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  • Jinchuan Zhang, Xin Qian, Yuting Wei, Tianzi Wang, Xuelong Fu, Sijie Luo, Yuanquan Chen, Leanne Peixoto, Zhaohai Zeng, Huadong Zang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.038
    Accepted: 2025-12-24

    Maize and soybean intercropping improve land use efficiency and plays a crucial role in ensuring food security. However, optimal field configuration parameters for maize and soybean strip intercropping remain unclear, particularly in the North China Plain where the system has been widely adopted. A two-year field experiment was conducted to evaluate the effects of four maize planting densities under two row configurations on the land equivalent ratio (LER), crop yields, and economic benefits. Our results demonstrated that intercropping consistently enhanced land use efficiency across all field configurations, with an average LER of 1.20. Under the M3S4 (three maize rows alternating with four soybean rows) configuration at 90% of the monocropping maize density, maize yields were sustained at up to 93.3% of monocrop, while simultaneously producing an additional 893 kg ha-1 soybean. Compared to the M2S4 configuration (two maize rows alternating with four soybean rows), the M3S4 increased maize yield by 12.2%, but led to a 17.1% reduction in soybean yield. Further, optimization of maize planting density improved land use efficiency, crop yields, and the net income. The optimal M3S4 configuration at 90% of the monocropping maize density increased the LER by 6.7%, maize yield by 5.6%, soybean yield by 8.1%, and net income by 8% compared to M3S4 at 100% density. These findings indicate that optimizing field configurations can significantly improve crop yields and farmers' economic benefits in maize-soybean strip intercropping. Our study highlights that optimized field configurations improve both yield potential and economic viability of mechanized maize and soybean strip intercropping, providing a scientific basis for its large-scale adoption.

  • Mengdi Guan, Wenxi Li, Wenjun Shi, Mengjing Wang, Lili Liu, Yujiao Xie, Huihui Kong, Yujie Li, Hongke Xu, Mingfeng Liu, Xuan Yang, Zhanshuai Li, Anran Ren, Jing Guo, Xuyong Li
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.043
    Accepted: 2025-12-23

    H13亚型禽流感病毒的主要宿主是水鸟家禽和哺乳动物中鲜有发现,目前对其流行病学动态及遗传特征的认知仍较为欠缺。为填补这一研究空白,本研究于2017-2024年在我国山东省主要候鸟栖息地开展了系统性的主动监测累计采集50016份候鸟样本,共分离到21H13亚型禽流感病毒(19H13N62H13N8。所有H13亚型病毒均发现于2021-2024年的春秋迁徙季,且绝大多数源自鸥类。贝叶斯系统发育分析显示,21病毒HA基因分属欧亚谱系和北美-欧亚谱系,而N6N8基因则均聚类于欧亚谱系。本研究还发现H13/H16-like病毒存在广泛的基因重配现象,如其内部基因片段参与高致病性H5N1毒株的形成,部分毒株的基因与感染人类的H10N5亚型病毒基因具有高度同源性。此外,H13病毒在小鼠体内复制能力较差,表明其公共卫生风险较低。本研究深化了对H13亚型禽流感病毒全球流行特征、地理分布、宿主范围及系统发育多样性的认知,同时也凸显了针对迁徙鸟类开展持续性监测的必要性。

  • Xinyu Yang, Wenzhen Qin, Ning Kong, Yuchang Liu, Guangzhi Tong, Tongling Shan
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.042
    Accepted: 2025-12-23

    冠状病毒是单链正义 RNA 病毒。在 PEDV 吸附和内化后及病毒负链 RNA 合成前,我们同时检测到了冠状病毒的正链和负链序列。为解释上述发现,本研究证实α、β和δ冠状病毒属的冠状病毒病毒粒子中包裹病毒的负链基因组。通过蔗糖密度梯度离心纯化,并经抗体和核酸酶处理的 PEDV 颗粒中,约 20% 至 46% 含有负链基因组,且这些病毒颗粒具备吸附和内化的能力。该研究解释了冠状病毒在吸附和内化后检测到病毒的负链RNA的发现,也表明了冠状病毒在组装过程中不仅包装病毒正链基因组,也会同时包装了病毒负链基因组。

  • Meiqi Zhong, Linjing Wei, Henghui Mo
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.041
    Accepted: 2025-12-23

    Cotton leaf diseases such as leaf spot, blight, and wilt are difficult to detect reliably in the field because lesions are small, low-contrast, and often obscured by complex backgrounds. We present RT-DETR-SDSL, a lightweight detector designed for real-world on-device deployment. Our main research line is a complementary three-part pipeline that aligns representation quality, lesion sensitivity, and edge efficiency: (i) we adopt MoCo v2 self-supervised pretraining on unlabeled field imagery to initialize the backbone and improve data efficiency under scarce labels; (ii) we propose a Decoupled Focused Self-Attention (DFSA) module that factorizes 2D attention along height and width and augments each axis with 1D dilated depthwise convolution, enlarging the effective receptive field around fine textures while suppressing background responses; and (iii) we propose a Teacher–Assistant–Student distillation framework coupled with a structured channel-pruning schedule to preserve accuracy while reducing parameters and storage for edge devices. To mitigate class imbalance and rare-lesion scarcity, we incorporate high-fidelity StyleGAN3 synthesis and targeted augmentations, and we use Grad-CAM++ to visualize decision evidence for interpretability. On challenging field datasets, RT-DETR-SDSL attains precision of 90.32%, recall of 87.52%, and mAP50 of 88.47%, outperforming strong baselines. The deployable model is 17.8 MB and runs at 14 fps on an NVIDIA Jetson Xavier NX, striking a practical balance between accuracy and efficiency for precision agriculture.

  • Yidi Sun, Tao Zong, Yuhao Zhou, Jianchang Yang, Xiaoping Xin, Weiyang Zhang, Wenhao Fang, Tong Shen
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.040
    Accepted: 2025-12-23

    Biochar (BC) demonstrates considerable potential for reducing nitrogen emissions and improving crop yield. However, it frequently exhibits limited capacity and may increase ammonia (NH3) volatilization. Nano-biochar (NBC) is attracting growing attention due to its higher surface energy, but there is a lack of information for rice production systems, especially under alternate wetting and drying (AWD). Thereforea two-year field experiment was conducted in 2023 and 2024, involving six treatments: continuous flooding (CF) without BC (ICFB0), AWD without BC (IAWDB0), AWD with 20 t ha-1 BC (IAWDB20), AWD with 5,10 and 20 t ha-1 NBC (IAWDNB5, IAWDNB10 and IAWDNB20). Their effects on reactive gaseous nitrogen losses (NH3 and N2O; Nr), floodwater nitrogen, soil environment variables, nitrogen uptake, grain yield, and nitrogen-related global warming potential (GWPN) were evaluated. Results showed that there was no significant difference in NH3 volatilization and grain yield between IAWDB0 and ICFB0 treatments, but AWD increased N2O emission by 41.71-53.25%. Compared with without BC addition, NBC application increased soil mineral nitrogen while decreasing floodwater NH4+-N, thereby reducing NH3 volatilization, N2O emission, Nr and GWPN by 5.92-34.41%, 9.95-25.49%, 6.37-33.39%, 12.20-26.11%, respectively, in AWD paddy fields. Compared to IAWDB20, IAWDNB20 reduced NH3 volatilization, N2O emission, Nr losses and GWPN by 12.97-13.45%, 9.47-17.26%, 13.69%, 9.95-17.89%, respectively, and IAWDNB10 showed no significant difference in 2023, but significantly reduced N2O emission, lowering GWPN by 7.81% in 2024. NBC also promoted aboveground dry matter and nitrogen accumulation in rice plants, ultimately increasing grain yield by 1.95-12.25%, and no significant difference was observed between IAWDNB10 and IAWDB20. Therefore, even with the biochar application rate halved, NBC can still enhance soil nitrogen content, thereby mitigating Nr losses and GWPN, while simultaneously improving grain yield in AWD paddy fields.

