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Convergent dynamics and shared mechanisms of three-pool soil carbon mineralization under different grassland managements
Junhao Feng, Ji Chen, Xiaowei Liu, Yudu Jing, Ke Liang, Qiang Yu, Changhui Peng, Liang Guo
2026, 25 (7): 3044-3057.   DOI: 10.1016/j.jia.2025.12.030
Abstract49)      PDF in ScienceDirect      

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

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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
2026, 25 (7): 3031-3043.   DOI: 10.1016/j.jia.2026.01.003
Abstract46)      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°C, 35°C 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.


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Multiomics integration identifies regulatory factors underlying reproductive disorders in geese
Qingyuan Ouyang, Cong Lan, Shenqiang Hu, Haizhou Gong, Bincheng Tang, Qingliang Chen, Zhiyu He, Junqi Wang, Tanze Liu, Shangmin Wang, Xi Zhang, Jiwei Hu, Hua He, Liang Li, Hehe Liu, Jiwen Wang
2026, 25 (7): 2936-2949.   DOI: 10.1016/j.jia.2024.05.030
Abstract119)      PDF in ScienceDirect      

Geese, descendants of migratory birds, have preserved the distinct reproductive and lipid metabolism traits of their wild ancestors.  Therefore, compared to other poultry, geese have lower egg production ability and greater susceptibility to fatty liver.  Recent research underscores the impact of lipid metabolism disorders on female reproductive health.  In this context, we observed reproductive disorders (RD) and lipid metabolism anomalies in certain geese populations.  This study systematically elucidated the differences between RD and normal geese at various levels, including genomics, transcriptomics, bile acid metabolomics, and microbiomics, revealing the crucial role of microorganisms.  Our study provides a thorough examination of the ovarian anatomical, histological, and transcriptomic profiles between normal and RD geese.  Genomic analyses pinpoint mutations in genes associated with bile acid metabolism, highlighting their potential role in RD pathogenesis.  The genomic discoveries are substantiated by precise bile acid assays and ileum transcriptome analyses, which expose a significant disruption in bile acid absorption, activation of FXR, and an increase in serum chenodeoxycholic acid (CDCA) concentrations within RD geese.  Notably, 16S rRNA sequencing uncovers significantly greater beta diversity in the ileum microbiota of RD geese than in the normal group.  Both Wilcoxon rank sum test and LEfSe analyses highlighted a marked increase in Romboutsia abundance in RD geese.  Experimental cultivation of microbiota with CDCA supplementation confirms the impact of CDCA on Romboutsia lituseburensis proliferation.  Gavage experiments with Rlituseburensis elucidate its involvement in primary follicle reduction via immune-mediated pathways.  Collectively, our multifaceted analysis unravels the intricate involvement of Romboutsia in goose RD, offering insights from genetic, physiological, and microbial dimensions.  Our findings not only deepen understanding of the etiology of RD in geese but also suggest potential avenues for therapeutic interventions targeting bile acid metabolism and modulation of specific microbiota components.

 

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A mutation in BrPRPL1 causes leaf yellowing by influencing chloroplast protein translation in Chinese cabbage
Xiaowei Ren, Xing Li, Jie Li, Jindi Fan, Mengyao Yuan, Yan Li, Daling Feng, Yin Lu, Hao Liang, Xiaofei Fan, Lei Sun, Kehui Ren, Mengyang Liu, Wei Ma, Jianjun Zhao
2026, 25 (7): 2836-2846.   DOI: 10.1016/j.jia.2025.12.029
Abstract62)      PDF in ScienceDirect      

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

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Filament-like plant protein 7 (FPP7) negatively regulates rice salt tolerance by enhancing abscisic acid sensitivity and disturbing sodium and ROS homeostasis
Fan Fan, Jin Chen, Lingyue Yan, Wenjie Hu, Xue Liu, Jia Zeng, Ling Liu, Ting Liu, Nenghui Ye, Dingyang Yuan, Meijuan Duan
2026, 25 (7): 2701-2713.   DOI: 10.1016/j.jia.2024.08.029
Abstract155)      PDF in ScienceDirect      

Filament-like plant proteins are intermediate filament proteins that play a major role in the development and growth of plants.  However, no studies have systematically identified or characterized the filament-like plant proteins (FPP) family in plants.  Fifty-nine FPP candidates were found in this study by analyzing the genomes of two dicots and four monocots.  Phylogenetic analysis and multicollinearity mapping showed the relatively conserved evolution of FPP genes in monocots.  In rice, eight OsFPPs were characterized and found to be induced or repressed by abiotic stresses.  Additional genetic evidence showed that OsFPP7-overexpressing rice exhibited increased sensitivity to abscisic acid during the germination stage, disrupted Na+/K+ homeostasis, and disrupted balance of reactive oxygen species during the seedling stage when exposed to salt stress.  Conversely, the knockout of osfpp7 alleviated abscisic acid (ABA) sensitivity, safeguarded the antioxidant system and sodium ion transport system, and thus enhanced rice salt tolerance.  In the cytoskeleton, the functions of FPPs in controlling salt stress and plant stress tolerance mechanisms are all further elucidated by our findings.

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Rapid and ultrasensitive point-of-care detection of ASFV antibodies using p30-Fc-labeled nanoparticle-based fluorescence strip-assisted portable immunosensor
Yang Yang, Jiayang Zheng, Yan Zhang, Qianming Zhao, Yafang Lin, Junjie Zhang, Zongjie Li, Ke Liu, Beibei Li, Donghua Shao, Yafeng Qiu, Zhiyong Ma, Jianchao Wei
2026, 25 (6): 2630-2633.   DOI: 10.1016/j.jia.2025.11.028
Abstract94)      PDF in ScienceDirect      
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Targeting ThyA: Investigating the mechanisms of 5-FU-induced inhibition of biofilm formation and virulence in Streptococcus suis through LuxS/AI-2 quorum sensing
Jing Zuo, Yingying Quan, Yue Li, Dong Song, Jinpeng Li, Yuxin Wang, Li Yi, Yang Wang
2026, 25 (6): 2510-2522.   DOI: 10.1016/j.jia.2024.07.007
Abstract135)      PDF in ScienceDirect      

Streptococcus suis is a significant zoonotic agent affecting both human and pig health and poses a substantial public health concern. The pathogenicity of S. suis is intricately linked to its ability to form biofilms and express virulence factors, which are regulated by the LuxS/AI-2 quorum sensing (QS) system. Herein, we uncover a novel therapeutic avenue by demonstrating that 5-fluorouracil (5-FU), an FDA-approved anti-cancer agent, effectively mitigates biofilm formation and attenuates the virulence of S. suis. Mechanistically, we observe a significant reduction in capsular polysaccharide and extracellular polysaccharide production upon 5-FU treatment, elucidating a potential mechanism for biofilm weakening. Additionally, 5-FU down-regulates virulence traits, diminishing S. suis's ability to adhere to host cells and evade phagocytosis. Crucially, our study identifies the thymidylate synthase regulatory gene thyA as a key mediator of 5-FU's effects on the LuxS/AI-2 QS system. Virtual molecular docking and gene knockout experiments provide compelling evidence that 5-FU modulates the LuxS/AI-2 QS system by targeting thyA. In vivo experiments further validate the therapeutic potential of 5-FU, showcasing a significant reduction in bacterial load and mitigation of tissue damage in a mouse model. In conclusion, our investigation unveils 5-FU as a potent disruptor of S. suis's biofilm formation and virulence, offering a promising avenue for the control of this devastating pathogen.

