dynamic genetic control. To dissect this dynamic genetic architecture, we performed unconditional and conditional QTL mapping using a recombinant inbred line (RIL) population derived from a cross between Yugu 18 and Jigu 19. Phenotypic analysis showed that PH followed an approximately sigmoidal growth curve, with the most rapid elongation occurring between the jointing and booting stages (T2–T3). Genotype × environment interaction (G×E) effects were also most pronounced at T3. A total of 57 QTL were identified and integrated by meta-analysis into 23 consensus loci. Among these loci, qPH9-1 on chromosome 9 was consistently detected across multiple developmental stages. Notably, this locus exhibited a stage-specific reversal of allelic effects: the Yugu 18 allele increased PH before T3, whereas the Jigu 19 allele increased PH from T3 onward. QTL-by-environment interaction (QEI) analysis further identified T3 as a stage of heightened environmental sensitivity. At this stage, qPH9-1 showed a significant QEI effect, explaining up to 14.06% of the phenotypic variance. Within the qPH9-1 interval, integrated analysis of gene annotation, differential expression in elongating internodes, and haplotype variation prioritized Seita.9G017500, Seita.9G018900, and Seita.9G019900 as high-confidence candidate genes. Collectively, these findings clarify the dynamic genetic architecture of PH in foxtail millet and provide a framework for targeted trait improvement and marker-assisted breeding.

Enhancing photosynthetic efficiency under fluctuating light is critical for improving crop productivity in intercropping systems; however, the role of phosphorus (P) nutrition in regulating photosynthetic induction remains poorly understood. Field and pot experiments with three P supply levels were conducted in a maize–soybean intercropping system to quantify gas exchange in soybean [Glycine max (L.) Merr.] during photosynthetic induction under controlled fluctuating light protocols and to identify P-related drivers of induction kinetics. Adequate P supply increased soybean yield by 26.7%–55.4% relative to P deficiency treatments and concurrently reduced carbon loss during the low-to-high light transitions by 26.5%–37.3%. Photosynthetic limitation analysis revealed that biochemical limitation dominated the induction response under P deficiency, accounting for 72.3% of the total limitation, with stomatal limitation playing a comparatively minor role. Foliar and chloroplast inorganic phosphate (P_i) contents both increased with P supply; notably, chloroplast P_i exhibited a strong, nonlinear relationship with induction performance. A critical threshold was identified at 0.18 mg g⁻⊃1; FW chloroplast P_i; below which induction time increased sharply. Collectively, these findings identify chloroplast P_i availability as a proximal physiological determinant of photosynthetic induction under fluctuating light and point to improving chloroplast P_i status as a promising strategy for reducing carbon loss and enhancing soybean productivity in intercropping systems exposed to highly dynamic light environments.

Soil alkalization, driven by bicarbonate stress, severely inhibits soybean (Glycine max L.) seed germination. While spermidine (Spd) is known to enhance plant tolerance to abiotic stress, whether and how it alleviates bicarbonate stress remains unclear. Here, we demonstrate that Spd treatment significantly alleviates bicarbonate stress experienced by in germinating soybeans, as evidenced by higher germination rates and greater root biomass. Physiological assays revealed that Spd diminishes accumulation of reactive oxygen species accumulation and malondialdehyde while promoting proline accumulation. Transcriptome and weighted gene co-expression network analysis (WGCNA) indicated that Spd continuously upregulates genes in the phenylpropanoid and flavonoid biosynthesis pathways in germinating seeds. Two key genes in these pathways, GmPAL1.1 (Phenylalanine Ammonia-Lyase 1.1) and GmCCR1 (Cinnamoyl-CoA Reductase 1), are associated with seed germination. Furthermore, natural variation in GmPAL1.1 and GmCCR1 is associated with adaptation to saline-alkaline soils: the elite haplotypes GmPAL1.1-Hap1 and GmCCR1-Hap3 are associated with favorable agronomic traits and improved adaptation to these soils. These findings reveal that Spd enhances bicarbonate tolerance by coordinating antioxidant defense mechanisms and activating the phenylpropanoid and flavonoid biosynthesis pathways. In addition, our results identify GmPAL1.1 and GmCCR1 as potential elite genes for breeding alkaline-tolerant soybean cultivars.

 Mulching is a widely adopted and effective agronomic practice that strongly influences soil properties and microbial activity. However, knowledge gaps exist regarding the effects of mulching on soil microbial dynamics, tea yield and quality under organic management. Here, we examined soil properties, microbial community structure, tea yield and quality across seasons under diverse mulching practices (RS: rice straw mulching; WBF: weed barrier fabric mulching; SC: living mulch with soybean and common vetch; Control: no mulching management) in organic tea plantations. Compared with CK, RS and WBF significantly increased soil organic carbon and total nitrogen by 21.6%-23.4% and 15.6%-24.4%. Microbial biomass carbon, bacterial richness and diversity were elevated under all mulching practices. β diversity and microbial community composition have markedly differed after mulching, attributed to changes in soil nutrients, pH, and soil water content. Importantly, RS and WBF enabled a shift from stochasticity to determinism in fungal community assembly. Moreover, mulching enhanced nitrogen cycling function by recruiting beneficial microorganisms, including Bradyrhizobium and Cupriavidus. RS and WBF also enhanced carbohydrate metabolism and energy metabolism of soil bacteria in organic tea plantations. Tea yield increased by 9.36% under RS and 13.7% under SC, while all mulching practices considerably increased water extracts content in tea leaves. In addition, RS and WBF increased the concentration of free amino acids in tea by 15.5% and 20.1%, respectively. The partial least squares path model further revealed that mulching improved tea quality indirectly by enhancing soil nutrient availability and enriching nitrogen-cycling microbial taxa. Overall, mulching can positively regulate the microbial community structure and improve tea yield and quality by influencing the soil environment.

The grain yield of foxtail millet is strongly shaped by sowing-season environments and ecotype adaptation, however the genetic basis of yield components across contrasting regimes remains incompletely resolved. Here, we developed a recombinant inbred line (RIL) population derived from a hybrid between the spring-sowing cultivar Jingu 21 and the summer-sowing cultivar Chuang29, and evaluated eight yield-related traits across eight environments during 2022–2023. Composite interval mapping was performed separately in each environment and 112 QTL signals were identified, which were consolidated into 74 non-redundant QTLs. Among these, 24 were detected in at least two environments, and 47 showed no overlap with previously reported QTL intervals compiled from the literature. QTL clustering revealed multiple co-localized regions, including a prominent chromosome-9 hotspot affecting seven traits and detected 17 times across trait–environment combinations. Homology-informed mining within refined intervals prioritized 27 candidate genes. Haplotype analysis with an independent natural population (n=1,844), identified significant associations for three genes—Seita.3G233000 (panicle length), Seita.4G281800 (thousand-grain weight) and Seita.5G068000 (panicle diameter). Analysis of additive effects found different contributions from the two parents, with Jingu21 contributing more TGW-increasing signals and Chuang29 contributing more PW/GWP-increasing signals across environments, which established the foundation pyramiding those super allele into an elite foxtail millet cultivar. Together, these results provide a cross-environment genetic framework for foxtail millet. They also offer actionable loci for marker-assisted improvement and gene discovery for yield-related traits.

