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Note: The papers published below will continue to be available from this page until they are assigned to an issue. To see an article, click its [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Selected articles' button. To see one abstract at a time, click its [Abstract] link. Please wait a minute... For Selected: Download Citations EndNote Ris BibTeX Toggle Thumbnails Select Engineering an efficient tomato spotted wilt virus mini-replicon system for high-throughput antiviral compound discovery Xingwang Zhang, Nan Zhou, Yulong Yuan, Qinhai Liu, Tianyi Zhang, Shenghan Zang, Yangliu Dai, Baoyue Zhang, Jia Li, Min Zhu, Xiaorong Tao, Mingfeng Feng DOI: 10.1016/j.jia.2026.02.025 Online: 11 February 2026 Abstract （1）      PDF in ScienceDirect       Plant viral diseases pose a persistent threat to global agriculture, requiring efficient platforms for antiviral agent screening to ensure sustainable crop protection. Here, we developed a simplified mini-replicon reverse genetics (RG) system for tomato spotted wilt virus (TSWV) based on co-expression of SR(+)eGFP replicon and L(+)opt genome in the absence of viral suppressors of RNA silencing (VSRs). Using this system, we demonstrated that the movement protein NSm and M(-)opt genome significantly enhance both the replication and cell-to-cell movement of the TSWV mini-replicon. We further constructed a tandem expression vector (SR(+)eGFP-M(-)opt), and established a novel dual-vector-driven TSWV RG system. Notably, this system achieved 100% systemic infection efficiency without requiring any VSR. This is unprecedented for plant negative-strand RNA virus reverse genetics. This optimized system enabled the screening of antiviral agents, among which ribavirin, ningnanmycin, chitooligosaccharide, cellobiose, azadirachtin, and copper sulfate (CuSO4) potently inhibited TSWV infection. Our study provides a new RG manipulation tool for functional genomics of plant negative-strand RNA viruses (NSVs) and a powerful platform for high-throughput antiviral agents discovery. Reference | Related Articles | Metrics Select Mining genomic regions and candidate genes underlying QTL Qfcr.caas.7A-2 conferring Fusarium crown rot resistance in wheat via integrated GWAS and BSE-Seq analysis Peipei Wu, Hui Zhao, Minghe Wang, Ziming Wang, Ziyu Zhao, Xianrui Guo, Chunyan Mai, Huili Li, Liqiang Yu, Li Yang, Hongwei Liu, Yang Zhou, Hongjun Zhang DOI: 10.1016/j.jia.2026.02.024 Online: 11 February 2026 Abstract （1）      PDF in ScienceDirect       Fusarium crown rot (FCR), a major soil-borne disease caused by Fusarium species, threatens global wheat production. This study identified quantitative trait locus (QTL) for FCR resistance in wheat using genome-wide association study (GWAS) on a panel of 299 wheat cultivars/lines and bulked segregant exome sequencing (BSE-Seq) on a recombinant inbred line (RIL) population. Phenotypic evaluation revealed five wheat accessions with resistance levels comparable to the resistant control Sunco. Fourteen putative QTLs were mapped on chromosomes B, 2B, 2D, 4A, 5D, 6D, 7A, 7B, and 7D by GWAS, with the phenotypic variation explained by 3.73-6.64%. A major QTL (Qfcr.caas.7A-2) on chromosome 7A was consistently detected across all replications. BSE-Seq analysis confirmed enrichment of associated polymorphisms on chromosome 7A, encompassing the Qfcr.caas.7A-2 interval. Within this region, TraesCS7A02G53500. (encoding an RGA5-like protein) was prioritized as a candidate gene based on expression and phylogenetic analysis. Two kompetitive allele-specific PCR (KASP) markers KASP-7079 and KASP-3538 were successfully developed and validated for Qfcr.caas.7A-2. These findings offer valuable insights into the genetic mechanisms underlying FCR resistance and provide valuable resistance resources and molecular markers for FCR resistance breeding.  