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Radiation use efficiency of maize under high-density optimal growth conditions in Jilin Province, China
E Li, Zhijuan Liu, Xiaomao Lin, Tao Li, Dengyu Shi, Huazhe Shang, Suliang Qiao, Guangxin Zhu, Wanrong Yang, Zhenzhen Fu, Jingjin Gong, Wanghua Yang, Zhenkang Yang, Xiaomeng Lu, Jingjing Wang, Lexuan Wang, Jin Zhao, Chuang Zhao, Xiaoguang Yang
2026, 25 (6): 2389-2395.   DOI: 10.1016/j.jia.2025.04.016
Abstract81)      PDF in ScienceDirect      

To evaluate the impact of climate change on maize production, accurately measuring the radiation use efficiency (RUE) of maize is critical.  This study focused on three maize cultivars in Jilin Province, China: Zhengdan 958 (ZD958), Xianyu 335 (XY335), and Liangyu 99 (LY99).  Under the optimal growing conditions for high density planting (9 plants m–2), the maize RUE was determined during the vegetative and reproductive phases, and the entire growth period.  The results showed that the canopy light interception for maize peaked during anthesis.  After anthesis, maize plant biomass continued to accumulate.  The maize RUE was calculated based on the absorbed photosynthetically active radiation (APAR).  During the entire growth period, maize RUE averaged 5.71 g MJ–1 APAR among the three cultivars, with a high-to-low order of ZD958 (5.85 g MJ–1 APAR)>XY335 (5.64 g MJ–1 APAR)>LY99 (5.07 g MJ–1 APAR).  Within the vegetative and reproductive growth periods, maize RUE averaged 6.85 and 5.64 g MJ–1 APAR, respectively.  When utilizing maize models that depend on RUE to predict aboveground biomass accumulation, such as APSIM, the current RUE value of 3.6 g MJ–1 APAR is considerably lower than the measured value obtained under high-density optimal growing conditions.  Consequently, to derive the optimal potential yield for maize in such planting conditions, we recommend adjusting the RUE to a range of 5.07–5.85 g MJ–1 APAR.

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The impact of digital technology use on relocated households’ income stability in China
Mingyue Liu, Wenying Zhang, Huanguang Qiu, Xiaolong Feng
2026, 25 (6): 2242-2254.   DOI: 10.1016/j.jia.2025.12.058
Abstract54)      PDF in ScienceDirect      

Ensuring the income stability of relocated households is essential for advancing rural revitalization and achieving common prosperity.  While existing research has explored the impact of digital technology on income, few studies have addressed how digital technology use affects income stability.  To fill this gap, based on survey data from relocated households in 16 counties across 8 provincial-level regions in China, this study examines the impact of digital technology use on the income stability of relocated households using Ordinary Least Squares (OLS) and Propensity Score Matching (PSM).  The results show that digital technology use improves both income and income stability, with stronger effects at higher levels of use.  This impact is driven by better access to information acquisition and enhanced human capital.  Additionally, digital technology helps stabilize the income of households facing downward volatility.  The income stabilizing effect is particularly significant among relocated households in central regions, rural resettlement areas, and those with higher education levels.  Furthermore, digital literacy amplifies the positive impact of digital technology on income stability.  These findings offer valuable insights for policymakers aiming to promote digital technology use to ensure the income stability of relocated households and foster common prosperity.

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Low-phosphorus stress induces GmSTOP1-3-mediated organic acid exudation to recruit phosphate-solubilizing bacteria for organic phosphorus mineralization in soybean rhizosphere
Qianqian Chen, Xing Lu, Guoxuan Liu, Tianqi Wang, Huiying Zhou, Jihui Tian, Qing Yao, Jinming He, Jiang Tian, Cuiyue Liang
2026, 25 (5): 2077-2092.   DOI: 10.1016/j.jia.2025.08.015
Abstract120)      PDF in ScienceDirect      

Root exudates serve a vital function in recruiting beneficial phosphate-solubilizing bacteria (PSB), thereby enhancing plant adaptation to phosphorus (P) deficiency.  The C2H2-type zinc finger transcription factor STOP1 (sensitive to proton rhizotoxicity 1) regulates root organic acid (OA) exudation in plants.  However, the impact of STOP1-regulated root OA exudation on rhizosphere microbial composition remains unexplored.  This study revealed enhanced vegetation properties of soybean with higher P content in P-rich soils, while rhizosphere organic acid concentrations were elevated in P-poor soils.  The soybean genotype YC03-3 in P-deficient soils specifically recruited three PSB in acid soils: Gammaproteobacteria_Incertae_Sedis, KF_JG30_C25, and Solirubrobacterales.  These PSB abundances correlated positively with rhizosphere oxalate and citrate concentrations.  Under P-sufficient conditions, GmSTOP1-3 overexpression in soybean plants increased oxalate and citrate exudation compared to YCO3-3 wild type (WT), leading to preferential colonization by the same three PSB species naturally present in P-deficient WT rhizosphere.  The population dynamics of these PSB demonstrated strong positive correlations with the abundance of key genes involved in P cycling, particularly those governing acid/alkaline phosphatase activities and organic-P mineralization.  Given the phosphate starvation-enhanced expression pattern of GmSTOP1-3, the findings indicate that specific PSB recruitment for organic-P remobilization in soybean rhizosphere depends on GmSTOP1-3-mediated oxalate and citrate exudation in P-deficient acid soils.  This research establishes GmSTOP1-3 as a crucial regulator of rhizosphere microbiome assembly and P-acquisition efficiency in acid soils.