Being one of the most crucial food crops globally, accurate yield prediction of wheat is essential for ensuring food security, enabling precision agricultural management, and addressing climate change challenges. Previous studies mainly focused on single-period feature extraction or time-series remote sensing features for yield prediction, but lacked in-depth explanation of the yield formation mechanism. Therefore, this study aimed to develop a yield prediction model based on growth curve parameters of aboveground biomass (AGB). A logistic S-shaped growth curve was fitted using measured AGB, and key growth parameters (K, V_max, S_GIP, S_RIP, S_SIP, V_GIP, V_RIP, V_SIP, etc.) were extracted and integrated into machine learning models for yield prediction. Results showed that this approach achieved high accuracy (R²=0.97, RMSE=355.38 kg ha^-1, MAE=255.74 kg ha^-1), and the extracted parameters had clear physiological significance. To enable rapid AGB acquisition, an AGB estimation model was further developed using multi-source remote sensing features, including vegetation indices (VIs), texture indices (TIs), canopy structure (CS), and canopy temperature (CT). As the growing season progressed, these multi-source features exhibited strong complementarity, reaching the highest accuracy at 30 days after anthesis (R²=0.83) and effectively alleviating the saturation problem of VIs. Moreover, growth parameters derived from the fitted curves of the estimated AGB also achieved accurate yield prediction (R²=0.87, RMSE=746.07 kg ha^-1, MAE=570.16 kg ha^-1). The model further demonstrated stable performance across different regions and years (R²=0.85, RMSE=784.52 kg ha^-1, MAE=569.56 kg ha^-1). In conclusion, this study introduced novel AGB growth curve parameters for wheat yield estimation, which improved prediction accuracy and enhanced physiological interpretability, providing insights for efficient field-scale management and yield prediction across regions.

Increasing spike number is essential for achieving high wheat yield under dense planting conditions. However, dense planting reduces the ratio of red to far-red light (R/FR) in the canopy, which inhibits productive tiller formation and spike development. Sufficient assimilate supply is essential for spike differentiation and seed setting, but the mechanism of low R/FR affects spike development remains unclear. In this study, a pot experiment was conducted with supplemental FR light from wheat stem elongation to heading to simulate a low R/FR environment and to analyze its impact on young spike differentiation and the physiology of leaves and stems. The results showed that low R/FR significantly reduced wheat yield, primarily due to a decrease in both spike number and grains per spike. The developmental failure of high-position tillers (tiller III) contributed to over 65% of the total yield loss. Under low R/FR, stem elongation and spike differentiation of tiller III were synchronously arrested, with most tillers aborting during the stamen and pistil primordium stage. Low R/FR treatment significantly reduced the net photosynthetic rate (P_n) of the fully expanded top leaves of the main stem and tillers, thereby decreasing the overall supply of assimilates. Furthermore, low R/FR inhibited the export of carbohydrates from leaves to stems, leading to a significant increase in soluble sugar content in leaves and a marked decline in stems. The limited assimilate supply intensifies nutrient competition among tillers, causing more carbohydrates to be allocated to low-position tillers and ultimately leading to the developmental failure of tiller III spikes. Hormonal analysis revealed that low R/FR significantly reduced cytokinin (CTK) levels in young spikes of tiller III by inhibiting its synthesis and promoting degradation, while simultaneously inducing abscisic acid (ABA) synthesis, thereby directly inhibiting the developmental progression of young spikes. In summary, low R/FR signaling alters the hormonal balance of CTK and ABA in the young spikes of high-position tillers, coordinately regulating the export and allocation of carbohydrates, ultimately leading to the termination of spike development in high-position tillers.

Global climate change is increasing the frequency of concurrent heat and drought events, highlighting the urgent need to elucidate their synergistic effects on crop root function and nutrient uptake. We subjected maize plants to normal condition (CK), heat stress (H), drought stress (D), and combined heat and drought stress (HD) at the 12^th fully expanded leaf stage (V12) for five days. The root-to-shoot ratio decreased under H but increased under D. Both single stresses induced “low-cost” root anatomical changes. Under HD, however, these anatomical alterations were most pronounced. They coincided with the strongest oxidative damage, the greatest suppression of root respiration, and the most severe cellular energy deficit. This energy limitation downregulated key nitrogen assimilation enzymes (NR, GS, and GOGAT) and impaired the compensatory upregulation of glutamate dehydrogenase observed under single stresses. Consequently, root nitrogen uptake efficiency declined by 9.0%, 10.4%, and 18.0% under H, D, and HD, respectively. Total plant nitrogen accumulation was lowest under HD, with nitrogen allocation increasingly skewed toward the shoot. Grain yield also lowest under HD. Collectively, these findings demonstrate that combined heat and drought cause oxidative damage, which in turn worsens the energy deficit in roots and suppresses nitrogen assimilation, thereby reducing nitrogen acquisition efficiency in maize.

Drought stress caused by abnormal climate is the main abiotic stress factor restricting maize planting and production, and its impact will expand with the intensification of climate change and threaten global food security. Since its rise, multi-omics technology has been widely applied to decipher the formation mechanism of maize drought resilience, laying a solid theoretical foundation for solving the problem of “how maize adapts to drought”. However, there is still a lack of summaries of the relevant research progress at present. Therefore, in this review, we summarize the progress of multi-omics research involving the mechanisms of maize drought resilience, especially the application of emerging technologies such as single-cell and spatial omics, as well as the discovery of new regulatory mechanisms. We also look forward to the feasibility of applying a series of cutting-edge technologies to multi-omics research. The effective integration of multi-omics with these cutting-edge technologies will greatly enhance the efficiency of analyzing the drought resilience mechanisms of maize and precisely breeding maize varieties with excellent drought resilience.

While excessive nitrogen fertilizer application enhances crop yields, it does so at the expense of ecosystem health, making the enhancement of nitrogen use efficiency (NUE) an imperative for sustainable agriculture. This study investigates the mechanisms underlying the response to low nitrate (LN) stress in two Brassica juncea genotypes: a high-NUE (H158) and a low-NUE (L159), aiming to identify genetic resources for improved NUE. Hydroponic experiments revealed that H158 displayed enhanced antioxidant capacity, nitrogen assimilation, and nitrogen uptake efficiency (NUpE) under LN conditions relative to L159. Field trials corroborated these findings, with H158 demonstrating higher yields and greater agronomic nitrogen use efficiency (ANUE) across a gradient of nitrogen application rates. Genomic analysis identified 1,654 genes associated with NUE, including NIN-LIKE PROTEIN 4 (BjuB04.NLP4), whose G/C variants influenced transcriptional regulation and root-to-shoot ratio responses to nitrogen availability. Notably, BjuB04.NLP4-HAP2 (H158) was predominant in low-nitrogen soils, while BjuB04.NLP4-HAP1 (L159) was more common in high-nitrogen soils. Collectively, our findings uncover and characterize valuable genetic resources for breeding rapeseed varieties with enhanced NUE, providing both elite germplasm and functional molecular markers.

Improving low-nitrogen adaptation is crucial for sustainable wheat production. In this study, we integrated transcriptome profiling, functional characterization, and large-scale haplotype dissection to investigate the genetic basis of wheat responses to low-nitrogen conditions. Transcriptome analysis revealed that TaNLP1-5A, TaNRT1.1B-1A, TaNFYA1-6B, and TaTCP19-6A were consistently and strongly induced under nitrogen deficiency, highlighting their central roles in nitrogen signaling and uptake. Overexpression of TaNLP1-5A significantly enhanced seedling tolerance to low nitrogen by increasing chlorophyll accumulation, shoot growth, and biomass. We systematically analyzed natural genetic variations within the 2-kb promoter regions and coding sequences of these four genes, leading to the development of functional markers (Indel-110, Indel-601, Indel-1829, and Indel-746). These markers were used to genotype a diverse wheat panel consisting of 307 accessions, and haplotype-trait association analysis revealed clear functional divergence among homoeologs. Four favorable haplotypes, TaNLP1-5A-HapII, TaNRT1.1B-1A-HapⅠ, TaNFYA1-6B-HapII, and TaTCP19-6A-HapII, demonstrated significant advantages in yield components, particularly under low-nitrogen conditions. Pyramiding these favorable haplotypes further enhanced low-nitrogen adaptability and yield-related traits. Collectively, this study identifies key nitrogen-responsive genes and provides functional markers and favorable haplotypes that can be applied in breeding wheat cultivars with improved low-nitrogen adaptation and enhanced agronomic performance. 