Reference | Related Articles | Metrics Select Characterization of defense responses in forage and food barley hosts during interaction with Epichloë endophyte Kamran Malik, Fangli Wei, Taixiang Chen, Chunjie Li DOI: 10.1016/j.jia.2026.02.023 Online: 11 February 2026 Abstract （1）      PDF in ScienceDirect       Endophytes are prevalent in plants and significantly contribute to plant growth and development. In the present study, Epichloë bromicola endophyte strain WBE1 was artificially inoculated into wild barley (Hordeum brevisubulatum, natural host) and cultivated barley (Hordeum vulgare, novel host) to obtain endophyte-barley symbionts. Physiological traits, such as callus formation, lignin content, cell mortality, early signaling molecules, second messenger endogenous signaling molecules, and the expression patterns of differential genes at different time periods were studied. The colonization rate of E. bromicola was 54.21% in wild barley and 9.91% in cultivated barley. Artificial endophytic infection enhanced callus growth, lignin content, and cell mortality in both hosts, with cultivated barley showing stronger resistance than wild barley. The infection induced the expression of early signaling molecules, and the O2- production rate as well as H2O2 and NO contents were increased in both hosts. During the early infection stage, mitogen-activated protein kinase (MAPK) activity in cultivated barley increased by 12.24% and 54.60% compared with wild barley at 2 and 4 days post-infection, respectively. Transcriptomic analysis revealed that cultivated barley triggered an earlier and targeted defense response than wild barley, characterized by the stage-specific upregulation of genes involved in resistance-related secondary metabolite biosynthesis and key signaling molecules. Expression patterns showed upregulation of signaling molecules alongside downregulation of genes associated to oxylipin biosynthesis, lipid oxidation, cellular responses to environmental stimuli, oxidoreductase activity, and heme binding. These findings indicated that E. bromicola infection effectively triggered an enhanced and timely defense response in cultivated barley.  Reference | Related Articles | Metrics Select Polymyxin B inhibits T3SS gene expression via WspR in Pseudomonas syringae pv. actinidiae Yudi Wang, Mingming Yang, Xianwei Xie, Bobo Zhao, Jinfang Zhou, Yuqing Yang, Yao Wang, Xihui Shen, Lili Huang DOI: 10.1016/j.jia.2026.02.022 Online: 11 February 2026 Abstract （1）      PDF in ScienceDirect       Kiwifruit bacterial canker (KBC), caused by Pseudomonas syringae pv. actinidiae (Psa), severely threatens the kiwifruit industry. The type III secretion system (T3SS) is a key virulence factor in Psa, but the regulatory mechanisms remain poorly understood. Polymyxin B1, the main component of polymyxin B, inhibits T3SS gene expression in Psa, yet its underlying mechanism is unclear. Cyclic diguanosine monophosphate (c-di-GMP), a crucial bacterial second messenger, is synthesized by diguanylate cyclases (DGCs) containing a GGDEF domain. In this study, we identified and characterized PSA_1379 (WspR), a GGDEF domain-containing protein in Psa. Biochemical assays demonstrated that WspR exhibits DGC activity. Virulence assays showed that WspR negatively regulates Psa virulence. RT-qPCR analyses revealed that polymyxin B induces wspR expression. Additionally, polymyxin B upregulates intracellular c-di-GMP levels and inhibits the expression of T3SS genes through WspR. Bacterial two-hybrid and GST pull-down assays confirmed that WspR interacts with the transcription factor PsrA. Both WspR and c-di-GMP inhibit the binding of PsrA to the promoter of the T3SS master regulator hrpL, thereby suppressing PsrA-mediated transcriptional activation of hrpL and ultimately repressing T3SS gene expression. This study provides new insights into Psa virulence regulation and suggests potential targets for KBC control through the WspR-c-di-GMP pathway. Reference | Related Articles | Metrics Select Impact of manure-derived dissolved organic matter on antibiotic transport in soil: A cross-scale study from molecular to column scale Xinyu Liu, Jianqiang Zhang, Xuyang Lu, Chen Liu DOI: 10.1016/j.jia.2026.02.021 Online: 11 February 2026 Abstract （0）      PDF in ScienceDirect       Land application of manure containing antibiotic residues poses significant environmental risks, primarily via leaching of these emerging contaminants into water resources. Despite extensive attention to antibiotic pollution, the mechanisms by which manure-derived