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FvVam6 is associated with fungal development and fumonisin biosynthesis via vacuole morphology regulation in Fusarium verticillioides
Jie Liu, Jie Zhang, Huijuan Yan, Tuyong Yi, Won Bo Shim, Zehua Zhou
2026, 25 (5): 1981-1991.   DOI: 10.1016/j.jia.2024.05.023
Abstract105)      PDF in ScienceDirect      
As the largest multifunctional and dynamic organelle in fungi, vacuoles are associated with different organelles through membrane contact sites and participate in various cellular processes.  Vacuole and mitochondria patch (vCLAMP), the membrane contact site that tethers vacuoles and mitochondria, is indispensable for reciprocal interplay between these two organelles.  The impairment of vacuoles and mitochondria significantly suppressed FB1 production in Fusarium verticillioides.  However, the understanding of how vCLAMP complex regulates fumonisin biosynthesis remained unknown.  Herein, the biological functions of vCLAMP component Vam6 were investigated in F. verticillioides. Our results showed that FvVam6 deletion mutant ΔFvVam6 exhibited palpable defects in fungal development, stresses responses and pathogenicity.  In addition, abnormal vacuolar morphology and significantly reduced FB1 production were observed in ΔFvVam6.  Furthermore, we demonstrated that two vacuolar sorting protein 39 (Vps39) domains and clathrin domain were critical for the biological functions of FvVam6, while clathrin and Vps39-2 domains played dominant roles in the regulation of virulence and FB1 production.  Taken together, our results advanced our understanding of vCLAMP in fumonisin biosynthesis in plant pathogenic fungus F. verticillioides.
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Identification of broad-spectrum B-cell and T-cell epitopes of H9 subtype avian influenza virus HA protein using polypeptide scanning

Keji Quan, Nan Zhang, Mengqi Lin, Yuan Liu, Yue Li, Qun Hu, Maoshun Nie, Tao Qin, Jingzhi Li, Hongwei Ma, Sujuan Chen, Daxin Peng, Xiufan Liu
2026, 25 (4): 1636-1646.   DOI: 10.1016/j.jia.2024.07.005
Abstract146)      PDF in ScienceDirect      

The H9N2 subtype avian influenza virus (AIV) hemagglutinin (HA) protein is a major immunogen in which HA1 is a genetic variant and HA2 is relatively conserved.  Identifying broad-spectrum antigen epitopes targeting HA1 is crucial for vaccine design and detection.  Based on the phylogenetic and serological analyses, we identified 2 antigenic groups and 3 representative viruses: A/chicken/Jiangsu/JY040218C/2019, A/pigeon/Jiangsu/JY020616/2019, and A/chicken/Jiangsu/WX090312/2018.  An overlapping peptide library was synthesized using HA1 amino acid sequences of the viruses as templates.  Through peptide scanning of the sera against different strains of H9N2 subtype AIV, we identified peptides from 4 regions (H9-2/3, H9-20/21, H9-26, and H9-29/30/31) that demonstrated broad-spectrum reactivity.  Immunological assay results demonstrated that H9-21 (219RIFKPLIGPRPLVNGLMGRI239), H9-26 (269SGESHGRILKTDLKMGSCTV289), and H9-30 (309YAFGNCPKYI GVKSLKLAVG329) effectively induced antibody generation and conferred partial protective efficacy against the parent virus JY040218C.  The results of lymphocyte proliferation and ELISpot assays indicated that peptides H9-15 (159MRWLTQKNNAYPTQDAQYTN179), H9-22 (229PLVNGLMGRINYYWSVLKP G249), and H9-23 (239NYYWSVLKPGQTLRIKSDGN259) could effectively stimulate the expression of interferon-gamma in peripheral blood lymphocytes of chickens immunized against different strains of H9N2 AIV.  Collectively, 5 novel cell epitopes H9-15, H9-22, H9-23, H9-26, and H9-30, including the best B cell epitope H9-26 and the best T cells epitope H9-22, were identified that could be targeted for vaccine design or detection approaches against H9N2 AIVs.

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Straw returning and night-warming improve grain yield and nitrogen use efficiency of winter wheat under rice–wheat rotation
Pan Hou, Qiang Gao, Yingkai Ren, Jinhong Yu, Lijun Gao, Xiaoxue Liu, Dong Jiang, Weixing Cao, Tingbo Dai, Zhongwei Tian
2026, 25 (4): 1418-1432.   DOI: 10.1016/j.jia.2024.12.012
Abstract74)      PDF in ScienceDirect      

Global climate warming is characterized by diurnal and seasonal asymmetry, with greater increases at nighttime and in winter and spring.  Growing evidence has recognized that night-warming in winter and spring significantly impacts winter wheat production.  Pre-crop straw returning is the principal method for straw utilization, but the interactions between straw returning and night-warming on wheat yield and N use efficiency (NUE) remain unclear.  Here, a consecutive three-year field experiment with two straw treatments (S0, straw removal; S1, straw returning) and two warming treatments (W0, no warming control; W1, night-warming) found that both S1 and W1 improved wheat grain yield and NUE, with W1 exhibiting more pronounced improvements.  Notably, the interaction between S1 and W1 (S1W1) further enhanced yield and NUE by 13.0 and 16.5%, respectively, compared to S0W0 through increasing grain number and 1,000-grain weight (three-year average).  Additionally, root growth and topsoil inorganic N content decreased in S1 before jointing, thereby reducing plant dry matter and N accumulation.  However, W1 exhibited an opposite trend, thereby mitigating these negative effects.  Simultaneously, under S1W1, increased N translocation to grain and post-anthesis dry matter accumulation, driven by greater N distribution to leaves and higher N metabolism enzyme activity, enhanced both yield and NUE.  This improvement was supported by better root morphology and biomass, particularly in the 0–40 cm soil layer, boosting plant N absorption.  Additionally, elevated soil N-acquiring enzyme activity after jointing increased the net N mineralization rate and microbial biomass N, enhancing soil N-supply capacity.  As a result, post-jointing inorganic N content rose in the 0–20 cm layer while decreasing at 20–60 cm, thus reducing the apparent N surplus.  Collectively, straw returning, night-warming, and their interactions enhanced root distribution and N-supply capacity after jointing in the topsoil layer, thereby increasing plant N uptake and its translocation to grains, along with post-anthesis dry matter accumulation, ultimately improving grain yield and NUE.

