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For Selected: Download Citations EndNote Ris BibTeX Toggle Thumbnails Select Stage-dependence of the impacts of grazing and mowing on temporal stability of grassland biomass Jiatao Zhang, Hongbin Xu, Xiao Tao Lü, Lei Zhang, Ting Yuan, Taogetao Baoyin, Zhuwen Xu DOI: 10.1016/j.jia.2025.11.018 Online: 14 November 2025 Abstract （5）      PDF in ScienceDirect       Ecosystem stability ensures the sustainable supply of ecosystem services. Our current understanding of ecosystem stability is mainly based on results from the initial stage after disturbance or experimental treatments, which reveal short-term responses. There is a big knowledge gap regarding whether the long-term responses would be consistent with such initial responses. We examined how grazing and mowing affect the temporal stability of aboveground biomass in a temperate semi-arid steppe and further clarified the differences in treatment impacts and primary drivers of stability between the initial four years and the subsequent five years. Both grazing and mowing significantly decreased the community stability across the nine years, and such impacts showed high stage-dependency. Grazing reduced community stability in the first four years but not in the following five. Mowing initially did not affect community stability but reduced it over the next five years. Community stability was driven by species asynchrony in the early stage, and later solely regulated by the dominant species stability. When Stipa krylovii and Cleistogenes squarrosa become dominant in the community following prolonged grazing, or when mowing leads to a notable decline in community stability over time, enclosure measures should be adopted to promote ecological recovery. Additionally, long-term enclosure may also lead to a decline in biomass, thereby affecting the maintenance of community functions. We recommend implementing a rational rotation of enclosure, grazing, and mowing in grassland management based on different stages, as a scientifically sound grassland management system is key to achieving sustainable utilization of grassland resources. Reference | Related Articles | Metrics Select Integrating meta-QTL analysis and VIGS to decipher GhPCMP-E17-mediated abiotic stress tolerance in upland cotton Qiwen Yang, Dandan Li, Yan Zhao, Xueli Zhang, Wenmin Yuan, Ying Li, Junning Yang, Junji Su, Caixiang Wang DOI: 10.1016/j.jia.2025.11.017 Online: 14 November 2025 Abstract （3）      PDF in ScienceDirect       Cotton (Gossypium spp.), a globally important cash crop, is increasingly threatened by abiotic stresses that significantly affect yield and fiber quality. In this study, data on 3,016 abiotic stress-related quantitative trait loci (QTLs) described in 31 published papers were integrated through meta-QTL analysis, a total of 34 MQTLs were identified. Nine major MQTLs with numerous initial QTLs, high R2 values, narrow confidence intervals (CIs), and close colocalizations were successfully detected. Combined with the transcriptome data, the candidate gene GhPCMP-E17 was identified. Through virus-induced gene silencing (VIGS) technology, the role of GhPCMP-E17 in the response to abiotic stress was clarified. Compared with the TRV:00 plants, the GhPCMP-E17-silenced plants presented more severe wilting and yellowing under drought and salt stress conditions. Silencing GhPCMP-E17 weakens the function of antioxidant enzymes, thereby increasing the accumulation of reactive oxygen species. These results indicate that downregulation of GhPCMP-E17 gene expression enhances the sensitivity of cotton plants to drought and salt stress. This research provides excellent genetic resources for adaptive abiotic crop breeding in upland cotton. Reference | Related Articles | Metrics Select Dissecting chromatin accessibility profiles of anatomically distinct skeletal muscles and different breeds in pigs at single-nucleus resolution Yiwu Chen, Yundi Zheng, Ziyu Chen, Geng Zhang, Chuang Tang, Fuwen Wang, Can Liu, Mingzhou Li, Long Jin DOI: 10.1016/j.jia.2025.11.016 Online: 14 November 2025 Abstract （3）      PDF in ScienceDirect       To dissect chromatin accessibility profiles in pig skeletal muscle at single-nucleus resolution, we performed single-nucleus ATAC-seq on longissimus dorsi and psoas major muscles of Large White pigs. After quality control, 26,225 nuclei were classified into seven major cell types, including myofibers, muscle stem cells, and immune cells, using snRNA-seq-based label transfer. We identified 158,438 accessible chromatin regions, with cell-type-specific differentially accessible regions (DAR) enriching for specific functions. Myonuclei subtypes (type I, IIA, IIB) showed distinct accessibility patterns, with SIX1 and MAF transcription factor motifs enriched in fast myofibers (type II). Comparative analysis between muscles revealed that myofiber composition drove chromatin differences, with psoas major featuring more type I myofibers. Cross-breed analysis (Rongchang vs. Large White) identified breed-specific DARs in myonuclei, linking MEF2-mediated regulation to myofiber hypertrophy. Pseudo-temporal analysis of myogenesis showed dynamic accessibility changes in key myogenic genes (e.g., MYF5, MYH1). This study unveils cell-type-resolved chromatin landscapes underlying myofiber specification, tissue heterogeneity, and breed-specific muscle development in pigs.   