While composted manure application typically boosts soil organic carbon (SOC) levels, the detailed understanding of its biochemistry at the molecular level remains largely unexplored. Here, we employed three biomarkers - free lipids, lignin phenols, and amino sugars, to characterize the changes in SOC biochemistry (i.e., composition, origins and degradation) after three decades of manure application in the Northern China Plain. Topsoil samples (0-20 cm) were collected from six treatments: control (CK), mineral fertilizers alone (NPK), low and high rates of traditional composted manures (TraM_l and TraM_h, with 7.5 and 15 t ha^-1 yr^-1), and low and high rates of bio-composted manures (BioM_l and BioM_h, with 7.5 and 15 t ha^-1 yr^-1). Results showed that TraM_l, TraM_h, BioM_l, and BioM_h increased SOC concentrations by 28%, 31%, 24%, and 47%, respectively, compared to CK. These compost treatments showed higher levels of plant-derived lipids (long-chain ≥C₂₀ and steroids) by 73%, 128%, 100%, and 156%, and microbial-derived lipids (short-chain <C₂₀ and simple sugars) by 54%, 110%, 86%, and 149% in TraM_l, TraM_h, BioM_l, and BioM_h compared to the control. Moreover, TraM_l, TraM_h, BioM_l, and BioM_h enhanced lignin phenols by 68%, 89%, 78%, and 109%, respectively, relative to control. The bacterial, fungal, and total microbial necromass ranked as BioM_h>TraM_h>BioM_l≈TraM_l>NPK>CK, highlighting the superior efficacy of microbial-derived components in bio-compost amended soils. Collectively, the application of composted manures, particularly bio-composts, can boost SOC levels through plant and microbial-derived biomolecules, providing a more efficient composting strategy for carbon sequestration and persistence in cropland soils.

干旱是限制水稻生产的主要非生物胁迫之一，严重威胁全球粮食安全。籼稻和粳稻作为亚洲栽培稻的两个亚种，在长期驯化过程中形成了对不同生态环境的适应性分化。籼稻主要分布于低纬度热带和亚热带地区，具有较强的高温适应能力，因而在耐旱性方面较粳稻可能具有潜在优势。然而，目前针对籼粳亚种间耐旱性差异的研究仍较为匮乏，其遗传基础尚不清晰。本研究基于292份水稻种质资源材料（含籼稻144份、粳稻148份），通过系统评价其在干旱胁迫下的表型和生理响应，证明了籼稻的苗期耐旱性显著强于粳稻，具体表现为较晚的叶片卷曲和较高的存活率，并且多项生理指标优于粳稻。基于253个已报道抗旱相关基因的群体分化与单倍型分析，发现74个基因在籼粳亚种间存在显著遗传分化，其中37个基因具有耐旱优势单倍型，并且多数耐旱优异等位基因通过在籼稻中较高的表达水平贡献了较强的耐旱性。本研究从表型、生理及遗传层面揭示了籼稻与粳稻苗期耐旱性差异的遗传和分子基础，为深入解析水稻亚种间抗旱性分化机制提供了新证据，并为水稻抗旱和耐高温协同遗传改良提供了理论参考。

The yield and quality of soybean (Glycine max [L.] Merr.), a globally important food and cash crop, are affected by a variety of environmental factors, one of which is low-light stress. In previous work, we demonstrated that knockout of the SEIPIN homolog FA9, whose encoded protein participates in lipid-droplet formation, reduced oil content and increased protein content in seeds. In this study, we compared the responses of gmfa9 knockout mutants (fa9-KO) and wild-type (WT) Dongnong 50 (DN50) soybean to low-light stress. Vegetative indices (GNDVI and CIGreen), spectral reflectance, and chlorophyll-fluorescence parameters were higher in fa9-KO than in the WT under low light. fa9-KO exhibited prolonged reproductive development and more pronounced morphological changes than WT soybean under low-light conditions; under all light conditions, it produced larger seeds with higher protein and sugar contents but had a lower total seed weight per plant. Transcriptome and RT-qPCR analyses demonstrated that FA9 mutation was associated with the downregulation of multiple genes involved in fatty acid synthesis and photosynthetic light reactions. These findings suggest that FA9 is an important genetic resource for breeding high-quality soybean varieties adapted to low-light environments.

The L-type amino acid transporter (LAT) family facilitates the cellular transport of amino acids and polyamines. However, the functions of LAT transporters in rice remain insufficiently characterized. In this study, we identified a significant negative association between OsLAT1 transcript levels and tiller number in rice. Transcriptional analysis revealed that OsLAT1 is predominantly expressed in leaves, basal tissues, and panicles. Subcellular localization assays showed that the OsLAT1 protein is localized to the endoplasmic reticulum and is strongly induced by Asp), Leu, spermidine (Spd), and spermine (Spm). Furthermore, under hydroponic conditions, moderate concentrations of arginine (Arg) and serine (Ser) partially promoted bud outgrowth and biomass in OsLAT1-overexpressing plants, whereas these effects diminished at higher Arg/Ser concentrations. In contrast, OsLAT1 facilitated the transport of spermidine (Spd) and spermine (Spm), thereby promoting axillary bud elongation and rice growth. These findings provide insights into amino acid transporter-mediated regulation of rice plant architecture and offer potential targets for yield improvement. 

In maize/peanut intercropping systems, shading from taller maize is a primary limiting factor for peanut yield. While the strip width largely constrains the shading magnitude, optimizing row orientation is crucial for improving the light environment and enhancing the yield of intercropped peanut. Field experiments were conducted during 2021–2022 to evaluate the effects of east-west (EW) and south-north (SN) orientations on peanut yield and quality in a maize/peanut strip intercropping system. The results showed that the daily photosynthetically active radiation (PAR) transmittance in EW orientation was on average 2.0 times that of the SN. Under the EW orientation, the optimized light environment suppressed main stem elongation and increased the branching number by 13.8% in during the pod-setting stage. Enhanced light capture drove superior photosynthetic performance, increasing vegetative and generative dry matter by an average of 16.9 and 18.6%, respectively, and boosted post-flowering dry matter transport to pods by 20.2%. Consequently, peanut yield in EW orientation was enhanced by an average of 17.3% without compromising maize productivity, and the land equivalent ratio (LER) increased from 1.20 in the SN orientation to 1.27 in the EW orientation, representing a 6.3% improvement. Furthermore, the EW orientation improved kernel quality, with crude fat and soluble sugar contents increasing by 4.7% and 3.3%, respectively. It also enhanced oleic acid and reduced linoleic acid, thereby maintaining a higher oleic/linoleic ratio (O/L). In conclusion, adopting an EW orientation in maize/peanut strip intercropping systems in the Huang-Huai-Hai region is a highly effective practice that simultaneously maximizes system productivity, land use efficiency, and crop quality through spatial light optimization. 