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Granulated organic amendment enhances recalcitrant carbon accumulation through soil aggregation in a barren paddy field
Yan Li, Xiaobin Guo, Yingnan Xian, Zhe Li, Haoyu Fu, Li Tang, Yuting Dai, Wei Gao, Yan Li, Ping Zhou, Shoulong Liu, Jinshui Wu
2026, 25 (3): 1194-1208.   DOI: 10.1016/j.jia.2025.05.004
Abstract129)      PDF in ScienceDirect      

Barren paddy fields characterized by poor soil structure, shallow tillage layers and low organic carbon content are a common limitation to rice production in subtropical China.  As a novel approach to soil improvement, granulated organic amendments offer significant potential.  Previous studies have shown that granulated straw can improve soil physicochemical properties and rapidly increase the soil organic carbon (SOC) content.  However, their effects on barren paddies remain underexplored.  This study evaluated four soil amendment strategies: no organic amendments (CK), 10 t ha–1 of composted manure (M10), 20 t ha–1 of granulated organic amendment (G20), and 40 t ha–1 of granulated organic amendment (G40).  The objective was to assess the effects of these amendments on soil structure, the contents of aggregate-associated carbon (AAC), particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and the chemical stability of MAOC among various size aggregates in both topsoil (0–20 cm) and subsoil (20–40 cm).  The results demonstrated that organic amendment inputs significantly increased the macroaggregate (>250 µm) proportion and improved soil structural stability.  These amendments also elevated the carbon concentration within aggregates of various sizes and facilitated the redistribution of organic carbon from microaggregates (53–250 µm) and silt+clay fractions (<53 µm) to macroaggregates.  The proportion of POC to AAC declined with decreasing aggregate size, whereas the proportion of MAOC increased.  In the topsoil, macroaggregate formation enhanced the protection of POC, supported the accumulation of non-hydrolyzable carbon within MAOC, and accelerated the formation of intra-microaggregates.  In the subsoil, mineral-bound organic carbon remained the dominant form of carbon sequestration.  In conclusion, the application of 40 t ha–1 of granulated organic amendment proved to be a successful tactic for enhancing soil physicochemical structure, increasing SOC content, and improving carbon stability.  This approach offers a promising and innovative solution for the sustainable management and restoration of barren paddy fields.  

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Rhizosphere flavonoids alleviate inhibition of soybean nodulation caused by shading under maize–soybean strip intercropping
Ping Lin, Shanshan Liu, Zhidan Fu, Kai Luo, Yiling Li, Xinyue Peng, Xiaoting Yuan, Lida Yang, Tian Pu, Yuze Li, Taiwen Yong, Wenyu Yang
2026, 25 (3): 952-964.   DOI: 10.1016/j.jia.2024.09.030
Abstract373)      PDF in ScienceDirect      

Flavonoids produced by legume roots act as signaling molecules that induce the expression of nod genes in symbiotic rhizobia.  However, the role of flavonoids in root exudates under intercropping systems in promoting soybean nodulation remains unclear.  Two consecutive years of field experiments were conducted using maize–soybean strip intercropping with interspecific row spacings of 30 cm (MS30), 45 cm (MS45), and 60 cm (MS60), along with sole cropping of soybean (SS) and maize (MM).  Root interactions were manipulated using either no root barrier (NB) or a polyethylene plastic barrier (PB) to assess the relationship between flavonoids in root exudates and soybean nodulation.  We found that root–root interaction between soybean and maize increased nodule number and fresh weight in intercropped soybean, with enhancement gradually increasing as interspecific distance widened.  The proportion of nodules with diameters exceeding 0.4 cm was higher in intercropped soybean under NB compared to PB.  Additionally, the expression of nodule-related genes - GmENOD40, GmNIN2b, and GmEXPB2 - was up-regulated.  Furthermore, compared to monocropping, isoflavone secretion by soybean roots decreased, whereas flavonoid and flavonol secretion by both maize and soybean roots increased under intercropping.  The abundance of differentially secreted flavonoid metabolites in the rhizosphere of both species declined when root contact was prevented by the barrier.  In soybean roots, the expression of GmCHS8 and GmIFS1 was up-regulated, while GmICHG was down-regulated under root interaction.  Most flavonoid and flavonol compounds showed positive correlations with nodule diameter.  Nodule number, fresh weight, and the proportion of nodules larger than 0.2 cm increased in diverse soybean genotypes treated with maize root exudates, which contributed to enhanced nitrogen fixation capacity.  Therefore, maize–soybean strip intercropping, combined with optimal row spacing, enhances the positive effects of underground root interactions and improves nodulation and nitrogen fixation in intercropped soybean.

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Exploring strategies for agricultural sustainability in super hybrid rice using the food–carbon–nitrogen–water–energy–profit nexus framework
Jun Deng, Ke Liu, Xiangqian Feng, Jiayu Ye, Matthew Tom Harrison, Peter de Voil, Tajamul Hussain, Liying Huang, Xiaohai Tian, Meixue Zhou, Yunbo Zhang
2026, 25 (2): 624-638.   DOI: 10.1016/j.jia.2024.07.025
Abstract152)      PDF in ScienceDirect      


The breakthrough in super hybrid rice yield has significantly contributed to China’s and global food security.  However, the inherent conflict between high productivity and environmentally sustainable agriculture poses substantial challenges.  Issues such as water scarcity, energy crises, escalating greenhouse gas emissions, and diminishing farm profitability threaten long-term agricultural sustainability.  In response, we applied a holistic food–carbon–nitrogen–water–energy–profit (FCNWEP) nexus framework to comprehensively assess the sustainability of distinct crop management strategies across three sub-sites in Central China.  Field experiments were conducted in Hubei and Hunan provinces from 2017 to 2021 using a widely adopted elite super hybrid rice cultivar (Y-liangyou 900). Four crop management treatments were implemented: a control (CK, 0 kg N ha−1), conventional crop management (CCM, 210–250 kg N ha−1, 7:3 basal:mid-tiller fertilizer ratio), and two integrated crop management (ICM) treatments (ICM1, 180–210 kg N ha−1, 5:2:3 basal:mid-tiller:panicle initiation fertilizer ratio; ICM2, 240–270 kg N ha−1, 5:2:2:1 basal:mid-tiller:panicle initiation:flowering fertilizer ratio).  Variables assessed included grain yield, carbon footprint, nitrogen footprint, water footprint, energy footprint, nitrogen use efficiency, and economic benefits.  Our results showed significant yield variations, with ICM2 consistently outperforming CCM and ICM1 across all three sites.  In Jingzhou, Suizhou, and Changsha, ICM2’s grain yield was 30.2, 24.7, and 13.3% higher than CCM, respectively.  Net profits under ICM2 exceeded those of CCM and ICM1 by 31.8 and 115.2% in Jingzhou, 32.2 and 109.9% in Suizhou, and 15.4 and 34.0% in Changsha, respectively.  Integrated crop management, particularly ICM2, demonstrated improved nitrogen and energy use efficiency, leading to reduced carbon, nitrogen, water, and energy footprints.  Overall, composite sustainability scores derived from the FCNWEP framework indicated that both ICM2 and ICM1 exhibited higher sustainability levels compared to CCM.  This study provides valuable insights into practical management methodologies and offers recommendations for enhancing agricultural sustainability.


