Home Browse Just accepted
Accepted

Accepted, unedited articles published online and citable. The final edited and typeset version of record will appear in the future.

Please wait a minute...
  • Select all
    |
  • Yating Fang, Hongyan Deng, Hehe Gu, Xin Cui, Shipeng Liao, Zhifeng Lu, Rihuan Cong, Xiaokun Li, Tao Ren, Jianwei Lu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.020
    Accepted: 2026-01-15

    Maintaining soil fertility through balanced fertilization is essential for ensuring high crop productivity in intensive paddy-upland rotation systems. In this study, a meta-analysis of 141 published studies was conducted to evaluate the effects of different fertilization regimes on soil chemical properties and crop yields in predominant paddy-upland rotation systems. Relative to balanced fertilization (BF), both no fertilization (CK) and unbalanced fertilization (UF) significantly reduced soil organic matter (SOM) (16.6% and 7.2%), total N (11.3% and 4.9%), total P (14.6% and 7.1%), available P (41.0% and 22.9%), and available K (13.0% and 11.0%). In contrast, the combined application of chemical fertilizer with organic manure (F+M) or straw return (F+S) significantly increased SOM (16.5% and 9.6%), total N (14.9% and 8.7%), total P (29.2% and 16.6%), available P (37.6% and14.7%), and available K (9.1% and 12.9%). Notably, the response of soil fertility to fertilization regimes differed between oilseed rape–rice (OR) and wheat–rice (WR) rotations. The WR rotation showed greater declines in SOM and total N under CK treatment than the OR rotation. While F+S treatment was more effective in improving soil available P in OR rotation, F+M treatment produced better outcomes in WR rotation. These soil responses were reflected in crop yields, with a more severe rice yield reduction under CK in the WR (45.0%) than in the OR rotation (29.2%). The greatest yield increases were associated with the F+S treatment in OR and the F+M treatment in WR. Random Forest analysis and linear regression identified SOM, available P, and total N as the primary factors governing rice yield. These results suggest that integrated nutrient management combining chemical fertilizers with organic amendments is crucial for sustaining soil fertility and productivity in paddy-upland rotations, and that tailored fertilization strategies should be developed based on specific rice-based cropping systems.

  • Yanan Xu, Chang Ye, Yi Tao, Deshun Xiao, Junlin Zhu, Wenli Liao, Song Chen, Guang Chu, Chunmei Xu, Jianliang Huang, Danying Wang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.019
    Accepted: 2026-01-15

    To elucidate the relationship between leaf color-changing and stem NSC translocation during grain filling and their impact on yield formation, two indica-japonica hybrid varieties with distinct leaf color change patterns were planted under three N fertilizer dosages (LN 0 kg ha−1; MN 150 kg ha−1; HN 300 kg ha−1). Leaf color change characteristics, photosynthetic productivity, stem NSC translocation, yield and harvest index were analyzed. The results showed that CY927 (slow leaf color change) achieved 10.45%−21.81% higher yields than YY1540 (fast leaf color change) under high-temperature conditions. Compared to YY1540, CY927 delayed the onset of leaf color-changing (T0) by 2.1−4.1 d, enhanced the final leaf color indicator at maturation (CIf) by 16.79−52.25%, contributing to 10.56−42.77% greater aboveground biomass accumulation through higher photosynthetic capacity, but significantly limited stem NSC remobilization, reduced total NSC translocation by 23.78−33.19% and NSC translocation ratio by 14.65−22.19%, resulting in a 2.66−8.43% lower harvest index. N application increased rice yield via a delay in leaf color-changing onset (T0), a reduced color-changing rate (Rm), a shortened color-changing duration (T100), and an improved final color index (CIf). This retardation of senescence enhanced photosynthetic capacity, which was associated with elevated sucrose content and sucrose synthase activity. However, N reduced stem α-amylase activity (14.83−62.07%) and NSC translocation ratio (5.44−16.30%) in both varieties. Correlation analysis revealed significant positive relationships between T0 and aboveground biomass (P<0.001), and between T100 and stem NSC translocation (P<0.001). In conclusion, rice variety and N application indirectly regulate the dynamic balances between leaf photosynthetic carbon metabolism and stem NSC translocation by influencing the leaf color-changing dynamic, ultimately affecting yield and resource use efficiency. This integrative framework, connecting leaf color-changing, carbon allocation, and yield performance, provides scientific guidance for optimizing rice cultivars and N fertilization strategies.

     

  • Xiaoyan Liang, Jiajia Li, Kuihua Yi, Yinyu Gu, Meng Li, Chuanjie Chen, Junlin Li, Rao Fu, Jialei Zhang, Shubo Wan
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.017
    Accepted: 2026-01-15

    Quinoa–peanut relay intercropping is a potential practice in saline-alkali land; however, quinoa varieties exhibit considerable variability, and a paucity of information regarding suitable varieties of quinoa for intercropping with peanuts. A field experiment with three intercropped peanut treatments (PSE, PMM, and PTL) with quinoa varieties of short-stemmed and early-maturing (QSE), medium-stemmed and medium-maturing (QMM), and tall-stemmed and late-maturing (QTL) was conducted in 2021–2022 to elucidate the effects of quinoa varieties on the root distribution, soil moisture content (SMC), electrical conductivity (EC), nutrient (N, P, and K) absorption, and pod yield of peanuts. The results showed the pod yield, pod dry weight, biomass, and 100-fruit weight of peanut under PSE were the highest, followed by PMM, and PTL was the lowest. The pod yield of PSE was 6.03–21.16% higher than that of PMM and PTL in 2021 and 2022. In the co-growth period of quinoa and peanut (CGP), the main stem height, branch number, leaf area (LA), dry matter weight, and nutrients absorption of peanut plants under PSE and PMM were all significantly higher than PTL; but no difference was observed between PSE and PMM. In the solo-growth period of peanut (SGP), the plant traits (except for the main stem height) and nutrient absorption of peanut under PMM were worse than PSE, and PTL was the worst, which was consistent with the variation of root length density (RLD) of peanuts. Meanwhile, PSE had the highest SMC at soil depths below 10 cm, nutrient contents in rhizosphere soil (K+, NO3, NH4+, PO43−, and TOC), also EC and Na+ contents compared with PMM and PTL. The RLD of peanut, SMC, EC, and nutrient contents in rhizosphere soil of peanuts were negatively correlated with the RLD of quinoa. Therefore, intercropping peanut with short-stemmed and early-maturing quinoa variety is more conducive to increasing peanut yield in saline-alkali soil.

  • Ruiyun Li, Shaopeng Yu, Jiayue Zhou, Ziyang Lu, Mingrui Zhao, Xuwen Su, Qinghua Yang, Yuhao Yuan, Jinfeng Gao, Baili Feng
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.018
    Accepted: 2026-01-15

    The frequent occurrence of extreme adverse climatic conditions worldwide has led to a significant increase in crop lodging, resulting in reduced yields and posing a threat to food security. Broomcorn millet is mainly cultivated in marginal land where agricultural practices are relatively less advanced. Improper sowing methods and density have exacerbated the lodging issue of broomcorn millet, hindering yield increase. The aim of this study was to explore the impact of different sowing methods and densities on the lodging resistance and yield of broomcorn millet, aiming to optimize cultivation techniques for enhanced lodging resistance and higher yields. The experiment was conducted using the Shaanxi broomcorn millet No. 2 variety, with three sowing methods (row sowing, hole sowing, and wide-range sowing) and three sowing densities (D1-D3, 6×105, 9×105, and 1.2×106 plants ha-1, respectively) to assess the impact on lodging-related characteristics and yield changes. The results showed that as sowing density increased, the total dry matter of broomcorn millet decreased. However, wide-range sowing maintained a larger leaf area and better growth status at higher densities. Wide-range sowing exhibited superior stem breaking resistance under all density conditions, optimizing both plant height and the height of the center of gravity, thereby enhancing overall lodging resistance. Furthermore, the mechanical tissue structure in wide-range sowing was superior to that in row and hole sowing at the same density, promoting lignin and cellulose accumulation, thereby strengthening broomcorn millet's lodging resistance. Based on these findings, it is recommended that local broomcorn millet production adopt wide-range sowing with a D2 density, as this combination results in a lower lodging rate and higher yields. This study provides a theoretical foundation for optimizing broomcorn millet planting strategies, demonstrating that a suitable combination of sowing method and density can effectively improve lodging resistance and yield.