Soil carbon sequestration plays a dual role in mitigating climate change and enhancing ecological resilience. Microbial necromass carbon (MNC) constitutes a critical component of soil organic carbon (SOC), yet its vertical distribution under straw mulching with fertilization remain poorly characterized. We conducted a 3 year field experiment on China's Loess Plateau, integrating straw (mulching (S) vs. removal (S₀)) with nitrogen fertilizer (no fertilizer (W), conventional urea (U), slow-release urea (RU)). The results indicate that SRU treatment drove surface enrichment of labile carbon fractions, triggering microbial diversity and microbial community assembly processes. Additionally, compared to S₀W, the SRU treatment significantly increased topsoil bacterial necromass carbon (BNC) by 22.2%, fungal necromass carbon (FNC) by 33.4%, and MNC by 28.9%. Conversely, the SRU treatment significantly decreased subsoil FNC content by 9.2%. In the 0-10 cm layer, compared to S₀W, both straw mulching combined with chemical fertilizer treatments (SU and SRU) significantly reduced the ratios of BNC/SOC, FNC/SOC, and MNC/SOC. Regarding carbon-degrading enzyme activities, at the 0-10 cm depth, the sole fertilization treatments (S₀U, S₀RU) significantly increased peroxidase (POD) activity, whereas straw mulching combined with fertilization (SU, SRU) had no significant effect in this layer. Meanwhile, compared to S₀W, both SU and SRU treatments significantly enhanced β-glucosidase (BG) activity, with increases of 200.5% and 122.2%, respectively. Additionally, relative to S₀W, the SRU treatment also significantly increased BG activity in the 10-20 cm and 20-30 cm layers, by 106.4% and 110.5%, respectively. Using partial least squares path modeling and optimal multivariate regression model, this study revealed that FNC exhibited a significantly positive correlation with SOC accumulation in the topsoil. In the subsoil layer, the 9.2% decrease in FNC accumulation may be associated with reduced nitrogen availability and the consequent decline in fungal activity. These findings suggest that straw-fertilizer drives vertical gradient interactions between edaphic biotic and abiotic factors, thereby regulating the spatial heterogeneity of carbon sequestration.

Cultivated soybean (Glycine max [L.] Merr.) is a major global source of vegetable protein and edible oil, yet its production is severely constrained by soybean cyst nematode (SCN, Heterodera glycines), with race 3 being the most prevalent and destructive pathotype in China. Zhongpin 03-5373 (ZP03) is an elite Chinese soybean line characterized by stable resistance to SCN3 (race 3, HG type 0) and superior agronomic performance. Here, we report a near-gapless de novo genome assembly of ZP03 generated using PacBio Revio (HiFi) long-read sequencing combined with Hi-C chromatin interaction mapping. The assembled genome spans 1,067.68 Mb with a Contig N50 of 35.36 Mb, anchoring 95.24% of sequences onto 20 chromosomes. Comparative genomic analyses revealed an extensive structural variation (SV) landscape associated with SCN3 resistance in ZP03. A 393-bp deletion-type SV located in the promoter region of GmSNAP11 was identified and was associated with increased gene expression following SCN3 infection. This allelic variation may contribute to differential transcriptional regulation under pathogen challenge. Using an SV-based genetic map constructed from a ZP03×Zhonghuang 13 (ZH13) recombinant inbred line population, we further identified a novel QTL qSCN3-16 contributing to SCN3 resistance, which explaining 7.51% of the phenotypic variance (LOD=3.42). Within this locus, Glyma.16G045900 (SYP16), encoding a t-SNARE protein, was prioritized as the candidate gene. Haplotype analysis across 2,214 diverse soybean accessions demonstrated that a favorable promoter SV in SYP16 is significantly associated with enhanced SCN3 resistance. Together, these results highlight the critical role of structural variation in shaping soybean immune responses and provide high-resolution genomic resources and functional markers, specifically the novel QTL qSCN3-16, to support precision breeding of SCN3-resistant soybean cultivars.

Glutathione reductase plays a crucial role in maintaining redox homeostasis and coordinating growth, development, and secondary metabolism in pathogenic fungi. However, its function in the wheat crown rot pathogen Fusarium pseudograminearum remains unclear. In this study, the glutathione reductase gene FpGlr1 was functionally characterized through targeted gene deletion. Compared with the wild-type strain, the ΔFpGlr1 mutant exhibited significantly reduced vegetative growth and asexual reproduction, accompanied by abnormal increases in conidial septation. In addition, the mutant showed enhanced sensitivity to multiple fungicides, including fluazinam, carbendazim, tebuconazole, and pyraclostrobin. The ΔFpGlr1 mutant also displayed increased sensitivity to Fe⊃2;⁺ and menadione, along with impaired antioxidant capacity, elevated lipid peroxidation, and accumulation of oxidized glutathione. Deletion of FpGlr1 markedly reduced virulence during host infection and completely abolished the ability to penetrate cellophane. Moreover, the mutant produced significantly lower levels of deoxynivalenol (DON) and exhibited defective toxisome formation, accompanied by downregulation of trichothecene biosynthetic (TRI) genes. Transcriptomic analysis revealed that differentially expressed genes in the ΔFpGlr1 mutant were significantly enriched in glutathione metabolism and carbohydrate metabolism related pathways. Consistently, metabolomic profiling demonstrated extensive metabolic reprogramming, particularly affecting carbohydrate, amino acid, energy, and purine metabolism, and revealed a decoupling between transcriptional activation and metabolite accumulation in key sugar metabolic pathways. Collectively, these findings demonstrate that FpGlr1 is essential for oxidative stress responses, secondary metabolism, and virulence in F. pseudograminearum, highlighting its importance in redox regulation and its potential as a target for controlling wheat crown rot.

Ovine pneumonia is a complex and economically devastating disease that results in approximately USD 4 billion in annual losses to the global livestock industry. Despite its substantial impact, the underlying pathogenic mechanisms and the host factors that confer resistance remain poorly understood. To address this knowledge gap, we employed an integrative multi-omics strategy to comprehensively investigate the genetic and microbial contributors to pneumonia resistance in sheep. To elucidate the pathogenic mechanisms underlying pneumonia resistance in sheep and to identify key host genetic and microbial determinants through the integration of multi-omics data with phenotypic information. We profiled the lung microbiome (metagenomics, n=61), host transcriptome (RNA-seq, n=61), and chromatin accessibility (ATAC-seq, n=14) in infected sheep. Whole-genome sequencing (WGS, n=61) data for the same animals were examined. Metagenomic profiling identified Jaagsiekte sheep retrovirus (JSRV) as the dominant pathogen across all samples, while disease severity was not driven by pathogen load. Transcriptomic analyses identified IL1R2 and CSF3 as key differentially expressed genes associated with resistance, with enrichment in cytokine-mediated immune pathways, including cytokine–cytokine receptor interaction and IL-17 signaling. ATAC-seq revealed globally increased chromatin accessibility in resistant sheep and significant enrichment of differentially accessible regions in immune-related pathways. Transcription factor footprinting revealed distinct regulatory landscapes, and high-resolution chromatin profiling identified dense binding of multiple transcription factors at the IL20RB promoter, including Hoxd12 and TF3A, indicating transcription factor–mediated regulation of IL20RB. Integrative multi-omics analysis identified IL1R2 as a central determinant of pneumonia resistance. IL1R2 expression was strongly correlated with chromatin accessibility at distal regulatory regions. A functional enhancer harboring the Single Nucleotide Polymorphism (SNP) chr3:99752986 exhibited increased accessibility and active histone marks in resistant sheep, and the protective A allele was significantly associated with reduced lung lesion severity. These findings were validated by Kompetitive Allele Specific PCR (KASP) genotyping and Quantitative real-time PCR (qRT-PCR). Functional assays further demonstrated that IL1R2 modulates host inflammatory responses. IL1R2 overexpression enhanced epithelial cell viability following Mycoplasma ovipneumoniae (M. ovipneumoniae) infection, whereas IL1R2 knockdown altered bacterial adhesion patterns, supporting its role in limiting excessive inflammatory signaling and maintaining epithelial integrity. This study emphasizes the importance of host-intrinsic factors in phenotypic variance in disease severity, identified key genetic and regulatory factors that could guide future therapeutic and breeding strategies.

