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2026 Vol. 25 No. 4 Previous Issue   

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Review
Crop Science
Horticulture
Plant Protection
Animal Science · Veterinary Medicine
Agro-ecosystem & Environment
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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, SlMYB32 was characterized as a transcriptional repressor in tomato fruit. Phenotype and metabolome analyses showed that knockout of SlMYB32 resulted in increased accumulation of flavonols and flavanones, especially about 1 mg g^–1 FW of rutin. Transcriptome and molecular biology experiments showed that SlMYB32 regulated expression of SlPAL6, Sl4CL3 and SlUGTs. This study provides new insights into improving bioactive compounds in fruit and understanding negative regulatory mechanisms in flavonol and flavanone biosynthesis. This cover picture illustrates that CRISPR/Cas9-mediated mutagenesis of SlMYB32 induced phenylpropanoid pathway and UGT activity to improve flavonol and flavanone levels, contributing to nutrition biofortification in fruit. This cover picture was provided by Prof. Xian Li and Mr. Ruining Zhang from Zhejiang University, China. For more details, please see pages 1463–1474.



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Review

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Global trends in the commercialization of genetically modified crops in 2024 Haohui Li, Xingru Cheng, Liqiang Wang, Pei Xie, Haiwen Zhang, Yadong Yang, Tao Liu, Youhua Wang 2026, 25(4): 1307-1315.  DOI: 10.1016/j.jia.2025.11.037 Abstract ( )   PDF in ScienceDirect   The ongoing commercialization of genetically modified (GM) crops continues to enhance global grain yields, improve crop quality, and reduce pesticide usage. These technological advancements have effectively propelled agricultural production systems toward sustainable transformation. Specifically, GM crops address core challenges such as pest infestations, weed proliferation, and arable land constraints, emerging as a pivotal new productive force in agriculture. This study systematically examines the global spatial distribution patterns of GM crops in 2024 and provides an indepth analysis of the driving forces and evolving regional trends, offering critical informational support and strategic guidance for innovation in agricultural science and technology. In 2024, the global GM crop cultivation area reached 209.8 million hectares, a 1.7% year-on-year increase. GM Glycine max (soybean) and Zea mays (maize) dominated the landscape, accounting for 50.0 and 32.5% of the total area, respectively. Among them, maize with stacked traits of insect resistance and herbicide tolerance accounts for 92.5% of GM maize. The share of cultivation in developing countries expanded substantially, with Brazil and Vietnam emerging as regional growth drivers. Policy support and the diffusion of advanced technologies were identified as core driving forces. Concurrently, applications of gene-editing technology accelerated, and several countries approved novel tr aits such as drought tolerance and disease resistance, marking substantial progress in the commercialization of next-generation GM crops. This research provides multidimensional insights and strategic guidance to support global agricultural biotechnology development, promoting the transition of biotechnology breeding into the ‘4.0 era’.

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Multi-objective integrated cotton cultivation (MOICC): A synergistic framework for sustainable production Yanjun Zhang, Jianlong Dai, Hezhong Dong 2026, 25(4): 1316-1329.  DOI: 10.1016/j.jia.2025.12.024 Abstract ( )   PDF in ScienceDirect   Global cotton production faces mounting pressure to reconcile rising fiber demand with urgent sustainability imperatives, including water scarcity mitigation, greenhouse gas reduction, and agrochemical pollution control.  Traditional practices, constrained by fragmented objectives and inherent trade-offs among yield, fiber quality, labor efficiency, and ecological impact, struggle to address these systemic challenges.  Building upon previous concept of collaborative cultivation, this review for the first time introduces and comprehensively elaborates multi-objective integrated cotton cultivation (MOICC)  - also referred to as integrated cotton cultivation (ICC) - a transformative framework centered on three pillars: dynamic trade-off management (e.g., region-specific priority adjustment), systematic technology integration (precision seeding, dense planting, chemical regulation, water-nutrient synergy, and targeted defoliation), and resource circularity (spatiotemporal optimization and waste recycling).  MOICC overcomes sustainability bottlenecks by leveraging key physiological mechanisms, including ethylene signaling to enhance stress-resilient seedling establishment, jasmonate-mediated pathways to improve water/nutrient efficiency, canopy light competition coupled with hormonal regulation to eliminate manual pruning, and growth regulators to concentrate boll maturation.  Case studies from diverse Chinese agro-ecosystems (e.g., Xinjiang, Yangtze/Yellow River basins) and intercropping systems demonstrate significant synergies: increased yield (8–22%), improved resource efficiency (water use efficiency increased by ≥20%, and nitrogen productivity up to 35 kg kg–1), and enhanced environmental performance (labor reduction of 30–40%, carbon footprint reduction of 24–37%, and agrochemical savings: nitrogen reduction of 15–20% and pesticides reduction of 25%).  Crucially, MOICC resolves core conflicts through integrated optimization: yield vs. quality (via ≥70% inner-position bolls), labor-saving vs. eco-safety (precision defoliant timing), and productivity vs. emissions (root-zone nitrogen monitoring).  Future research priorities include deciphering multi-scale stress adaptation, developing intelligent decision-support systems (e.g., AHP-NSGA-II integration), advancing carbon-neutral value chains, addressing socio-economic adoption barriers, and fostering policy synergy.  Overall, MOICC establishes a conceptually globally scalable pathway toward high-yield, superior-quality, resource-efficient, and ecologically sustainable cotton production, with potential applicability to other major cropping systems.

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High-fidelity gut metagenome: A new insight of identification of fuctional probiotics Yuhui Wang, Peiwen Gao, Chenying Li, Yuxi Lu, Yubo Zhang, Yu Zhou, Siyuan Kong 2026, 25(4): 1330-1342.  DOI: 10.1016/j.jia.2024.05.011 Abstract ( )   PDF in ScienceDirect   Probiotics are considered to exert beneficial effects in humans and animals by modulating the structure and metabolic functions of the gut microbiota.  Therefore, the identification of functional probiotics and in-depth exploration of the characteristics and applicability of probiotics are of paramount significance for the development of more effective probiotic products and the formulation of personalized probiotic treatment strategies in the fields of human health and livestock farming.  However, due to current limitations in sequencing technologies and considering that microbial communities may encompass closely related lineages, rendering metagenome assembly complex, the generation of complete metagenome-assembled genomes (cMAGs) is hindered.  This limitation constrains our comprehensive resolution at the probiotic strain level.  In this review, we summarized the effects of probiotics on gut microbiota balance and host health from a functional perspective.  The technical methods of functional probiotics identification were summarized from the technical point of view.  Furthermore, we introduced methods for microbial metagenome assembly to elucidate the associated progress and advantages and disadvantages of these approaches.  Finally, we highlight more advanced metagenomic assembly techniques that may help us assemble high-fidelity intestinal metagenomes, providing powerful tools for the identification of functional probiotics.