  • Xue Li, Bo Jiang, Depiao Kong, Deqiang Zang, Ya Chen, Changkun Wang , Huanjun Liu, Chong Luo
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.016
    Accepted: 2026-01-15

    Soil organic matter (SOM) is a core indicator of soil fertility and ecosystem function. However, in regions where Mollisol and non-Mollisol coexist, high-precision spatial mapping faces significant challenges due to pronounced terrain heterogeneity and redundancy in high-dimensional covariates. This study proposes a “remote sensing zoning-feature selection optimization-random forest (RSZ-FSO-RF)” framework. By integrating Landsat-8 multi-temporal imagery from 2014-2023 with topographic and climatic factors, and leveraging the Google Earth Engine (GEE) platform, it achieves high-precision remote sensing zoning of Mollisol and non-Mollisol areas (overall accuracy: 92.13%, Kappa coefficient: 0.70). Subsequently, local Random Forest (RF) regression models were established within each zone for SOM prediction, with predictive variables optimized using Recursive Feature Elimination (RFE). Results demonstrate that compared to FAO-zone-based modeling, the RSZ-FSO-RF framework significantly enhances prediction accuracy (R2=0.619, RMSE=6.849 g kg-1). And further feature optimization continued to enhance model performance (R2=0.627, RMSE=6.781 g kg-1). Notably, optimal predictor combinations varied significantly across zones, with SOM spatial variability generally higher in non-Mollisol areas than in Mollisol regions. By organically integrating remote sensing zoning with feature selection, this framework effectively mitigates covariate redundancy while accounting for local heterogeneity, significantly enhancing the accuracy and stability of high-resolution SOM mapping. Furthermore, this study provides scientific basis and decision support for soil resource management and sustainable agricultural development under complex topographic conditions.

  • Shiyan Peng, Jiangyao Fu, Kuanyu Zhu, Weiyang Zhang, Zhiqin Wang, Junfei Gu, Jianhua Zhang, Jianchang Yang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.015
    Accepted: 2026-01-15

    Brassinosteroids (BRs) are a novel class of plant hormones that play important roles in regulating plant growth and development, as well as in responding to biotic and abiotic stresses. However, little is known whether and how BRs mediate phosphorus (P) acquisition and utilization in rice. This study investigated the question. Both hydroponics and field experiments were conducted in 2019-2024 by using rice varieties either with strong tolerance to low P (SVs) or with weak tolerance to low P (WVs). The results showed that the SVs had higher levels of BRs including 24-epibrassinolide (24-EBL) and 28-homobrassinolide (28-HBL) in both roots and leaves than WVs at each growth stage and under a low P (LP) condition. Levels of 24-EBL and 28-HBL were very significantly and positively correlated with the parameters reflecting P acquisition and utilization, such as P content, activities of acid phosphatase and proton-pumping adenosine triphosphatase, and P remobilization, leading to more P accumulation and higher P harvest index, internal P use efficiency, and grain yield for SVs. In contrast, levels of other phytohormones including cytokinins (zeatin+zeatin riboside), indole-3-acetic acid, gibberellic acids (GA1+GA4), abscisic acid, jasmonic acid, and ethylene were neither markedly different between SVs and WVs nor significantly correlated with the parameters reflecting P acquisition and utilization under LP. Applying 24-EBL prominently increased BRs levels in plants, improved the parameters reflecting P acquisition and utilization, up-regulated expression of the genes involved in P uptake and transport, and increased P remobilization, internal P use efficiency, and grain yield, whereas applying brassinazole, an inhibitor of BRs synthesis, exhibited opposite effects. These findings shed light on the role and mechanism of BRs in mediating P acquisition and utilization, and provide a strategy for synergistically improving grain yield and P use efficiency through increasing BRs levels in the plants in rice breeding and crop management.

  • Jiyu Wang, Xiang Li, Xiaoxue Liang, Yingying Chen, Lei Cao, Qiong Li, Zhiqiang Cheng, Yan Guo, Junlong Fan, Wenwen Mao, Chen Luo, Lili Li, Panqiao Wang, Luming Yang, Juan Hou, Jianbin Hu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.014
    Accepted: 2026-01-14

    Melon is a globally important cucurbit crop, but its functional genomics are hindered by inefficient genetic transformation. Virus-induced gene silencing (VIGS) enables rapid gene analysis and high-throughput screening. In this study, we evaluated the silencing efficiency of three viral vectors delivered via vacuum infiltration and cotyledon injection. We developed an optimized tobacco ringspot virus (TRSV)-mediated VIGS system using vacuum infiltration, which exhibited remarkable silencing efficiency and accelerated phenotypic manifestation in melon. The reporter gene CmPDS (phytoene desaturase) was effectively silenced, resulting in complete photobleaching across the entire leaf surface. This method achieved 95.2% silencing efficiency with 80% transformation frequency, completing the entire process from seed treatment to observable phenotype within just 11 days. Supplementing with tenoxicam (TNX, oxicam-type nonsteroidal anti-inflammatory drugs NSAIDs) during co-culture significantly enhanced transformation frequency to 93.3% across diverse genotypes. qRT-PCR showed TNX may boost transformation by attenuating plant immunity. To validate the system’s broad applicability, we silenced the Mg-chelatase H subunit (CmChlH) gene, resulting in the expected yellow-leaf phenotype. The VIGS system developed herein provides a powerful tool for investigating gene function during early melon development. Also, this work establishes a foundational framework for VIGS system construction and accelerates genetic research in other cucurbit species.

  • Junmei Huang, Dafeng Dong, Tao Wang, Zhidan Chen, Peitao Lü, Weijiang Sun, Wen Zeng
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.013
    Accepted: 2026-01-14

    Tea trichomes are rich in secondary metabolites and play a crucial role in the stress resistance and quality formation of tea plants. However, the specific metabolites involved and their regulatory mechanisms remain largely unknown. Here, we employed ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) to conduct a comprehensive targeted metabolomic analysis of the trichomes and corresponding defoliated leaves from the buds of Fudingdahao (FDDH) white tea. Our analysis identified a total of 2,425 metabolites, with 1,537 differentially accumulated metabolites (DAMs) between the trichomes and leaves. Notably, flavonoids, particularly kaempferol and its derivatives, were found to be more abundant in trichomes. Transcriptomic analysis revealed 447 genes specifically highly expressed in trichomes, with significant enrichment in phenylpropanoid and flavonoid biosynthesis pathways. Further chromatin accessibility analysis identified an ERF transcription factor, CsRAP2.3, as a key regulator. DNA affinity purification sequencing and luciferase reporter assays demonstrated that CsRAP2.3 binds to the promoter of the CsUGT78A14 gene, which is involved in kaempferol glycosylation. Transient overexpression of CsRAP2.3 in tobacco leaves increased flavonol metabolites. Our results suggest that CsRAP2.3 may regulate the expression of CsUGT78A14, thereby influencing the accumulation of flavonols in trichomes of tea plants. This study provides insights into the molecular mechanisms underlying the accumulation of flavonol metabolites in white tea trichomes and offers a foundation for improving tea stress resistance and quality.

  • Junjie Zhong, Ruoyan Li, Yuan Liu, Shuquan Chen, Huibao Wen, Teng Tang, Cong Luo, Xinhua He
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.012
    Accepted: 2026-01-14
    The CONSTANS/CONSTANS-LIKE (CO/COL) gene family plays important roles in plants flowering and stress response. In this study, two variants of the MiCOL14B gene were identified from two different mango cultivars; they were designated as MiCOL14B-GQ and MiCOL14B-JH, which exhibited significant differences in sequence and B-box domain. Both genes are expressed in various tissues of mango, localized in the nucleus, and responsive to drought and salt stress. In transgenic Arabidopsis thaliana, MiCOL14B-GQ delayed flowering, while MiCOL14B-JH promoted flowering. This phenotypic divergence stemmed from their molecular regulatory specificity. Yeast one-hybrid (Y1H) and dual-luciferase reporter assays demonstrated that both variants directly bind to the promoters of florigen genes (MiFTs), with MiCOL14B-GQ repressing their transcription and MiCOL14B-JH enhancing it. Altered expression levels of MiFTs in the roots of transgenic mango further validated this mechanism. Moreover, both MiCOL14B-GQ and MiCOL14B-JH improved stress tolerance under drought and salt conditions in transgenic A. thaliana as well as in transgenic mango roots. These variants significantly increased stress tolerance by increasing proline (Pro) content and superoxide dismutase (SOD) activity, while reducing malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) accumulation. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays revealed that MiCOL14B-GQ and MiCOL14B-JH interact with several stress-related proteins. This study demonstrates for the first time the potential function of MiCOL14B gene sequence variation in regulating flowering and stress responses, providing valuable genetic resources for mango molecular breeding.