RNA interference (RNAi) offers a precise and environmentally sustainable approach to crop protection, yet its widespread field application is constrained by the rapid degradation of double-stranded RNA (dsRNA), inefficient pathogen uptake, and variable performance of both host-induced and spray-induced gene silencing strategies. In this review, we propose synthetic microbial communities (SynComs) as microbially integrated delivery systems designed to overcome these limitations. We introduce a functional framework in which SynCom members are rationally assigned specialized roles dsRNA producers, stabilizers, carriers, and helpers to enable continuous in situ RNA production, protection against nucleases and environmental stressors, and targeted delivery to pathogens across the rhizosphere, phyllosphere, and endosphere. We discuss niche-specific design principles, microbiome engineering strategies, and biosafety considerations essential for translating SynCom-mediated RNAi into robust field applications. Importantly, we address the emerging challenges, posed by agro-environmental pollutants such as microplastics, heavy metals, and pesticide residues and propose how engineered pollutant-tolerant SynComs can maintain RNAi efficacy in contaminated agroecosystems. Finally, we present a phased translational roadmap that progresses from combined SynCom-dsRNA sprays toward programmable self-regulating SynComs capable of adaptive dsRNA delivery. By bridging RNAi biotechnology, microbial ecology, and synthetic biology, this integrated SynCom-based platform offers a scalable, durable, and ecologically resilient strategy to reduce reliance on synthetic chemical inputs and enhance crop protection under real-world field conditions.

Sakuranetin is the flavonoid phytoalexin to defense blast pathogen infection in rice (Oryza sativa L.). Although sakuranetin biosynthesis has been characterized, the transcriptional regulation of sakuranetin biosynthetic genes remains elusive. A transcription factor OsMYB133 is identified here to coexpress with sakuranetin biosynthetic gene OsNOMT and exhibits highly inducible expression in response to the infection of blast fungus Magnaporthe oryzae. Overexpression of OsMYB133 elevated blast resistance and knockout lines showed more susceptible to M. oryzae infection. OsMYB133 directly bound to the OsNOMT gene promoter and enhanced its gene expression, leading to increased sakuranetin accumulation and blast resistance. OsMYB133 also directly regulates momilactone biosynthesis genes OsKSL4 and OsCYP99A3 to increase corresponding gene expression and momilactone accumulation in the overexpression rice line. This study identified the OsMYB133 as the key transcription factor to regulate flavonoid and diterpenoid phytoalexin biosynthesis and provided the insights for comprehensive characterization of chemical defense mechanism and molecular breeding to increase pathogen resistance in rice.

猪伪狂犬病（Pseudorabies, PR）是由伪狂犬病病毒（Pseudorabies virus, PRV）引起的一种重要动物传染病，不仅给全球养猪业造成重大经济损失，还存在感染人并引发脑炎的人兽共患风险。近年来，新型PRV变异株的出现降低了传统疫苗的保护效果，因此建立快速、简便的现场检测方法对防控该病具有重要意义。为此，本研究将重组酶辅助扩增（RAA）与CRISPR/Cas12a系统相结合，针对PRV的gE基因设计特异性引物与crRNA，建立了一管法核酸检测体系，并优化了反应条件，进而评价了该方法的灵敏度、特异性及临床样本检测一致性。结果显示，所建立的RAA-CRISPR/Cas12a方法可在50分钟内完成检测，对重组质粒的检测限为5拷贝/μL，对PRV病毒的检测限为7.96×10^-2 TCID₅₀/反应；该方法与猪瘟病毒（CSFV）、非洲猪瘟病毒（ASFV）、猪丁型冠状病毒（PDCoV）等其他常见猪病原体均无交叉反应，表现出高度特异性；在临床样本验证中，本方法与实时定量聚合酶链式反应（qPCR）检测结果完全一致，具有良好的临床符合性。综上所述，本研究成功建立了一种基于RAA与CRISPR/Cas12a系统的PRV核酸检测方法，具有快速、灵敏、特异、操作简便等优点，适用于资源有限条件下的现场检测，为PR的临床诊断提供了有力工具。

研究背景：代谢物水平是连接遗传变异与复杂性状的关键分子信息，解析其遗传基础有助于理解遗传变异影响复杂性状的作用机制。其中血清作为全身循环系统的物质交换媒介，能够反映多组织的代谢信息，是研究复杂性状代谢基础的重要材料。然而，目前针对鸭血清代谢物遗传结构的研究仍较为有限。因此，本研究整合273只330日龄母鸭的血清非靶向代谢组、基因组变异、多组织调控变异资源（eQTL、sQTL、apaQTL）及46个复杂性状，旨在鉴定血清代谢物相关遗传位点（mQTL），并评估其在复杂性状遗传解析中的应用潜力。

主要结果：基于液相色谱-质谱联用技术，本研究共注释出403种血清代谢物，涵盖脂质、氨基酸、核苷酸等8个大类。遗传力分析显示，超过80%的代谢物遗传力低于0.268，表明血清代谢物整体以低遗传力为主。通过mGWAS分析，在40种代谢物中鉴定到175个独立的mQTL。将上述mQTL与调控变异资源进行共定位分析，发现19个mQTL与调控变异共享遗传信号，提示这些位点可能通过调控基因表达、可变剪接或3′UTR使用等分子过程影响血清代谢物水平。进一步整合复杂性状的GWAS结果，发现11个mQTL与12种复杂性状显著相关，其中3个mQTL同时关联复杂性状与调控变异：（1）4_24700740位点可能通过影响肝脏中AADAT的可变剪接，调控血清氨基己二酸水平，进而影响蛋黄重量；（2）16_943465位点可能通过影响输卵管壳腺中TFIP11的3′UTR使用，调控L-谷氨酰胺水平，影响胫围；（3）1_59979162位点则可能通过影响脾脏中MKRN1的表达，调控L-缬氨酸水平，影响肝脏重量。最后，将所有表型相关mQTL作为固定效应引入GBLUP模型后，发现多数复杂性状的预测准确性均有所提高。

研究结论：本研究系统解析了鸭血清代谢物的遗传结构，并通过多维组学数据整合，揭示了3条“遗传变异-基因调控-代谢物水平-复杂性状”的候选遗传作用通路。这些结果表明，整合mQTL信息有助于将关联信号转化为清晰的机制假设，同时也能为基因组预测提供有价值的功能位点。

The gut microbiota plays a critical role in regulating host fat deposition, yet the underlying mechanisms remain poorly understood. To investigate this question, this study employed germ-free (GF) and fecal microbiota transplantation (FMT) piglet models to systematically elucidate how microbiota-derived metabolites modulate fat deposition via N⁶-methyladenosine (m⁶A) RNA methylation. Although the FMT group showed no significant change in body weight compared with the GF group, it exhibited markedly increased subcutaneous and intramuscular fat deposition, as evidenced by larger adipocyte size (P<0.001), elevated serum and longissimus dorsi muscle triglyceride levels (P<0.05), and upregulated expression of adipogenic genes (P<0.05). Non-targeted metabolomics revealed elevated levels of bile acids, including hyodeoxycholic acid (HDCA), 12-ketodeoxycholic acid (12KDCA), and 3b-hydroxy-5-cholenoic acid (3b-h5-CA), as well as tryptophan metabolites indoxyl sulfate (IS) and L-kynurenine (L-Kyn) in the FMT group, and these metabolites were significantly correlated with lipid metabolism parameters. Mechanistic studies showed that these metabolites reduced m⁶A modification levels in mouse stromal vascular fraction (SVF) cells and fibro-adipogenic progenitor (FAPs) cells by upregulating fat mass and obesity-associated protein (FTO) and downregulating methyltransferase-like 3 (METTL3) (P<0.05), consistent with the in vivo observations in piglets. Furthermore, Bacteroides, Lactobacillus, Parabacteroides, and Akkermansia were identified as key genera involved in bile acid and tryptophan metabolism. Together, these findings reveal a gut microbiota–metabolite–m⁶A regulatory axis in fat deposition in pigs, providing new insights into host–microbiota interactions and offering potential strategies for improving metabolic health and meat quality in livestock.