     

  • Pei Yang, Cao Cheng, Peng Yan, Fubin Liang, Jingshan Tian, Yali Zhang, Chuangdao Jiang, Wangfeng Zhang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.039
    Accepted: 2025-12-23

    Chilling stress is a major abiotic factor that limits the yield and quality of cotton (Gossypium hirsutum L.), particularly during the flowering and boll-setting stages. Developing a scientific and precise evaluation system for chilling tolerance is important for the screening and breeding of tolerant cultivars. In this study, 14 early maturing upland cotton cultivars were subjected to a three-day chilling stress treatment (15°C/10°C, day/night) during the flowering and boll-setting stages. Physiological and biochemical parameters, including photosynthetic pigments, gas exchange, chlorophyll fluorescence, antioxidant enzyme activities, and membrane lipid peroxidation, were measured in both the main and sympodial leaves. A comprehensive evaluation index (D-value) was constructed based on principal component analysis (PCA) and membership function and validated by the resistance coefficient of whole-plant biomass (RCBM). Systematic cluster analysis was used to classify chilling tolerance levels, and partial least squares regression (PLSR) was applied to identify key physiological indicators. The results showed that chilling stress significantly suppressed photosynthesis and induced oxidative damage, with sympodial leaves being more sensitive than main stem leaves. PCA revealed that main-stem leaves primarily relied on a “photosynthesis–antioxidant coordinated defense” mechanism, while sympodial leaves exhibited a “damage signal-driven” response pattern. The D-value based on main-stem leaf traits was highly correlated with the whole-plant biomass resistance coefficient (R⊃2;=0.92, P<0.001), indicating that it is the most effective indicator for assessing plant chilling tolerance. PLSR analysis identified the net photosynthetic rate (Pn) and peroxidase (POD) activity as the core indicators shared by both leaf types. Furthermore, the resistance coefficient of boll–leaf system photosynthesis [Pn(BLS)] was also significantly correlated with RCBM (R⊃2;=0.84, P<0.001), suggesting its great potential as a simple and efficient indicator for rapid screening. This study developed a reliable and systematic evaluation strategy for chilling tolerance in cotton, highlighted the predictive value of main stem leaf traits, and proposed Pn(BLS) as a mechanistic indicator reflecting systemic photosynthetic responses under chilling stress.

  • Kaili Duan, Yutong Shi, Hanru Gong, Qifang Shen, Chunlan Wu, Aliang Xia, Ping Xiang, Cong Jiang, Guanghui Wang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.037
    Accepted: 2025-12-23

    Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a globally destructive fungal disease that not only reduces cereal crop yields but also threatens food safety due to mycotoxin contamination. In this study, we systematically characterized histone acetyltransferases in F. graminearum and revealed the overlapping functions between FgSas3 and FgRtt109. The double deletion mutant Fgsas3 Fgrtt109 showed severely impaired vegetative growth, conidiation, mycotoxin production, as well as complete loss of sexual reproduction and pathogenicity. Furthermore, integrated transcriptome and metabolome analyses revealed that this double mutant had significant dysregulation in carbohydrate metabolism, particularly in the disaccharides to monosaccharides conversion. This metabolic shift was evidenced by the reduced disaccharide concentrations, accumulated monosaccharide and their derivatives, and enhanced growth on disaccharide-supplemented medium in the Fgsas3 Fgrtt109 double mutant. Taken together, our results demonstrate that FgSas3 and FgRtt109 synergistically regulate carbohydrate metabolism, which in turn modulates fungal development, and plant infection.

  • Chenchen Zhang, Yan Wang, Lu Chen, Xixi Wang, Sheng Teng
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.036
    Accepted: 2025-12-23

    Synthetic biology is an interdisciplinary field that applies engineering principles to design and construct novel biological systems or organisms. Initially focused on microbial systems, its applications have expanded to include plants. Plant synthetic biology offers promising solutions to pressing global challenges in agriculture and human health. As a staple crop for much of the world’s population and a model species in plant science, rice has emerged as a pivotal platform in this domain. Significant progress has been achieved in genome engineering through multiplex genome editing, synthetic hybrid rice systems, induction of apomixis, reconstruction of photosynthesis and nitrogen-fixation pathways, and biosynthesis of micronutrients, pharmaceuticals, and therapeutic proteins or peptides. This review summarizes recent advances in rice synthetic biology, outlines current developments, and discusses future research directions.

  • Liang Feng, Ruoxing Liao, Muhammad Umair Hassan, Xin Liu, Xinghao Chen, Xuyang Zhao, Xinhui Lei, Tian Pu, Yushan Wu, Taiwen Yong, Feng Yang, Xiaochun Wang, Wenyu Yang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.035
    Accepted: 2025-12-23

    Narrow-wide row soybean-maize intercropping systems can improve crop yield. Particularly, the mechanisms underlying the maize yield advantage associated with the source-flow-sink theory are unclear. Effect of optimized nitrogen (N) fertilizer application strategies on intercrops yield still needs to be further studied. This study revealed the mechanism of wide-row N application strategy to enhance the yield of intercropped maize through the trade-off relationship of source-flow-sink. Field experiments were conducted from 2023 to 2024, in a typical soybean maize intercropping region of the Sichuan Basin, China. The study was contained different fertilizer application sites: narrow rows (A1), wider row sites 10 cm (A2), 20 cm (A3) and 30 cm (A4) away from the maize plants, respectively, and different N rates (N0, 0 kg ha-1; N1, 225 kg ha-1; N2, 300 kg ha-1; N3, 375 kg ha-1). Specifically, compared to A1N2, optimized fertilization A3N2 treatments significantly enhanced the leaf biomass (11.44%), net photosynthetic rate (11.04%), SPAD (13.24%), root bleeding saps intensity (RBSI, 54.1%), number of vascular bundles (VB, 7.0%), soluble sugars (SS, 12.6%) and amino acids (16.3%), apparently, A3N2 also significantly enhanced the root morphology and maize yield (17.4%). Structural equation modeling showed that the N site and N rate interaction effect significantly increased the number of vascular bundles, soluble sugars and amino acids, which promoted root morphology, sped up grain filling (GF) and extended the active grain filling period by 2 d, ultimately leading to higher intercropped maize yields. Random forest modeling also revealed that factors such as GF, RBSI, SS and VB made a main contribution to the intercropped maize yield effect. Collectively, optimization of trade-offs in source-flow-sink relationships facilitates intercropped maize to achieve increased yield at 20 cm wide row distance with 300 kg ha-1 N application rates. These findings enriched the knowledge of source-flow-sink of strip intercropped maize under the condition of optimal N fertilizer application. It offers critical insights for the optimized application of N fertilizers in large-scale field production of strips intercropped maize.

  • Haiwang Yu, Guangzhou Liu, Xiaoyu Li, Yanhong Cui, Zhen Gao, Xiong Du
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.034
    Accepted: 2025-12-23

    Climate warming during early spring usually increases the kernel number per spike (KNS) of winter wheat in North China. However, the underlying physiological mechanisms remain unclear. Therefore, field warming experiments were conducted in early spring (late wintering period) using mobile plastic greenhouses for three consecutive growing seasons from 2020 to 2023. Warming treatment (WT) advanced wheat regreening and reduced the daily mean temperature (DMT) during subsequent growth stages, with a decrease of 1.4–1.9 °C from regreening to maturity compared to CK. Consequently, WT extended the duration of spike differentiation and the active growth period of winter wheat, significantly increased spike length, flag leaf area, and leaf area index. WT exhibited increased contents of indole-3-acetic acid and gibberellin A3 along with decreased abscisic acid levels in both flag leaves and spikes. Furthermore, WT increased the content of water-soluble carbohydrates (WSC) of different organs, which significantly enhanced the dry matter accumulation (DMA) and the contribution rate of stored assimilates in vegetative organs to grains. Compared to CK, WT led to significant increases of the number of fertile spikelets (NFS), fertile florets (NFF), and KNS by 9.1–19.5%, 6.8–8.4%, and 17.1–18.9%, respectively. In conclusion, WT extended the active growth period and spike differentiation duration of winter wheat, increased photosynthetic area, and regulated hormone levels, thereby increasing WSC and DMA in the spike. These promoted spike development and differentiation, ultimately significantly increase KNS. These findings provide new insights into the wheat KNS formation in the North China Plain under climate warming.