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MicroRNA-mediated modulation of immune genes facilitates Metarhizium anisopliae infection in the red imported fire ant, Solenopsis invicta
Yating Xu, Junaid Zafar, Liangjie Lin, Hongxin Wu, Zehong Kang, Jie Zhang, Rana Fartab Shoukat, Yongyue Lu, Rui Pang, Fengliang Jin, Xiaoxia Xu
2026, 25 (1): 192-206.   DOI: 10.1016/j.jia.2025.02.009
Abstract179)      PDF in ScienceDirect      

The red imported fire ant, Solenopsis invicta Buren, is a highly invasive eusocial insect pest that threatens native biodiversity, agriculture, and human health.  The innate immune system and intricate social immune responses of Sinvicta pose challenges to the development of effective control strategies.  MicroRNAs (miRNAs) play critical roles in the post-transcriptional regulation of gene expression, which influences various biological processes, including immunity and host-pathogen interactions.  While the miRNA-mediated response of insects to pathogens has been extensively studied in solitary insects, little is known about the innate immune responses of individual members within a colony.  To address this gap, we constructed small RNA libraries from Metarhizium anisopliae-infected Sinvicta workers and investigated the temporal dynamics of miRNA-mediated immune responses to the entomopathogen.  Several differentially expressed miRNAs were identified, and they were found to regulate genes involved in the Toll, IMD, and melanization immune pathways.  Quantitative real-time PCR (qRT-PCR) was employed to analyze the spatiotemporal dynamics of key miRNAs/target genes, specifically miR-71/ModSP1-Relish and miR-7/Lysozyme2-Serine protease7.  A dual luciferase assay (in vitro) was performed to validate the interactions between miRNAs and their target genes.  Overexpression of miR-71 and miR-7 (via miRNA mimics) efficiently suppressed their target genes, impaired the antifungal immune response of Sinvicta and increased the susceptibility to Manisopliae infection compared to controls.  Furthermore, RNA interference-based gene silencing elucidated the roles of these immune genes in regulating fungal susceptibility, thus providing vital clues for developing virulent and effective mycoinsecticides using modern genetic engineering tools.  

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Performance and functional responses of the thelytokous and arrhenotokous strains of Neochrysocharis formosa to Tuta absoluta, a globally severe tomato pest 
Guifen Zhang, Hao Wang, Yibo Zhang, Xiaoqing Xian, Cong Huang, Wanxue Liu, Fanghao Wan
2026, 25 (1): 180-191.   DOI: 10.1016/j.jia.2025.04.023
Abstract157)      PDF in ScienceDirect      

The native thelytokous (TH) and arrhenotokous (AR) strains of Neochrysocharis formosa (Westwood) (Hymenoptera: Eulophidae) are promising biocontrol agents against the invasive tomato pest Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae).  This study assessed the performance and preferences of these strains in choice experiments involving five host instar ratios and evaluated their functional responses to seven densities of 1st instar larvae (5 to 40 hosts).  In host-attacking behavior assays, an increasing proportion of 1st instar larvae led to a significant rise in host mortality rates for both strains.  Both strains exhibited strong preferences for parasitizing and attacking 1st instar larvae over later instars, with the TH strain demonstrating significantly greater host-killing efficacy than the AR strain.  Functional response experiments revealed that the attack rates of both strains were positively correlated with host density.  Parasitism by both strains and host-stinging behavior by the TH strain showed type III functional responses, while host-feeding by both strains and host-stinging by the AR strain followed type II functional responses.  Early establishment of the TH strain in tomato agroecosystems could enhance the management of Tabsoluta.  These findings provide critical insights into the functional dynamics of the TH and AR strains of Nformosa that can inform the development of effective biocontrol programs for this globally significant pest.

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Optimizing nitrogen application and planting density improves yield and resource use efficiency via regulating canopy light and nitrogen distribution in rice
Zichen Liu, Liyan Shang, Shuaijun Dai, Jiayu Ye, Tian Sheng, Jun Deng, Ke Liu, Shah Fahad, Xiaohai Tian, Yunbo Zhang, Liying Huang
2026, 25 (1): 81-91.   DOI: 10.1016/j.jia.2024.04.006
Abstract336)      PDF in ScienceDirect      

Coordinating light and nitrogen (N) distribution within a canopy is essential for improving rice yield and resource use efficiency.  However, limited research has examined light and N distribution in response to planting density and N rate, and their relationships with grain yield, radiation use efficiency (RUE), and N use efficiency for grain production (NUEg) in rice.  A two-year field experiment was conducted with two hybrid varieties under three N levels, 0 kg ha–1 (N1), 90 kg ha–1 (N2) and 180 kg ha–1 (N3), and two planting densities, 22.2 hills m–2 (D1) and 33.3 hills m–2 (D2).  Results showed 3.4% higher yield and 4.4% higher NUEg under N2D2 compared with N3D1.  The extinction coefficient for N (KN) and light (KL) and their ratio (KN/KL) at heading stage were significantly influenced by N rate, planting density, and their interaction.  KN decreased with the increase of N input or planting density.  Compared to N1, KN decreased by 43.5 and 58.8% under N2 and N3, respectively, while KN under D2 decreased by 16.0% compared to D1.  Higher KL and KN/KL values occurred under low N rates, with opposite trends under high N rates.  Increased planting density led to decreased KL and KN/KL values.  N2D2 demonstrated higher KL and KN, and thus comparable KN/KL, compared to N3D1.  Correlation analysis revealed KL negatively correlated with RUE, while KN and KN/KL positively correlated with NUEg.  These findings indicate that increasing planting density under reduced N input could maintain rice yield while enhancing resource use efficiency through regulation of canopy light and N distribution.

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Automatic diagnosis of agromyzid leafminer damage levels using leaf images captured by AR glasses
Zhongru Ye, Yongjian Liu, Fuyu Ye, Hang Li, Ju Luo, Jianyang Guo, Zelin Feng, Chen Hong, Lingyi Li, Shuhua Liu, Baojun Yang, Wanxue Liu, Qing Yao
2025, 24 (9): 3559-3573.   DOI: 10.1016/j.jia.2025.02.008
Abstract275)      PDF in ScienceDirect      

Agromyzid leafminers cause significant economic losses in both vegetable and horticultural crops, and precise assessments of pesticide needs must be based on the extent of leaf damage.  Traditionally, surveyors estimate the damage by visually comparing the proportion of damaged to intact leaf area, a method that lacks objectivity, precision, and reliable data traceability.  To address these issues, an advanced survey system that combines augmented reality (AR) glasses with a camera and an artificial intelligence (AI) algorithm was developed in this study to objectively and accurately assess leafminer damage in the field.  By wearing AR glasses equipped with a voice-controlled camera, surveyors can easily flatten damaged leaves by hand and capture images for analysis.  This method can provide a precise and reliable diagnosis of leafminer damage levels, which in turn supports the implementation of scientifically grounded and targeted pest management strategies.  To calculate the leafminer damage level, the DeepLab-Leafminer model was proposed to precisely segment the leafminer-damaged regions and the intact leaf region.  The integration of an edge-aware module and a Canny loss function into the DeepLabv3+ model enhanced the DeepLab-Leafminer model’s capability to accurately segment the edges of leafminer-damaged regions, which often exhibit irregular shapes.  Compared with state-of-the-art segmentation models, the DeepLab-Leafminer model achieved superior segmentation performance with an Intersection over Union (IoU) of 81.23% and an F1 score of 87.92% on leafminer-damaged leaves.  The test results revealed a 92.38% diagnosis accuracy of leafminer damage levels based on the DeepLab-Leafminer model.  A mobile application and a web platform were developed to assist surveyors in displaying the diagnostic results of leafminer damage levels.  This system provides surveyors with an advanced, user-friendly, and accurate tool for assessing agromyzid leafminer damage in agricultural fields using wearable AR glasses and an AI model.  This method can also be utilized to automatically diagnose pest and disease damage levels in other crops based on leaf images.