Reference | Related Articles | Metrics Select Development stage-specific recovery of remedial nitrogen fertilizer application after waterlogging in maize through photosynthetic capacity and nitrogen allocation Yifei Sun, Shancong Wang, Meiyu Chen, Xinru Hu, Reda M.M. Ahmed, Fanzheng Meng, Yulou Tang, Qinghua Yang, Shenjiao Yang, Ruixin Shao DOI: 10.1016/j.jia.2025.11.015 Online: 14 November 2025 Abstract （3）      PDF in ScienceDirect       Waterlogging stress (WS) significantly threatens summer maize production. Although supplemental nitrogen (N) fertilization is a common remediation strategy, the differences in N regulation pathways across developmental stages are still unclear. The maize hybrid ‘Zhongkeyu 505’ was used as the experimental material in a 3-year field localization experiment investigating the responses and N-mediated recovery pathway in maize at the jointing stage (V6) and blister stage (R2) to WS. Over three experimental years, compared to control, WS significantly decreased grain yield at V6 and R2 by an average of 27.6 and 23.0%, respectively. Structural equation modeling showed that WS decreased grain number at V6 by inhibiting leaf photosynthetic capacity, and reduced grain capacity at R2 by limiting N allocation to grains. However, post-waterlogging nitrogen application (WF) effectively mitigated these losses, increasing grain number by 19.1% at V6 and improving grain sink capacity by 23.4% at R2. The recovery at V6 was driven by enhanced photosynthetic capacity with average increases of 23.6% in total chlorophyll content, 36.3% in phosphoenolpyruvate carboxylase activity, and 24.8% in Rubisco activity. Differently, the recovery at R2 was due to improve N utilization, where N allocation in grains increased to 73.1%, and nitrate reductase and glutamine synthetase activities in grains increased by an average of 31.7 and 35.6%, respectively. Transcriptomic analysis further confirmed upregulation of protein-processing genes (e.g. hsp18a and hsp18c), facilitating N allocation and utilization. In conclusion, the N-mediated recovery pathway varied across maize development stages, with the photosynthetic capacity and grain number restored at V6 and N allocation to grains and sink capacity was increased at R2. This study will provide significant theoretical and practical value for enhancing tolerance in maize to WS at V6 and R2. Reference | Related Articles | Metrics Select Optimizing plastic film mulching and nitrogen fertilizer strategies for spring maize in Loess Plateau through field experiments and enhanced AquaCrop modeling Yu Liu, Gang Cheng, Yaosheng Zhang, Tingting Huang, Hongzheng Shen, Weibin Zhang, Xiaoyi Ma DOI: 10.1016/j.jia.2025.11.014 Online: 14 November 2025 Abstract （3）      PDF in ScienceDirect       Plastic film mulching (PM) is widely used to improve soil temperature and moisture in rainfed agriculture, but the combined effects of PM proportions and nitrogen (N) fertilization on spring maize under different hydrological conditions remain unclear. We conducted a two-year field experiment (2021 and 2022) in the Loess Plateau and improved the AquaCrop model by incorporating stage-specific temperature-increase compensation coefficients for full and wide PM treatments. Results showed that PM increased soil temperature by 2.11–3.59°C and water content by 14.3–21.2% during the first 90 days after sowing, requiring compensatory temperature increases during the sowing-tasseling stage. The modification reduced normalized root-mean-square error values of canopy cover and biomass from 14.2 and 7.6% to 8.1 and 6.2%, respectively. Using 40 years of hydrological simulation, we identified the optimal PM–N combinations: FN180 (100% PM+180 kg N ha−1) for dry years to maximize precipitation use efficiency (+35.3%), and WN225 for normal and wet years to balance yield and nitrogen fertilizer agronomic use efficiency (>14 kg kg−1). Our results demonstrate that tailoring PM proportions and N rates to hydrological conditions enhances water–nutrient synergy, providing a climate-resilient management approach for sustainable maize production in semi-arid agroecosystems. Reference | Related Articles | Metrics Select The yellow‑green plant (Clygp) encodes a signal recognition particle 54 kDa protein regulating chloroplast development and photosynthesis in watermelon