     

  • Junhao Feng, Ji Chen, Xiaowei Liu, Yudu Jing, Ke Liang, Qiang Yu, Changhui Peng, Liang Guo
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.030
    Accepted: 2025-12-22

    The mineralization dynamics of soil organic carbon (SOC) in grasslands are crucial to terrestrial biogeochemical cycles. However, the regulatory mechanisms underlying extracellular enzyme metabolism and microbial community structure during SOC mineralization across different carbon pools remain poorly understood. In this study, a 553-day incubation experiment was conducted to examine temporal changes in CO2 emissions, extracellular enzyme activities, microbial biomass, and microbial community composition in soils from both enclosed and grazed grasslands. Using a three-pool model, SOC dynamics were quantified within active, slow, and passive carbon pools, revealing a shift in the dominance of mineralization from the active carbon pool to the passive carbon pool during the long-term carbon turnover, with differences observed across grassland management strategies. Compared to grazed grasslands, enclosed grasslands exhibited an approximately 110% larger active carbon pool and higher initial SOC mineralization rates (significantly higher during the first 113 days), yet long-term microbial and enzymatic regulatory mechanismsparticularly shifts in microbial strategies, enzyme activity patterns, and their interactions with carbon pools—were similar across both management regimes. The observed shifts in carbon pool dynamics were driven by enhanced microbial capacity to decompose passive carbon, associated with substantially increased oxidative enzyme production (e.g., mass-specific oxidase activity increased by 190.6% in enclosed soil and by 256.1% in grazed soil) and elevated nitrogen and phosphorus demands. Notably, microbial communities shifted from fast-growing copiotrophic taxa (e.g., Proteobacteria, Bacteroidetes, Ascomycota) to slower-growing oligotrophic taxa (e.g., Acidobacteria, Actinobacteria, Planctomycetes, Basidiomycota), with the oligotroph-to-copiotroph ratio increasing by 55.5–62.6% for bacteria and 96.9–247.5% for fungi. These changes were closely linked to shifts in enzyme activity profiles and stoichiometric ratios. Overall, this study provides mechanistic insights into how microbial ecological strategies and enzyme activities interact to regulate SOC mineralization across different pools under contrasting grassland management regimes. These findings advance our understanding of SOC turnover and improve predictive capabilities for carbon cycling, with broader implications for global climate change feedbacks.

  • Xiaowei Ren, Xing Li, Jie Li, Jindi Fan, Mengyao Yuan, Yan Li, Daling Feng, Yin Lu, Hao Liang, Xiaofei Fan, Lei Sun, Kehui Ren, Mengyang Liu, Wei Ma, Jianjun Zhao
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.029
    Accepted: 2025-12-22

    Leaf color directly influences the appearance quality and nutritional quality of leafy vegetables, determining their economic value. Here, we identify a golden leaf mutant, Mut298, from an ethyl methanesulfonate (EMS)-induced mutant library of Chinese cabbage. Through the approach of forward genetics, it has been demonstrated that the phenotype of Mut298 is due to a single nucleotide substitution from C to T change glycine to arginine in the conserved domain of BrPRPL1, which encodes the large subunit ribosomal protein L1 of the chloroplast. Due to the PRPL1 mutation result in embryonic lethality in Arabidopsis, the function of PRPL1 in leaf development remains elusive. In this study, the mutation of BrPRPL1 causes a substantial reduction in the expression of key chloroplast-encoded proteins (RbcL, PsaA, and PsaB), and causing abnormal chloroplast development. Moreover, the chlorophyll content and photosynthetic parameters are significantly lower in Mut298 plants than in wild type plants, resulting in golden yellow leaves in Chinese cabbage. This study details the impact of PRPL1 mutation on ribosome translation within chloroplasts and sets a foundation for future research into the regulatory roles of PRPL1 in plant growth and development.

  • Erhan Hai, Boyuan Li, Yukun Song, Jian Zhang, Bingbing Xu, Yongbin Liu, Jiaxin Zhang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.033
    Accepted: 2025-12-19

    Ferroptosis is the primary form of regulated cell death in cashmere goat sperm during the freeze-thaw process, which significantly hinders the efficacy and application of frozen semen technology, yet its specific regulatory mechanisms remain unclear. Here, we found it activated during the cooling-equilibration phase, linked to the degradation of critical ferroptosis inhibitory proteins like ferritin heavy chain 1 (FTH1). Freezing causes superoxide anion accumulation via cytochrome b (CYTB) upregulation and reduced mitochondrial antioxidants, unblocked by ferrostatin-1 (Fer-1). Superoxide anions dose-dependently induce ferroptosis, mitigated by Fer-1. Autophagy/ferritinophagy inhibitors alleviate it, implicating ferritinophagy. This identifies superoxide anions as key mediators, offering new targets for sperm cryopreservation.

  • Tiantian Yuan, Yulin He, Minghao Cao, Dong Li, Yulong Wang, Lin Zhang, Xiang Li, Rongrong Ding, Gongshe Yang, Taiyong Yu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.032
    Accepted: 2025-12-19

    The Bamei pigs (BM), an indigenous breed in Northwest China, is renowned for its superior meat quality. To uncover the genetic basis of its traits, we analyzed whole-genome sequencing data from 61 BM. Our results revealed that BM have a good genetic conservation status and distinct genomic divergence from Western breeds. We identified MALSU1 as a new candidate gene associated with intramuscular fat (IMF) by integrating selection signature analysis with public databases, such as PigGTEx, PigBiobank, and PigQTL. Overexpression and interference experiments of MALSU1 demonstrated that it regulates IMF by inhibiting the proliferation and promoting the differentiation of porcine intramuscular adipocyte primary cells. RNA-seq results further revealed that MALSU1 regulates IMF by inhibiting lipid metabolism and promoting lipid synthesis. Interestingly, a missense mutation (p.Arg10Leu) in the coding region of the MALSU1 gene was identified, which could promote the proliferation of intramuscular preadipocytes, suggesting an important role in IMF deposition.

  • Chongbin Zhao, Jiale Huang, Yuanyuan Jiang, Jie Jiang, Wenbing Su, Shunquan Lin, Guibing Hu, Xianghui Yang, Ze Peng
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.031
    Accepted: 2025-12-19

    Flowering time and subsequent fruiting significantly influence the economic value of fruit trees. However, the regulatory mechanisms underlying the vegetative-to-reproductive transition remain understudied, particularly at single-cell and spatial levels. Here, we present a single-nucleus (snRNA-seq) and spatial transcriptomic (stRNA-seq) atlas of shoot apices in loquat (Eriobotrya japonica), a perennial fruit crop with both nutritional and medicinal importance. From the snRNA-seq dataset, 42,546 nuclei were profiled and resolved into 22 clusters corresponding to seven major cell types. Pseudotime analysis reconstructed developmental trajectories, revealing bifurcated lineages toward external and internal tissues, and identified genes dynamically associated with cell differentiation. Comparative analysis between the pre-initiation and onset stages of floral bud initiation uncovered 3,329 differentially expressed genes, including 67 homologs of Arabidopsis flowering-related genes, with the most pronounced transcriptional changes observed in epidermal and shoot meristematic cells, underscoring their central roles in floral initiation. Moreover, 43 key candidate genes, such as EjCRY2 and EjAGL79, associated with pseudotime branch points critical for cell fate decisions were predicted to act within a regulatory network dominated by photoperiod- and circadian rhythm-related pathways. Finally, integration with stRNA-seq demonstrated well concordance with snRNA-seq results and supported cell-type annotations particularly for epidermal and shoot meristematic cells. Collectively, the marker genes and associated datasets generated here provide a valuable resource for advancing single-cell and spatial transcriptomic research in loquat and potentially other fruit tree species. In addition, the identified candidate genes represent promising targets for in-depth functional studies and for breeding strategies aimed at manipulating flowering and fruiting time in loquat.

  • Shuzhen Jiao, Yaping Huang, Shixiong Lu, Han Wang , Yanmei Li, Juan Mao, Baihong Chen
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.028
    Accepted: 2025-12-19

    Drought stress negatively affects grapevine growth and development. Grafting with rootstock is widely used to improve the quality of grape fruits and confer drought stress tolerance, but the underlying genetics and regulatory mechanism is unclear. Hence, we investigated the physiologic and transcriptomic profiles in the leaves of grafted SM/1103P (SM shoot/1103P root) and self-rooted SM (Shine Muscat) as well as roots of grafted SM/1103P and self-rooted 1103P under drought stress conditions. The results indicated that grafted grapevine effectively attenuated drought damage in grape leaves by increasing phytohormone levels and antioxidant enzyme activity, reducing H2O2 and MDA content. Transcriptomic profiling revealed a total of 11,855 and 11,197 differentially expressed genes (DEGs) were identified in grape leaves and roots respectively. Weighted correlation network analysis (WGCNA) was performed based on the RNA-seq data, and five modules (greenyellow, black, turquoise, salmon and blue) were significantly correlated to drought stress. Pathway analysis showed that DEGs were enriched in the plant hormone signal transduction and MAPK signaling pathway. 916 transcription factor genes (TFs) belonging to different gene families were detected that may participate in regulating the drought stress. Quantitative real-time polymerase chain expression analysis of twelve drought stress responsive DEGs were used to verify the transcriptome data. Furthermore, overexpression of VvMYBPA1 in Arabidopsis thaliana and grape callus improved drought tolerance. Our findings provided new insights into to the regulation of mechanism for improving grapevine adaptation to drought. 