  • Jingjing Cao, Yongpan Qian, Jianying Guo, Hongwei Wang, Jianguo Fu, Yibo Zhang, Wanxue Liu, Fanghao Wan, Rui Wang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.011
    Accepted: 2026-01-14

    A central challenge in invasion biology is to determine whether disjunct distributions of invasive species stem from secondary spread from an initial introduction bridgehead or from recurrent, human-mediated introductions. The devastating alien weed Amaranthus palmeri, with its large-scale disjunct distribution across China, provides an ideal system to address this question. We tested the competing hypotheses of bridgehead-mediated expansion (originating from the initial introduction in Beijing, 1985) versus multiple independent introductions. By integrating genetic analyses with stable isotope geolocation, we treated propagules from imported soybean shipments as direct, traceable links to potential source populations. Newly field-collected populations in China harbored significantly higher nucleotide diversity (π=(0.78 ± 0.18) × 10-3) and haplotype diversity (Hd = 0.47 ± 0.04) than both the initial introduced population and the pooled propagules from the primary source, the United States (US). Significant genetic differentiation (FST > 0.20was observed both among newly field-established populations and between them and the initial introduction. Non-significant neutrality tests, coupled with multimodal mismatch distributions (Raggedness index = 0.0946, P > 0.05), indicated that these populations did not undergo a recent demographic expansion or selection. Genetic diversity and structure correlated with regional soybean import volume (r = 0.59, P < 0.05but not with environmental distance (Mantel r = 0.24, P > 0.05). Our findings demonstrate that recurrent transcontinental introductions, mediated by global grain trade, are the dominant force shaping the genetic pattern and invasion process. This study provides a framework for reconstructing invasion pathways and highlights the need for proactive, source-targeted biosecurity strategies to manage invasions in the Anthropocene.

  • Dongmei Xue, Jinglei Wang, Lanxin Xiang, Xiaoxian Peng, Ke Jin, Yunting Fang, Xiangzhen Li, Yidong Wang, Zhongliang Wang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.010
    Accepted: 2026-01-14

    Denitrification plays a critical role in mitigating anthropogenic nitrate (NO3-) accumulation in JIA-2025-1634 Jinke slj ZR.docxecosystems. The isotopic composition of NO3- (δ15N and δ18O) serves as a powerful tracer for identifying N sources and transformation processes. Denitrification often superimposed on the isotope effects of NO2- oxidation, resulting in parallel enrichment of δ15N- and δ18O-NO3- (Δδ18O:Δδ15N trajectory) that causes them to be either below or above 1. This study compared the Δδ18O:Δδ15N trajectory during denitrification, functional genes (narG, napA, and nxrA), and carbon sources from metabolites in the Δδ18O:Δδ15N trajectories below or above 1 in unsaturated zones. The results revealed that NO3- reduction was more important for variation in the Δδ18O:Δδ15N trajectory because the difference in isotope effects (15εNO3 reduction and 18εNO3 reduction) between the two Δδ18O:Δδ15N trajectory groups was significant, whereas the difference in isotope effects (15εnxr and 18εnxr) upon NO2- oxidation was not. Carbon sources in the group with Δδ18O:Δδ15N trajectories below 1 facilitated more efficient electron production to promote NO3- reduction because of their low molecular weight and simple structure. Conversely, the lower electron production efficiency due to the high molecular weight and complex structures of carbon sources in the group with Δδ18O:Δδ15N trajectories above 1 downregulated the expression of the three functional genes (narG, napA, and nxrA). The group with Δδ18O:Δδ15N trajectories below 1 showed significantly higher levels of 15εNO3 reduction, 18εNO3 reduction, NO2- oxidation ratio, and copy numbers of narG, napA, and nxrA genes compared to the other group, revealing that NO3- reduction at the cellular level was more active in the former group. This study elucidated the integrated influence of isotope effects, NO3- reductase and NO2- oxidoreductase activities, and carbon sources from metabolites. These findings are significant for understanding the Δδ18O:Δδ15N trajectories of N cycling in terrestrial ecosystems and support groundwater conservation by improving carbon supplementation approaches that stimulate denitrification, with Δδ18O:Δδ15N trajectories serving as effective tracers for assessing denitrification performance in terrestrial environments.

  • Jing Cao, Yunfei Tian, Longfei Han, Xiaoping He, Liming Niu, Jiawei Liu, Fangyuan Zhang, Dongyue Wang, Jiangnan Li, Changjiang Weng, Jiajun Wu, Li Huang, Shaobin Shang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.009
    Accepted: 2026-01-08

    African swine fever (ASF) is a highly lethal hemorrhagic disease of swine caused by African swine fever virus (ASFV). Development of safe and effective ASFV subunit vaccine relies on the identification of protective antigens. In this study, we systematically evaluated the antigenicity of ASFV non-structural protein pA151R recognized by T cells from immune-protected pigs. Recombinant pA151R (rpA151R) was expressed in E. coli and used to generate anti-rpA151R polyclonal antibodies (pAb). This pAb bound both eukaryotically-expressed and native viral pA151R, confirming that rpA151R retains its native antigenicity. Using ASFV attenuated vaccine-immunized pigs, we further analysed the kinetics and functions of pA151R-specific T cells as well as their epitope recognition. The results showed that pA151R-specific T cell responses peaked at 14 days post-immunization in pigs, and secreted IFN-γ, TNF-α, IL-2, and perforin simultaneously, with multifunctional characteristics. T-cell epitope mapping identified seven peptides recognized by these pA151R-specific T cells. Among them, three peptides (P2, P4, and P5) were exclusively recognized by CD4⁺ T cells, four peptides (P6, P10, P12, and P13) were specific for CD8⁺ T cells whereas P1, P7, and P9 were recognized by both CD4⁺ and CD8⁺ T cells. These peptide-specific CD4⁺ or CD8⁺ T cells showed cytotoxicity, killing peptide-pulsed autologous target cells in a dose-dependent manner. These findings demonstrated that pA151R-specific swine T cells are able to contribute to protective immunity against ASFV and pA151R is a potential protective antigen for vaccine development. This study established a benchmark for screening and defining more ASFV protective antigens.

  • Song Liang, Shaoyan He, Shidan Zhang, Jiqi Song, Yubing Wang, Xinyi Liu, Lei Dai, Jinxiu Wang, Youzhi Xie, Huochun Yao, Guangjin Liu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.008
    Accepted: 2026-01-08

    Streptococcus suis (S. suis) is an important global zoonotic pathogen that can cause meningitis, arthritis, and even death in humans and pigs. Hainan, as the only tropical island in China, experiences a year-round prevalence of S. suis in swine and a high risk of human infection. This work aimed to investigate the molecular epidemiological and phenotypic characteristics of S. suis isolates from pigs in Hainan. Between 2022 and 2024, a total of 298 S. suis isolates were recovered from 639 samples (629 from healthy pigs and 10 from sick pigs) collected across Hainan Island. Serotype 16 (22.15%) and 2 (11.74%) strains exhibited the highest prevalence, followed by serotypes 7 (6.04%) and 31 (5.37%), while 17.79% of the strains belonged to non-classical serotypes. Whole-genome sequencing was conducted on 63 representative strains, and the genome data showed that 65.08% of the strains belonged to novel sequence types, which reflects the distinctive evolutionary relationships of strains originating from Hainan. Notably, D74-2 and D77-1, isolated from healthy pigs, exhibited high virulence with 106 virulence-associated genes (VAGs), and had the closest evolutionary relationship to the human strains 98HAH33 and 05ZYH33, which were responsible for two human outbreaks in China. Further, two new NCL subtypes (NCL3-3, NCL29-2) were identified from diseased pig-derived strains. Furthermore, 98.41% of sequenced strains exhibited multidrug resistance, irrespective of whether they originated from healthy or diseased pigs. Interestingly, all SS2/ST1 and SS7/ST29 strains were classified as highly virulent, whereas all SS16 strains were categorized as lowly virulent in zebrafish infection experiments. Nevertheless, our data showed that some strains lacking combinations of virulence markers (mrp/sly/epf, srtF/ofs, and NisR/K) still exhibited high virulence. In conclusion, the results presented above illustrate the diverse molecular epidemiological and phenotypic characteristics of S. suis in Hainan, providing a targeted scientific basis for the development of prevention and control strategies for this zoonotic pathogen in the Chinese tropical region