Shixiang Duan, Yaomiao Guo, Lin Deng, Qishuai Kang, Changbao Shen, Xiaohang Xue, Junling Dou, Dongming Liu, Sen Yang, Xingping Zhang, Yun Deng, Huayu Zhu, Yongdong Sun, Luming Yang DOI: 10.1016/j.jia.2025.11.013 Online: 14 November 2025 Abstract （4）      PDF in ScienceDirect       Photosynthesis serves as the primary source of nutrients synthesized in higher plants, and enhancing photosynthetic efficiency can significantly improve crop yield and fruit quality. Leaf color mutants, which are ideal materials for studying chloroplast development and photosynthesis mechanisms, have been extensively investigated in field crops. However, the study on their application in watermelon remains limited. In this study, we identified a yellow-green phenotype mutant, PKH352, from an EMS mutagenesis watermelon mutant library. The chlorophyll content and maximal photochemical efficiency in PKH352 was significantly reduced. Genetic analysis showed that the mutated trait was controlled by a single nuclear gene, which named as Clygp (Citrullus lanatus yellow-green plant). Through MutMap and linkage analysis in an F2 population of 440 plants, we identified a single nucleotide polymorphism (SNP) mutation in ClG42_04g0106300, which encoded a signal recognition particle 54 kDa protein, as the causal variant for the yellow-green phenotype. Further validation using a CRISPR/Cas9-mediated system confirmed that knockout of ClG42_04g0106300 results in the yellow-green phenotype in watermelon. In addition, comparative transcriptomic analysis revealed that the ClG42_04g0106300 mutations greatly affected the expression of key genes associated with chloroplast development and photosynthesis, providing strong evidence that it plays a critical role in these biological pathways. Taken together, these findings provide insights into the molecular mechanisms underlying chloroplast development and photosynthetic efficiency, offering a theoretical basis for breeding watermelon varieties with high photosynthetic efficiency. Reference | Related Articles | Metrics Select Functional analysis of CsAGL6 in flower development and pigmentation in cucumber (Cucumis sativus L.) Li Qin, Zheyuan Liu, Shuai Li, Guanghua Cai, Jie Wang, Xueyong Yang, Jinjing Sun DOI: 10.1016/j.jia.2025.11.012 Online: 14 November 2025 Abstract （4）      PDF in ScienceDirect       Cucumber (Cucumis sativus L.) is a major vegetable crop worldwide, and its yield and quality are closely linked to flower development. AGAMOUS-LIKE 6 (AGL6), a member of the ancient MADS-box transcription factor family, plays a crucial role in flower development. However, the specific functions of its homolog in cucumber remain poorly understood. In this study, we demonstrate that CsAGL6 is predominantly expressed in flowers, with high expression levels observed in all floral organ primordia during the early stages of floral development. The petals of Csagl6 mutants exhibit a greener color compared to wild-type plants, along with a significant increase in total chlorophyll content. Additionally, the mutants show abnormal petal morphology, including changes in size and shape, as well as enlarged sepals resembling leaves occasionally. Molecular analysis reveals that the A-class gene CAULIFLOWER (CAL) and the E-class gene SEPALLATA 4 (SEP4) are significantly downregulated in the mutants, while the chlorophyll synthesis gene Early Light-Induced Protein 1 (ELIP1) and several stress-related genes in the chloroplasts are dramatically upregulated. Our findings provide novel insights into the functional role of CsAGL6 in regulating sepal and petal development, and offer a potential avenue for understanding the genetic control of flower pigmentation and organ morphology in Cucumis species. Reference | Related Articles | Metrics Select CRISPR/Cas9-mediated mutagenesis of transcriptional repressor SlMYB32 improves flavonols and flavanones accumulation in tomato fruit Ruining Zhang, Yunlin Cao, Tong Zhang, Yingyue Ma, Jiajia Li, Kunsong Chen, Xian Li DOI: 10.1016/j.jia.2025.11.011 Online: 14 November 2025 Abstract （5）      PDF in ScienceDirect       Flavonols and flavanones are important bioactive compounds with multiple pharmacological activities and health benefits. Transcriptional activation of flavonol and flavanone biosynthesis has been studied extensively, while little is known about the negative regulators. CRISPR/Cas9 gene-editing technology, with the advantage of precise genetic modification, is a desirable tool for breeding biofortified materials and exploring potential molecular mechanisms. In this study, a transcriptional repressor, SlMYB32, was characterized in tomato fruit. Phenotype and metabolome analysis confirmed that knockout of SlMYB32 resulted in increased accumulation of flavonols and flavanones, especially about 1 mg g-1 FW of quercetin 3-O-rutinoside (rutin). Transcriptome analysis indicated that expression of key genes SlPAL6, Sl4CL3 and Sl4CL4 as well as five candidate SlUGTs were significantly up-regulated in slmyb32 mutants. Dual-luciferase and EMSA assay indicated SlMYB32 could bind to and repress promoter activities of SlPAL6 and Sl4CL3. Expression of 27 transcription factors belonging to twelve families was significantly changed in slmyb32 mutants, among which two SlMYBs, two SlNACs, two SlAP2s and one SlWRKY were clustered with known flavonoid regulators. Our results provide new insights into improving bioactive compounds in fruit and understanding negative regulatory mechanisms in flavonol and flavanone biosynthesis.   