  • Qihong Zou, Bokun Zhou, Yilan Hu, Ping Li, Qi zhao, Hu Tang, Yujie Jiao, Xinzhuan Yao, Lin Chen, Litang Lu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.027
    Accepted: 2025-12-19

    Theanine content in tea plants is reduced by heat stress, but its molecular mechanism is still unclear. In this study, a temperature gradient treatment (20°C, 25°C, 30°C, 35°C) was performed to unveil the effect of heat stress on biosynthesis and accumulation of theanine. It was found that heat stress triggered metabolic alterations characterized by reduced theanine and increased catechin levels. In addition, heat stress up-regulated the expression of class B heat shock transcription factor gene CsHSFB2c, while significantly suppressing the transcription of key theanine biosynthetic genes CsTS1 and CsGS1. Functional studies showed that silencing CsHSFB2c increased theanine content, while its overexpression significantly reduced theanine levels. Consistent with these changes, silencing CsHSFB2c up-regulated the expression of CsTS1 and CsGS1, while overexpression of CsHSFB2c resulted in their down-regulation. Yeast one-hybrid (Y1H) and dual-luciferase reporter gene (Dual-LUC) assays showed that CsHSFB2c directly binds to the promoters of CsTS1 and CsGS1 and inhibits their expression. These results demonstrate that CsHSFB2c mediates heat-induced suppression of theanine biosynthesis by directly inhibiting the expression of CsTS1 and CsGS1. This study provides a theoretical basis for improving heat resistance and quality of tea plants through molecular breeding.

  • Fan Yang, Ge Gao, Cheng Wang, Jingyue Guan, Hongyan Qi
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.022
    Accepted: 2025-12-17

    Low temperature is involved in regulating plant growth, development, and quality formation. The mechanism by which low temperature affects sucrose accumulation in oriental melon fruit is currently unclear. Here, ‘HS’ (High Sucrose) melons were used as the research material and treated at temperature of 30/18℃ (day/night) and 22/10℃ (day/night) at the stage of ethylene is about to be released. Low temperature significantly inhibited ethylene release and sucrose accumulation in melon fruit, while ethephon treatment at low temperature partially restored the ethylene production and sucrose content. Through Yeast One-Hybrid (Y1H), GUS activity analysis, and Luciferase assay, we found that the transcription factor CmCBF3 could bind to CmACO1 (ACC oxidase 1) promoter and inhibit its activity, thereby suppressing ethylene production. Overexpression CmCBF3 at low temperature significantly inhibited the synthesis of ethylene and sucrose. Further research had shown that low temperature promoted CmERFV-2 expression, and CmERFV-2 could bind to CmCBF3 promoter to further inhibit ethylene synthesis. In addition, CmMYB44, as a transcription factor that negatively regulated fruit ethylene production and sucrose accumulation, could inhibit the expression of CmACO1 and CmSPS1 (sucrose phosphate synthase 1). CmERFV-2 further affected the expression of CmACO1 and CmSPS1 by binding to CmMYB44 promoter, thereby regulating ethylene and sucrose content at low temperature. In summary, this study revealed the mechanism by which CmERFV-2 affects ethylene release and sucrose accumulation in oriental melon fruit, laying the foundation for cultivating high-quality melon varieties in low-temperature environment.

  • Tiaohong Su, Yong Jin, Shangrong Wu, Shiwei Ruan, Hong Cao, Hu Zhong, Yongli Guo, Shaoxiong Guo, Hanxiao Meng, Yingbin Deng
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.025
    Accepted: 2025-12-17

    To improve the accuracy of regional rapeseed yield simulations, in this study, a new assimilation system for estimating rapeseed yield based on a four-dimensional variational (4DVar) algorithm was proposed. In this assimilation system, the state variable that bridges crop models and remote sensing observations is the total photosynthetic area index (TPAI), which is composed of the leaf area index (LAI) and silique peel area index (SPAI) and can describe the characteristics of photosynthesis and component succession in the rapeseed canopy. First, on the basis of the proposed new bridging parameter, the crop model localization method was improved, and a crop model localization method combining the TPAI and specific pod area (SPA) was proposed. Second, on the basis of the proposed new bridging parameter, a rapeseed yield estimation system was constructed in which the TPAI inverted from the SAR data was assimilated. Finally, the system was applied to single-point and regional scales rapeseed yield estimation in the main rapeseed-producing areas of Hengyang city and Yongzhou city in the middle and lower reaches of the Yangtze River Basin in China. The results revealed that at the single-point scale, the R2 values between the simulated total dry weight of storage organs (TWSO) and total above-ground biomass (TAGP) and the yield measured in the field were 0.6313 and 0.7327, respectively, whereas the root mean square error (RMSE) values reached 807.6795 and 885.3617 kg ha-1, respectively. At the regional scale, the R2 values for the simulated TWSO and TAGP in relation to the yield measured in the field were 0.6456 and 0.6894, respectively, whereas the RMSE values reached 953.6547 and 1,238.4942 kg ha-1, respectively. The accuracy of the yield simulation using the TPAI as the bridging parameter is greater than that using the LAI as the bridging parameter. Additionally, the regional assimilation results were verified via county-level rapeseed grain yield data from the National Bureau of Statistics. The R2 value between the simulated mean county TWSO and the statistical value of rapeseed grain yield reached 0.8348, with an RMSE of 867.2809 kg ha-1. These results indicate that using the TPAI as a parameter to bridge crop models and remote sensing observations can result in high rapeseed yield estimation accuracy at both single-point and regional scales, providing a new technical methodology for monitoring regional rapeseed growth and forecasting yield.

  • Yanjun Zhang, Jianlong Dai, Hezhong Dong
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.024
    Accepted: 2025-12-17

    Global cotton production faces mounting pressure to reconcile rising fiber demand with urgent sustainability imperatives, including water scarcity mitigation, greenhouse gas reduction, and agrochemical pollution control. Traditional practices, constrained by fragmented objectives and inherent trade-offs among yield, fiber quality, labor efficiency, and ecological impact, struggle to address these systemic challenges. Building upon previous concept of collaborative cultivation, this review for the first time introduces and comprehensively elaborates Multi-objective Integrated Cotton Cultivation (MOICC) —also referred to as Integrated Cotton Cultivation (ICC)—a transformative paradigm centered on three pillars: dynamic trade-off management (e.g., region-specific priority adjustment), systematic technology integration (precision seeding, dense planting, chemical regulation, water-nutrient synergy, targeted defoliation), and resource circularity (spatiotemporal optimization, waste recycling). MOICC leverages key physiological mechanisms—ethylene signaling enhancing stress-resilient seedling establishment; jasmonate-mediated pathways improving water/nutrient efficiency; canopy light competition coupled with hormonal regulation eliminating manual pruning; and growth regulators concentrating boll maturation—to overcome sustainability bottlenecks. Case studies from diverse Chinese agro-ecosystems (e.g., Xinjiang, Yangtze/Yellow River basins) and intercropping systems demonstrate significant synergies: yield gains (8–22%), resource efficiency improvements (water use efficiency increased by ≥20%, nitrogen productivity up to 35 kg kg-1), and enhanced environmental performance (labor reduction 30–40%, carbon footprint reduction 24–37%, agrochemical savings: nitrogen reduction of 15–20%, pesticides reduction of 25%). Crucially, MOICC resolves core conflicts through integrated optimization: yield versus quality (via≥70% inner-position bolls), labor-saving versus eco-safety (precision defoliant timing), and productivity versus emissions (root-zone nitrogen monitoring). Future research priorities include deciphering multi-scale stress adaptation, developing intelligent decision-support systems (e.g., AHP-NSGA-II integration), advancing carbon-neutral value chains, addressing socio-economic adoption barriers, and fostering policy synergy. MOICC establishes a conceptually globally scalable pathway toward high-yield, superior-quality, resource-efficient, and ecologically sustainable cotton production, providing a viable framework for sector-wide sustainability transition and demonstrating adaptability to other major cropping systems.