  • Lianjie Wan, Fei Ma, Jianmin Zhou, Changwen Du
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.007
    Accepted: 2026-01-08
    Modern agriculture faces unprecedented challenges: a growing global population, limited arable land, freshwater scarcity, and inefficient agrochemical use have triggered severe environmental degradation.  Pollutants including pesticides, heavy metals, microplastics, antibiotics, nutrient runoff, and greenhouse gases threaten ecosystem stability, food security, and human health.  Metal-organic frameworks (MOFs), with their tunable structures, high porosity, and versatile functionality, emerge as promising materials to address these issues.  This review comprehensively summarizes recent advances in MOFs-based solutions for agriculture.  It covers green synthesis strategies to enhance structural stability and promote circular economy principles.  Applications span three primary domains: pollutant remediation, sustainable technologies (e.g., atmospheric water harvesting, seawater desalination, and green ammonia synthesis), and smart agricultural systems.  The latter enables controlled agrochemical release and real-time sensing and monitoring.  Finally, challenges - such as high costs, biosafety concerns, and scalability limitations - are discussed, alongside forward-looking perspectives including AI-assisted design, improved recyclability, scalable production, and multifunctional integration toward green and smart agriculture.
  • Zhengqin Ye, Wenqiang Wang, Zhenbang Zhu, Wei Wen, Hu Suk Lee, Xiangdong Li
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.006
    Accepted: 2026-01-08

    猪繁殖与呼吸综合征(PRRS)是威胁全球养猪业的重要疫病。近年来,NADC34-like毒株因其复杂的重组背景和多变的致病性备受关注。本研究旨在通过全球视野下的全基因组分析,明确NADC34-like毒株的遗传多样性、时空分布特征及重组规律,为该毒株的精准防控提供理论依据。本研究从GenBank数据库中检索并筛选了截至20256月的1,598PRRSV全基因组序列,最终聚焦于来自中国、美国和韩国的176NADC34-like毒株序列。利用IQ-TREE软件构建最大似然系统发育树进行分类研究;采用RDP4(集成7种算法)及Simplot软件对重组事件进行系统鉴定与验证;并结合时间与地理信息,分析了不同国家毒株重组热点的演化趋势。遗传分类显示,NADC34-like毒株内平均核苷酸距离为5.68%,而与其他谱系距离均超过14.89%。重组分析发现,在176条毒株中,重组毒株占比56.82%100/176),已成为该亚群的主要存在形式。研究界定了12种重组模式(R1–R12),其中NADC34-R1是美国最流行的模式,且具有明显的地域聚集性。发现中国NADC34-like毒株的重组热点存在显著的时空转移:2017-2019年重组多发生于结构蛋白区(ORFs 2-7),而2020年后则主要集中在ORF1a区域,这与美国和韩国毒株持续集中于ORF1ab的特征显著不同。谱系1.8Lineage 1.8)被鉴定为全球范围内最主要的次要亲本贡献者(占比54.84%),是驱动该毒株遗传多样化的核心引擎。NADC34-like PRRSV在全球范围内呈现高度的遗传多样性和复杂的区域演化特征。虽然重组模式与毒株毒力间的直接联系尚待明确,但重组株的广泛流行及其演化热点的漂移提示该毒株具有极强的环境适应性。首次在全球尺度下对NADC34-like毒株进行了系统的全基因组重组模式分类,确立了R1-R12评价框架。揭示了中国毒株重组热点从结构基因向非结构基因区转移的独特演化规律。明确了Lineage 1.8作为通用亲本在驱动全球NADC34-like毒株多样性中的关键作用。

  • Lele Jin, Xiaoyue Wang, Yu Luo, Jie Zheng, Francisco Dini-Andreote, Chao Liang, Yuji Jiang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.005
    Accepted: 2026-01-08

    The interactions between nematodes and fungi are important for soil carbon cycling. However, their cascading effects on soil organic carbon (SOC) accrual remain unclear, particularly the role of soil aggregates and manure amendments in mediating this trophic cascade. Using a 19-year fertilization experiment, we examined how nematode predation influences fungal necromass carbon (FNC) and glomalin-related soil proteins (GRSPs), and quantified their contributions to SOC across soil aggregates under different manure amendments. Our findings showed that nematode predation significantly enhanced fungal biomass and promoted deterministic assembly of fungal communities. These effects were strongly dependent on aggregate size, with the most pronounced responses observed in the large macroaggregate (LA) fraction. A complementary microcosm experiment confirmed that nematode predation increased fungal biomass by over 6%, particularly in the LA fraction. Manure amendments further stimulated fungal growth and reinforced deterministic community assembly, thereby enhancing trophic cascade-driven accrual of FNC and GRSPs. Of the two fungal-derived carbon sources, FNC contributed more substantially to SOC (40%) than GRSPs (17%), with the greatest contribution found in the LA fraction. Path analysis further revealed that nematode-induced changes in fungal communities mediated the positive effects of manure amendments on fungal-derived carbon accrual. Overall, these findings underscore the pivotal role of nematodes in driving positive trophic cascade impact on SOC accrual. Our study offers new insights into aggregate-scale carbon dynamics and biologically mediated strategies for soil carbon management.

  • Archita Sahu, Rohit Bharati, Piotr Trebicki, Jiban Kumar Kundu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.004
    Accepted: 2026-01-08

    Oilseed crops of the genus Brassica rank third globally in vegetable oil production and contribute substantially to global oil supplies for both food and industrial purposes, including lubricants, biofuels, and cosmetics. Despite advances in high-yielding cultivars and modern agronomic practices, the productivity of oilseed Brassica species remains significantly constrained by a range of pathogens, particularly viral agents such as turnip yellows virus (TuYV), turnip mosaic virus (TuMV), and cauliflower mosaic virus (CaMV). Climate change further exacerbates these challenges by influencing plant physiology, virus biology and vector ecology. Rising temperatures enhance virus-vector interactions and increase the risk of disease outbreaks, while elevated atmospheric CO₂ concentrations can alter plant nutritional profiles, potentially stimulating vector feeding behaviour and promoting virus transmission. Although natural sources of resistance offer partial protection, their effectiveness may be compromised under abiotic stress conditions such as heat stress, highlighting vulnerabilities in plant defence. This mini-review addresses three major challenges to Brassica oilseed production: the impact of principal viral pathogens, climate-driven shifts in host-virus-vector dynamics, and the environmental robustness of genetic resistance. The review also outlines knowledge gaps and research priorities for developing climate-resilient Brassica oilseed genotypes.

  • Yan Gao, Yansheng Li, Zhenhua Yu, Zhuxiu Liu, Jinyuan Zhang, Xiaojing Hu, Jun Wang, Hanting Cheng, Rong Li, Caixian Tang, Junjie Liu, Junjiang Wu, Guanghua Wang, Xiaobing Liu, Yueyu Sui, Jian Jin
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.003
    Accepted: 2026-01-08
    Soil microbial response to warming may potentially contribute to the positive priming effect, i.e. accelerating the decomposition of native soil organic carbon (SOC) under the outsourced carbon (C) input. Investigating microbiota that metabolize the outsourced C is essential to deciphering the mechanism of priming effect in response to warming and thus mitigating the SOC loss under warming climate. In this work, we monitored the priming effect at 25, 35 and 45°C over four weeks with weekly addition of 13C-glucose, and subsequently revealed microbial assemblage metabolizing glucose with the DNA stable-isotope probing (DNA-SIP) method. Warming initially inhibited the priming effect, and decreased bacterial α-diversity, K/r-strategists ratio (K/r)  and recalcitrant C/labile C gene ratio (R/L) in week 1, suggesting that at the onset of the outsourced C input, the increased proportion of r-strategists preferentially utilize the added glucose over SOC to meet their C and energy demands. Yet, in week 4, positive priming effects were intensified by warming with up to 3.8-fold increase at 45°C. Additionally, the primed C was positively correlated with K/r, R/L, and the abundances of chitin degradation genes in week 4. These functions concurred with an increase in the abundance of resource-acquisition strategists such as Streptomyces affiliated to Actinobacteria under warming conditions over time. From week 1 to 4, warming induced a distinctive change in glucose-assimilating bacterial community compositions with a particular decrease in the relative abundance of Actinobacteria while an enriched abundance of Chloroflexi. Taken together, warming-triggered change of priming effect depended on alternation of microbiota and metabolic function over time. These findings provide important insights of how warming mediates microbial metabolic use of fresh C and subsequent SOC mineralization, reflecting the positive feedback between soil C emission and climate warming.