Reference | Related Articles | Metrics Select Sex-specific and functional differentiation between OR23h and OR109d in aggregation pheromone detection in Riptortus pedestris Xiaotong Zhang, Jiahang Wei, Xuanpu Luan, Ian W. Keesey, Xin Chen, Qi Yan, Shuanglin Dong, Jin Zhang DOI: 10.1016/j.jia.2025.11.009 Online: 10 November 2025 Abstract （11）      PDF in ScienceDirect       The bean bug, Riptortus pedestris, is a major pest of soybeans in East Asian countries. Male-released aggregation pheromones attract both adults and nymphs, offering potential for eco-friendly pest control. However, the molecular mechanisms underlying the detection of the aggregation pheromones remain unclear. In the present study, functional analysis using the Xenopus oocyte expression system demonstrated that two ORs (OR23h and OR109d) were responsible for sensing aggregation pheromones, with the primary component (E)-2-hexenyl (E)-2-hexenoate (E2HE2H) being shared by the two ORs. Further quantitative PCR (qPCR) profiling indicated that OR109d was expressed only in male antennae, while OR23h was expressed in both sexes at similar levels. RNA interference assays demonstrated that dsOR23h-treatment significantly reduced the Electroantennographic (EAG) response of (E)-2-hexenyl (Z)-3-hexenoate (E2HZ3H) in both sexes. Furthermore, simultaneous RNAi knockdown of the two ORs significantly reduced the male EAG response to E2HE2H and abolished male attraction to this compound. These results were consistent with the sex expression profile, demonstrating the sex and functional differentiation between the two ORs. Taken together, this study characterizes the ORs responsible for chemical perception and the associated aggregation behaviors driven by these pheromones. Thus, this study enhances our understanding of olfactory signaling in a hemipteran insect and contributes to the knowledge required for improved pest management. Reference | Related Articles | Metrics Select Integrative fertilizer nitrogen management mitigates nitrogen leaching and gray water footprint in a subtropical vegetable rotation system Fen Zhang, Xiaopeng Gao, Xiao Ma, Hailing Cao, Fabo Liu, Tao Liang, Xinping Chen, Xiaozhong Wang DOI: 10.1016/j.jia.2025.11.008 Online: 10 November 2025 Abstract （5）      PDF in ScienceDirect       Nitrogen (N) leaching is a major pathway of N loss in subtropical crop production systems, contributing to groundwater pollution and thus posing serious threats to human health. However, the characteristics of annual N leaching in subtropical open-field vegetable systems and the effectiveness of integrative N fertilization management practices in reducing N leaching remain poorly understood. In this study, two plot-based field experiments were conducted with open-field Chinese cabbage-pepper rotation system in subtropical southwest China to quantify annual N leaching and evaluate the effectiveness of integrated N fertilization management practices. Experiment 1 compared five N fertilizer application rates using conventional urea, while Experiment 2 compared different N sources including conventional urea, organic fertilizer, nitrification inhibitor-based fertilizer, and controlled-release urea which were all applied at the optimized N rate. Results showed that the annual N leaching under farmers’ N practice (FNP) was 251 kg N ha−1, with contributions of 55, 31, and 14% from the pepper season, Chinese cabbage season, and fallow period, respectively. Total N leaching increased exponentially with N rate. The seasonal N leaching factor was 32% for pepper and 17% for Chinese cabbage in the FNP treatment, respectively. Compared to FNP, optimizing N rate based on crop requirement and soil supply significantly reduced N leaching by 68% and gray water footprint by 66−75%, while improving N use efficiency (NUE) from 35% to 54%. In Experiment 2, mixing organic and inorganic fertilizers, applying nitrification inhibitor, and using controlled-release urea further reduced annual N leaching by 27, 54, and 25%, respectively, compared to conventional urea. These practices also improved crop yields by 2−11% and NUE by 10−13%, and lowered gray water footprint by 28−58%. In summary, integrative N stewardship practices, particularly use