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Methyl donor micronutrients orchestrate lipid metabolism: The role of DNA methylation modification Li Han, Qiyu Tian, Qi Han, Yulong Yin, Jie Yin, Xingguo Huang 2026, 25(4): 1343-1358.  DOI: 10.1016/j.jia.2024.11.001 Abstract ( )   PDF in ScienceDirect   DNA methylation, a key epigenetic modification, plays a crucial role in regulating lipid metabolism.  Consistent correlations have been observed between aberrant DNA methylation patterns and lipid metabolic disorders.  Emerging evidence indicates that methyl donor micronutrients could influence DNA methylation patterns, consequently exerting an influence on lipid metabolism.  Specifically, the deficiency or excesses of methyl donor micronutrients (folate, choline, betaine, B vitamins and methionine) have been associated with altered DNA methylation patterns linked to lipid metabolism.  These alteration in DNA methylation levels, occurring globally and within promoter regions, could affect gene expression related to lipid metabolism.  However, the mechanisms through which methyl donor micronutrients regulate lipid metabolism via the DNA methylation modification and the role of methyl donor micronutrients supplementation on DNA methylation profiles remain unclear.  In this review, we summarized the regulatory role of DNA methylation in lipid metabolism, and highlighted recent findings investigating the impact of methyl donor micronutrients on lipid metabolism, as well as DNA methylation-mediated adipogenesis and adipose deposition.  Taken together, this review deepened our understanding of how the complex interplay between methyl donor micronutrients, DNA methylation, and lipid metabolism, and provides valuable information for accurately regulating lipid metabolism of livestock and poultry, thereby improving meat quality, and promoting the development of animal husbandry.

Crop Science

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Multi-trait genome-wide association studies reveal novel pleiotropic loci associated with yield and yield-related traits in rice Chunhai Liu, Chao Wu, Zheming Yuan, Bingchuan Tian, Peiyi Yu, Deze Xu, Xingfei Zheng, Lanzhi Li 2026, 25(4): 1359-1372.  DOI: 10.1016/j.jia.2024.07.026 Abstract ( )   PDF in ScienceDirect   Rice yield is a complex trait affected by many related traits.  Traditional single-trait genome-wide association studies (GWAS) have limitations when studying complex traits, as they cannot account for the genetic relationships among multiple traits.  Multi-trait GWAS can consider the relationships among multiple traits and identify pleiotropic loci, so it is more suitable for complex traits such as rice yield than single-trait GWAS.  In this study, we conducted a multi-trait GWAS on 11 two-trait combinations of yield and yield-related traits with 575 hybrid rice varieties across two environments.  All these yield-related traits showed significant genetic correlations with yield (YD), including filled grains per panicle (FGPP), 1,000-grain weight (KGW), tillers per plant (TP), primary branch number (PB), secondary branch number (SB), and main panicle length (MPL).  In total, we identified 44 pleiotropic quantitative trait loci (pQTLs), including 29 new pQTLs not found in a single-trait GWAS.  We then screened 23 pQTLs showing common effects in two traits as key pQTLs.  These key pQTLs were subsequently analyzed by haplotype analysis, which identified 13 pleiotropic candidate genes.  Finally, we identified two optimal yield-enhancing allele combinations by pyramiding the superior haplotypes: GS3-GL3.1-OsCIPK17 for the YD-KGW combination and GNP12 for the YD-FGPP and YD-SB combinations.  This study provides pleiotropic candidate genes and allele combinations that exhibit superior differences in both yield and yield-related traits, offering valuable information for future high-yielding rice breeding.

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High-resolution mapping through whole-genome resequencing identifies two novel QTLs controlling oil content in peanut Nian Liu, Huaiyong Luo, Li Huang, Xiaojing Zhou, Weigang Chen, Bei Wu, Jianbin Guo, Dongxin Huai, Yuning Chen, Yong Lei, Boshou Liao, Huifang Jiang 2026, 25(4): 1373-1383.  DOI: 10.1016/j.jia.2024.08.028 Abstract ( )   PDF in ScienceDirect   Increasing the oil content is a key objective in peanut breeding programs.  Accurate identification of quantitative trait loci (QTLs) with linked markers for oil content can facilitate marker-assisted selection for high-oil breeding.  In this study, a high-density bin map was constructed by resequencing a recombinant inbred line (RIL) population (ZH16×J11) consisting of 295 lines.  The bin map contained 4,212 loci and had a total length of 1,162.3 cM.  Ten QTLs for oil content were identified in six linkage groups.  Notably, two of these QTLs, qOCB03.1 and qOCB06.1, were consistently detected in a minimum of three environments and explained up to 13.62% of the phenotypic variation.  They have not been reported in previous studies and thus are novel QTLs.  The combination of favorable alleles from qOCB03.1 and qOCB06 in the RIL population could increase oil content across multiple environments from 1.50 to 2.46%.  Two insertions/deletions (InDels) markers linked to qOCB03.1 and qOCB06.1 were developed, and their association with oil content was validated in another RIL population (ZH10×ICG12625) with diverse phenotypes.  In addition, the high-resolution map allowed for the precise positioning of qOCB03.1 and qOCB06.1 within a 1.77 Mb interval on chromosome B03 and a 1.51 Mb interval on chromosome B06, respectively.  The annotation of genomic variants, analysis of transcriptome sequencing, and evaluation of the allelic effects in 292 peanut varieties revealed two candidate genes associated with oil content for each of the two QTLs.  The candidate genes identified in this study can enable the map-based cloning of key genes controlling oil content in peanut.  Furthermore, these novel and stable QTLs and their tightly linked markers are valuable for marker-assisted breeding for greater oil content in peanut.

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The mitochondrial genes orf113b and orf146 from Xinjiang wild rapeseed cause pollen abortion in alloplasmic male sterility Man Xing, Bo Hong, Chunyun Guan, Mei Guan 2026, 25(4): 1384-1401.  DOI: 10.1016/j.jia.2024.09.018 Abstract ( )   PDF in ScienceDirect   Nsa CMS is a type of cytoplasmic male sterility (CMS) in rapeseed that originated from the cross between Xinjiang wild rapeseed (Sinapis arvensis) and Xiangyou 15 (Brassica napus L.).  Although this CMS variant shows promising applications, the factors contributing to its sterility and their underlying mechanisms remain unclear.  To the best of our knowledge, we successfully assembled and analyzed the mitochondrial genome of 1258A (Nsa CMS) for the first time.  This mitochondrial genome spans 263,010 bp and contains 91 genes, including 33 protein-coding and 36 orf genes.  Our analysis identified a novel mitochondrial gene, orf113b, and a mutated, truncated gene, orf146, both likely linked to the sterility observed in 1258A.  ORF113b and ORF146 were found to impede cell growth, disrupt gene expression associated with complexes I, III, and V of the mitochondrial oxidative phosphorylation pathway, and trigger reactive oxygen species (ROS) production.  In addition, transcriptome data analysis revealed key nuclear genes co-expressed with orf113b and orf146, suggesting that their aberrant expression may be influenced by retrograde signaling from the mitochondria.  This signaling could lead to atypical programmed cell death (PCD) in the tapetum layer, resulting in pollen sterility.  In conclusion, our study not only provides the first characterization of the Nsa CMS mitochondrial genome but also identifies orf113b and orf146 as crucial for pollen sterility.  Furthermore, it suggests that the ROS induced by these mitochondrial genes may play a central role in the abnormal regulation of nuclear genes essential for pollen development, thus offering new insights into the molecular mechanisms underlying Nsa CMS.