The rumen's microbial community is vast and intricate, playing a key role in animal health and eco-friendliness. Drawing from studies over the past five years, we highlight progress in diversity, early community formation, host-microbe links, diet tweaks, and methane reduction strategies. Metagenomics points to a stable core of Bacteroidota and Firmicutes, featuring genera like Prevotella, Butyrivibrio, and Ruminococcus with shared roles across hosts. Succession happens in young animals and during weaning, while functions show adaptability through varied carbohydrate-digesting enzymes. Diets reshape the mix—fats and plant compounds trigger clear changes in structure and activity. Host factors shine through: milk-producing cows boost bugs for fat and protein breakdown, but imbalances fuel issues like ketosis or acidosis. For cutting emissions, methanogens are prime targets. Overall, this microbiome is tunable via smart feeding and fixes to boost output and curb pollution.

Powdery mildew disease caused by the host-adapted fungal pathogen Blumeria graminis f. sp. tritici (Bgt) threatens the yield and quality of bread wheat (Triticum aestivum L.). Air humidity is a key environmental influence affecting the occurrence of plant diseases, but chemical mechanism underlying the response of compatible wheat-Bgt interaction to the air humidity changes remains largely unknown. This study reveals that transcription factor TaEPBM1 governs the humidity-responsive biosynthesis of wheat cuticular wax and salicylic acid (SA) to fine-tune the wheat susceptibility to Bgt. Partially redundant β-ketoacyl-Coenzyme A reductase TaKCR1s were demonstrated to catalyze the biosynthesis of wheat cuticular wax. Transcription factor TaEPBM1 directly targets TaKCR1s and the SA biosynthesis gene TaICS1, and recruits TaADA2 to promote histone acetylation at TaKCR1s and TaICS1 promoters, thereby epigenetically activating cuticular wax and SA biosynthesis. In addition, we showed that high air humidity suppresses TaEPBM1 gene transcription and attenuates the epigenetic activation of cuticular wax and SA biosynthesis. Importantly, very-long-chain (VLC) aldehydes and SA were identified as the humidity-responsive chemical cues provided by the TaADA2-TaEPBM1-TaKCR1/TaICS1 circuit for fine-tuning the compatible wheat-Bgt interaction. These findings support that transcription factor TaEPBM1 governs the humidity-responsive biosynthesis of wheat cuticular wax and SA to fine-tune the wheat susceptibility to Bgt, providing valuable information for the wheat powdery mildew control.

Straw amendments can improve soil fertility by loading organic carbon (C) into soils, but whether and how biological nitrogen fixation (BNF) occurs in long-term rice straw (RS)-incorporated paddy fields remain poorly understood. To fill this gap, we explored the effects of three rates of straw incorporation (0, 3 and 6 t ha^-1; RS₀, RS₃ and RS₆) on soil BNF activities inferred from acetylene reduction assay (ARA) and diazotrophic communities at three rice growth stages (tillering, elongation, and maturation) based on a 10-year field experiment. The ARA activities increased significantly in response to increasing straw incorporation rates across all three rice growth stages, while the effect decreased as rice growth progressed. Soil BNF was associated with key diazotrophs, such as Dechloromonas, Bradyrhizobium, and Azospirillum. Straw incorporation increased diazotrophic abundance, diversity and interactions, which consequently improved soil BNF activities and rice yields. Straw incorporation increased rice yield by 12.6% in RS₃ and by 15.5% in RS₆ compared with the control. Structural equation models (SEMs) suggested that microbial C turnover and nitrogenase gene expression were the key factors affecting soil stage-specific BNF associated with the decomposition of straw. These results revealed that C-rich straw incorporation reconfigured soil N dynamics, enabling simultaneous improvement of soil fertility and rice yields through demand-driven BNF patterns in paddy fields.

Vapor pressure deficit (VPD), defined as the difference between the actual water vapor pressure and the saturation vapor pressure in the air, is a core indicator of atmospheric aridity. High VPD induces intensified water loss via plant transpiration, thereby constraining water uptake and photosynthetic capacity. The dynamic functions and molecular regulatory mechanisms of plasma membrane intrinsic proteins (PIPs), key aquaporins mediating rapid transmembrane water transport, remain unclear during plant responses to high VPD stress. In this study, we elucidated the regulatory role of SlPIP1;7 in regulating the multi-level adaptation strategy of tomato (Solanum lycopersicum) at the morphological, physiological, and molecular levels under high VPD conditions. The results indicate that, compared to wild-type (WT) plants, SlPIP1;7 overexpressing (OE) plants exhibit superior growth performance under high VPD conditions. The overexpression of SlPIP1;7 significantly enhances the reactive oxygen species (ROS) scavenging efficiency, effectively protecting plant cells from oxidative damage. This protective mechanism for maintaining ROS homeostasis is closely associated with stomatal function. The overexpression of SlPIP1;7 can regulate stomatal morphology, size, and aperture dynamics, thereby promoting efficient utilization of water and carbon dioxide and enhancing the overall physiological regulatory capacity of plants under stress conditions. Additionally, we identified the ethylene response factor SlERF4 as an upstream regulatory factor in this adaptive network. Yeast one-hybrid (Y1H) and dual-luciferase (LUC) assays demonstrate that the transcription factor SlERF4 can bind to the SlPIP1;7 promoter, enhancing its expression and functionality. This interaction further underscores the pivotal role of SlPIP1;7 in combating high VPD stress. In summary, our study elucidates the crucial function of SlPIP1;7 in plant response and acclimation to high VPD stress. These findings expand our understanding of the molecular mechanisms underlying plant acclimation to environmental stresses and provide a reference for future breeding strategies aimed at developing drought-resistant crops.

Motivated by growing concerns about excessive agrochemical use and the resulting environmental pollution in China, this study explores the importance of online agricultural information for chemical fertilizer and pesticide use decisions among grain farmers. In particular, we focus on the functional agricultural information used for productive purposes for smallholders. Based on a survey dataset of 1,833 family farms across five Chinese provinces, we employ a propensity score matching (PSM) approach to estimate treatment effects of online agricultural information. The results reveal that online acquisition of agricultural information does not reduce the expenses of chemical fertilizers and pesticides in our sample; rather, the opposite is true. The use of online agricultural information significantly increased agrochemical expenses, particularly among smallholders. Within our sample region, the limited evolution of online information content and the inherent challenges faced by smallholder farmers are the major barriers to the beneficial effects of online agricultural information in reducing agrochemical use. Our findings emphasize the need for targeted interventions and educational efforts to bridge the knowledge gaps of smallholders. Furthermore, there is a need to raise awareness among information providers to ensure that their recommendations avoid encouraging overdoses of agrochemicals. In addition, enhancing farmers’ digital literacy will be a future task of development policy.