of nitrification inhibitors under optimized N rates, effectively reduced N leaching while achieving high NUE and vegetable yields, providing a promising strategy for sustainable subtropical vegetable production. Reference | Related Articles | Metrics Select SlWRKY42 positively promotes proline accumulation by regulating SlP5CS1 to enhance tomato salt stress tolerance Xiaoyan Liu, Pengyu Duan, Chunyu Shang, Qingpeng Li, Jianyu Yang, Jiahui Yan, Guo Chen, Guobin Li, Xiaohui Hu, Songshen Hu DOI: 10.1016/j.jia.2025.11.007 Online: 10 November 2025 Abstract （4）      PDF in ScienceDirect       Tomato (Solanum lycopersicum L.) is an important vegetable crop worldwide. Throughout its growth cycle, tomato is susceptible to various abiotic stresses. Among these stresses, salt stress is one of the most detrimental abiotic factors to plant growth and development. In this study, we identified a WRKY transcription factor, SlWRKY42, which is induced by salt stress. We then characterized the function of SlWRKY42 in transgenic materials under salt stress and found that SlWRKY42 positively regulates salt tolerance in tomato. Transcriptome sequencing analysis revealed that genes involved in proline biosynthesis were significantly enriched in SlWRKY42-overexpressing (SlWRKY42 OE) plants. The proline biosynthesis genes (SlP5CS1 and SlP5CS2) and proline contents were significantly upregulated in SlWRKY42 OE lines. We discovered that the promoter of the proline biosynthesis gene SlP5CS1 contains a W-box element. Further yeast one-hybrid (Y1H), luciferase, electrophoretic mobility shift assay (EMSA), and chromatin immunoprecipitation quantitative polymerase chain reaction (ChIP-qPCR) assays verified that SlWRKY42 could specifically bind to the W-box element in the promoter of SlP5CS1 and activate its expression, thereby promoting proline biosynthesis. In summary, SlWRKY42 enhances salt tolerance in tomato by regulating the expression of SlP5CS1, thereby elucidating the molecular mechanism by which the SlWRKY42 transcription factor controls salt tolerance in tomato. Reference | Related Articles | Metrics Select Modelling spatio-temporal dynamics of soil organic carbon in paddy soil by coupling digital soil mapping with a process model Zheng Wang, Songchao Chen, Ruiying Zhao, Jie Xue, Qiangyi Yu, Danqing Wei, Wei Chen, Qichun Zhang, Zhou Shi DOI: 10.1016/j.jia.2025.11.006 Online: 10 November 2025 Abstract （4）      PDF in ScienceDirect       Soil organic carbon (SOC) plays a crucial role as a nutrient trigger and directly impacts soil health and agricultural productivity. In China, the Well-facilitated Farmland Construction (WFC) project is a comprehensive agricultural management strategy, changing the soil environment and then influencing the SOC dynamics. However, the long-term trajectory of SOC under the implementation of the WFC project remains unclear. To address this knowledge gap, this study focused on farmland in southeastern China that completed the WFC project in 2022. A total of 202 topsoil samples (0-20 cm) were collected from the regional paddy soil in 2023. Using digital soil mapping (DSM) and the CENTURY model, we delineated key soil properties and simulated the spatio-temporal changes of SOC density (SOCD). The results revealed that the SOCD ranged from 1.23 to 6.35 kg m-2, with an average value of 3.68 kg m-2 in 2023. Soil pH, clay, and sand content were primary factors influencing SOCD distribution. According to CENTURY model simulations, SOCD exhibited a declining trend from 2010 to 2021, while it was projected to increase from 2022 to 2030 following the WFC implementation, which could be attributed to enhancements in irrigation and straw incorporation. Besides, the scenario without WFC results shows that SOCD would decline from 2022 to 2030, underscoring the project’s effectiveness in preventing SOC loss for paddy soil. The spatial patterns of SOCD in 2021 and 2030 were similar, and the low-value areas showed faster increase rates than the areas with high SOCD levels, indicating that the specific field plots with lower SOCD levels could sequester more carbon with improved soil management. In conclusion, the WFC project can potentially increase SOC sequestration in the paddy soil and grain yield, ensuring food security and addressing climate change. Reference | Related Articles | Metrics Select Stabilization of plant-derived carbon from different green manure species mediated by carbon-decomposition genes Tingyu Li, Wei Feng, Tianshu Wang, Yili Meng, Shuihong Yao, Xinhua Peng DOI: 10.1016/j.jia.2025.11.005 Online: 10 November 2025 Abstract （3）      PDF in ScienceDirect       The integration of green manure (GM) crops into traditional cropping systems has regained attention for its potential to improve soil organic carbon (SOC) content in an environmentally sustainable way. However, the effects of carbon (C) input