 = 0.72, RMSE = 0.73, MAE = 0.54). Furthermore, LAI values were used to predict tomato yield across developmental stages, with the strongest correlation observed during the fruiting stage (R2 = 0.90). Altogether, this study demonstrates how coupling interpretable deep learning with porosity-based modeling to enhance the accuracy, efficiency, and applicability of LAI retrieval and yield estimation in protected horticultural systems.

BACKGROUND:Plant citrate synthase (CSY) is involved in the iron deficiency (-Fe) response and aluminum (Al) detoxification. However, knowledge of CSY function in responding to excess iron (+Fe) or Al stress (+Al) is still limited. METHODS:The CDS and promoter of GmCSY3 were isolated from soybean and bioinformatically analyzed. The GmCSY3 expression was detected by qRT-PCR and GUS assay. The growth of GmCSY3 recombinant yeast under +Fe or +Al was detected. The phenotype, CSY activity, citric acid concentration, chlorophyll content, MDA, H2O2, O2- contents, GST, CAT, SOD, and POD activities were examined in GmCSY3 overexpressed and RNAi-suppressed soybean chimeras under +Fe or +Al. Perls and Hematoxylin stained the roots, and the FCR activity was determined. RESULTS:GmCSY3 was induced by +Fe or +Al, but not by -Fe. GmCSY3 enhanced yeast's acid production and resistance to +Fe or +Al. GmCSY3 overexpression in soybean significantly enhanced CSY activity, promoted growth, alleviated oxidative damage caused by +Fe or +Al, with less free Fe3+ and Al3+, and reduced FCR activity, while GmCSY3 RNAi-suppressed showed the opposite effect. CONCLUSIONS:GmCSY3 promotes the process of citrate synthesis, chelates Fe3+ and Al3+, alleviates oxidative damage caused by +Fe or +Al, and modulates iron absorption in plants.

Rapeseed is one of the most important oil crops in the world. Its yield and quality are severely restricted by biotic stress and abiotic stress. Rapeseed seeds play a crucial role in the propagation process, and the microorganisms in the seeds can be vertically passed on to the next generation, which greatly affects the quality, yield and growth of rapeseed. However, from a group perspective, there is currently a lack of systematic research on the composition of seed-associated microbiome within rapeseed seeds. This study utilized the transcriptome data of 218 rapeseed seeds that have been published, focusing on analyzing and comparing the dynamic changes and functional differences in the composition of seed-associated microbiome in rapeseed seeds under normal growth and development, biologic stress and abiotic stress conditions. Since we used public transcriptome data without surface sterilisation control, we refered to the detected microorganisms as seed-associated microbiome. The advantage of this study lies in its application of this method to a large-scale sample of rapeseed populations, which systematically revealed the response characteristics of seed-associated microbiome under different stress conditions. Interestingly, some widely distributed genera were not detected, while rare taxa were found under specific conditions, warranting further verification. Since these microorganisms originated from the seeds, their compatibility with plants and colonization ability may far exceed those of soil-derived agents. In the future, high-throughput screening of strains with excellent antagonistic or repellent effects against major diseases and pests of rapeseed can be conducted from these unique seed-associated microbiome. These strains that were confirmed by culture-based, amplicon or metagenomic approaches can then be used to develop seed coating agents or soil inoculants.