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Proteomic investigation reveals the molecular mechanisms of plant height regulation in foxtail millet Zhiying Zhao, Wanting Li, Yifei Wang, Meng Jin, Wenqiang Tang, Jiayi Li, Renliang Zhang, Yaxian Zhang, Peiyong Xin, Jinfang Chu, Yingjie Gao, Sha Tang, Xianmin Diao, Baowen Zhang 2026, 25(4): 1402-1417.  DOI: 10.1016/j.jia.2024.06.014 Abstract ( )   PDF in ScienceDirect   Plant height is an essential characteristic of agronomic traits, and an ideal plant height is essential for achieving high crop yields.  Foxtail millet (Setaria italica) has become a novel diploid C4 model crop.  The proteomic profiles of the internode, node, and leaf in two foxtail millet varieties with different heights, Ci846 and Yugu 18, were investigated at the jointing stage in this study.  There were different degrees of enrichment in various processes, such as plant hormone signal transduction, the MAPK signaling pathway, and others.  In particular, the proper content of auxin could activate downstream SiARFs-SiSAURs expression, which enhances the length of internodes.  Haplotype analysis of SiSAUR-like revealed two differential haplotypes of associated plant height, Hap1 and Hap2.  The molecular marker SiSAUR-like-FCM1-2 can effectively separate materials into Hap1 and Hap2.  Two additional genes, designated SiGH3 and SiTCH4, were found to be associated with plant height regulation.  In conclusion, this study not only uncovers the crucial role of auxin regulators in modulating plant height during the jointing stage but also provides molecular markers that will be invaluable for molecular breeding efforts.  The findings of this research help to elucidate the molecular mechanisms of plant height determination that can be used for crop variety innovation and breeding.

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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 Abstract ( )   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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Nitrogen redistribution during the grain-filling stage and its correlation with senescence and TaATG8 expression in leaves of winter wheat Guoming Li, Xiaotian Ren, Shengyan Pang, Changjie Feng, Yuxi Niu, Yanjie Qu, Changhong Liu, Xiang Lin, Dong Wang 2026, 25(4): 1433-1442.  DOI: 10.1016/j.jia.2024.12.024 Abstract ( )   PDF in ScienceDirect   Nitrogen is a key nutrient for wheat (Triticum aestivum L.) growth and yield, particularly during the grain-filling stage, where most nitrogen is redistributed from vegetative organs to the grain, significantly influencing yield.  However, it remains unclear during which period the nitrogen translocation from the vegetative phase to grain maturation occurs and how it correlates with flag leaf senescence.  In this study, a field experiment was conducted using the winter wheat cultivar ‘Xinong 511’ under two nitrogen fertilizer treatments: regular nitrogen supply (240 kg ha–1 (N240)) and no nitrogen supply (0 kg ha–1 (N0)).  The results revealed that nitrogen accumulation in wheat flag leaves peaked at 7–14 days, with a nitrogen content 4.55%, after which nitrogen was redistributed to the grains.  Nitrogen content in flag leaves decreased by 56% during 21–35 days, while that in the grains increased by 51%.  The plant analysis development value (relative chlorophyll content), photosynthetic rate, free amino acid concentration, and soluble protein content in flag leaves peaked at 7–14 days, indicating nitrogen transportation from the flag leaves to the grains.  Nitrogen application significantly increased the nitrogen remobilization rate in flag leaves by 20% compared with that of N0, reduced reactive oxygen species accumulation by 21%, and delayed flag leaf senescence.  Under nitrogen deficiency, autophagy was induced earlier, with a 5–7-fold increase in the expression of autophagy-related genes (TaATG8), suggesting that regulation of the autophagy pathway and enhancement of autophagy activity can optimize nitrogen fertilization.  Our study demonstrates that the remobilization of nitrogen from vegetative parts to grains initiates leaf senescence and is closely correlated with the expression of autophagy-related genes.

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Dense planting and nitrogen fertilizer management improve drip-irrigated spring maize yield and nitrogen use efficiency in Northeast China Guoming Li, Xiaotian Ren, Shengyan Pang, Changjie Feng, Yuxi Niu, Yanjie Qu, Changhong Liu, Xiang Lin, Dong Wang 2026, 25(4): 1443-1450.  DOI: 10.1016/j.jia.2024.09.032 Abstract ( )   PDF in ScienceDirect   Farmers in China often use nitrogen (N) fertilizers to ensure adequate crop growth.  However, inappropriate applications have increased the risk of environmental pollution, lowered maize yields, and reduced profits for farmers.  Proper N fertilizer management is crucial for improving yield and nitrogen use efficiency (NUE).  This study conducted a three-year experiment involving nine N treatments (0, 45, 90, 135, 180, 225, 270, 315, and 360 kg ha–1) on a field under nitrogen fertilizer precision management (NFPM) in Northeast China.  The results were compared with studies published within the past decade that analyzed yield and dry matter (DM) content under two management practices in Northeast China: conventional nitrogen fertilization management (CNFM) and water-saving fertilization management (WSFM).  The findings reveal that maize yield increases with rising N application rates up to 270 kg ha–1, after which yield decreases.  The kernel number (KN) and kernel weight (KW) of maize grown under NFPM were 13.7 and 14.7% higher than those grown under WSFM, respectively.  Furthermore, they surpassed crops grown under CNFM by 38.4 and 21.2%, respectively.  The maximum total yield of the NFPM treatment was 41.8 and 78.8% higher than under WSFM and CNFM, respectively.  In addition, compared with CNFM and WSFM, NFPM significantly increased NUE across the various N-level treatments.  Optimizing nitrogen management can help farmers to achieve higher yields and promote sustainable agricultural development.

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Cultivar mixtures of maize enhance grain yield and nitrogen use efficiency by promoting canopy photosynthetically active radiation and root growth Xucun Jia, Fuli Li, Zhengyan Miao, Xiaoyong Li, Leikang Sun, Yuepeng Wei, Kangna Yang, Hangzhao Guo, Rui Song, Haipeng Shang, Xianli Feng, Yuxia Li, Rongfa Li, Qun Wang 2026, 25(4): 1451-1462.  DOI: 10.1016/j.jia.2024.11.002 Abstract ( )   PDF in ScienceDirect   Cultivar mixtures increase crop diversification and grain yield stability.  Achieving high grain yield and nitrogen use efficiency (NUE) with environmentally friendly practices is a major challenge, but it is currently unclear whether maize cultivar mixtures can improve NUE.  A two-year field experiment was conducted using two maize cultivars with different roots angles and leaf angles planted in monoculture or in mixtures under four nitrogen levels N0 (0 kg N ha–1), N140 (140 kg N ha–1), N280 (280 kg N ha–1) and N340 (340 kg N ha–1).  Cultivar mixtures significantly increased light interception of the middle canopy, dry matter accumulation and total root length under N0, N140, and N280 conditions.  Light interception of the middle canopy was positively related to dry matter accumulation and thus increased grain yield.  In addition, light interception of the whole canopy was positively related to total lateral root length, while the greater total lateral root length of outer nodal roots significantly improved nitrogen accumulation and NUE.  Thus, cultivar mixtures promoted an optimal canopy structure and good root growth, thereby improving grain yield and NUE.  These findings deepen our understanding of the facilitating effect of canopy structure and root traits of cultivar mixtures on the combined promotion of grain yield and NUE.

Horticulture

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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 2026, 25(4): 1463-1474.  DOI: 10.1016/j.jia.2025.11.011 Abstract ( )   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 metabolomic analyses 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 assays indicated SlMYB32 could bind to and repress promoter activities of SlPAL6 and Sl4CL3.  Expression of 27 transcription factors belonging to 12 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.