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Editing of the APETALA2/ethylene responsive factor confers improvements in seed shattering and quality in rice
Saisai Xia, He Liu, Ying Liu, Guangheng Zhang, Deyong Ren, Qian Qian
2025, 24 (8): 3282-3286.   DOI: 10.1016/j.jia.2025.02.022
Abstract153)      PDF in ScienceDirect      
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Establishment of goat infection model of the peste des petits ruminants virus isolated in China for vaccine efficacy evaluation
Xue Wang, Hefeng Chen, Xianfeng Zhang, Zhengshuang Wu, Shuai Zhang, Lei Shuai, Lulu Wang, Weijie Li, Jinliang Wang, Wenxing Liu, Xijun Wang, Zhiyuan Wen, Jinying Ge, Yuntao Guan, Xijun He, Weiye Chen, Zhigao Bu
2025, 24 (8): 3199-3211.   DOI: 10.1016/j.jia.2024.02.016
Abstract256)      PDF in ScienceDirect      

In 2013, peste des petits ruminants (PPR) re-emerged in China and spread to the majority of provinces across the country.  The disease was effectively controlled through a vaccination campaign employing live attenuated vaccines, although sporadic cases still occurred.  However, limited information is currently available regarding the peste des petits ruminants virus (PPRV) endemic in China.  Here, a PPRV strain (HLJ/13) was isolated from a field sample in China using Vero cells expressing goat signalling lymphocyte activation molecule.  Phylogenetic analysis indicated that HLJ/13 belonged to lineage IV.  Subsequent intranasal and subcutaneous inoculation of goats with a dose of 2×106 TCID50 of HLJ/13 resulted in the development of typical clinical symptoms of PPR, including pyrexia, ocular and nasal discharges, stomatitis, and diarrhea.  All infected goats succumbed to the disease by day 8.  To gain further insight, viral loading, pathological examination and immunohistochemical analyses were conducted, elucidating the main targets of HLJ/13 as the respiratory system, digestive tract and lymphoid organs.  Employing the goat infection model established above, the goat poxvirus-vectored PPR vaccine, which was previously developed and could be used as DIVA (differentiating infected from vaccinated animals) vaccine, provided complete protection against the challenge of HLJ/13.  It is important to note that this study represents the first comprehensive report delineating the biology and pathogenicity characterization, and infection model of PPRV isolated in China. 

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Characterization and functions of temperature stress-associated microRNAs in invasive insect Bemisia tabaci Mediterranean cryptic species
Xiaona Shen, Jianyang Guo, Fanghao Wan, Zhichuang Lü, Jianying Guo, Wanxue Liu
2025, 24 (7): 2719-2731.   DOI: 10.1016/j.jia.2024.09.021
Abstract221)      PDF in ScienceDirect      

With the development of international trade and frequent personnel exchanges, biological invasion is showing a rapidly growing trend worldwide.  Insects are ectothermic animals, so their geographical distribution is due largely to their high and low temperature tolerances.  To study the temperature response mechanisms of Bemisia tabaci Mediterranean cryptic species (MED), miRNA-seq technology was used to unravel the miRNA library of Btabaci MED in three field populations (TP, HB, and HK) from cities with different environmental temperatures.  We identified 12 differentially expressed miRNAs in response to temperature stress, and Bta-miR-998 and Bta-miR-129 were shown to be associated with temperature tolerance.  In addition, we predicted and verified the target genes associated with the temperature tolerance imparted by Bta-miR-998 and Bta-miR-129.  The results showed that the down-regulated target gene of Bta-miR-129, BtMGAT3, significantly reduced the heat tolerance and another down-regulated target gene, BtRGS7, affected the cold tolerance of Btabaci MED.  These results indicate that gene expression regulated by miRNAs is an important temperature response mechanism in Btabaci MED.  This study reveals the important regulatory role of miRNA in insect temperature adaptation and provides a new avenue for studying the regulation of insect gene expression by miRNA


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Ppbbx24-del mutant positively regulates light-induced anthocyanin accumulation in the ‘Red Zaosu’ pear (Pyrus pyrifolia White Pear Group)
Shuran Li, Chunqing Ou, Fei Wang, Yanjie Zhang, Omayma Ismail, Yasser S. G. Abd Elaziz, Sherif Edris, , He Li, Shuling Jiang
2025, 24 (7): 2619-2639.   DOI: 10.1016/j.jia.2024.11.005
Abstract264)      PDF in ScienceDirect      

Red fruit peel is one of pear’s most valuable economic traits and is mainly determined by anthocyanins.  Many pear cultivars with a red peel originated from bud sports; however, little is known about the genetic mechanisms underlying this trait.  We have previously identified a mutant PpBBX24 containing a 14-nucleotide deletion in the coding region (Ppbbx24-del) as the only known variant associated with the red coloration of the mutant ‘Red Zaosu’ pear (Pyrus pyrifolia White Pear Group).  Herein, we analyzed the role of the mutant gene in red coloration and its mechanism of action.  The results showed that light promoted red peel coloration in the ‘Red Zaosu’ pear, and Ppbbx24-del positively affected light-induced anthocyanin biosynthesis, while normal PpBBX24 had the opposite effects.  Transient and stable transformation experiments confirmed that Ppbbx24-del could promote anthocyanin accumulation in pear fruit peels, calli, and tobacco flowers.  Due to the loss of nuclear localization sequence (NLS) and viral protein (VP) domains, Ppbbx24-del co-localized in the nucleus and cytoplasm, whereas PpBBX24 localized only in the nucleus.  Real-time PCR and transcriptome analyses indicated that PpMYB10 and PpHY5 are highly expressed in the ‘Red Zaosu’ pear.  In yeast one-hybrid and dual-luciferase assays, Ppbbx24-del and PpHY5 independently promoted the expression of PpCHS, PpCHI, and PpMYB10 by binding to their promoters; however, PpBBX24 did not affect the expression of these genes.  Additionally, we found that Ppbbx24-del and PpHY5 had additive effects on the expression of PpCHS, PpCHI, and PpMYB10, as they promote the expression of anthocyanin synthesis genes separately.  The co-expression of PpBBX24 and PpHY5 inhibited the activation of downstream genes by PpHY5, which was attributed to the interaction between the two loci.  In conclusion, our results clarify the molecular mechanism by which mutant Ppbbx24-del and PpBBX24 exert opposite effects in regulating anthocyanin accumulation in pear.  These findings lay an important theoretical foundation for using Ppbbx24-del to create red pear cultivars.

