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Note: The papers published below will continue to be available from this page until they are assigned to an issue. To see an article, click its [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Selected articles' button. To see one abstract at a time, click its [Abstract] link. Please wait a minute... For Selected: Download Citations EndNote Ris BibTeX Toggle Thumbnails Select Functional analysis and epitope recognition of African swine fever virus pA151R antigen-specific T cells 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 DOI: 10.1016/j.jia.2026.01.009 Online: 08 January 2026 Abstract （18）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Molecular epidemiological and phenotypic characteristics of Streptococcus suis isolated in Hainan Island of China Song Liang, Shaoyan He, Shidan Zhang, Jiqi Song, Yubing Wang, Xinyi Liu, Lei Dai, Jinxiu Wang, Youzhi Xie, Huochun Yao, Guangjin Liu DOI: 10.1016/j.jia.2026.01.008 Online: 08 January 2026 Abstract （6）      PDF in ScienceDirect       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 Reference | Related Articles | Metrics Select Green agriculture enabled by versatile metal-organic frameworks: A review Lianjie Wan, Fei Ma, Jianmin Zhou, Changwen Du DOI: 10.1016/j.jia.2026.01.007 Online: 08 January 2026 Abstract （12）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Genetic diversity and recombination analysis of NADC34-like porcine reproductive and respiratory syndrome viruses Zhengqin Ye, Wenqiang Wang, Zhenbang Zhu, Wei Wen, Hu Suk Lee, Xiangdong Li DOI: 10.1016/j.jia.2026.01.006 Online: 08 January 2026 Abstract （4）      PDF in ScienceDirect       Reference | Related Articles | Metrics Select Macroaggregates magnify the positive feedback of trophic cascades on carbon accrual Lele Jin, Xiaoyue Wang, Yu Luo, Jie Zheng, Francisco Dini-Andreote, Chao Liang, Yuji Jiang DOI: 10.1016/j.jia.2026.01.005 Online: 08 January 2026 Abstract （7）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Oilseed Brassica under threat: viral pathogens and the compounding effects of climate change Archita Sahu, Rohit Bharati, Piotr Trebicki, Jiban Kumar Kundu DOI: 10.1016/j.jia.2026.01.004 Online: 08 January 2026 Abstract （9）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Warming alters fresh-carbon assimilating bacterial community relevant to priming effect in Mollisols 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 DOI: 10.1016/j.jia.2026.01.003 Online: 08 January 2026 Abstract （7）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Risk assessment and residue behavior of a novel pesticide cyetpyrafen and its metabolites from fresh tea leaves to tea infusion Yue Hu, Yating Ning, Yan Zhao, Yaqi Wang, Fengjian Luo , Li Zhou, Xinzhong Zhang DOI: 10.1016/j.jia.2026.01.001 Online: 08 January 2026 Abstract （9）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Impacts of Bacillus velezensis inoculation on exogenous organic carbon mineralization and bacterial community composition in fumigated continuous-cropping obstacle soils 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 DOI: 10.1016/j.jia.2025.12.076 Online: 02 January 2026 Abstract （21）      PDF in ScienceDirect       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, B. velezensis 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 B. velezensis 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. Reference | Related Articles | Metrics Select Vacuolar metabolomic and proteomic profiling reveals vacuole composition of ripe juice sacs and functions of CsTST2 and CsERDL6 for sugar accumulation in citrus Youfu Fan, Wenxin Shangguan, Rong Hu, Yong Liu, Li Yang, Wei Hu, Jie Song, Jingheng Xie, Yingjie Huang, Mingjun Li, Dechun Liu, Liuqing Kuang DOI: 10.1016/j.jia.2025.12.074 Online: 02 January 2026 Abstract （11）      PDF in ScienceDirect       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.   