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The TEI (Tomato Elongated Internode) gene encodes a GA20ox protein conferring internode elongation in tomato Xinyi Jia, Hexuan Wang, Chunying Feng, Xinyi Zhang, Guohao Yang, Ping Zhang, Qingjun Fu, Te Wang, Jingfu Li, He Zhang, Jingbin Jiang, Ke Wen, Xiangyang Xu, Huanhuan Yang 2026, 25(4): 1475-1487.  DOI: 10.1016/j.jia.2025.12.055 Abstract ( )   PDF in ScienceDirect   The ideal plant architecture is a critical factor in achieving high yields in tomato (Solanum lycopersicum) cultivation.  The length and number of internodes directly influence plant height.  Therefore, investigating the regulatory mechanisms of internode morphology is essential for the genetic enhancement of tomatoes.  We identified a naturally occurring field mutant, tomato elongated internode (tei), characterized by longer internodes and darker leaf color.  Physiological hormone and microscopic studies revealed that, compared to wild-type (WT) plants, the tei mutant exhibited increased endogenous GA3 levels, enhanced photosynthetic capacity, and elongation of stem internode cells.  RNA-seq analysis results of tei and WT indicated enrichment in the gibberellin pathway.  We employed BSA-seq for mapping analysis on tei, WT, and F2 populations, leading to the fine mapping of the candidate gene designated as TEI (Tomato Elongated Internode).  This gene encoded a gibberellin 20 oxidase (GA20ox) protein and was identified as Solyc09g042210.  Additionally, we discovered numerous SNPs and InDel mutations in the TEI promoter region, with expression levels of TEI in tei stems significantly higher than those in WT.  Furthermore, knocking out the TEI gene eliminated its role in elongating internodes.  We proposed that TEI serves as the primary effector gene regulating the internode elongation phenotype associated with tei.  This discovery offered researchers a novel target for enhancing crop plant varieties by modulating gibberellin homeostasis, ultimately contributing to the breeding of superior tomato varieties.

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Increasing fruit weight and altering flavour of pitaya by supplementing blue light during fruit growth Qingming Sun, Juncheng Li, Satish Kumar, Ran Yao, Honghua Su 2026, 25(4): 1488-1500.  DOI: 10.1016/j.jia.2025.11.034 Abstract ( )   PDF in ScienceDirect   Supplemental light is often used in fruit production, but few studies have been conducted on pitaya.  In this study, supplemental blue light was applied to pitaya for four hours each night in the field from flowering to fruit ripening to examine changes in peel and pulp physicochemical parameters and metabolites.  Blue light treatment significantly increased fruit weight, improved fruit firmness by increasing pectin content and retarding hemicellulose degradation, and enhanced antioxidant enzyme activity.  Blue light had minor effects on primary metabolites but more pronounced effects on volatiles.  By affecting alanine, aspartate and glutamate metabolism, blue light treatment resulted in significant fruit growth, increased accumulation of bioactive ingredients in the peel, and significantly altered the accumulation of flavor-associated volatile compounds, such as organic acids, esters and terpenes in the pulp.  Our results provide an important reference for improving the yield and quality of pitaya production using supplemental light in the field.

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Transcriptomic changes and VvMYBPA1 function analysis reveal the molecular mechanism of drought tolerance in grapevine Shuzhen Jiao, Yaping Huang, Shixiong Lu, Han Wang, Yanmei Li, Juan Mao, Baihong Chen 2026, 25(4): 1501-1518.  DOI: 10.1016/j.jia.2025.12.028 Abstract ( )   PDF in ScienceDirect   Drought stress negatively affects grapevine growth and development.  Grafting with rootstock is widely used to improve the quality of grape fruits and confer drought stress tolerance, but the underlying genetics and regulatory mechanisms are unclear.  Hence, we investigated the physiologic and transcriptomic profiles in the leaves of grafted SM/1103P (SM shoot/1103P root) and self-rooted SM (‘Shine Muscat’) as well as roots of grafted SM/1103P and self-rooted 1103P under drought stress conditions.  The results indicated that grafted grapevine effectively attenuated drought damage in grape leaves by increasing phytohormone levels and antioxidant enzyme activities, reducing H2O2 and MDA contents.  Transcriptomic profiling revealed a total of 11,855 and 11,197 differentially expressed genes (DEGs) were identified in grape leaves and roots respectively.  Weighted correlation network analysis (WGCNA) was performed based on the RNA-seq data, and five modules (greenyellow, black, turquoise, salmon and blue) were significantly correlated to drought stress.  Pathway analysis showed that DEGs were enriched in the plant hormone signal transduction and MAPK signaling pathway.  916 transcription factor genes (TFs) belonging to different gene families were detected that may participate in regulating the drought stress.  Quantitative real-time PCR (qRT-PCR) expression analysis of twelve drought stress responsive DEGs was used to verify the transcriptome data.  Furthermore, overexpression of VvMYBPA1 in Arabidopsis thaliana and grape callus tissues improved drought tolerance.  Our findings provided new insights into to the regulatory mechanism for improving grapevine adaptation to drought.

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Identification of CsAK as a critical caffeine-related upstream gene in tea accessions through genome-wide association study Kaixin Rao, Yuting Ouyang, Yanjun Chen, Xiaojing Wang, Ting Liu, Qinfei Song, Shaojuan Zhang, Biao Xiong, Suzhen Niu 2026, 25(4): 1519-1530.  DOI: 10.1016/j.jia.2025.06.026 Abstract ( )   PDF in ScienceDirect   Caffeine (CAF), a primary flavor component in tea, is one of the main reasons for the popularity of tea beverages.  As an important secondary metabolite in tea plants, the CAF content varied greatly among different tea accessions.  However, the genetic mechanisms underlying the CAF biosynthesis were still unclear.  In this study, we performed a genome-wide association study (GWAS) on 359 tea accessions in the Guizhou Plateau to identify genetic variation associated with CAF content.  A total of 19 significant single nucleotide polymorphisms (SNPs) and key gene (CsAK) involved in CAF biosynthesis were identified.  Subcellular localization revealed that the CsAK-GFP fusion protein was located on the cell membrane.  Antisense oligodeoxynucleotide (AsODN) targeting the CsAK gene to the buds and leaves revealed that the expression levels of the CsAK gene were significantly reduced, and the corresponding CAF content was also decreased in AsODN-treated tea plants.  Overexpression of the CsAK gene in eukaryotic cells resulted in the accumulation of key intermediate product (L-methionine) during CAF biosynthesis process.  These findings offered a theoretical foundation for future tea breeding programs aimed at cultivating excellent germplasm with high or low levels of CAF.