from different GM species on the SOC accumulation and recalcitrant C fractions across soil profile remain inadequately understood. This three-year North China Plain study assessed SOC changes and C fractions of easily oxidizable organic carbon (EOC) and recalcitrant organic carbon (ROC) in fallow, rye, rapeseed, and vetch systems, with δ13C analysis for GM-derived C fraction and microbial C-decomposition functional genes. Our results show that SOC was significantly increased by GMs. Rapeseed was the only species that improved SOC at 20-40 cm, the rapeseed-derived C contributed 2.48% of the SOC. Rye enhanced EOC and ROC at topsoil, rapeseed increased ROC at 20-60 cm, and vetch increased EOC at 40-60 cm. At the topsoil, the abundances of cellulose- and pectin-decomposition gene were increased in vetch and decreased in rye. At 20-40 cm, the pectin- and lignin-decomposition genes were markedly improved by rapeseed, while at 40-60 cm, the chitin-decomposition gene was increased in vetch, indicating the microbial promoting effects by deep roots of vetch and rapeseed. Our results suggest GM species influence SOC deposition depth and the recalcitrance of SOC decomposition, thereby affecting the distribution of SOC accumulation through microbial-driven C decomposition activities. Reference | Related Articles | Metrics Select Identification and selection of evaluation indices for soybean shade tolerance via high-throughput phenotyping platforms and machine learning Xiuni Li, Menggen Chen, Shuyuan He, Jie Chen, Xiangyao Xu, Panxia Shao, Yahan Su, Lingxiao He, Wenjing Zhang, Nanli Du, Mei Xu, Yao Zhao, Wenyu Yang, Wouter H. Maes, Weiguo Liu DOI: 10.1016/j.jia.2025.11.004 Online: 10 November 2025 Abstract （5）      PDF in ScienceDirect       Intercropping is a promising cultivation strategy that enhances the sustainable use of water and land resources while contributing to national food and oil security. To improve the yield stability of soybeans in intercropping systems, there is an urgent need to develop a scientific and efficient framework for evaluating shade tolerance. In this study, we propose an integrated shade tolerance assessment method based on high-throughput phenotyping, multienvironment trials, and machine learning (ML) approaches. Utilizing multivariate analysis, we evaluated 202 soybean accessions and partitioned their performance under intercropping into two distinct capacities, namely, shade tolerance during the cogrowth stage and recovery ability during the independent growth stage, each of which was classified into five levels from weak to strong. Preliminary trait selection was performed through correlation analysis and broad-sense heritability estimation, followed by the application of six ML models to identify the key shade tolerance traits across different growth stages. The robustness and generalizability of the selected traits were validated in three environments—a field pot, an open field, and a greenhouse—using soybean varieties with known shade tolerance levels. The results revealed that three traits—the side canopy area (SCA), top canopy area at stage 3 (TCA3), and top-view mixed entropy (TME)—were strongly associated with shade-tolerant varieties. These traits presented two distinguishing features: significantly higher values under shaded conditions and greater increases during the recovery phase. The prediction models constructed with these three traits achieved strong performance, with coefficients of determination of R²=0.776 for shade tolerance and R²=0.959 for recovery ability. In summary, this study demonstrates the potential for integrating high-throughput phenotyping with ML to efficiently identify the key indicators of shade tolerance. By measuring only three indicators—SCA, TCA3, and TME—soybean shade tolerance at the seedling stage, recovery ability during later growth, and overall shade tolerance across the full growth period can be rapidly and accurately evaluated. This method offers a powerful and practical tool for implementing shade tolerance evaluations, gene discovery, and targeted breeding of soybean cultivars that are suitable for intercropping systems. Reference | Related Articles | Metrics Select Functional analysis of tomato SlPP2C-A gene Subfamily, highlighting SlPP2C7's role in regulating saline-alkali stress tolerance Songshen Hu, Yixuan Shang, Ruoxi Ding, Junxiao Li, Xiaohui Hu DOI: 10.1016/j.jia.2025.11.003 Online: 10 November 2025 Abstract （8）      PDF in ScienceDirect       The Type A protein phosphatase 2C (PP2C-A) gene family is vital for regulating the ABA signaling pathway and plant stress responses. In this research, 14 SlPP2C-A genes were identified in the tomato genome, distributed across six chromosomes. Most SlPP2C-A genes contain cis-acting elements associated with growth, development, light, hormones, and stress responses. Collinearity analysis