Walnut is an important economic woody oil tree species, and anthracnose caused by Colletotrichum gloeosporioides is a devastating disease affecting walnut production in China. The MAPK-WRKY signaling pathway plays an important role in regulating plant disease resistance. However, the MAPK-WRKY pathway in walnut and the mechanism involved in anthracnose resistance remain unclear. Using 'Taile' and 'Xiangling' with significant differences in anthracnose resistance as materials, we identified a potential JrMAPK3-JrWRKY22 pathway related to anthracnose resistance through transcriptomics. Further analysis using yeast two-hybrid, bimolecular fluorescence complementation, pull-down, and in vitro phosphorylation assays revealed that JrWRKY22 interacts with and is phosphorylated by JrMAPK3. Transient injection results in walnut fruit revealed that overexpression of JrWRKY22 can inhibit Colletotrichum gloeosporioides infection, increase fruit anthracnose resistance, and significantly promote the expression of the β-1,3-glucanase gene JrGLU of the PR-2 family and the pathogenesis-related gene JrPR1. In contrast, silencing JrWRKY22 resulted in a significant increase in lesion size caused by Colletotrichum gloeosporioides and a corresponding decrease in gene expression levels. A dual-luciferase assay confirmed that JrWRKY22 can activate the promoter activity of JrPR1 and JrGLU and that phosphorylation by JrMAPK3 increases this activation. Further analysis using yeast one-hybrid assays, ChIP-PCR, and EMSA demonstrated that JrWRKY22 can bind to W-box elements in the promoters of JrPR1 and JrGLU. These findings elucidate the molecular mechanism by which the JrMAPK3-JrWRKY22 module increases walnut anthracnose resistance, broaden the understanding of resistance mechanisms, and provide a scientific basis for molecular breeding in the context of walnut disease resistance.

Northern corn leaf blight, a globally significant maize disease, is caused by the heterothallic fungus Setosphaeria turcica, which relies on mating type for its sexual reproduction. The mating-type locus (MAT) genes StMAT1-1 and StMAT1-2 determine three mating types (A, a, and Aa) of S. turcica. The sexual cycle of S. turcica in natural ecosystems has garnered substantial research interest; however, the functional dynamics of its sexual reproduction-including regulatory mechanisms and adaptive significance-remain uncharacterized. From 2011 to 2023, a 13-year continuous monitoring of S. turcica in major Chinese corn-producing regions identified the a mating type (with StMAT1-2) as the field-dominant type. Laboratory analyses of artificially induced F1 populations confirmed that a mating-type strains exhibit superior fitness (enhanced sporulation, faster mycelial growth, stronger pathogenicity) compared with A mating-type strains (with StMAT1-1). Generation of mating-type gene mutants demonstrated that StMAT1-1 and StMAT1-2 are essential for sexual reproduction in S. turcica. Transcriptome analysis further revealed that StMAT1-2 regulates a larger set of genes involved in metabolism-related pathways. Mechanistically, StMAT1-2 directly binds to the promoter of pheromone receptor gene StSte2 to modulate its expression. Silencing StSte2 disrupted sexual reproduction and downregulated downstream MAPK pathway genes, while exogenous pheromone partially rescued these defects, verifying the pheromone pathway's role in S. turcica sexual reproduction. Notably, silencing of StMAT1-2 and StSte2 was associated with reduced sporulation and pathogenicity. Collectively, StMAT1-2 regulates sexual reproduction and pathogenicity by targeting StSte2, driving the field dominance of the a mating type. This study advances understanding of mating-type distribution bias in heterothallic fungi.

Soil nutrient supply during crop growth is a key determinant of crop yield in agricultural ecosystems. However, the critical growth stage most influencing yield formation and the associated microbial mechanisms under straw incorporation remain unclear. A 6-year field experiment (2019–2024) was conducted with four treatments: conventional tillage (CT, 20 cm), deep tillage (DT, 35 cm), conventional tillage with straw incorporation (CTS), and deep tillage with straw incorporation (DTS). Soil samples were collected from topsoil (0–20 cm) and subsoil (20–35 cm) at maize jointing (JS), grain-filling (GS), and maturity (MS) to elucidate the microbial mechanisms by which straw incorporation influences maize yield. Results showed that CTS and DTS significantly increased maize yield by 8.3% and 17.6%, respectively, compared to CT. Straw incorporation elevated soil organic carbon (SOC, 7.0–28.7%), available nutrients (nitrogen, phosphorus (P), and potassium) and microbial biomass stoichiometric ratios (microbial biomass carbon/microbial biomass nitrogen, MBC/MBN; and microbial biomass carbon/microbial biomass phosphorus, MBC/MBP), alleviating microbial C (0.7–3.2%) and P (0.2–4.6%) limitations in the 0–35 cm soil layer, with DTS exhibiting a more pronounced effect in the subsoil. Furthermore, straw incorporation increased the relative abundance of Proteobacteria (3.0–39.4%) and Ascomycota (7.8–40.3%) in the 0–35 cm soil layer, and enhanced bacterial diversity in the subsoil by increasing the contribution of stochastic assembly processes. Notably, nutrient availability at GS was identified as the primary driver of yield formation. By boosting available nutrients during this critical period, straw incorporation directly enhanced yield. Indirectly, by enhancing available nutrients and microbial biomass stoichiometric ratios (MBC/MBN and MBC/MBP), straw incorporation alleviated microbial C and P limitations. This, in turn, improved bacterial community structure, promoted SOC accumulation, and ultimately boosted yield. These findings elucidate the stage-specific microbial mechanisms under straw incorporation and provide a basis for optimizing farmland management practices to enhance soil productivity.

Water footprint (WF) of crop production is an advanced water consumption metric that can decouple the source of the water (i.e., green and blue water) in time and space over the crop growing period at both regional and product levels. Several machine learning models have been developed for crop WF accounting, however, the transferability of existing models has not been adequately validated, which constrains wider application and implementations across different crops, scenarios, and broader spatiotemporal domains. Here a comprehensive multi-scale machine learning modeling framework was constructed. Using the Yellow River Basin in China as the baseline training area, prediction models for 21 crops were developed based on 2000–2019 data, focusing on eight core indicators including yield per unit area, unit blue and green WFs (uWF_b and uWF_g), total yield, and total WF. Cross-regional validation in the Colorado River Basin for the basin scale, and mainland China for national scale confirmed the spatial transferability of the model. Long-term crop WF scenarios for 2020-2100 were then simulated for Yellow and Colorado river basins under four climate change projection pathways. In total, 5,112 machine learning modeling scenarios were constructed, and through grid search, over one billion parameter combinations were optimized, ultimately yielding 392 optimal models. Results demonstrates excellent accuracy across all scales and with spatial transferability, with the coefficient of determination (R²) exceeding 0.9 at both provincial and county levels. Incorporating human activity indicators and the Fast-Track approach data significantly improved model performance. The error distribution exhibits a pronounced scale-dependent characteristic, indicating systematic differences in the deviation of observed values for the same crop across varying scales. Long-term future crop WF scenarios show downward trends for unit WF for each crop, whereas increased total blue WFs in both considered basins. This study provides an innovative methodological framework for multi-scale agricultural water resource management.