  • Guorui Li, Jinghua Zhang, Xiong Wang, Qian Zhang, Yuqing Meng, Yueshan Song, Yaru Pang, Zhiqiang Lu, Weiyan Wang, Tong Li, Yuncheng Liao, Xiaoxia Wen
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.023
    Accepted: 2025-12-17

    Tillage practices and cropping systems affect crop production by altering the soil environment. Due to the sparse rainfall and lack of soil nutrients on the Loess Plateau, it is necessary to explore suitable tillage practices and cropping systems that can improve soil moisture and nutrient conditions, thereby maintaining crop yields. Based on a long-term experiment that was initiated in 2009 on the Loess Plateau, we explored the effects of different tillage practices (chisel plow tillage, CPT; zero tillage, ZT; plow tillage, PT) and cropping systems (summer maize (Zea mays L.)-winter wheat (Triticum aestivum L.), MW; summer soybean (Glycine max L.) -winter wheat, SW) on winter wheat growth, yield, soil moisture, and soil nutrients during three winter wheat growing seasons (2020-2023). Conservation tillage practices (CPT and ZT) increased soil moisture, nitrate nitrogen, ammonium nitrogen, available phosphorus (AP), soil organic carbon, and total nitrogen in topsoil (0-20 cm) compared with that under PT. The CPT among the two conservation tillage practices was more pronounced for soil nutrients and wheat production, increasing 0-1 m AP stocks and wheat yields by 3.3-31.9% and 1.2-27.6%, respectively, compared to ZT. SW positively affected soil nitrogen availability and AP content, as well as early winter wheat growth under conservation tillage practices. The combination of CPT and SW positively affected soil AP stocks and water storage across the three growing seasons, while increasing winter wheat yield in 2022-2023. Structural equation modeling indicated that soil water storage and available nutrient stocks positively regulated winter wheat yield by influencing yield components. Overall, CPT positively affected soil quality and wheat productivity under both the MW and SW cropping systems. This is a suitable strategy for promoting sustainable agricultural development in dryland regions.

  • Rongchun Zheng, Faxi Li, Qiong Wang, Yingde Li, Youlei Shen, Zhibiao Nan, Tingyu Duan
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.021
    Accepted: 2025-12-09

    Continuous cropping presents various challenges including land degradation, the proliferation of soilborne pathogens, diminished yields. However, it can also foster the development of positive plant–soil feedbacks. The related microbial mechanisms and the potential impact of aboveground diseases on its formation remain unclear. This study systematically assessed the growth, occurrence of disease, soil properties and complexity and stability of the rhizosphere microbial network of common vetch (Vicia sativa L.) across different continuous cropping years. In this study, although continuous cropping decreased crop yield and quality, it reduced disease prevalence. The establishment of disease suppression was linked to a decrease in the incidence of disease, reduction in the soil nitrogen, decrease in microbial diversity and asymmetric alterations in the complexity and stability of the microbial network. Key beneficial microorganisms recruited in rhizosphere, such as Bacillus, Sphingomonas and Arthrobacter, were identified as potential contributors to disease suppression. The microbial-mediated soil legacy of anthracnose-infected modulated the growth-defense trade-off of common vetch by influencing the allocation of N and activating the plant's induced systemic resistance. The study underscores the significance of microbial-driven suppression in modulating the beneficial microbiome and offers novel insights into sustainable strategies of disease management in agricultural systems.

  • Ke Ding, Weihong Huang, Kehui Sun, Huali Tang, Xi Li, Surong Wang, Hao Peng, Zhiyang Han, Xiaohui Li#, Yueming Yan, Ke Wang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.020
    Accepted: 2025-12-09

    High-molecular-weight glutenin subunits (HMW-GS) play a key role in determining wheat processing quality, but their contribution to NCSB quality has not been systematically elucidated. In this study, near-isogenic lines and chromosome substitution lines differing in HMW-GS compositions at the Glu-B1 and Glu-D1 loci were utilized to comprehensively assess the impact of gluten proteins on gluten microstructure, flour functionality, and NCSB quality through multiple analytical methods.  Unextractable polymeric protein content (%UPP), disulfide bond content, TGA, rapid viscosity analyzer (RVA) profiles, gluten aggregation behavior, and steamed bread-making trials were used to evaluate gluten structure and functional performance. CLSM and LCM-Raman analyses demonstrated that CB037B and SL/B significantly increased junction density, protein network area, and β-sheet content, while reducing lacunarity and α-helix content.  Steamed bread-making trials combined with dough rheological assessments revealed that although CB037B exhibited strong-gluten characteristics, the resulting steamed bread quality was lower than that of CB037A, supporting the concept that superior NCSB quality does not necessarily depend on higher gluten strength.  TGA further indicated that the weight loss pattern at 150°C (CB037A>CB037B>SL/B>CS) aligned with steamed bread quality rankings, whereas weight loss at 600°C corresponded more closely with conventional bread quality. Overall, this work provides valuable insights into the structure–function relationships of HMW-GS in wheat and introduces novel indicators for predicting both steamed bread and bread quality, offering guidance for breeding programs aimed at improving wheat processing performance in northern China.

  • Pei Yu, Qian Luan, Jing Wang, Fei Lao, Haiming Shi, Xuebing Xu, Chunming Liu, Jihong Wu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.019
    Accepted: 2025-12-09

    The occurrence of fruity and fermented off-flavors significantly diminishes the quality and consumer acceptance of cold-pressed peanut oil (CPO). This study investigated the effects of freeze-thaw stress (0, 3, and 6 cycles) on the flavor of cold-pressed peanut oil and found that fruity and fermented off-flavors were significantly increased. Quantitative analysis and odor activity value (OAV) calculations confirmed ethyl 3-methylbutanoate (OAV=248) and ethyl 2-methylbutanoate (OAV=195) for fruity off-flavors, while butanoic acid (OAV=93) and 3-methylbutanoic acid (OAV=81) were key drivers of the fermented off-flavors. Crucially, the S-curve method revealed a synergistic interaction between ethyl 3-methylbutanoate and butanoic acid. Molecular docking revealed a preferential binding of ethyl 3-methylbutanoate to olfactory receptor OR11G2 (-7.2 kcal mol-1) driven by hydrophobic interactions. Butanoic acid was preferentially anchored in OR52E1 (-6.5 kcal mol-1), stabilized by a hydrogen bond to the receptor backbone and complementary hydrophobic interactions. These findings provide a scientific basis for improving the quality of cold-pressed peanut oil and preventing off-flavors.

  • Hongbo Zeng, Guangmin Zhao, Taohong Shao, Bindan Chen, Wentao Lyu, Yue Zhang, Qian Lin, Hua Yang, Yingping Xiao
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.018
    Accepted: 2025-12-09

    This study aimed to explore the quality characteristics and lipid profiles of egg yolks from Linwu and Shaoxing ducks using untargeted lipidomics based on UPLC-MS/MS. No significant difference in shell strength and Haugh unit between Linwu and Shaoxing duck eggs. The appearance of Linwu and Shaoxing duck eggs are markedly different, Linwu duck egg yolks exhibited higher total cholesterol and polyunsaturated fatty acids levels. Shaoxing duck egg yolks had higher water content and monounsaturated fatty acids levels. Lipidomics analysis revealed that triglyceride (TG) and phosphatidylcholine (PC) were the most abundant lipids, followed by phosphatidylethanolamine (PE) and ceramides in Linwu and Shaoxing duck egg yolks. Linwu duck egg yolks had higher TG and PC levels, whereas Shaoxing duck egg yolks had higher PE level. The differential lipids between the Linwu and Shaoxing duck egg yolks exhibited higher carbon chain lengths and were mainly enriched in membrane components, lipid-mediated signaling, and transition functions. Furthermore, integrating of lipidomics with co-occurrence network analysis indicates that TG (19:1_18:1_20:3), PC (16:0_22:6), and PE (18:0e_18:1, 18:1e_20:1, and 18:1e_22:3) were potential indicators for differentiating Linwu and Shaoxing duck egg yolks. This study provides an important data support for improving quality and nutrition of egg products.

  • Yan Li, Qiong Yao, Chuan Huang, Jing Wen, Siwei Wang#
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.017
    Accepted: 2025-12-09

    Litchi is renowned for its distinctive appearance, flavor, and nutrient composition. This study investigated the potential of nocturnal white LED light exposure, applied from the pre-second physiological fruit drop stage to harvest, to enhance the quality of ‘Feizixiao’ litchi. We focused on understanding its effects on the physical-chemical properties, aromatic profile, and gene activity. Our results showed that LED treatment significantly improved internal fruit quality by increasing the sugar/organic acid ratio in the litchi pulp and delaying the postharvest loss of key aroma compounds like 2,4-nonadienal and rose oxide isomers. Metabolomic analysis of the pulp identified 254 differentially accumulated metabolites (DAMs), primarily associated with amino acid biosynthesis. Additionally, LED treatment altered the anthocyanin profile in the pericarp, significantly elevating the level of cyanidin-3-O-glucoside, a key contributor to red pigmentation, even as it reduced the overall content of procyanidins. Transcriptomic data indicated that this shift may be attributed to LED-induced regulation of flavonoid biosynthesis genes. This work demonstrates LED light profoundly shapes litchi quality, offering valuable insights for balancing flavor and appearance in horticultural practices. 