  • Yue Hu, Yating Ning, Yan Zhao, Yaqi Wang, Fengjian Luo , Li Zhou, Xinzhong Zhang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2026.01.001
    Accepted: 2026-01-08

    China has limited acaricide options for tea plantations. Cyetpyrafen, a novel domestic acaricide with high efficacy, low toxicity and a negative temperature coefficient, offers an alternative for tea pest control; however, its residue fate in tea remains unclear. This study developed a method to simultaneously detect cyetpyrafen and its metabolites (M-309, M-325-1, and M-409-3) in different tea matrices to investigate their fate. Recoveries of compounds ranged from 73.4% to 106.2% with the relative standard deviations (RSDs) below 12.0%. During tea cultivation, the dissipation half-life of cyetpyrafen was 0.59 d, with M-309 as a major metabolite. The residues of cyetpyrafen and M-309 were affected by different processing stages, especially water loss and high temperatures during fixing, drying and withering. The total processing factors ranged from 1.39 to 1.71 for green tea and 1.48 to 2.28 for black tea (processed from fresh tea leaves sampled at 1, 5, and 7 d), respectively. The leaching rates of cyetpyrafen from green tea and black tea into tea infusions were 7.4% and 6%, respectively. The risk associated with cyetpyrafen intake from tea consumption was low, with risk quotient values below 100%. However, theoretical calculation indicated potential harm to non-target organisms from its metabolites. This research provides a reference for the safe and efficient use of cyetpyrafen in tea gardens.

  • Yixian Liu, Runa Zhang, Shuai Ding, Shuang Wang, Liang Wei, Cuiyan Wu, Wensheng Fang, Qiuxia Wang, Dongdong Yan, Aocheng Cao, Jianping Chen, Tida Ge, Zhenke Zhu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.076
    Accepted: 2026-01-02
    Chemical fumigants such as dazomet (DZ) and dimethyl disulfide (DMDS) effectively suppress soil-borne pathogens but  there  is  uncertainty  regarding  the  restoration  of  soil  ecological  functions  in  continuous  cropping  obstacles  after fumigation, such as microbe-mediated organic carbon cycling.   However, the mechanism by which microbial remediation measures enhance carbon mineralization activity after soil fumigation remains unclear.   In  this study, we conducted microcosm experiments to investigate the impacts of Bacillus velezensis inoculation on exogenous organic carbon (EOC) mineralization and bacterial community composition and interactions following chemical fumigation.  Relative to fumigation alone, Bvelezensis addition increased cumulative EOC mineralization by 27% in DZ-treated soils and by 22% in DMDS- treated soils.  This enhancement was associated with the enrichment of core taxa and keystone species, which collectively increased microbial activity.   Structural equation modeling further confirmed that core taxa (OTU56, belonging to Bacillus) induced positive interactions with indigenous species, which drove the observed enhancement in EOC mineralization. We conclude that Bvelezensis facilitates the rapid recovery of soil carbon mineralization after fumigation by selectively reshaping the bacterial community and strengthening bacterial cooperative networks.   This work provides a mechanistic framework for microbially driven ecological restoration of fumigant-impacted continuous-cropping obstacle soils and informs the development of sustainable soil-management practices in chemically challenged agroecosystems.


  • Youfu Fan, Wenxin Shangguan, Rong Hu, Yong Liu, Li Yang, Wei Hu, Jie Song, Jingheng Xie, Yingjie Huang, Mingjun Li, Dechun Liu, Liuqing Kuang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.074
    Accepted: 2026-01-02

    Vacuolar composition, particularly the type and abundance of metabolites and tonoplast proteins, critically determines fruit quality and flavor. However, the specific vacuolar composition of fruits with different flavors at the fully ripe stage, especially regarding sugar accumulation, remains unclear. In this study, we established an optimized protocol to overcome technical barriers in isolating intact vacuoles from four types of fresh ripe citrus juice sacs. Subsequently, quasi-targeted metabolomics analysis and 4D-label-free proteomic analysis were conducted, identifying 640 metabolites and 1,782 proteins, respectively. Notably, amino acids, flavonoids, lipids, carbohydrates, and organic acids collectively represented 70% of the total vacuolar metabolites. Pummelo MJY vacuoles exhibited the highest sucrose accumulation, whereas tangerine NFMJ showed minimal sucrose content. Proteomic profiling revealed vacuolar proteins participating in protein fate determination, metabolism, vesicle trafficking, solute transport, and energy supply. Comparative analysis demonstrated significantly greater protein abundance variation between MJY and NFMJ than between other varieties. In total, 158 transport proteins, including sugar-related transporters, were identified, and most of them were more abundant in MJY vacuoles. The protein abundance of CsTST2 and CsERDL6 was greater in MJY vacuoles compared to other varieties, and the relative expression patterns of their encoding genes were consistent with sugar accumulation during fruit ripening. Subcellular localization analysis confirmed their tonoplast localization. Importantly, transgenic tomato fruits overexpressing these genes demonstrated both enhanced gene expression and increased sugar content. This study systematically revealed cultivar-specific vacuolar composition and sugar accumulation strategies in ripe citrus fruits and provided key tonoplast proteins responsible for fruit quality improvement.

     

  • Min Yin, Yi Zheng, Haotong Zeng, Zheyu Yan, Anqi Sun, Kuang Ma, Xiangling Gong, Jing Li, Qianlin Xiao, Zhizhai Liu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.079
    Accepted: 2025-12-31

    Starch, the predominant component in sorghum grains and a key component for utilization, is primarily regulated by spatiotemporally specific starch biosynthesis-related genes (SBRGs) with poorly characterized transcriptional mechanisms. This study elucidates the functional role of the NAC-type transcription factor (TF) SbNAC22 in starch biosynthesis in sorghum grains. SbNAC22 exhibits preferential expression levels in developing grains and demonstrates co-expression trends with multiple sorghum SBRGs. SbNAC22 possesses nuclear targeting, autoactivation activity, and intrinsic activity domain. The integrated results of DAP-seq, dual-luciferase analysis, and EMSA imply that SbNAC22 could bind to the conserved motif of 5-CACGCAA-3’, influencing the promoter activities of the corresponding SBRGs. Transient overexpression assays revealed that SbNAC22 can also upregulate critical SBRGs of SbAGPLS1, SbGBSSI, and SbSSI, while suppress SbISA1 in sorghum. Heterologous expression in rice further demonstrates the conserved regulatory capacity of SbNAC22, elevating transcript levels of rice SBRGs, enhancing grain length and weight, and significantly increasing the starch content in rice grains. The findings of this study identify SbNAC22 as a key transcriptional regulator that orchestrates starch biosynthesis by differentially activating and repressing SBRGs, positioning SbNAC22 as a prime target for novel molecular breeding strategies designed to enhance both grain yield and quality in sorghum.

  • Junli Yang, Haiming Han, Baojin Guo, Shenghui Zhou, Jinpeng Zhang, Weihua Liu, Xinming Yang, Lihui Li
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.078
    Accepted: 2025-12-31

    Wheat is a major staple crop worldwide, and with the ongoing changes in dietary patterns, the demand for improved nutritional quality in wheat has been increasing. Black-grained wheat is a promising germplasm rich in nutrients. Agropyron cristatum (2n = 4x = 28, PPPP) is a wild relative of wheat that carries several desirable genes for genetic improvement. Here, we identified black-grained lines PB31334 and PB31340 from wheat–A. cristatum derivatives, which exhibited significantly higher anthocyanin content and possibly increased amino acid content compared with common wheat. These lines were identified as wheat–A. cristatum 6P (6A) disomic substitution lines, with the alien chromosome 6P from A. cristatum responsible for the black grain trait, as revealed by genetic analysis of four segregated populations created by crossing PB31334 and PB31340 with Fukuho and Xinong979. Additionally, three lines were identified, including telosomic lines carrying the short arm (6PS) and the long arm (6PL) of alien chromosome 6P, as well as a 6PL-deletion line lacking a partial segment of the long arm (bin 6–17). The line with 6PL displayed the black grain trait, whereas the other two did not. The gene was localized to the 6PL (bin 6–17) region without affecting the grain number per spike or thousand-grain weight. Notably, the total anthocyanin content increased in 6PL telosomic line and was positively correlated with grain coloration. The newly identified 6PL chromosomal region is a valuable resource rich in anthocyanins, offering a promising avenue for increasing the nutritional content of wheat.