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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 2026, 25(4): 1531-1543.  DOI: 10.1016/j.jia.2025.11.002 Abstract ( )   PDF in ScienceDirect   Floral scent is an important ornamental trait in garden plants.  Monoterpenes, a major class of terpenoids, constitute the primary volatile components of lily floral scents.  1-Deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the second enzymatic step in the MEP pathway, which supplies precursors for monoterpene biosynthesis.  However, the functional role of the DXR gene in floral monoterpene production in Lilium Oriental Hybrid ‘Sorbonne’ remains unclear.  In this study, ‘Sorbonne’ was used as the experimental material, and a differentially expressed LiDXR gene was identified from early transcriptomic data, showing high temporal correlation with the synthesis and emission dynamics of floral volatiles during flowering.  The LiDXR gene was cloned and subjected to bioinformatics analysis, revealing that it encodes a protein of 472 amino acids.  LiDXR expression peaked at the half-open floral stage and was significantly higher in petals than in other floral organs.  Subcellular localization analysis indicated that the LiDXR protein is targeted to chloroplasts in leaf epidermal cells.  VIGS of LiDXR reduced monoterpene levels by downregulating the expression of downstream TPS genes in the MEP pathway.  Consistently, headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) revealed a significant decrease in total volatile terpene content in silenced lilies.  Transgenic Arabidopsis thaliana and petunia plants overexpressing LiDXR exhibited enhanced growth vigor and accelerated flowering.  GC-Murashige and Skoog’s (MS) analysis of transgenic petunias showed a 78% increase in total volatile terpenes compared to wild-type plants.  Overexpression of LiDXR also modulated the expression of other MEP pathway genes, thereby influencing the biosynthesis of downstream terpenoids, including monoterpenes.  This study elucidates the functional role of LiDXR in terpenoid metabolism and provides a theoretical foundation for floral scent breeding in lily and other ornamental plants.

Plant Protection

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Elucidating the mechanisms of Fusarium oxysporum f. sp. tuberosi inhibition using functionalized multi-walled carbon nanotubes: A comprehensive analysis of biophysical and molecular interactions Sadia Manzoor, Asma Irshad, Saira Azam, Ijaz Ali, Ayesha Latif, Abdul Qayyum Rao, Samina Hassan, Ahmad Ali Shahid, Muhammad Danish Ali, Ameni Brahmia 2026, 25(4): 1544-1555.  DOI: 10.1016/j.jia.2024.07.010 Abstract ( )   PDF in ScienceDirect   The study explores the antifungal properties of functionalized multi-walled carbon nanotubes (f-MWCNTs) against Fusarium oxysporum f. sp. tuberosi, revealing a concentration-dependent impact, with the lowest concentration suppressing mycelial development.  The peaks at 2θ°=7.92° and 25.85° reveal the presence of MWCNTs.  Furthermore, the bonding extremes at 3,194 and 2,441 cm–1 and the peak at 3,573 cm–1 are hydrogen-bonded.  The peak at 3,756 cm–1 demonstrates the vibration of OH stretching to confirm the functionalization of MWCNTs.  MWCNTs at 308 nm show a peak with much higher UV energy.  This is because of the different plasmonic vibrations that the free electrons of multi-wall carbon nanotubes exhibit at about 308 nm.  Scanning electron microscope (SEM) analysis revealed mycelial structure distortions, revealing inhibitory mechanisms of f-MWCNTs and their interaction with F. oxysporum f. sp. tuberosi, providing insights into their complex behavior.  Multi-walled carbon nanotubes (MWCNTs) showed anti-oxidative properties, indicating potential multifaceted modes of action, as evidenced by 2´,7´-dichlorofluorescein diacetate dye testing.  The current study analyzed bioactive molecules in F. oxysporum f. sp. tuberosi extracts by gas-chromatography-mass spectrometry (GC-MS) analysis, showing six metabolites having antimicrobial, cytotoxic, and antioxidant properties.  However, exposure to f-MWCNTs reduced these potent molecule concentrations, highlighting the significant impact of f-MWCNTs on F. oxysporum f. sp. tuberosi biochemical arsenal.  This is the first report that checked the antifungal, and antioxidant activity and of a lesser concentration of metabolites produced after the action of f-MWCNTs in F. oxysporum f. sp. tuberosi.  This research highlights the potential of f-MWCNTs as antifungal agents, paving the way for innovative strategies in combating fungal pathogens and developing effective treatments.

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A Fusarium pseudograminearum secreted protein, Fp00392, is a major virulence factor during infection and identified as a PAMP Qian Yang, Jing Wang, Jixiang Sun, Sijing Gao, Hang Zheng, Yuemin Pan 2026, 25(4): 1556-1565.  DOI: 10.1016/j.jia.2025.02.030 Abstract ( )   PDF in ScienceDirect   As a main causal agent of wheat crown rot, Fusarium pseudograminearum secrets numerous proteins into the host during the infection process to regulate host immune responses and contribute to the virulence of F. pseudograminearum.  In this study, the secreted protein Fp00392 from F. pseudograminearum was found to trigger cell death in Nicotiana benthamiana.  Purified Fp00392 protein could activate the ROS burst, callose deposition, and the upregulation of defense-related genes in N. benthamiana.  Moreover, the VIGS assay in N. benthamiana showed that Fp00392-triggered cell death is independent of BAK1 and SOBIR1.  Furthermore, the transcript level of Fp00392 was significantly induced during F. pseudograminearum infection.  Knockout of Fp00392 significantly attenuated the pathogenicity of F. pseudograminearum on wheat coleoptiles.  Deletion of Fp00392 affected the sensitivity of F. pseudograminearum to H2O2 and Congo Red.  Overall, these results indicate that Fp00392 can not only induce plant immune response as a PAMP, but it can also promote F. pseudograminearum infection as a virulence factor.

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A novel effector of Aphelenchoides besseyi, AbPFN3, interacts with multiple host proteins to facilitate parasitic nematode and sustain infection in rice Xin Huang, Yuankai Chi, Wei Zhao, Wenkun Huang, Deliang Peng, Rende Qi 2026, 25(4): 1566-1574.  DOI: 10.1016/j.jia.2024.08.013 Abstract ( )   PDF in ScienceDirect   The rice white tip nematode (RWTN) Aphelenchoides besseyi secretes effectors that manipulate host plant cells to facilitate successful parasitism and sustain infection.  Although the number of identified RWTN effectors remains limited, their mechanisms of interaction with host plants are largely unknown.  Profilins (PFNs) function as molecular hubs that regulate complex interaction networks.  To advance understanding of PFN3 in plant-parasitic nematodes, we identified an effector from A. besseyi, designated AbPFN3.  AbPFN3 is transcriptionally upregulated during the juvenile stage of the nematode, and in situ hybridization localized its expression to the esophageal glands.  Three rice (Oryza sativa) proteins, ADP/ATP carrier protein 1 (OsAAC1), B-cell receptor-associated protein 31 (OsBAP31) and Small Auxin Up RNA 50 (OsSAUR50), were identified as interactors of AbPFN3, with interactions occurring in distinct cellular compartments, including the endoplasmic reticulum, cytoplasm, and plasma membrane.  Transgenic analyses revealed that AbPFN3 expression significantly increased plant height and upregulated AAC1 and BAP31, while downregulating RGA2 and SAUR50.  This study characterizes AbPFN3 as a novel effector secreted by A. besseyi that interacts with multiple host proteins, highlighting its potential role in modulating host defense responses and cell development processes.