  • Jiale Li, Wenna Shuai, Ziqiang Guo, Meng Luo, Liwei Li, Yanjun Zhou, Yifeng Jiang, Guangzhi Tong, Yifan Zeng, Jinbin Wang, Fei Gao
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.016
    Accepted: 2025-12-09

    Porcine reproductive and respiratory syndrome virus (PRRSV), the etiological agent of porcine reproductive and respiratory syndrome (PRRS), has caused substantial  economic losses to the global swine industry. In recent years, frequent genetic recombination and mutation events in PRRSV have given rise to numerous genetic  variants, presenting significant challenges for PRRS containment and eradication programs. In the present investigation, a novel PRRSV strain, designated FJNP22-1, was successfully isolated from an affected pig farm in Fujian Province, China, during a 2023 disease outbreak. Comprehensive phylogenetic analysis of the complete genome sequence identified FJNP22-1 as a member of Lineage 8 within the PRRSV-2. Notably, ORF5-based phylogenetic characterization revealed its classification within  Sub-lineage 1.8 of PRRSV-2. Genomic recombination analysis revealed that FJNP22-1 was a recombination strain derived from HP-PRRSV (Lineage 8, major parental strain) and NADC30-like (Lineage 1, minor parental strain), with seven distinct recombination breakpoints identified across Nsp2, Nsp3, ORF2, and ORF4 gene regions. Pathogenicity evaluation demonstrated that FJNP22-1 infection induced 100% morbidity in piglets, with clinical manifestations including pyrexia, anorexia and severe growth retardation. Necropsy findings confirmed marked pulmonary lesions, supporting the conclusion that FJNP22-1 exhibits high pathogenicity in swine. Furthermore, a novel recombinant PRRSV-vectored vaccine candidate (rPRRSV-E2), engineered via reverse genetics to express the classical swine fever virus (CSFV) E2 glycoprotein, conferred robust protection against FJNP22-1 challenge in piglets. This study enhances our understanding of PRRSV molecular epidemiology and provides valuable insights for vaccine development and PRRS control strategies in China.

  • Teng Hui, Zhengfeng Fang, Yong Yang, Tao Liu, Teng Pan
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.015
    Accepted: 2025-12-09

    Soy sauce is a traditional Chinese seasoning with a history spanning 3,000 years Increasing the utilization efficiency of soy sauce-separated oil (SSO), a by-product of soy sauce processing, is essential for promoting its application potential. Therefore, this study is the first to investigate the use of SSO instead of soybean oil (SO) in the diets of finishing pigs (SSO-SO) to evaluate its impact on the safety and nutritional value of roasted pork meat via systemic tests (from breeding to processing and digestion). The results indicated that regarding nutrition, the SSO-SO reduced the ∑n-6/∑n-3 in the roasted meat and digestion product by 15 and 14%, respectively, and increased the essential amino acids (∑EAAs) content in the digestion product by 6%. In terms of safety, the SSO-SO promoted protein oxidation and non-polar heterocyclic amine (HAs) formation to some extent, while reducing the thiobarbituric acid reactive substance (TBARs) value by 20% and decreasing cholesterol oxide product (COPs) content by 20-70% in the roasted meat. This study suggests that SSO shows promise as an alternative oil for n-3 polyunsaturated fatty acid (PUFA)-rich pork processing without compromising safety and nutrition.

  • Yinan Ma, Junzhou Li, Jing Liu, Sasa Zheng, Peipei Wang, Wen Zeng, Jiaqi Zhang, Kaiji Liao, Hailei Wei
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.014
    Accepted: 2025-12-09

    Tobacco bacterial wilt and black shank, caused by Ralstonia solanacearum and Phytophthora nicotianae, respectively, severely threaten global tobacco production. Although the rhizosphere microbiome has emerged as a key factor in disease suppression, limited knowledge is available regarding how mixed infections by these pathogens reshapes microbial communities or affects soil health. Most existing studies focus on single-pathogen interactions, leaving a critical gap in understanding the complex microbiome responses to dual infections. Here, we investigated rhizosphere microbiome dynamics under single and mixed infections with these pathogens to identify microbial resources for disease suppression and growth enhancement. Using an amplicon-qPCR combined method, we demonstrated the restructuring of the microbiome. Healthy soils exhibited higher diversity and enrichment of beneficial taxa, including Sphingomonas and Rhizobium, whereas diseased soils were dominated by pathogens such as Ralstonia, with intensified diversity losses in mixed infected samples. Network analyses revealed collapsed microbial connectivity in diseased soils, indicating destabilized community resilience. Among the 2,048 rhizosphere isolates, Burkholderia orbicola ZY288 was identified as a potent biocontrol agent that suppressed pathogens and provided control effect by 53%–57% in greenhouse trials. Strain ZY288 also promoted plant growth via phosphate solubilization, protease activity, and ammonia synthesis, significantly increasing tobacco biomass and height. Phylogenetic and amplicon data linked strain ZY288 to disease-suppressive rhizosphere taxa, validating its ecological niche. Our findings highlight pathogen-driven microbiome shifts in tobacco soils and suggest that strain ZY288 is a sustainable biocontrol agent with plant-protective and growth-promoting capacities. This study advances microbiome-guided strategies for managing soil-borne diseases and promotes the integration of microbial ecology into agriculture.

  • Xiaoqian Wang, Chenchen Zhao, Qinglan Wei, Chengdao Li, Zhong-Hua Chen, Rajeev Varshney, Sergey Shabala, Meiqin Lu, Yunlong Pang, Meixue Zhou
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.013
    Accepted: 2025-12-09

    Septoria tritici blotch (STB), caused by the fungal pathogen Zymoseptoria tritici, poses a major threat to global wheat production, adversely affecting both yield and grain quality. To identify the genetic loci controlling STB resistance, a genome-wide association study (GWAS) was conducted using 13,098 high-quality SNPs across a diverse panel of 318 wheat accessions including Australian commercial varieties, Australian Grains Genebank, Chinese commercial varieties, and Chinese landraces. Disease resistance was evaluated over two consecutive years under field conditions. Population structure and principal component analyses revealed distinct genetic differentiation between Chinese landraces and other groups. Notably, Chinese landraces exhibited the highest proportion of resistant accessions. We identified a total of 14 quantitative trait loci (QTLs) associated with STB resistance. Notably, three QTLs (qSTB-3B.1, qSTB-4A.2, and qSTB-6B) were consistently detected across all environments, with qSTB-4A.2 as a major resistance locus. Selection for the qSTB-4A.2 allele reduced the average disease score from 5.4 to 3.9. Furthermore, an additive effect was observed, where accessions carrying resistance alleles at both qSTB-4A.2 and qSTB-6B exhibited significantly lower disease scores than those with only the qSTB-4A.2 allele. Candidate gene analysis within these stable QTLs identified 27 promising genes including homologs of known disease resistance-related genes such as Lr34/Yr18/Pm38, and OsWAK1. These findings enhance our understanding of STB resistance genetics and provide robust markers and candidate genes for marker-assisted selection in breeding durable and disease-resistant wheat cultivars.


  • Minru Du, Wenhao Yue, Lingdan Lian, Sidi Wu, Jie Wang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.012
    Accepted: 2025-12-09

    Phenylpropanoid metabolism plays an essential role in storage stability of edible mushrooms. Phenylalanine ammonia-lyase (PAL) is the rate-limiting enzyme of this metabolic pathway. However, its special mechanisms in regulating postharvest quality of Pleurotus eryngii remain to be determined. This study aimed to investigate the roles of hot air (HA) and PAL inhibitor (AOPP) on the postharvest storage stability of P. eryngii to reveal the potential regulatory mechanism of PAL. Results showed that HA treatment inhibited the increase in water loss, browning, electrolyte leakage rate and malonaldehyde (MDA) content in P. eryngii. It also elevated the contents of phenylpropanoid metabolites and enhanced the activities and expression levels of the key enzymes in basic phenylpropanoid pathway. However, the activated phenylpropanoid metabolism induced by HA treatment was inhibited by AOPP treatment, leading to severe quality deterioration. To further analyze the role of PAL, the overexpression and silencing transformants of PePAL2, one of the PAL homologous genes in P. eryngii, were constructed. The overexpression of PePAL2 up-regulated the expression of genes downstream of PAL and boosted the contents of secondary metabolites, whereas PePAL2-silenced transformants showed the opposite effect, indicating that PePAL2 was crucial to the regulation of phenylpropanoid metabolism. Overall, the results suggested that HA treatment activated the phenylpropanoid metabolism through PePAL2, thereby improving the storage stability of P. eryngii