  • Qi Liu, Zhidong Qi, Chaofan Li, Zhenghan Chen, Wenqian Liu, Baoshen Liu, Chaozhong Zhang, Jiajie Wu, Juan Qi, Fei Ni
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.077
    Accepted: 2025-12-31

    大麦(Hordeum vulgare L.)是全球第四大谷物作物,也是酿造工业的重要原料和畜牧业的主要饲料来源。杂种优势利用是提升作物产量的重要途径,而雄性不育基因及其突变体为杂交种选育或生产提供了关键遗传资源。本研究所用雄性不育材料N13401来源于大麦品种Tamalpais的甲基磺酸乙酯(EMS)诱变群体,表现出完全雄性不育;其不育表型由单隐性基因msgN13401控制。细胞学观察显示,突变体绒毡层与中间层可正常降解,但花粉粒淀粉积累异常并最终导致雄性不育。利用两个F₂分离群体,我们将msgN13401定位在侧翼标记pMS124M17pMS124M16之间约0.9 cM的遗传区间内,对应Morex V3参考基因组中约576.9 Kb的物理区域。该区间共注释有38个基因,其中23个为高置信度基因在这些高置信度基因中,有17个在花药中表达。对N13401进行重测序并与Tamalpais参考基因组比较,我们发现仅有一个高置信度基因存在序列变异。此外,在15个低置信度基因中,有两个基因也检测到碱基突变。基于上述突变特征与表达模式,我们筛选出三个候选突变:包括一个编码吡咯啉-5-羧酸还原酶(pyrroline-5-carboxylate reductase, P5CR)基因启动子区的突变、一个编码螺旋-发夹-螺旋(helix-hairpin-helix, HhH)基序基因的移码突变,以及一个编码液泡铁转运类似蛋白(vacuolar iron transporter-like, VTL)的错义突变。这三个候选基因均不同于已鉴定的大麦雄性不育基因位点,相关研究结果为进一步解析花粉淀粉积累的分子机制及推进大麦杂交育种提供了有效线索和遗传材料。

  • Xiaohui Yin, Guoyi Yang, Shuo Han, Xiaowen Han, Ting Huang, Limeng Dong, Junliang Yin, Lu Hou, Yujiao Liu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.075
    Accepted: 2025-12-31

    Faba bean is a vital food and industrial crop, yet its production is increasingly threatened by various stresses. SWEETs, a class of plant-specific genes, play essential roles in plant stress responses. However, knowledge regarding Vicia faba SWEETs remains limited. In this study, 27 VfSWEETs were identified from the faba bean genome. A comprehensive analysis revealed that these genes are under strong purifying selection and primarily encode hydrophobic proteins localized to the plasma membrane, featuring the characteristic MtN3_slv domain. Promoters of VfSWEETs were found to contain numerous stress-responsive cis-elements, suggesting their involvement in stress responses and growth regulation in faba bean. Notably, VfSWEET19 and VfSWEET26 were upregulated under drought and salt stress; both encode plasma membrane-localized galactose transporters. These transporters attenuate plant immunity by inhibiting pattern-triggered immunity (PTI) and disrupting ROS homeostasis, thereby facilitating pathogen infection. Additionally, they enhance drought and salt tolerance by reducing stomatal aperture and improving water retention, which contributes to better water status, scavenging ROS, and alleviating leaf wilting under stress. In conclusion, this study highlights the dual role of galactose transporters VfSWEET19 and VfSWEET26 in attenuating plant immunity while enhancing drought and salt tolerance, offering valuable candidate genes for resistance breeding.

  • Yingao Zhang, Huike Li, Siqing Wan, Yongheng Zhang, Dan Chen, He Zhang, Yezi Xiao, Lu Liu, Pengjie Wang, Youben Yu
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.073
    Accepted: 2025-12-31

    The tea plant (Camellia sinensis) is an economically important leaf crop in which the flowering process consumes substantial nutrients, thereby negatively impacting tea yield and quality. Therefore, deciphering the molecular basis of floral transition is essential for enhancing tea cultivars and optimizing plantation management. The natural mutant ‘Ziyang 1’ (ZY1H, which had not flowered for years) and its wild-type cultivar ‘Ziyang’ (ZYQT, normal flowering) were used to study the molecular mechanisms underlying the non-flowering phenotype in ZY1H. Phenotypically, ZY1H exhibited shortened internodes, prolonged vegetative growth, and failure to develop floral meristems. Chromosomal analysis confirmed that ZY1H maintains a normal diploid chromosome number (2n=30), excluding triploidy as a cause of its sterility. Transcriptome analysis revealed defective vegetative-to-reproductive transition in ZY1H, manifesting as insufficient expression of SPL genes and sustained high expression of flower-inhibiting AP2-like genes. Additionally, elevated expression of the flowering repressor SVP and reduced expression of the flowering integrator FT further disrupted the integration of floral induction signals. Notably, brassinosteroid (BR) levels and CsBZR2 expression were elevated in ZY1H. Functional assays showed that CsBZR2 directly interacts with the CsFLC promoter and suppresses its expression, thereby blocking the flowering process. These findings suggest that the floral transition defect in ZY1H is driven by dysregulated BR signaling and excessive vegetative growth, to provide novel insights into the molecular mechanisms of flowering regulation in tea plants and valuable theoretical support for cultivar improvement.

  • Huihui Zhu, Liqiong Jia, Yuzhi Bai, Junqiang Xu, Xulu Luo, Wei Fan, Weiwei Chen, Jianli Yang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.072
    Accepted: 2025-12-31

    The composition and function of root exudates in rhizosphere iron (Fe) mobilization are significantly influenced by environmental pH conditions. While the role of organic acids in Fe solubilization is well-recognized, the molecular mechanisms underlying this pH-dependent process remain poorly understood. Here, we demonstrate that under weakly acidic conditions, proton excretion alone is insufficient to solubilize sparingly soluble Fe. Instead, a pH-dependent ligand specificity emerges as a critical factor in Fe mobilization. Notably, within the pH range of 5.0-6.0, citric acid exuded by roots exhibits superior Fe solubilization efficacy compared to oxalic acid and malic acid. We identified SlFRDL1, a gene induced by Fe deficiency, as a key player in this process. SlFRDL1 encodes a plasma membrane-localized protein with citrate permeability, as confirmed by its functional expression in Xenopus oocytes. Knockout mutants of SlFRDL1 displayed exacerbated Fe deficiency symptoms, which were associated with a significant reduction in citrate secretion from roots. Furthermore, we discovered that SlSTOP1, a transcription factor, binds to the promoter region of SlFRDL1 and activates its expression. Slstop1 mutants exhibited leaf chlorosis symptoms similar to those observed in Slfrdl1 mutants, highlighting the functional interplay between these two genes. Interestingly, while Fe deficiency triggers the FER-mediated Fe uptake system across both acidic and alkaline conditions, the SlSTOP1-SlFRDL1 module is specifically activated only in acidic environments. This pH-specific regulation underscores the importance of the SlSTOP1-SlFRDL1 pathway in root-mediated Fe solubilization under acidic conditions. 

  • Chunrui Chen, Licheng Xiao, Yaling Wang, Rong Huang, Sunan Gao, Wenran Su, Jiajun Ran, Lei Song, Taotao Wang, Jie Ye, Yongen Lu, Zhibiao Ye, Jinhua Li, Junhong Zhang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.071
    Accepted: 2025-12-31

    Global climate warming and extreme high-temperature events significantly impact crop growth, development, and economic productivity. Plants typically enhance heat tolerance by regulating heat shock transcription factors (HSFs) and antioxidant enzymes to reduce the detrimental impacts of heat stress. However, the precise regulatory mechanisms by which HSFs confer heat tolerance in tomato remain to be elucidated. In this study, we investigated the role of the heat-induced transcription factor SlHSFA3 in tomato heat tolerance. We demonstrated that knockout of SlHSFA3 increases tomato plants' sensitivity to heat stress, while enhanced expression of SlHSFA3 improves heat tolerance by promoting reactive oxygen species (ROS) scavenging through increased ascorbate peroxidase (APX) activity. Similarly, overexpression of SlAPX1 enhances heat tolerance in tomato by reducing ROS accumulation, whereas its knockout increases heat stress sensitivity. Furthermore, SlHSFA3 interacts with SlAPX1 to further augment APX activity. Molecular analysis revealed that SlHSFA3 directly upregulates the expression of SlAPX1 by binding to its promoter region. In summary, our findings elucidate the molecular mechanism of the SlHSFA3-SlAPX1 regulatory pathway in tomato heat tolerance, providing a theoretical foundation for developing advanced biotechnological and breeding strategies to improve crop adaptation under elevated temperature conditions.

  • Jiangyue Long, Wei Tan, Chunzhi Zhang, Guangtao Zhu, Zhong Zhang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.070
    Accepted: 2025-12-31

    Potato is a vital global food source, yet the metabolic and transcriptional regulation governing tuber development and quality remains poorly understood. Here, we performed integrated metabolomic and transcriptomic analyses on wild and cultivated potato tubers, revealing dynamic and distinct metabolic accumulation patterns. The 849 metabolites exhibited 10 distinct temporal accumulation patterns, including six shared patterns between accessions and four genotype-specific patterns. The wild genotype exhibited an early decrease in lipids, followed by an increase in phenolic acids, whereas the cultivated genotype displayed an early increase in phenolic acids, accompanied by a decrease in some phenolic acids, amino acids, and flavonoids. A comparative analysis highlighted a key metabolic trade-off: the cultivated genotype exhibited significantly lower levels of bitter steroidal glycoalkaloids (SGAs) but higher levels of beneficial flavonoids compared to its wild counterpart. Co-expression network analysis revealed 35 SGA- and 57 phenylpropanoid-related genes that underlie metabolite dynamics. Notably, we functionally validated that the transcription factor StMYB113 plays a previously unknown role in positively regulating phenolic acid biosynthesis in tuber flesh. Our work provides a comprehensive map of tuber metabolism and a valuable resource of high-confidence targets for accelerating the genetic improvement of key potato quality traits.