Reference | Related Articles | Metrics Select Brassinosteroid signaling regulates floral transition defects in Camellia sinensis 'Ziyang 1' via CsBZR2-mediated suppression of CsFLC Yingao Zhang, Huike Li, Siqing Wan, Yongheng Zhang, Dan Chen, He Zhang, Yezi Xiao, Lu Liu, Pengjie Wang, Youben Yu DOI: 10.1016/j.jia.2025.12.073 Online: 31 December 2025 Abstract （7）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Proton-responsive SlSTOP1-SlFRDL1 regulatory pathway modulates citrate-driven iron acquisition in tomato roots Huihui Zhu, Liqiong Jia, Yuzhi Bai, Junqiang Xu, Xulu Luo, Wei Fan, Weiwei Chen, Jianli Yang DOI: 10.1016/j.jia.2025.12.072 Online: 31 December 2025 Abstract （10）      PDF in ScienceDirect       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.  Reference | Related Articles | Metrics Select The heat shock transcription factor SlHSFA3 enhances heat tolerance in tomato by directly modulating both APX activity and SlAPX1 expression 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 DOI: 10.1016/j.jia.2025.12.071 Online: 31 December 2025 Abstract （24）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Multi-omics analyses unveil dynamic metabolic and transcriptomic changes of swelling potato tubers Jiangyue Long, Wei Tan, Chunzhi Zhang, Guangtao Zhu, Zhong Zhang DOI: 10.1016/j.jia.2025.12.070 Online: 31 December 2025 Abstract （7）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Geographical origin authentication of fruits: A decadal review (2014-2024) of technological progress and outlook Jiyun Nie, Mengying Shuai, Yihui Liu, Xiaoming Li, Mingyu Liu, An Li, Duoyong Zhao, Qiusheng Chen, Xiaoli Liu, Zhichao Li DOI: 10.1016/j.jia.2025.12.069 Online: 31 December 2025 Abstract （12）      PDF in ScienceDirect       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.  Reference | Related Articles | Metrics Select Multi-omics analysis reveals WRKY31 and MATE as key regulators of flavonoid-based waterlogging tolerance in Welsh Onion (Allium fistulosum L.) Yueting Li, Pengtao Yang, Yu Yuan, Chao Yan, Yue Jia, Yongqin Wang, Yue Liu, Zhonghua Zhang, Bingsheng Lv DOI: 10.1016/j.jia.2025.12.068 Online: 31 December 2025 Abstract （9）      PDF in ScienceDirect       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.  Reference | Related Articles | Metrics Select BrRRG affects leaf size by regulating cell cycle gene expression in Chinese cabbag Qianyun Wang, Rui Yang, Daling Feng, Yongcheng Li, Rui Li, Mengyang Liu, Yiguo Hong, Na Li, Wei Ma, Jianjun Zhao DOI: 10.1016/j.jia.2025.12.067 Online: 31 December 2025 Abstract （9）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Farmers’ preferences for agricultural drone services under uncertainty: A Choice Experiment in Hubei, China Hua Zhang, Lena Kuhn, Hang Xiong, Zhanli Sun DOI: 10.1016/j.jia.2025.12.066 Online: 31 December 2025 Abstract （7）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Epigenomic regulation of flowering in apple: Insights from two contrasting cultivars Jiahui Song, Lin Li, Jiahe Wang, Yuqing Xia, Heyu Zhang, Jingwen Li, Juanjuan Ma, Do Zhang, Jiangping Mao, Na An, Libo Xing DOI: 10.1016/j.jia.2025.12.065 Online: 31 December 2025 Abstract （9）      PDF in ScienceDirect       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. Reference | Related Articles | Metrics Select Distinct decomposition dynamics of heterogeneous carbon components in cultivated agricultural soils controlled by flexible microbial substrate utilization strategy Wanqi Wang, Xuefeng Zhu, Yuzhu Li, , Shuhan Dong, Yan Liu, Kaikai Min, Huijie Lü, Wei Zhang, Hongbo He, Xudong Zhang DOI: 10.1016/j.jia.2025.12.063 Online: 31 December 2025 Abstract （10）      PDF in ScienceDirect       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 soils developed 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.  Reference | Related Articles | Metrics page Page 1 of 19 Total 373 records First page Prev page Next page Last page