  • Xianghua Xu, Bo Li, Lu Jing, Xuewen Xu, Shengsong Xie, Changchun Li, Xinyun Li, Xiaosong Han, Jinxue Ruan
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.011
    Accepted: 2025-12-09

    碱基编辑器(BEs)在生物医学研究、疾病治疗和动植物分子育种等领域展现出重大应用价值。然而,如何在猪细胞中实现高效精准的多重基因编辑仍是一个亟待解决的重要问题。为解决这一问题,本研究成功开发了基于EBNA1/oriP附加体元件的CBE4max基因编辑系统(命名为epiCBE4max),该系统能够在猪细胞中实现高效精准的一步式多重碱基编辑。通过将具有自主复制功能的附加体元件整合至CBE4max系统骨架,epiCBE4max能够持久维持碱基编辑元件的高水平表达,从而显著提升编辑效率。研究团队针对与家畜生长性状和抗病能力相关的五个关键基因(ANTXR1ANPEPCD163CALRMSTN),设计并筛选出具有高活性的sgRNAs,随后在U6启动子调控下,将这些sgRNAs串联克隆至epiCBE4max载体,成功构建了五基因同时编辑载体:epiCBE4max-5×(U6+sg)。实验结果显示,将该系统通过电穿孔技术导入猪胎儿成纤维细胞(PFF)后,在获得的18个单克隆细胞系中,有高达94.44%17/18)的细胞系在所有五个靶基因位点都表现出有效的编辑效果其中CALR基因位点的编辑效率尤为显著(达89.67%;其中44.44%8/18)的细胞系在五个靶位点均实现纯合编辑,且未检测到明显的脱靶效应。本研究建立的epiCBE4max编辑技术为猪细胞提供了高效、可靠的多重基因编辑新工具,不仅为家畜遗传改良、疾病模型构建提供了技术支撑,也为异种器官移植和功能基因组学研究开辟了新途径,具有重要的科学价值和应用前景。后续研究将把该方法与体细胞核移植技术相结合,培育高品质基因编辑猪,从而推动畜牧育种等领域的可持续发展。

  • Yarong Zhang, Jianhong Ren, Shanshan Liu, Xinru Zhang, Guangzhou Liu, Xiong Du, Yanhong Cui, Zhen Gao
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.010
    Accepted: 2025-12-09

    Low light stress during the flowering stage has become a limiting factor in high-density maize production. Understanding the combined effects of shading and planting density on maize yield is essential for improving productivity.  A three-year field experiment was conducted using six consecutive days of shading (25% light transmittance) initiated at tasseling, under three planting densities (4.5, 6.75, and 9.0 plants m-2; D1, D2, and D3).  Grain yield, photosynthetic rate, stem carbohydrate availability, silk growth dynamics, and sucrose metabolism and hormonal changes in silks were measured. Results indicated that shading-induced yield penalties were more severe at higher planting densitiy. Compared with ambient light conditions, shading reduced maize yield by 57.9, 59.0, and 84.2% at D1, D2, and D3, respectively, across the three years.  The reduction in kernel number per ear was the primary cause of yield decline.  The occurrence of barren ear tips indicated ovary fertilization failure rather than post-fertilization grain abortion.  Pollen viability remained unaffected by shading, whereas the number of silks emerging from the husk declined significantly, especially at higher densities.  A strong positive linear correlation was observed between kernel number per ear and emerged silk count (R2=0.94).  Furthermore, random forest analysis identified the number of emerged silks as the most influential factor affecting kernel set.  These findings together indicated that silk growth arrest determined final kernel number under shading at tasseling.  Further analysis revealed that shading induced carbon deficiency in maize, reducing sucrose content in silks.  This disruption impaired hormone-mediated cell expansion and consequently limited silk growth.  The mechanism of yield loss under the synergistic interaction of shading and planting density was thus elucidated, with silk growth arrest governing final kernel number.  Paying attention to accelerating silk growth is critical for maize production under low light conditions caused by high planting density, continuous rainfall, or similar stresses.

  • Yubei Wang, Ranran Xu, Yanyan Ma, Zhilei Zhao, Yuhong Gu, Jiankang Cao
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.009
    Accepted: 2025-12-09

    Cold storage of amber-fleshed black plums induced the biosynthesis and accumulation of anthocyanin in plum fruit, which caused the color change of the flesh tissue when stored at low temperature. bHLH transcription factors had potential functions in response to cold induction and anthocyanin biosynthesis. To investigate the role of bHLH genes, two amber-fleshed and black-skinned cultivars (Prunus salicina Lindl. cv. Friar and cv. Angeleno) were selected as fruit material to conduct transcriptomic and bioinformatics analysis. The differentially expressed bHLHs genes were identified via RNA sequencing and verified by qRT-PCR. Ten bHLHs genes, containing 5 up-regulated and 5 down-regulated, were identified as the most significantly altered during cold-induced flesh reddening. The structure of these 10 bHLH proteins was characterized, and a phylogenetic tree was constructed. Among them, the gene evm.TU.Chr8.2504, identified as PsbHLH3, exhibits low temperature responsiveness and contains MYB-binding sites. Further experiments involving transient overexpression were performed to validate the function of PsbHLH3 in facilitating anthocyanin biosynthesis. The yeast two-hybrid and bimolecular fluorescence complementation demonstrated that PsbHLH3 interacts with PsMYB10.1. Dual-luciferase assay showed that PsbHLH3 promoted the activation of PsMYB10.1 on the promoter of PsUFGT, and consequently augmenting the transcription of structural genes related to anthocyanin biosynthesis. The study indicated that low temperatures induced the up-regulation of PsbHLH3, facilitating the opening of ON/OFF molecular switch responsible for the flesh-reddening of plum fruit. This elucidates the role of PsbHLH3 in postharvest regulation of anthocyanin biosynthesis in plums trigged by cold storage.

  • Lin Cheng, Haili Zhang, Xiaoai Zhang, Pei Huang, Xinlan Chen, Fangxu Li, Wujian Li, Wei Liu, Hualei Wang, Sandra Chiu, Zengguo Cao
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.008
    Accepted: 2025-12-09

    琅琊病毒(Langya henipavirus, LayV)是一种新发的、人兽共患亨尼帕病毒。副粘病毒科亨尼帕病毒属成员均具有极高的致病性,感染人和动物后可引起严重疾病,如同为亨尼帕病毒属的亨德拉病毒(Hendra virus, HeV)和尼帕病毒(Nipah virus, NiV)均可引起人类的高致死性疾病。为实现对LayV的高效、快速检测,本研究根据LayV核蛋白基因的保守序列,分别对基于重组酶聚合酶扩增原理设计引物和探针进行特异性生物标记并结合一次性核酸可视化检测装置,建立了一种针对LayV的现场可视化检测方法将携带LayV核蛋白基因质粒梯度稀释后,作为评价方法的阳性模板,使用本研究建立的方法进行扩增,结果显示该方法的灵敏度可达1.22 copies/μL使用HeVNiV、仙台病毒(Sendai virus, SeV)的RNA作为扩增模板,评价该方法的特异性,结果显示,该方法对上述病毒无交叉反应,具有较好的特异性。此外,将在LayV感染的细胞和鼩鼱组织样品中提取的病毒RNA作为检测对象,分别使用建立的RT-qPCR方法和可视化检测方法进行检测,结果显示,两种方法的检测结果一致。但由于本研究建立的可视化检测方法无需特殊的仪器,且更易操作,因此更具实用性。同时开展双盲试验,使用本研究建立的可视化检测方法对LayV阳性和阴性的鼩鼱组织进行检测,并平行进行RT-qPCR方法检测,结果显示,可视化检测结果与RT-qPCR检测结果吻合的同时,与阳性和阴性样品的实际结果一致,证明本研究建立的可视化检测方法可以完成临床样品的检测。综上所述,上述检测方法具有操作简便、灵敏度高、特异性强等优势,作为检测LayV的可靠方法,具有较大的应用潜力,尤其适用于需要“现地快检”的应用场景

  • Hongchao Zhao, Xiangpeng Ding, Hongyang Dong, Baizhao Ren, Peng Liu, Jiwang Zhang, Junwen Chen, Bin Zhao, Jinyan Zhang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.007
    Accepted: 2025-12-09