revealed high homology between the tomato and Arabidopsis PP2C-A gene families. Tissue-specific expression analysis indicated that SlPP2C7 is highly expressed in flowers, leaves, and mature fruits, and is significantly induced by saline-alkali stress. Gene-edited SlPP2C7 knock-out mutants subjected to saline-alkali stress confirmed that SlPP2C7 negatively regulates saline-alkali tolerance in tomato. Combined transcriptomic and metabolomic analyses showed that under saline-alkali stress, metabolic pathways such as flavonoid biosynthesis, isoflavonoid biosynthesis, flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and phenylalanine metabolism were significantly enriched. These outcomes imply that SlPP2C7 may enhance tolerance to saline-alkali stress through modulating flavonoid biosynthesis pathways. This research reveals comprehension of the physiological and molecular mechanism responsible for saline-alkali stress tolerance mediated by SlPP2C7 in tomato. Reference | Related Articles | Metrics Select Cloning and functional characterization of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (LiDXR) gene in oriental lily (Lilium ‘Sorbonne’) Xinyue Zhang, Jingqi Dai, Fan Jiang, Tao Yang, Jinzhu Zhang, Jie Dong, Jinping Fan DOI: 10.1016/j.jia.2025.11.002 Online: 10 November 2025 Abstract （3）      PDF in ScienceDirect       Floral scent is an important ornamental shape of garden plants. Monoterpenes in terpenoids are the main components of lily floral scents. 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) plays a role in the second enzymatic reaction of methylerythritol phosphate (MEP) pathway, which is responsible for monoterpene synthesis. However, the function of DXR gene in the floral monoterpene synthesis pathway of Lilium 'Sorbonne' remains unclear. In this study, the Lilium oriental 'Sorbonne' was used as the experimental material, and the differentially expressed LiDXR gene was selected using the early transcriptomic data. It was found that it had a high consistency with the rater rate process from synthesis to termination of floral substances in the flowering stage of lily. Therefore, the LiDXR gene was cloned and bioinformatics analyzed. A total of 472 amino acids are encoded. The expression of LiDXR gene was the highest at the Sorbonne half opening stage, and the expression of LiDXR gene in petals was significantly higher than that in other flower organs. The results of subcellular localization showed that LiDXR protein was localized in chloroplasts of leaf epidermal cells. A virus-induced gene silencing (VIGS) assay showed that silencing LiDXR can reduce monoterpene levels by down-regulating TPS gene expression downstream of the MEP pathway. Meanwhile, the results of HS-SPME-GC-MS showed that the total volatile terpene content of lily decreased significantly after silenced. The results of overexpressed plants A. thaliana and petunia showed that the transgenic plants had stronger growth potential and advanced flowering time. The GC-MS results of transgenic petunias showed that the content of volatile total terpenes in transgenic strains was 78% higher than that of wild type. Overexpression of LiDXR gene would affect the expression level of MEP pathway genes, and then affect the synthesis of terpenes including monoterpenes downstream of MEP pathway. The purpose of this study was to analyze the function of LiDXR gene and provide theoretical basis for floral breeding of lily and ornamental plants. Reference | Related Articles | Metrics Select A single nucleotide mutation in BrECB2 impaired RNA editing efficiency and early chloroplast biosynthesis Zifan Zhao, Feng Pan, Tianxiang Zhao, Luyao Zhang, Qingli Hou, Tianer Tang, Nan Wang, Chong Tan, Yun Zhang, Zhiyong Liu DOI: 10.1016/j.jia.2025.11.001 Online: 05 November 2025 Abstract （10）      PDF in ScienceDirect       Chloroplasts are important organs for photosynthesis, which is essential for increasing the yields of pak choi. In this study, we evaluated a delayed chloroplast development mutant ‘M136’ during self-crossing of the pak choi inbred ‘136’. The newborn true leaves of ‘M136’ were yellow and gradually green with maturation. Chloroplast development, pigment contents and photosynthesis parameters were impaired and gradually recovered with growth in ‘M136’, and chlorophyll fluorescence parameters were also impaired in ‘M136’. Based on genetic analysis and bulk segregant analysis (BSA)-seq, the mutant phenotype was controlled by a single recessive gene, identified as BraA06g011520.3.5C (BrECB2), which encoded a DYW-type pentatricopeptide repeat (PPR) protein. In ‘M136’, a T-to-C single nucleotide polymorphism (SNP) in the 4th PPR motif of BrECB2 caused a Threonine-to-Isoleucine amino acid substitution. BrECB2 was mainly expressed in young leaves. The chloroplast RNA editing efficiency of ‘M136’ was affected and fully recovered after the