  • Jiyun Nie, Mengying Shuai, Yihui Liu, Xiaoming Li, Mingyu Liu, An Li, Duoyong Zhao, Qiusheng Chen, Xiaoli Liu, Zhichao Li
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.069
    Accepted: 2025-12-31

    Food fraud is an increasing deliberate act of deception for profits. Hence, it is highly necessary to develop powerful analytical approaches to assess the authenticity of foods. In recent years, the geographical origin authenticity of fruits has become a particular public concern. The geographical origin of fruit is generally determined based on specific indicators such as elements, stable isotopes, and metabolites. Many studies have demonstrated that mineral elements and stable isotope ratios are effective indictors for geographical origin authentication as they are directly related to the geographical environment. Some other techniques, such as spectroscopy and chromatography, have shown potential in identifying geographical origin and assessing the authenticity of fruits. Nonlinear PCA, PLS-DA, and LDA are commonly used for geographical origin authentication of fruits. A modern approach for data classification is machine learning, including SVM, RF, and ANN, which have been applied to identify the origin of fruits with high accuracies. 

  • Yueting Li, Pengtao Yang, Yu Yuan, Chao Yan, Yue Jia, Yongqin Wang, Yue Liu, Zhonghua Zhang, Bingsheng Lv
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.068
    Accepted: 2025-12-31

    Waterlogging poses a major challenge to Welsh onion (Allium fistulosum L.) production, exacerbated by climate change-induced extreme weather. Unraveling the molecular mechanisms of waterlogging tolerance is essential for breeding resilient cultivars. Here, we compared two Welsh onion varieties: BJQC (tolerant) and YZDC (sensitive). Waterlogging treatment revealed that YZDC exhibited higher accumulation of reactive oxygen species (ROS), including hydrogen peroxide (H2O2), superoxide ions (O2⁻), and malondialdehyde (MDA), leading to increased mortality. In contrast, BJQC demonstrated enhanced waterlogging tolerance, attributed to its ability to upregulate flavonoid biosynthesis genes, resulting in higher flavonoid accumulation under waterlogging stress. Transcriptomic analysis identified that the activation of flavonoid pathway-related genes in BJQC was central to this response. In addition, genes associated with jasmonic acid and gibberellin signaling were also activated. Weighted gene co-expression network analysis (WGCNA) revealed that WRKY31 and MATE likely play critical roles in regulating flavonoid biosynthesis under waterlogging conditions. Genome-wide association study (GWAS) results from natural populations further supported the significance of these genes in waterlogging tolerance. Our comprehensive multi-omics analysis, including phenotypic, physiological, transcriptomic, and genomic approaches, provides new insights into the molecular mechanisms underlying Welsh onion responses to waterlogging. These findings highlight WRKY31 and MATE as key candidates for improving waterlogging tolerance in crop breeding programs. 

  • Qianyun Wang, Rui Yang, Daling Feng, Yongcheng Li, Rui Li, Mengyang Liu, Yiguo Hong, Na Li, Wei Ma, Jianjun Zhao
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.067
    Accepted: 2025-12-31

    Chinese cabbage (Brassica rapa subsp. pekinensis) is a significant leafy vegetable in the Brassica genus of the Brassicaceae family. The size of edible leaves is an essential trait that determines its economic and nutritional values. However, current understanding of leaf development in Chinese cabbage is limited. Here, through forward genetic analyses of the mutant mini24 with defective leaf and root development, we identified the BrRRG gene, which regulates cell division in Chinese cabbage by map-based cloning. We demonstrated that BrRRG impacts leaf size by regulating the expression of E2Fa transcription factors and cell cycle-related genes in Chinese cabbage. Furthermore, BrRRG was found to modulates Chinese cabbage responds to IAA hormones and cytokinins, revealing distinct regulatory mechanisms by which BrRRG controls underground root and aboveground leaf development. Thus, these results suggest that BrRRG mutant causes damage to plant growth and development in Chinese cabbage.

  • Hua Zhang, Lena Kuhn, Hang Xiong, Zhanli Sun
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.066
    Accepted: 2025-12-31

    Agricultural drones can improve productivity, save labor, and reduce environmental impacts by offering digital multifunctions in agricultural production. Yet, the lagging adoption among smallholders is still prevalent. Existing literature commonly explains it by lack of capital, land fragmentation, and digital illiteracy, with little delving into specific adoption modes under uncertainty. In this study, we demonstrate the potential of hiring agricultural drone services and investigate the role of supplier uncertainty in the adoption decision. We conduct a discrete choice experiment among 338 farmers in Hubei Province, China. Mixed logit models are used to analyze farmers’ preferences for the agricultural drone service (ADS) and its attributes. The results show that the large majority of sampled farmers are willing to adopt ADS. Besides low prices, farmers prefer services with local suppliers and contracts. Potential adopters in this choice experiment are characterized by youth, high education, owning poor-topography farms, drone learning via word-of-mouth, and adoption experience. The willingness to pay analysis indicates that farmers would like to spend 25 CNY per mu (53 USD per ha) on average for ADS. Notably, farmers value the localness of suppliers more than the form of agreements when choosing a particular drone service. These findings suggest that the mode of hiring ADS can effectively motivate farmers’ adoption intention, thereby, the supply-side incentives and uncertainty-reducing promotion strategies needed to enhance smallholders’ access to and adoption of agricultural drones.

  • Jiahui Song, Lin Li, Jiahe Wang, Yuqing Xia, Heyu Zhang, Jingwen Li, Juanjuan Ma, Do Zhang, Jiangping Mao, Na An, Libo Xing
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.065
    Accepted: 2025-12-31

    Flowering is a necessary condition and the basis for yield in the life cycle of woody fruit trees. Although there has been considerable interest in the regulatory mechanisms underlying floral induction and flowering, the associated epigenetic modifications remain poorly characterized. We identified genome-wide DNA methylation changes and the transcriptional responses in axillary buds of ‘Qinguan’ (QA) and ‘Fuji’ (FA) varieties with contrasted flowering behaviors. The DNA methylation levels were19.35, 62.96 and 17.68% for FA, and 19.64, 62.49 and 17.86% for QA in the CG, CHG and CHH contexts, respectively. The number of hypermethylated or hypomethylated DMRs in different regions contributed to significantly up/downregulated gene expression. DNA methylation can positively or negatively regulate gene expression depending on the CG, CHG and CHH contexts and their locations in different regions. Additionally, the huge differences in transcription of MIKCc-Type MADS-box genes, and multiple flowering genes in multiple flowering pathways (i.e., light, age, GA and sugar) by changing DNA methylation, contributed to contrasted flowering behaviors in both QA and FA. Specifically, the floral meristem identity genes (i.e., FT, LEAFY, AP1 and SOC1) were significantly higher expression in QA than FA, but the floral repressor (i.e., SVP, AGL15, and AGL18) showed the opposite trend. Significant differences in multiple hormone levels were due to DEGs and their DMRs in their synthesis pathways, leading to both contrasted axillary bud outgrowth and flowering behaviors. These findings reflect the diversity in the epigenetic regulation of gene expression and may be helpful for elucidating the epigenetic regulatory mechanism underlying the axillary bud flowering in apple.