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Field identification of cowpea variety resistance against Megalurothrips usitatus and the metabolomics-based resistance mechanism Yunchuan He, Yang Gao, Qiulin Chen, Zheyi Shi, Hainuo Hong, Jiamei Geng, Ying Zhou, Zengrong Zhu 2026, 25(4): 1575-1585.  DOI: 10.1016/j.jia.2025.05.007 Abstract ( )   PDF in ScienceDirect   Megalurothrips usitatus causes significant economic losses in the regional cowpea industry in Hainan Province, China.  However, reports on M. usitatus-resistant varieties remain limited globally.  To address this gap, this study assessed the resistance of 210 cowpea germplasm resources through field experiments over two consecutive years, and comprehensively investigated the resistance mechanism of a selected resistant variety against M. usitatus.  Physiological measurements revealed that the resistant variety IZJU0044 had higher levels of total flavonoids and tannins, as well as lipoxygenase and β-1,3-glucanase activities, both before and after thrips feeding.  Thrips feeding stimulated flavonoid biosynthesis in cowpea flowers, and the contents of both constitutive and inducible luteolin in the resistant variety IZJU0044 were higher than those in the susceptible variety IZJU0120.  Laboratory toxicity tests confirmed the lethal effect of luteolin on thrips.  Moreover, thrips feeding strongly induced luteolin synthesis-related genes (chalcone isomerases, CHIs) in IZJU0044, indicating that luteolin likely conferred higher resistance to M. usitatus.  This study provides a theoretical basis for using thrips-resistant varieties in cowpea molecular breeding programs.

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Monitoring agricultural arthropod diversity by eDNA metabarcoding from plant cleaning fluid Xiaoxiao Song, Cong Dang, Ran Li, Fang Wang, Hongwei Yao, David W. Stanley, Gongyin Ye 2026, 25(4): 1586-1596.  DOI: 10.1016/j.jia.2025.07.014 Abstract ( )   PDF in ScienceDirect   Arthropods serve essential roles in crop production as pollinators, predators, and pests.  Understanding arthropod biodiversity is crucial for assessing agroecosystem health, functions, and services.  Traditional survey methods are labor-intensive, costly, and rely on diminishing taxonomic expertise, limiting their agricultural applications.  Environmental DNA (eDNA) metabarcoding of diverse samples provides comprehensive species composition data through efficient and non-invasive sampling.  However, this method remains underutilized in rice field studies.  This research examined four sample substrates - rice plant cleaning fluid (RPCF), rice pollen, soil, and water - using various barcoding primers to identify optimal substrates for monitoring rice paddy arthropod diversity.  The method was implemented in Bt rice and non-Bt rice fields to evaluate its biomonitoring potential.  Results indicate that the COI primer (mlCOIintF/jgHCO2198R) identified the highest number of rice field arthropod species.  The eDNA collected from RPCF detected 15% more arthropod species compared to vacuum sampling of whole arthropods.  Rice pollen collection during the heading stage also revealed considerable arthropod diversity.  Alpha diversity and taxonomic composition remained consistent between Bt and non-Bt rice fields, aligning with traditional survey findings.  These results suggest that eDNA metabarcoding of plant cleaning fluid offers an effective approach for monitoring agricultural arthropod communities, contributing to agricultural production optimization.

Animal Science · Veterinary Medicine

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Rapid on-site genotyping of the ovine prolific FecBB mutation using a CRISPR/Cas12a-based detection system Tingjie Wu, Jiayuan Sun, Lijin Lu, Chen Wang, Shiwei Zhou, Yulin Chen, Xinjie Wang, Xiaolong Wang 2026, 25(4): 1597-1605.  DOI: 10.1016/j.jia.2024.05.013 Abstract ( )   PDF in ScienceDirect   BMPR1B is a pivotal gene that influences reproductive performance in sheep.  The sheep populations that carry the FecBB mutation within this gene exhibit significantly higher lambing rates compared to wild-type populations.  Therefore, screening for individuals carrying the FecBB mutation is crucial for effective sheep breeding programs.  This study aims to establish a rapid, precise, and visualised on-site detection method for genotyping the prolific FecBB mutation in sheep.  We combined the CRISPR/Cas12a system with the recombinase-polymerase amplification (RPA) technique.  We introduced an additional nucleotide mismatch on the amplification primers to form a Cas12a-recognised protospacer adjacent motif (PAM) sequence.  In addition, mismatches were introduced in CRISPR-derived RNA (crRNA) to enable naked-eye differentiation of the assay results.  Subsequently, we validated the accuracy of the method by examining additional blood samples from 56 sheep representing four breeds.  The results of using our developed system were highly consistent with the Sanger sequencing.  Overall, the CRISPR/Cas12a-based detection provides a rapid and more versatitle method for FecBB genotyping.  It holds promise in enhancing efficiency in livestock breeding programmes for any single nucleotide mutations.

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Multi-omic analysis for dietary supplementation of different ratios of soluble and insoluble fiber on intestinal microbiota, metabolites and inflammation of weaned piglets Yetong Xu, Chengyu Zhou, Yingying Lu, Xutong Guo, Minyue Zong, Junwei Zhu, Pan Zhou, Jiaman Pang, Xie Peng, Zhihong Sun 2026, 25(4): 1606-1618.  DOI: 10.1016/j.jia.2025.05.013 Abstract ( )   PDF in ScienceDirect   Different types of dietary fiber (DF) play important roles in enhancing intestinal health and overall performance in animals.  This study investigated the effects of high-DF diets containing different ratios of soluble to insoluble dietary fiber (SDF:IDF) on growth performance, intestinal barrier integrity, microbiota, and metabolite profiles in weaned piglets.  The four dietary treatments consisted of a basal diet (CON) and three high-DF diets with SDF:IDF ratios of 0.37, 0.25, and 0.13 (designated HF-0.37, HF-0.25, and HF-0.13, respectively).  On days 14 and 28, colonic tumor necrosis factor-α, interleukin-1β, interleukin-6, and interleukin-8 concentrations were higher in the HF-0.37 group than in the CON, HF-0.25, and HF-0.13 groups (P<0.05).  Plasma D-lactate and endotoxin levels were lower in the HF-0.25 group compared to the CON group at both time points (P<0.05).  Furthermore, colonic zonula occludens 1 expression was upregulated in the HF-0.25 and HF-0.13 groups compared to the CON and HF-0.37 groups on day 14 (P<0.05).  At the transcriptional level, all three high-DF diets modulated signaling pathways associated with inflammation and immune responses in the colon.  Notably, DF supplementation particularly the HF-0.25 diet upregulated colonic levels of 3-indole butyric acid, nicotinic acid, and 3-methylthiopropylamine on d 14 and reduced certain peptide levels by d 28.  These findings indicate that DF supplementation, especially at an SDF:IDF ratio of 0.25, exerts beneficial effects on intestinal integrity in weaned piglets, potentially mediated by alterations in colonic metabolite profiles, whereas HF-0.37 and HF-0.13 exhibited limited impacts on intestinal barrier function.