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Optimizing planting density and nitrogen application to mitigate yield loss and improve grain quality of late-sown wheat under rice–wheat rotation
Zhongwei Tian, Yanyu Yin, Bowen Li, Kaitai Zhong, Xiaoxue Liu, Dong Jiang, Weixing Cao, Tingbo Dai
2025, 24 (7): 2558-2574.   DOI: 10.1016/j.jia.2024.01.032
Abstract308)      PDF in ScienceDirect      

Late sowing is a critical factor that hinders achieving high-yield, good-quality wheat under rice–wheat rotation.  Understanding the physiological basis and regulatory pathways that lead to high yield and sound quality late-sown wheat is crucial for developing effective cultivation strategies.  A 2-year field experiment was conducted to investigate the effects of sowing date, nitrogen (N) application rate, and planting density on wheat yield, grain quality, population characteristics, and the underlying physiological factors.  The results revealed significant interactions among the sowing date, planting density, and N application in regulating both yield and quality.  Late sowing reduced grain yield primarily by reducing the number of spikes and kernels.  However, the latter was improved by increasing N application and the planting density, thus mitigating the yield losses caused by late sowing.  Moreover, the grain protein content (GPC) and wet gluten content (WGC) increased with delayed sowing dates and higher N rates but decreased with increased planting densities.  For wheat yields over 9,000 or 7,500 kg ha–1, the latest sowing date should not be later than Nov. 4 or 15, respectively.  In addition, specific criteria should be met, including a maximum of 1.5 and 1.0 million stems and tillers ha–1, a maximum leaf area index of 6.7 and 5.5, and a dry matter accumulation (DMA) at anthesis of 14,000 and 12,000 kg ha–1, respectively.  For high-yield, good-quality late-sown wheat, the optimal combination is a 25% increase in the N rate (300 kg N ha–1) and a planting density of 2.25 million (N300D225) or 3.75 million (N300D375) plants ha–1 for 10- or 20-day delays in sowing, respectively.  These combinations result in a higher leaf net photosynthetic rate, higher activities of leaf nitrate reductase, glutamine synthetase, grain glutamic pyruvic transaminase, and a lower sugar-N ratio during post-anthesis.

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Overexpression of TuABCC4 is associated with abamectin resistance in Tetranychus urticae Koch
Mingmei Wu, Rui Dong, Yan Zhang, Haojie Liao, Tian Tian, Dandan Xu, Youjun Zhang, Zhaojiang Guo, Shaoli Wang
2025, 24 (6): 2299-2310.   DOI: 10.1016/j.jia.2024.07.020
Abstract262)      PDF in ScienceDirect      

Pesticide resistance greatly limits control efficacy after the long-term application of pesticides.  The two-spotted spider mite, Tetranychus urticae Koch, is a notorious agricultural pest worldwide that is resistant to various pesticides, including abamectin.  While some studies of abamectin resistance have investigated target resistance related to glutamate-gated chloride channels (GluCls), studies on the metabolic resistance mechanisms are still limited.  In this study, we identified an ABCC subfamily gene, TuABCC4, that was overexpressed in resistant populations of Turticae, based on the analysis of previously obtained transcriptomic and RNA-seq data.  No consistent nonsynonymous mutations in the TuABCC4 gene were found between the susceptible and resistant populations, although TuABCC4 expression was significantly increased in all the resistant populations that were studied.  Synergistic experiments with the inhibitor verapamil and gene expression analysis of the susceptible and resistant populations confirmed the key role of TuABCC4 in abamectin resistance.  In addition, an increase in the expression of the TuABCC4 gene was shown by RNA interference and genetic association analysis to be closely related to the resistance of Turticae to abamectin.  In conclusion, overexpression of TuABCC4 was shown to be involved in abamectin resistance in Turticae.  These results can help us to better understand the molecular basis of pest resistance to abamectin.


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Genetic diversity of the self-incompatibility locus in diploid potato
Xinyu Jing, Duoduo Qian, Xiuhan Jiang, Pei Wang, Huihui Bao, Dianjue Li, Yanhui Zhu, Guangtao Zhu, Chunzhi Zhang
2025, 24 (4): 1448-1460.   DOI: 10.1016/j.jia.2024.12.011
Abstract242)      PDF in ScienceDirect      
Re-domestication of diploid potato (Solanum tuberosum) into a seed crop is an innovative breeding method to accelerate genetic improvement.  Seed propagation would allow hybrid production and mix superior alleles.  However, almost all diploid potatoes in nature are self-incompatible (SI).  Gametophytic self-incompatible (GSI) is a widespread SI in Solanaceae and is controlled by the S locus that contains a ribonuclease (S-RNase) and multiple F-box (SLFs); however, the genetic diversity of the S locus in potato is unclear.  This study identified 21 S-RNase alleles involved in SI from 194 diploid potato accessions by large-scale transcriptome sequencing.  The levels of amino acid similarity among different S-RNase proteins varied from 31.3 to 95.8%.  S2 allele is the most widespread in 194 diploid potatoes and is mainly distributed in the Stuberosum Group Phureja.  Based on genomic annotation and expression analysis, we identified 12 potential functional SI male-determinant genes, S-locus F-box (SLFs), encoding F-box proteins in the S2 locus on a genomic region of approximately 13 Mb.  Comparative genomics analysis showed that eight SLF genes are relatively conserved among four homozygous S locus.  The Ka and Ks analysis suggested that S-RNase and intra-haplotypic SLF genes have co-evolved.  These findings help select suitable pollinators, combine more hybrid combinations, and fully use heterosis to accelerate diploid potato breeding.