Wheat (Triticum aestivum L.), one of the world’s three major staple crops, continues to face challenges in yield enhancement to ensure food security. Photosynthesis, the most fundamental energy conversion process on Earth, provides the primary source of biomass formation in plants. The first “Green Revolution” in the mid-20th century employed dwarfing genes such as Rht-B1b or Rht-D1b, which reduced plant height by 30-50% and significantly enhanced lodging resistance. Combined with the widespread adoption of fertilizers and pesticides, these advancements led to substantial increases in global wheat yields. However, the yield benefits derived from dwarfing genes have since plateaued, creating a bottleneck for further improvement through height reduction while exacerbating environmental costs of fertilizer-intensive agriculture. With the FAO predicting a 60% increase in global wheat demand by 2050, there is an urgent need for innovative technological strategies to achieve a second leap in productivity. Improving photosynthesis, the core driver of biomass accumulation, offers a promising pathway to overcome current yield limitations. This review synthesizes recent advances in wheat photosynthesis research, focusing on the relationship between photosynthetic carbon assimilation and grain yield. It also identifies key scientific questions, outlines future research directions, and proposes technological strategies for enhancing wheat through photosynthetic optimization. Wheat breeding is now ushering in a second “Green Revolution” era, one powered by the efficient use of solar energy.

Maize landraces, shaped by long-term adaptation to diverse environments, represent an invaluable but underexplored resource for modern breeding. Despite their potential, the genetic architecture and breeding value of Chinese maize landraces remain poorly characterized. In this study, we established a global diversity panel comprising 3,187 maize landraces, including 2,042 accessions from China, and integrated genomic data from teosintes and modern inbred lines to trace the evolutionary and breeding history of maize. We delineated Chinese landraces into seven distinct genetic groups, whose spatial distribution closely aligns with major agro-ecological zones in China, revealing a genetic structure profoundly influenced by local adaptation. Notably, TreeMix and f_d analyses revealed significant gene flow between the Chinese landrace group CL3, which primarily distributed in the Huang-Huai-Hai plain, and the Sipingtou (SPT) inbred lines. Furthermore, XP-CLR analysis indicated that the selected regions encompass genes associated with abiotic stress response, flowering and photoperiod regulation, and growth processes, highlighting the functional relevance of landrace-derived alleles. Through genome-wide association studies (GWAS), we identified numerous candidate genes for key traits, including known flowering regulator ZCN8 and disease resistance gene OPR8. Although modern breeding has efficiently accumulated favorable alleles for desired traits, landraces retain unique favorable alleles, particularly in flowering time and disease resistance, which are largely untapped. This study provides a comprehensive genetic resource and unveils the evolutionary and breeding dynamics of Chinese maize landraces. Our findings underscore the necessity of targeted utilization of landrace diversity to broaden the genetic base and enhance resilience in future maize breeding.

Achieving stable and sustainable soybean production under increasing climate variability and soil degradation remains a global challenge. Straw mulching is promoted to increase soybean seed yield in arid and semi-arid agricultural systems, but its long-term impacts on soil fertility and yield stability remain poorly quantified. We conducted a long-term field experiment, involving three treatments: straw removing (SR), straw mulching (SM), and straw crushing (SC). SM increased soil enzymes activity and improved topsoil nutrients. Among the three treatments, the SM exhibited the highest mean weight diameter (2.12), while the lowest soil solid phase proportion (49.09%). SM resulted in the longest chlorophyll retention duration in soybean leaves (135.55 d), followed by the SC (120.81 d) and SR (95.25 d). Furthermore, at the R1 stage, the SM exhibited the highest leaf area index (LAI) and biomass, both of which showed a significant positive correlation with seed yield. Compared with SR and SC, SM increased seed yield, yield stability, and yield sustainability by an average of 17.76, 73.64, and 15.42%, respectively. Long-term retention of crop residues represents a scalable, low-input strategy to rebuild soil fertility, buffer climatic stress, and secure yield stability – contributing to global goals for sustainable agriculture and food security.

Heat stress (HT) during grain filling severely constrains maize yield formation by disrupting whole-plant carbon allocation. Although salicylic acid (SA) is known to enhance crop thermotolerance, its role in coordinating source–flow–sink carbon dynamics under HT remains poorly understood. In this study, two waxy maize hybrids were pre-sprayed with SA and subsequently exposed to 15 days of HT treatment during grain filling. HT reduced post-anthesis dry matter accumulation and translocation, inhibited sucrose metabolism in leaves and grains, down-regulated sugar transporter genes in the stem and grains, and consequently decreased ¹³C allocation to developing grains and grain yield. SA reprogrammed source–flow–sink coordination under HT by simultaneously enhancing carbon supply, transport capacity, and sink utilization. At the source, SA sustained assimilate accumulation and maintained sucrose phosphate synthase, sucrose synthase, and invertase activities in leaves. Along the transport pathway, SA up-regulated key sucrose transporter genes in stems, thereby improving sucrose loading and long-distance translocation. At the sink, SA stabilized sucrose metabolism and transporter expression in grains, resulting in increased carbon partitioning to developing kernels. Partial least squares path modeling further identified coordinated regulation of sucrose metabolism in leaves and grains, together with sucrose transport in the stem and grains, as the main pathways through which SA mitigated heat-induced yield loss. Overall, exogenous SA alleviated the adverse effects of HT in waxy maize by reprogramming source–flow–sink carbon coordination, thereby stabilizing carbon allocation and maintaining yield under HT conditions.

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease worldwide. Wild rice serves as an invaluable reservoir of BB resistance genes, and introgressing them into cultivated varieties provides a cost-effective, environmentally sustainable strategy for control. Automated, non-destructive, and low-cost screening of BB-resistant wild rice germplasm is crucial for breeding BB-resistant rice varieties. This study proposes an AI-driven approach for screening elite BB-resistant wild rice germplasm to support breeding efforts. An AI-driven workflow for BB resistance screening in wild rice is developed, enabling in-field, repeated evaluations, and is implemented in a portable backpack apparatus costing approximately 890 USD. A computer vision algorithm is designed to segment lesions, measure lesion lengths, and evaluate BB-resistance levels, thereby screening elite BB-resistant wild rice. The lesion segmentation model, with only 0.85M parameters and 4.33G FLOPS, achieves an IoU of 94.14%. Comprehensive evaluations, including BB resistance level evaluation, field testing, and generalization testing, demonstrated high accuracy (92.0, 94.0, and 95.6% respectively) and efficiency gains. This method will support high-throughput screening of large-scale wild rice germplasm for BB resistance, accelerating the exploration of wild rice germplasm.

Soil organic carbon (SOC) is a key indicator of soil health and agricultural sustainability. Yet, SOC remains low in the Loess Plateau, and carbon sequestration efficiency (CSE) has not been systematically quantified across cropland systems spanning dominant climate zones. Here, we analyzed the spatiotemporal variability of carbon input and CSE from 1983 to 2023 across three agroecologically distinct counties in Shanxi Province, China: Yingxian (north), Shouyang (central), and Yongji (south). Using geostatistical methods, Random Forest, and path analysis, we identified key drivers of SOC accumulation and CSE under varying climates and amendment regimes. Our results revealed a clear north-to-south increase in SOC stocks, from 20.1±6.5 t ha^-1 in the north to 23.1±6.3 t ha^-1 in the central and 24.5±6.3 t ha^-1 in the south in 2023. Overall, carbon input also exhibited an increase from north to south, i.e., from 2.2 to 2.5 and 4.2 t ha^-1 yr^-1 whereas CSE declined from north to south, from 9.7 to 7.4 and 5.2% over 1983-2023. Our analyses suggest that elevation, temperature, initial SOM, and manure carbon input were dominant drivers of spatial divergence. The extremely low CSE values in the Eastern Loess Plateau may be partly attributable to carbon loss driven by persistent soil erosion. These findings underscore the need for erosion-sensitive, carbon-informed management strategies that better account for key biogeochemical processes to enhance soil health and resilience in the croplands of the eastern Loess Plateau.