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Dietary β-hydroxybutyrate sodium alters rumen microbiome and nutrient metabolism in the rumen epithelium of young goats Yimin Zhuang, Guanglei Liu, Chuyun Jiang, Mahmoud M ABDELSATTAR, Yuze Fu, Ying Li, Naifeng Zhang, Jianmin Chai 2026, 25(4): 1619-1635.  DOI: 10.1016/j.jia.2024.11.016 Abstract ( )   PDF in ScienceDirect   The role of β-hydroxybutyric acid (BHBA) includes providing energy, regulating signaling pathways, and ameliorating the gut microbiota in the host, while its nutrient mechanism to improve rumen epithelium development in young ruminants is still unclear.  In this study, a total of 12 female Haimen goats with 30 d of age were chosen and divided into two groups.  One group was fed with basic diet (CON), and the other group was fed a basal diet supplemented with 6 g d–1 dietary β-hydroxybutyrate sodium (BHBA-Na).  The experimental period was 30 d, and all goats were slaughtered at 60 d of age.  The joint analysis of multi-omics, including rumen microbiota, rumen epithelial transcriptome and rumen epithelial metabolomics in young goat model, was performed to systematically investigate the effect of dietary BHBA-Na on rumen development in young goats.  As the results, we found that dietary BHBA-Na improved the growth performance of young goat including body weight, average daily gain (ADG) and dry matter intake (DMI) (P<0.05).  Dietary BHBA-Na also increased the weight of rumen, and promoted the growth of rumen epithelium development (P<0.05).  The abundance of several beneficial bacteria was increased (Fibrobacter, Succinivibrio, Clostridiales, etc.).  The rumen epithelium transcriptome and metabolomics indicated that BHBA-Na supplementation showed a remarkable effect on the nutrient metabolism of the rumen epithelium.  Specifically, the pathways of “fatty acid metabolism”, “cholesterol homeostasis”, “reactive oxygen species (ROS) pathway” and “peroxisome” were activated in response to BHBA-Na addition (P<0.05).  Moreover, the genes (HMGCS2, ECSH1, ACAA2, ECH1, ACADS etc.) and metabolites (succinic acid, alpha-ketoisovaleric acid, etc.) involved in these pathways were also regulated positively (P<0.05).  The rumen epithelium obtained the energy for its development from the process of volatile fatty acids (VFAs) decomposition.  Finally, we observed the close correlations among the phenotypes, ruminal microbiota, host genes and epithelial metabolites.  Overall, our results revealed that the BHBA-Na promoted the growth and rumen development of young goats possibly by enhancing DMI and regulating the rumen microbiota and the metabolisms of VFA and amino acid in the rumen epithelium.

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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 Abstract ( )   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.

Agro-ecosystem & Environment

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Straw tissue quality influence the formation pathways of soil organic carbon via living microbes or microbial necromass in a Mollisols, Northeast China Qilin Zhang, Xiujun Li, Guoshuang Chen, Nana Luo, Shufeng Zhang, Ezemaduka Anastasia Ngozi, Xinrui Lu 2026, 25(4): 1647-1663.  DOI: 10.1016/j.jia.2025.09.020 Abstract ( )   PDF in ScienceDirect   Soil organic carbon (SOC), representing the largest terrestrial organic carbon pool, significantly influences soil quality.  The incorporation of residues is widely recognized as a method to regulate SOC sequestration.  A 365-day incubation experiment was conducted to evaluate the contribution of straw-derived carbon (SDC) of varying quality to SOC fractions (free-floating particulate organic carbon (fPOC), occluded POC (oPOC) and mineral-associated OC (MAOC)), and examine the relationships between microorganisms and SOC fractions by incorporating 13C-labelled maize stem straw (ST), leave straw (LE), sheath straw (SH) (1%) in Chinese Mollisols.  Results indicated that compared to control (CK), ST, LE and SH treatments enhanced SOC, fPOC and MAOC by 4.8–19.5, 35.7–49.5 and 1.6–3.9%, respectively.  The SDC-SOC and MAOC content of LE were 29.1–38.1% and 17.5–44.5% higher than ST and SH, respectively.  The SDC-oPOC content of SH was 3.1% higher than LE.  The PLFA concentration decreased steadily throughout the incubation period, while necromass remained in-fluctuating until an obvious increasing trend observed at later stage.  Furthermore, structural equation model (SEM) revealed that lignin to nitrogen ratio (LigN) of ST exhibited negative association with SDC-fPOC, and bacterial diversity in SH showed negative correlation with LigN and positive correlation with SDC-oPOC, while demonstrating positive correlation between microbial necromass and SDC-MAOC in LE.  These findings indicated that POC dynamics correlated with straw chemical traits, while MAOC showed links to both microbial necromass traits and straw chemical characteristics.  These findings advance our understanding of how straw residue quality influences SOC turnover and stabilization through microbial community interactions, contributing to the development of policies to improve soil fertility, and promote the rational and efficient utilization of straw.

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Biodegradable mulch films support root proliferation and yield in water-saving rice production Haihe Gao, Changrong Yan, Joann K. Whalen, Wenqing He, Hongjin Liu, Jixiao Cui, Daozhi Gong, Karen Mancl, Qin Liu, Xurong Mei 2026, 25(4): 1664-1674.  DOI: 10.1016/j.jia.2025.07.015 Abstract ( )   PDF in ScienceDirect   Water-saving rice systems must maintain yield targets while reducing water consumption. Applying biodegradable film to cover the soil surface reduces water loss through evapotranspiration, establishing a warmer, more humid microenvironment for rice growth compared to traditional paddy rice systems.  This study examined soil water regimes for rice production in Northeast China, comparing rice growth with and without biodegradable mulch film under continuous flooding, drip irrigation, and controlled irrigation conditions.  The implementation of biodegradable mulch film elevated soil temperature and sustained soil moisture during early rice development.  Continuous flooding with biodegradable mulch film yielded the highest rice production (9.4 Mg ha–1) and net profit of approximately 11,800 CNY ha–1.  Drip irrigation with biodegradable mulch film achieved maximum water efficiency, demonstrating the highest water productivity (1.25 kg m–3) and minimum water consumption (235 mm).  Root length, weight, and surface area in the 0–40 cm soil layer exhibited positive correlations with water productivity, shoot dry matter, and yield, indicating that root morphological characteristics, particularly during the panicle initiation stage, enhanced rice production and water conservation.  The findings demonstrate that biodegradable mulch film created favorable soil conditions for root proliferation, enabling higher yields in water-saving rice systems.

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Plant community micronutrients mediate the soil carbon stock by altering plant growth, reproduction and survival trade-offs Yi Zhou, Shenghua Chang, Xiaojuan Huang, Wenjun Wang, Fujiang Hou, Yanrong Wang, Zhibiao Nan 2026, 25(4): 1675-1686.  DOI: 10.1016/j.jia.2025.06.015 Abstract ( )   PDF in ScienceDirect   Despite the essential role of micronutrients in plant metabolic processes and carbon cycle, the mechanisms by which micronutrients regulate plant community traits remain poorly understood.  Here, we used a long-term experiment to explore the potential mechanisms of plant community micronutrients and traits along a precipitation gradient.  Our results showed that plants shifted toward lateral growth and asexual reproduction over time.  From 1985 to 2022, the plant community Fe content increased by 18.8% in the north but declined by 25.2% in the south of the typical steppe.  Furthermore, plant community growth and reproduction were sensitive to both micronutrient contents and uptake efficiencies in the north of the typical steppe.  While plant community Mn and Zn contents enhanced growth longitudinally, Zn and Fe uptake efficiencies hindered sexual reproduction.  Furthermore, soil moisture and GDP per capita were the key drivers of micronutrient variation in the north and south of the typical steppe, respectively.  Precipitation fluctuations primarily regulated community traits across all sites.  In the arid site, micronutrient-driven shifts in reproduction stabilized the soil carbon stock by balancing biomass allocation.  These findings can help us to better understand the coupling of plant micronutrients, traits, and soil carbon stocks, thereby providing the basis for a scientific grassland conservation strategy under global change scenarios.