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16S amplicon sequencing and untargeted metabolomics reveal changes in rumen microorganisms and metabolic pathways involved in the reduction of methane by cordycepin
Haokai Ma, Dengke Liu, Rui Liu, Yang Li, Modinat Tolani Lambo, Baisheng Dai, Weizheng Shen, Yongli Qu, Yonggen Zhang
2025, 24 (4): 1310-1326.   DOI: 10.1016/j.jia.2024.04.014
Abstract201)      PDF in ScienceDirect      
As a major contributor to methane production in agriculture, there is a need for a suitable methane inhibitor to reduce ruminant methane emissions and minimize the impact on the climate.  This work aimed to explore the influence of cordycepin on rumen fermentation, gas production, microbiome and their metabolites.  A total of 0.00, 0.08, 0.16, 0.32, and 0.64 g L–1 cordycepin were added into fermentation bottles containing 2 g total mixed ration for in vitro ruminal fermentation, and then the gas produced and fermentation parameters were measured for each bottle.  Samples from the 0 and 0.64 g L–1 cordycepin addition were selected for 16S rRNA gene sequencing and metabolome analysis.  The result of this experiment indicated that the addition of cordycepin could linearly increase the concentration of total volatile fatty acid, ammonia nitrogen, the proportion of propionate, valerate, and isovalerate, and linearly reduce ruminal pH and methane, carbon dioxide, hydrogen and total gas production, as well as the methane proportion, carbon dioxide proportion and proportion of butyrate.  In addition, there was a quadratic relationship between hydrogen and cordycepin addition.  At the same time, the relative abundance of Succiniclasticum, Prevotella, Rikenellaceae_RC9_gut_group, NK4A214_group, Christensenellaceae_R_7_group, unclassified_F082, Veillonellaceae_UCG_001, Dasytricha, Ophryoscolex, Isotricha, unclassified_Eukaryota, Methanobrevibacter, and Piromyces decreased significantly after adding the maximum dose of cordycepin.  In contrast, the relative abundance of Succinivibrio, unclassified_Succinivibrionaceae, Prevotellaceae_UCG_001, unclassified_Lachnospiraceae, Lachnospira, Succinivibrionaceae_UCG_002, Pseudobutyrivibrio, Entodinium, Polyplastron, unclassified_Methanomethylophilaceae, Methanosphaera, and Candidatus_Methanomethylophilus increased significantly.  Metabolic pathways such as biosynthesis of unsaturated fatty acids and purine metabolism and metabolites such as arachidonic acid, adenine, and 2´-deoxyguanosine were also affected by the addition of cordycepin.  Based on this, we conclude that cordycepin is an effective methane emission inhibitor that can change the rumen metabolites and fermentation parameters by influencing the rumen microbiome, thus regulating rumen methane production.  This experiment may provide a potential theoretical reference for developing Cordyceps byproduct or additives containing cordycepin as methane inhibitors.


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Inclusion of sorghum grain rich in condensed tannins in the diet of steers did not affect the nitrogen utilization efficiency but increased the urine nitrous oxide emissions
Biao Xie, Changfa Mao, Xu Shen, Yufeng Liu, Qingyue Liang, Guangyong Zhao
2025, 24 (4): 1296-1309.   DOI: 10.1016/j.jia.2023.11.035
Abstract192)      PDF in ScienceDirect      
The objectives of this study which included two experiments were to investigate the effects of dietary inclusion of sorghum grain rich in condensed tannins (CT) (18.9 g kg–1 dry matter (DM)) on nitrogen (N) metabolism and urine nitrous oxide (N2O) emissions of beef steers.  In experiment 1, six Limousin×Luxi crossbreed steers with an initial liveweight of (245.0±18.7) kg were used as experimental animals.  Three levels of sorghum grain, i.e., 0, 167 and 338 g kg–1 DM were included in diets as experimental treatments.  The animals and the treatments were randomly assigned to a replicated 3×3 Latin square design.  In experiment 2, static incubation technique was used to determine the N2O emissions of the urine samples collected in experiment 1.  The results of experiment 1 showed that dietary inclusion of sorghum grain linearly increased the faecal N excretion (P=0.001), the total N excretion (P=0.010) and the faecal N to N intake ratio (P=0.021), but it did not affect the N retention and the N utilization efficiency (P>0.10).  The plasma metabolomic data showed that dietary inclusion of sorghum grain increased the relative concentrations of phenolic acid (N1, N5, N10-tris-trans-p-coumaroylspermine and prenyl cis-caffeate) and carnitine (3-hydroxyisovalerylcarnitine and linoelaidyl carnitine).  The results also showed that dietary inclusion of sorghum grain linearly increased the urinary urea excretion (P=0.010) and decreased the urinary excretion of purine derivatives (P=0.041) as well as the estimated rumen microbial N supply (P=0.012) based on urinary purine derivatives.  The results of experiment 2 showed that including sorghum grain in the diet linearly increased the average concentrations of NH4+-N (P=0.012), NO2-N (P=0.009), NO3-N (P=0.001) and the total inorganic N (P<0.001) in the soil enriched with urine samples.  The urine sample N2O-N flux (P=0.001), the estimated steer urine N2O-N flux (P=0.021) and the N2O-N to urinary N ratio (P=0.038) linearly increased with increasing inclusion of sorghum grain in the diet.  In conclusion, dietary inclusion of sorghum grain containing high CT at 167 and 338 g kg–1 DM did not affect the N utilization efficiency of steers but increased the urine N2O-N emissions by 5.7 and 31.4%, respectively.  For reducing the N2O emissions to the environment, high levels of sorghum grain should not be included in the diet of steers.


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Comparative genomics study between high and low laying goose breeds reveals the important role of ESR1 in laying abilit
Qingyuan Ouyang, Hengli Xie, Shenqiang Hu, Cong Lan, Mingxia Ran, Jiwei Hu, Hua He, Liang Li, Hehe Liu, Hao Qu, Jiwen Wang
2025, 24 (3): 1167-1180.   DOI: 10.1016/j.jia.2023.05.028
Abstract336)      PDF in ScienceDirect      

The low egg production of goose greatly limits the development of the industry.  China possesses the most abundant goose breeds resources.  In this study, genome resequencing data of swan goose (Anser cygnoides) and domesticated high and low laying goose breeds (Anser cygnoides domestiation) were used to identify key genes related to egg laying ability in geese and verify their functions.  Selective sweep analyses revealed 416 genes that were specifically selected during the domestication process from swan geese to high laying geese.  Furthermore, SNPs and Indels markers were used in GWAS analyses between high and low laying breed geese.  The results showed that RTCB, BPIFC, SYN3, SYNE1, VIP, and ESR1 may be related to the differences in laying ability of geese.  Notably, only ESR1 was identified simultaneously by GWAS and selective sweep analysis.  The genotype of Indelchr3:54429172, located downstream of ESR1, was confirmed to affect the expression of ESR1 in the ovarian stroma and showed significant correlation with body weight at first egg and laying frequency of geese.  CCK-8, EdU, and flow cytometry confirmed that ESR1 can promote the apoptosis of goose pre-hierarchical follicles ganulosa cells (phGCs) and inhibit their proliferation.  Combined with transcriptome data, it was found ESR1 involved in the function of goose phGCs may be related to MAPK and TGF-beta signaling pathways.  Overall, our study used genomic information from different goose breeds to identify an indel located in the downstream of ESR1 associated with goose laying ability.  The main pathways and biological processes of ESR1 involved in the regulation of goose laying ability were identified by cell biology and transcriptomics methods.  These results are helpful to further understand the laying ability characteristics of goose and improve the egg production of geese.


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