leaf turned green, and the editing efficiency was partially restored in complementary lines. The plastid-encoded RNA polymerase activity was not affected in ‘M136’. Functional complementation analyses revealed that the transient overexpression of BrECB2 partially rescued the mutant phenotype and the RNA editing efficiency of ‘M136’. In summary, this study indicate that BrECB2 is involved in early chloroplast development and RNA editing, providing a theoretical basis for understanding the regulatory network involved in chloroplast development in pak choi. Reference | Related Articles | Metrics Select Development and characterization of monoclonal antibodies against p72 protein of African swine fever virus reveals a novel conserved B-cell epitope Hua Cao, Mengjia Zhang, Junhua Dong, Pengfei Li, Ahmed H Ghonaim, Xuexiang Yu, Yongtao Li, Suphot Wattanaphansak, Wenjuan Du, Anan Jongkaewwattana, Chao Kang, Pan Tao, Qigai He, Wentao Li DOI: 10.1016/j.jia.2025.10.024 Online: 05 November 2025 Abstract （11）      PDF in ScienceDirect       African swine fever (ASF), caused by African swine fever virus (ASFV), is a highly contagious disease that has spread globally, posing a significant threat to swine production and international trade. As rapid diagnosis is crucial for controlling ASF, its major capsid protein, p72, has become a key target for diagnostic and vaccine development. In this study, we generated five monoclonal antibodies (mAbs) against the p72 protein by immunizing mice with inactivated virus. Using phage display technology, we identified the epitope for one mAb as a novel linear B-cell epitope within amino acids 130-152 of the p72 protein. Structural and homology analyses revealed that this epitope is highly conserved across diverse ASFV genotypes and is exposed on the surface of the p72 trimer. Importantly, the epitope showed strong reactivity with sera from ASFV-positive swine. These findings offer a foundation for creating improved serological diagnostics and designing epitope-based vaccines against ASFV. Reference | Related Articles | Metrics Select Analysis of the characteristics of walnut cultivars and construction of the suitability evaluation model for soluble proteins processing Shanshan Li, Xue Hei, Shinuo Cao, Jing Zhou, Chao Wu, Qizhai Li, Yonghao Chen, Bo Jiao, Benu Adhikari, Aimin Shi, Xiaojie Ma, Qiang Wang DOI: 10.1016/j.jia.2025.10.023 Online: 05 November 2025 Abstract （14）      PDF in ScienceDirect       Thirty-six walnut cultivars were analyzed for apparent, nutritional, processing and protein properties. Systematic cluster analysis (SCA) was applied to classify 36 walnut cultivars, while multivariate linear regression (MLR) analysis was used to develop a model for evaluating walnut protein solubility. The walnut cultivars were classified into three distinct clusters. Wen 185 and Xinguang had protein purity of 64.42, 70.57, and solubility of 27.04, 30.04%, respectively. Wen 185 and Xinguang were identified as the more suitable cultivars for extracting and processing soluble proteins. The MLR model revealed critical factors influencing protein solubility, such as arginine (Arg), glutamic acid (Glu), threonine (Thr), lysine (Lys), histidine (His), and crude fat. Glu (r=-0.64) and Arg (r=-0.57) showed a significant negative correlation with solubility. With a R2 of 0.832 between predicted and experimental values, the model was validated. This study has improved the efficiency of walnut protein during the processing and pointed out the direction for the processing and utilization of different cultivars of walnuts. Reference | Related Articles | Metrics Select The Nicotiana benthamiana microtubule-associated E3 ubiquitin ligase degrades a host immune regulator and a viral effector to enhance antiviral defense Kun Wang, Shuai Fu, Yuchong Tan, Liang Wu, Yaqin Wang, Xueping Zhou DOI: 10.1016/j.jia.2025.10.022 Online: 05 November 2025 Abstract （7）      PDF in ScienceDirect       Geminiviruses mainly infect economically important dicot plants and cause serious damages in agriculture. Here we report that the dicot plant Nicotiana benthamiana microtubule-associated E3 ligase (MEL) plays a dual role in regulating geminivirus infection in N. benthamiana. On the one hand, NbMEL functioned as a defense factor to mediate resistance against geminiviruses with single-stranded, circular DNA genomes by promoting the degradation of plant immune negative regulator. On the other hand, NbMEL could specifically recognize geminivirus-encoded V2 protein, a viral gene silencing suppressor and effector, for polyubiquitination and degradation to suppress geminivirus infection. These findings provide a fundamental basis for utilizing MEL to generate crop for broad-spectrum resistance in dicot plants. Reference | Related Articles | Metrics page Page 1 of 17 Total 338 records First page Prev page Next page Last page