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Improved selected soil properties predictions using MIR and pXRF sensor fusion Junwei Wang, Qi Zou, Huimin Yuan 2026, 25(4): 1687-1699.  DOI: 10.1016/j.jia.2025.09.028 Abstract ( )   PDF in ScienceDirect   The timely and accurate assessment of soil nutrient information is essential for ensuring global food security and sustainable agricultural development.  This study evaluated the individual and fusion performance of mid-infrared (MIR) and portable X-ray fluorescence (pXRF) spectroscopy for predicting selected soil properties.  Four sensor fusion strategies were implemented: direct concatenation (DC), feature-level fusion using stability competitive adaptive reweighted sampling (sCARS) and least absolute shrinkage and selection operator (LASSO) algorithms (sCARS-C and LASSO-C), multi-block fusion via sequential orthogonal partial least squares (SO-PLS), and Granger-Ramanathan model averaging (GRA) method to enhance prediction accuracy for 13 soil properties.  The findings revealed that single sensor models using either MIR or pXRF provided accurate estimations for soil organic matter (SOM), total nitrogen (TN), available phosphorus (AP), calcium (Ca), iron (Fe), manganese (Mn), and pH, but showed limitations for total potassium (TK), magnesium (Mg), copper (Cu), zinc (Zn), available potassium (AK), and total phosphorus (TP).  The DC model significantly improved predictions for Mg (Rp2=0.76, RMSEp=358.76 mg kg–1, RPDp=2.03) and TK (Rp2=0.75, RMSEp=775.96 mg kg–1, RPDp=2.00).  The LASSO-C model demonstrated superior prediction accuracy compared to the DC model for AP, AK, TP, Zn, Mn, and Cu, achieving optimal results for AP (Rp2=0.89, RMSEp=21.37 mg kg–1, RPDp=3.01) and Zn (Rp2=0.80, RMSEp=9.88 mg kg–1, RPDp=2.32).  This enhancement is attributed to LASSO's effective selection of feature information from the complete MIR and pXRF spectra.  The GRA models achieved the highest prediction accuracy for TP, pH, AK, and Cu, with Rp2 values of 0.80, 0.82, 0.82, and 0.65, RMSEp values of 129.21 mg kg–1, 0.13, 48.38 mg kg–1, and 3.87 mg kg–1, and RPDp values of 2.23, 2.34, 2.37, and 1.67, respectively.  For single-sensor applications, MIR spectra are recommended for predicting SOM, TN, and Ca (Rp2≥0.88, RPDp≥2.87), while pXRF is more cost-effective for measuring Ca, Fe, and Mn (Rp2≥0.80, RPDp≥2.22).  This research demonstrates the effectiveness of MIR and pXRF sensor fusion in enhancing soil nutrient assessment accuracy, particularly for available nutrients and micronutrients.

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Enhancing soil organic matter mapping in saline-alkali and black soil areas with prior knowledge and multi-temporal remote sensing Depiao Kong, Chong Luo, Huanjun Liu 2026, 25(4): 1700-1715.  DOI: 10.1016/j.jia.2025.06.003 Abstract ( )   PDF in ScienceDirect   Soil organic matter (SOM) monitoring using remote sensing is critical for effective land resource management and environmental protection.  Mapping SOM in areas where saline and black soils are intertwined, with complex soil types and significant environmental variability, remains a challenging task.  This study integrated prior knowledge and classified Jilin Province, China, into saline-alkali and black soil areas.  All available Sentinel-2 images from 2019 to 2023 during the bare soil period (April to July) were collected, and the images were categorized into three time windows: day of year (DOY) 90–120, DOY 120–150, and DOY 150–180.  The potentials of these time windows, spectral indices (salinity index and vegetation moisture index), environmental variables (topography and climate), and local regression models for SOM mapping in the saline-black soil transition areas were then systematically evaluated.  The results revealed four key findings: (1) the optimal time window for SOM mapping in both the saline-alkali area and black soil area was DOY 90–120; (2) including the salinity index improved SOM mapping accuracy in the saline-alkali area but reduced it in the black soil area, whereas the vegetation moisture index enhanced accuracy in both areas; (3) incorporating environmental variables improved the SOM mapping accuracy in all areas, with topographic variables being more influential in the black soil area and climatic variables being more significant in the saline-alkali area; and (4) local regression models based on the saline-alkali area and black soil area outperformed the global regression model in terms of SOM mapping accuracy, although they exhibited higher uncertainty.  This study demonstrates that the integration of prior knowledge and multi-temporal remote sensing images significantly enhance SOM mapping accuracy in areas where saline and black soils intersect, thus providing a scientific foundation for the precise management and protection of areas with different soil types.

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Monitoring of agricultural drought based on multi-source remote sensing data in Heilongjiang Province, China Chenfa Jiang, Changhui Ma, Sibo Duan, Xiaoxiao Min, Youzhi Zhang, Dandan Li, Xia Zhang 2026, 25(4): 1716-1730.  DOI: 10.1016/j.jia.2025.04.027 Abstract ( )   PDF in ScienceDirect   Agriculture is the foundation of socio-economic development and is highly influenced by weather and climate conditions.  Drought is one of the most significant threats to agricultural development and food security.  Currently, in-situ drought monitoring based on weather stations and based on remote sensing data has limitations, including infrequent updates, limited coverage, and low accuracy.  This study leverages multi-source remote sensing data to monitor agricultural drought in Heilongjiang Province, China.  We developed multi-source composite drought indices (MCDIs) at various timescales (3, 6, 9, and 12 months) by integrating precipitation, land surface temperature, soil moisture, and vegetation indices.  Utilizing remote sensing data from various sources, we calculated a series of single drought indices, which are the precipitation condition index, soil moisture condition index, vegetation condition index, and temperature condition index.  These are then integrated into MCDIs using a multivariable linear regression approach.  The analysis reveals that MCDIs correlate more with standardized precipitation evapotranspiration index (SPEI) than single drought indices.  When examining the correlation between different MCDIs and the affected area of crops and major grain production, MCDI-9 showed the highest correlation with the affected area of crops, while MCDI-12 showed the highest correlation with grain production.  This suggests that these two MCDIs at different timescales are better indicators of agricultural drought.  The spatio-temporal analysis of MCDI indicates that drought in Heilongjiang Province primarily occurs in early spring, gradually spreading from the Greater Khingan Mountains region to the southeastern plains.  The drought gradually alleviates during the summer, ending by the autumn harvest period.  Therefore, the MCDIs constructed in this study can serve as effective methods and indicators for drought monitoring in Heilongjiang Province and similar regions.

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Identification and fine mapping of the male sterility gene msgN13401 reveals defective pollen starch accumulation in barley Qi Liu, Zhidong Qi, Chaofan Li, Zhenghan Chen, Wenqian Liu, Baoshen Liu, Chaozhong Zhang, Jiajie Wu, Juan Qi, Fei Ni 2026, 25(4): 1731-1735.  DOI: 10.1016/j.jia.2025.12.077 Abstract ( )   PDF in ScienceDirect

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A rapid and visual detection method for porcine deltacoronavirus with single-copy sensitivity based on the CRISPR/Cas12a assay Zezhao Cao, Zi Li, Kaikai Jin, Zanheng Huang, Ruijie Hu, Junchao Shi, Huabo Yu, Gaili Wang, Wenqi He, Hualei Wang, Yungang Lan, Haili Zhang 2026, 25(4): 1736-1739.  DOI: 10.1016/j.jia.2025.07.030 Abstract ( )   PDF in ScienceDirect