    Increasing planting density is an effective strategy for enhancing the yield potential of summer maize; however, it substantially elevates the risk of lodging under adverse weather conditions such as heavy rainfall and strong winds.  Under these circumstances, potassium fertilizer plays a progressively critical role in improving lodging resistance.  Previous studies have primarily focused on the individual effects of planting density and potassium fertilizer application rate on maize lodging resistance and yield, with less emphasis on their integrative effects in the lodging resistance process.  In this study, two maize varieties differing in lodging resistance—Denghai 605 (DH605, lodging-resistant) and Xianyu 335 (XY335, lodging-susceptible)—were used as experimental materials. Three treatments were established: T1 (density, 67,500 plants ha-1; K2O, 180 kg ha-1), T2 (density, 82,500 plants ha-1; K2O, 180 kg ha-1), and T3 (density, 82,500 plants ha-1; K2O, 270 kg ha-1), to examine the mechanism through which concurrent increases in planting density and potassium fertilizer application rate affect lodging resistance and yield formation of summer maize.  In terms of yield improvement, the T3 treatment demonstrated a significant advantage, increasing the two-year average yield of DH605 and XY335 by 18.65 and 16.05%, respectively, compared to T1, and by 7.25 and 14.36% relative to T2.  In terms of lodging resistance, T3 promoted stem thickening and root system expansion while enhancing the activity of lignin biosynthesis-related enzymes (PAL, TAL, and CAD) in both stems and brace roots.  This facilitated increased synthesis and accumulation of lignin, thereby strengthening mechanical properties.  Consequently, the T3 treatment reduced lodging rate by 30.45% (DH605) and 29.42% (XY335) compared to T1, and by 51.21 and 55.90% compared to T2.  Overall, concurrent increases in planting density and potassium fertilizer application rate achieved dual improvements in both yield and lodging resistance in summer maize.  This approach provides a crucial reference for mitigating lodging risks under projected extreme weather events and ensuring high and stable production of summer maize.

  • Zihan Wang, Shiduo Niu, Xiaoyu Yao, Guoqing Chen, Jian Guo, Guanghao Li, Dalei Lu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.006
    Accepted: 2025-12-09

    Increasing maize plant density (PD) is key to enhancing grain yield (GY), and one-time application of slow-release fertilizers represents an efficient and resource-saving practice.  However, the interaction between PD and fertilization mode (FM) in waxy maize production remains poorly understood.  This study systematically evaluated the interactive effects of PD and FM on dry matter (DM) and nitrogen (N) accumulation, translocation, and distribution, and their relationships with GY and N use efficiency (NUE) in waxy maize.  Two waxy maize varieties were grown across five PD levels (D1-D5: 4.5×104, 5.25×104, 6.0×104, 6.75×104, and 7.5×104 plants ha-1) and four FMs (F0, no fertilization; F1, conventional compound fertilizer at sowing plus urea topdressing at the six-leaf stage; F2, one-time application of amino acid compound fertilizer [Amino acid compound fertilizer (ACF)] at sowing; F3, one-time application of ACF at the six-leaf stage; total N-P2O5-K2O=225-75-75 kg ha-1) during the 2021-2023 growing seasons.  Although higher PD reduced kernel weight and kernels per plant, increased population density compensated for these reductions, resulting in greater GY.  Among all treatments, the D5F3 treatment (7.5×104 plants ha-1 with F3) achieved the highest GY, total score, and sustainability index.  This outcome was driven by greater post-silking DM and N accumulation, an improved harvest index, and enhanced leaf reserve translocation.  Given uniform fertilization rates across treatments, the higher yield under D5F3 led to superior N agronomic efficiency, N internal efficiency, N recovery efficiency, and N partial factor productivity.  In conclusion, increasing PD and postponing ACF application enhance GY primarily by improving post-silking DM and N accumulation and harvest index, while concurrently increasing NUE.  Field management strategies should therefore prioritize maximizing post-silking DM and N uptake to simultaneously improve yield and NUE in spring-sown waxy maize.

  • Maxinzhi Liu, Xinyao Ma, Bingbing Zhang, Xinyu Kong, Mudi Sun, Zhensheng Kang, Jie Zhao
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.005
    Accepted: 2025-12-09

    New races are responsible for the breakdown of stripe rust-resistant wheat cultivars. Sexual reproduction of Puccinia striiformis f. sp. tritici, the cause of wheat strip rust, can generate new races with virulence variation. However, the role of inter-racial hybridization in generating new races and population genetic diversity has remained unknown. So, we hybridized two single-urediospore P. striiformis f. sp. tritici isolates, 4-14 and b-5, on barberry (Berberis aggregata) seedlings to establish single-aeciospore F1 progenies, and selfed the F1 progeny 1-2 to establish 85 single-aeciospore F2 progenies. All isolates were phenotyped on 26 Yr-single gene lines as differentials, and genotyped with the 20K genotyping-by-target sequencing (GBTS) chip for P. striiformis f. sp. tritici. The results showed that 58 different virulence phenotypes (VPs, VP1-VP58) were identified, and 57 VPs were new, showing high virulence variation (98.3-100%). Overall F2 progenies displayed different avirulence and virulence segregation ratios at 13 of 26 Yr loci tested, at which avirulence was controlled by one dominant or recessive gene, or by two genes with different gene effects. All F2 progenies showed a high level of heterozygosity (0.07-0.64), with a great difference of genotypic distribution, presenting a rich genetic diversity from sexual recombination. Genetic variation of the F2 progenies mostly occurred among individuals rather than among populations. A low correlation was detected between phenotype and genotype in the F2 progenies (R2=0.0257). This study provides an insight into understanding the role of sexual recombination in the origin of new races and high level of genetic diversity as well as evolution of the stripe rust. 

  • Huifang Song, Bingshuai Du, Xinyan Zhao, Kaiyue Feng, Lingyun Zhang, Yibo Cao
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.004
    Accepted: 2025-12-09

    Soil salinization is a growing challenge for highbush blueberry (Vaccinium corymbosum) production, but knowledge about its physiological and molecular responses to salt stress remains limited. To address this, we performed Gene Ontology (GO) enrichment analysis and weighted gene co-expression network analysis (WGCNA) on differentially expressed genes from the roots and leaves of the salt-tolerant cultivar ‘Duke’ and the salt-sensitive cultivar ‘Sweetheart’. GO analysis revealed significant enrichment of ion transport and cellular ion homeostasis in the roots under salt stress. WGCNA identified a strong correlation between Na+ and K+ contents and the expression of hub genes VcHAK5, VcNHX1, and VcNHX2 under salt stress. These genes were significantly upregulated in the roots of the salt-tolerant cultivar. VcHAK5 encodes a K+-selective ion transporter in the plasma membrane, and VcNHX1 and VcNHX2 encode Na+- and K+-/H+ antiporters in the tonoplast. Knockdown mutants of these genes in blueberry calli showed hypersensitivity to salt stress. Furthermore, reciprocal grafting between salt-sensitive and salt-tolerant blueberry cultivars demonstrated that lower root Na+ content and Na+/K+ ratios are crucial for salt tolerance. This study provides the first comprehensive insights into blueberry responses to salt stress, identifies target genes and highlights the critical role of salt-resistant roots.

  • Meiqi Guo, Tongtian Guo, Chuan Guo, Jiqiong Zhou, Gaowen Yang, Yingjun Zhang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.003
    Accepted: 2025-12-09

    While chemical fertilization offers a direct solution to restore soil fertility in degraded ecosystem, revegetation through legume introduction represents a more sustainable management strategy. However, the mechanisms by which legume introduction influence soil phosphorus (P) transformation, and how these processes respond to nutrient fertilization, remain poorly understood. Using one-time sampling from an 11-year field experiment, we investigated how the introduction of a legume (Medicago falcata L.) influenced rhizosphere soil P fractions, both alone and in combination with nitrogen (N; 5 g m-⊃2; yr-⊃1;) and P (3.2 g m-⊃2; yr-⊃1;) fertilization. Our findings reveal that legume introduction stimulated the mobilization of soil P by increasing organic acid concentrations and microbial P demand, as indicated by the microbial biomass N:P ratio. This resulted in significant changes in P pools, marked by a 97.4% increase in labile inorganic P, a 22.9% decrease in moderately labile inorganic P, a 9.6% decrease in moderately labile organic P, and a 3.7% decrease in non-labile P pool. In contrast, while N fertilization promoted the solubilization of moderately labile inorganic P and the dissolution of the non-labile P pool by lowering soil pH and enhancing the abundance of genes for inorganic P solubilization, it ultimately led to a 10.6% depletion of the labile P pool. Phosphorus fertilization increased labile inorganic P, moderately labile inorganic P, and non-labile P, yet it inhibited microbial P transformation processes. Importantly, legume introduction mitigated the negative impacts of N fertilization on bioavailable P and the negative effects of P fertilization on microbial P mineralization genes. These findings suggest that legume introduction is a sustainable practice to stimulate P cycling in natural grassland, highlighting the importance of activating microbial functions in grassland management and restoration.