  • LIU Yi-fang, WANG Xiao-juan, HU Ya-xian, XIE Chao-ping
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.064
    Accepted: 2025-12-31

    Global agricultural trade helps to balance the supply and demand for food worldwide, stimulating economic growth and promoting political stability. However, agriculture’s inherent vulnerability to extreme weather events and other natural disasters has a significant impact on the industry amplified by trade, which can threaten global food security. This study examines both the deaths and economic losses caused by natural disasters and identifies the mechanisms and effects of these disasters on international agricultural trade from 2002 to 2023. The results show that natural disasters cause a decline in the volume of agricultural exports from affected countries, which is much larger than that of other industries. Despite the high demand inelasticity of agricultural products, which typically leads to increased export prices when production declines, the value of exports still declined significantly over the study period, implying an average annual export loss of $6.21 billion and 39,359 jobs. Geological disasters primarily hinder agricultural exports by increasing transportation costs, climatic disasters by damaging production systems, and biological disasters by increasing storage and compliance costs. We show that disasters have a more devastating effect on agricultural production in less developed countries, diminishing global product competitiveness for those countries, reducing export prices and intensifying disaster impacts. We also show that countries with low disaster risk, which lack emergency response experience, incur up to $ 2.053 million in agricultural export losses due to disasters. In addition, political risks interact with natural disasters, thereby amplifying the negative impact of natural disasters on agricultural exports. In terms of product heterogeneity, we find the destructive impact of disasters on primary agricultural products extends through the supply chain to processed agricultural goods, affecting both their production and export. We show that disasters exert an even more extended influence on the agricultural system through secondary effects that are 2.83 times greater than the direct impacts. Our findings provide valuable insights that should motivate countries affected by disasters to establish disaster prevention and recovery mechanisms to help minimize agricultural trade losses and safeguard global food security.

  • Wanqi Wang, Xuefeng Zhu, Yuzhu Li, , Shuhan Dong, Yan Liu, Kaikai Min, Huijie Lü, Wei Zhang, Hongbo He, Xudong Zhang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.063
    Accepted: 2025-12-31

    Improving soil organic matter (SOM) maintenance is crucial for terrestrial carbon (C) sequestration and ecosystem functioning. Conservation tillage favors SOM pool buildup; however, it remains unclear how the decomposition of heterogeneous components is manipulated by microbial substrate utilization strategy from the view of SOM stability. Here, a one-year microcosm incubation was conducted using surface soildeveloped under 12 years of conservation tillage (high-C soil) and maize residue removal (low-C soil). Temporal changes in lignin phenols, neutral sugars, and amino sugars in the soil were monitored along with microbial phospholipid fatty acids (PLFAs) and enzyme activities. Throughout incubation, lignin phenols declined more (20.8-26.3%) than the SOM (12.3-14.5%) and amino sugars (10.6-12.3%), highlighting the key role of plant debris in SOM mineralization, and complementarily, the greater contribution of microbial necromass to SOM stabilization. Moreover, the decomposition dynamics of neutral sugars and lignin were strongly influenced by C availability. In the low-C soil, these two types of compounds decomposed with similar temporal patterns and extents, and such substrate co-metabolism was dominantly mediated by actinomycetes. In contrast, in the high-C soil, a lower oxidases-to-carbohydrolases ratio regulated the sequential decomposition of labile neutral sugars followed by recalcitrant lignin. Such microbial substrate selectivity was associated with a shift in microbial community from bacterial dominance toward increased fungal contribution. Overall, our findings underscore the significant interplay between soil C availability and flexible microbial substrate utilization strategy in regulating decomposition of heterogeneous SOM components, as well as their distinct contributions in SOM turnover and stabilization. 

  • Xiaoting Sun, , Wei He, Jiajie Ma, Bo Chu, , Xianming Yang, Kongming Wu#
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.050
    Accepted: 2025-12-30

    The oriental fruit moth, Grapholita molesta Busck, is a major pest of fruit trees worldwide, it is necessary to develop green control technology instead of the traditional chemical pesticide. Although the sterile insect technique (SIT) is a safe and effective method for controlling G. molesta, the high cost of mass rearing irradiated pupae hinders its widespread adoption. In this study, we identified the optimal sub-sterilizing X-ray dose for G. molesta adults and evaluated its effects on the mating competitiveness of males, growth and reproduction of the F1 generation population, and the sterility rate of field-caught males. The results showed that the sub-sterilizing dose of 1-day-old male was 130 Gy, which rendered most males sterile (76.34%) and females nearly sterile (97.41%). Moreover, the sterile trait of the male parents that had been irradiated with 130 Gy of X-rays was successfully transmitted to the F1 generation, whose sterility rate (84.13–93.61%) exceeded that of F0 males. The F1 generation population exhibited significantly lower values for the net reproductive rate (R0), intrinsic rate of increase (r), and finite rate of increase (λ) compared to the non-irradiated group. Furthermore, the competitive mating index and sterility rate of irradiated males were highest when they were paired with unirradiated males and females at a release ratio of 20:1:1. The irradiating wild males captured by sex pheromones in pear orchards with the sub-sterilizing dose achieved a 75.69% sterility rate, comparable to the laboratory-reared population. This study introduces a novel X-ray irradiation method for adult G. molesta captured in the orchard field and lays a theoretical foundation for promoting the wide application of the SIT.

  • Hexuan Wang, Xinyi Zhang, Guohao Yang, Xinyi Jia, Jiayi Gao, Haoran Wang, Jingbin Jiang, Jingfu Li, He Zhang, Xiangyang Xu, Huanhuan Yang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.045
    Accepted: 2025-12-30

    The evolutionary development of adventitious roots (ARs) in plants enhances their capacity to adapt to various stress conditions. A thorough analysis of the influencing factors in its morphological construction holds significant theoretical value and practical guidance for overcoming rooting obstacles in cuttings, as well as for cultivating superior varieties characterized by broad adaptability and stress resistance. In this study, we investigated the molecular mechanisms underlying the development of ARs in tomato (Solanum lycopersicum).by performing transcriptome sequencing (RNA-seq). We analyzed the transcription profiles of relevant genes in the "Y962" strain, which exhibits spontaneous AR formation, and the "W961" strain, which does not form ARs. Our findings indicate that the AR induction stage represents an active phase of development, during which we identified 1,676 overlapping genes across the three comparison groups, highlighting the most differentially expressed genes. Functional enrichment analysis showed that they were most closely related to response to auxin, and were also dependent on the crosstalk between other hormones and carbohydrates. Furthermore, through the measurement of endogenous auxin levels and the induction tests with exogenous auxin, it was established that the formation of ARs is closely linked to the accumulation and transport of auxin. Notably, the auxin efflux SlPIN3, which was enriched in the auxin response pathway, exhibited significantly high expression during the induction phase of ARs. The slpin3 mutant, generated using the CRISPR/Cas9 editing system, exhibited a significant reduction in the number of ARs, highlighting the close relationship between polar transport regulated by SlPIN3 and auxin-induced AR formation. In summary, this study not only enriches the developmental network of AR formation in tomatoes with a wealth of data but also elucidates the potential mechanisms for promoting AR development by targeting SlPIN3

  • Fenggang Zan, Zhuandi Wu, Chengcai Xia, Long Zhao, Qi Liu, Zihao Wang, Yanjie Lu, Meiling Zou, Yong Zhao, Peifang Zhao, Xuan Luo, Jiayong Liu, Zhiqiang Xia
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.044
    Accepted: 2025-12-30

    Increasing the sucrose content of sugarcane, a major sugar crop, is a breeding objective. However, the complex genetic background of sugarcane affects development of sugarcane hybrids. In this study, we sequenced 292 sugarcane germplasm accessions and identified 2,542,965 single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). We performed a genome-wide association analysis of two important sugarcane traits—sucrose content and stem diameter. Both traits conform to a normal distribution and exhibit typical characteristics of quantitative traits. Population structure analysis revealed Four subpopulations with an average genetic distance of 0.236 were identified. Genome-wide association analysis of the sucrose content revealed 27 SNPs. After annotating genes at or near significant loci, 17 candidate genes were screened. For stem diameter, genome-wide association analysis revealed 19 SNPs, from which 9 candidate genes were identified. These results improve our understanding of genetic mechanisms affecting sucrose content in sugarcane, and identify important genetic resources to accelerate breeding of new sugarcane varieties with high sucrose content.

  • Rong Chen, Lei Xu, Jinyong Guo
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2025.12.062
    Accepted: 2025-12-30

    Scholars have explored various ways to improve farmers' e-commerce performance from different perspectives. However, the debate between "marketable product" and "marketing ability" in practice remains insufficiently addressed in academic research. To further explore this issue, based on dual-micro survey data from consumers and fruit farmers regarding five major fruits in Jiangxi Province, this study applies Data Envelopment Analysis (DEA) to assess farmers' e-commerce performance. The study tests the direct and interaction effects of product online adaptability ("marketable product") and e-commerce marketing ability ("marketing ability"), and examines the moderating role of industry clustering. The results show that improving product online adaptability boosts e-commerce performance, especially for medium-level performers. E-commerce marketing ability promotes performance, displaying a "Matthew effect". Product online adaptability and marketing ability act synergistically. Marketing ability has a stronger effect on performance than product online adaptability. Industry clustering amplifies the effects of both product online adaptability and marketing ability on performance. This study offers a new perspective on farmers' e-commerce performance and guidance for optimizing rural e-commerce development paths.