dissolved organic matter (MDOM) influences their transport remain poorly understood. Using integrated techniques including fluorescence quenching and density functional theory (DFT) calculations, this study investigated molecular-scale interactions between eight typical antibiotics from five categories and four DOM species (humic acid, L-tryptophan, chicken MDOM and pig MDOM). These molecular interactions were linked to field-relevant conditions via soil column experiments and hydraulic modeling. Results demonstrated that the extent of antibiotic-DOM binding was determined by molecular HOMO-LUMO energy gaps (ΔE), following the order: quinolones (QLs)>tetracyclines (TCs)>macrolides (MLs)>sulfonamides (SAs)>chloramphenicols (CAPs). Protein-like species exhibited stronger antibiotic affinity than humic acid (HA), with chicken MDOM showing higher reactivity than pig MDOM. MDOM impact on antibiotic leaching strongly depended on their molecular binding strength, governing soil-water interface behavior. MDOM acted as a mobile carrier for weakly-bound antibiotics, facilitating transport via competitive adsorption, whereas it enhanced the retention of strongly-bound antibiotics through co-adsorption. These findings bridge molecular interactions and macroscopic leaching behavior in soil, providing a scientific basis for improving risk assessment and sustainable manure management in agricultural systems. Reference | Related Articles | Metrics Select First report of leaf vein death caused by Pantoea ananatis on rice in Jiangsu Province, China Xian Chen, Chunyang Xue, Oluwatoyin Oluwakemi Afolabi, Bao Tang, Yancun Zhao DOI: 10.1016/j.jia.2026.02.020 Online: 11 February 2026 Abstract （0）      PDF in ScienceDirect       Reference | Related Articles | Metrics Select Linked swine feed balanced strategy and manure management systems: Dual mitigation of nutrient element excretion and composting gaseous emissions Xiaomin Shi, Lin Lu, Shengkai Li, Haitao Wei, Ming Liu, Xiangfang Zeng, Shiyan Qiao, Junyan Zhou DOI: 10.1016/j.jia.2026.02.019 Online: 11 February 2026 Abstract （0）      PDF in ScienceDirect       Intensive swine production causes nutrient losses and enhanced gaseous emissions during manure management, which disrupts nutrient cycling within agricultural systems and threatens agroecosystem sustainability. Prior research has typically examined feeding and manure management as isolated processes, failing to integrate these two components to improve system performance, and this gap limits the design of integrated agricultural systems. Here, we implemented a low-protein balanced diet (LPBD) system and compared it with a high-protein traditional diet (HPTD) to evaluate impacts on swine growth performance and nutrient-use efficiency, followed by sawdust co-composting of the resulting manures. System responses were quantified through integrated monitoring of nutrient excretion, compost physicochemical properties, and gaseous emissions, together with metagenomic profiling of microbial communities and functional genes and subsequent path modeling to resolve key interaction pathways across the feed–compost agricultural system. We found that LPBD improved C/N digestion synchronization, reduced protein/energy excretion, and maintained swine productivity, while markedly decreased CO₂, CH₄, N₂O and NH₃ emissions during composting. Metagenomics indicated that LPBD enriched N-cycling genes (nirK, nosZ, nifH) and restructured CAZyme repertoires and microbial communities, patterns consistent with lower NH₃ emissions and enhanced carbon cycling. Path modeling further indicated that diet-driven shifts in compost composition altered environmental factors and indirectly regulated gas emissions via enzymatic and genetic pathways. Overall, this integrated feed–compost strategy links livestock nutrition with environmental management, enhances nutrient cycling efficiency at the agroecosystem level, and provides a basis for sustainable, low-emission circular livestock systems. Reference | Related Articles | Metrics Select A comprehensive survey reveals high viral diversity and novel infections in pea and broad bean crops in Yunnan Province, China Wenhui Li, Shuting Yu, Changfang Long, Guanlin Tan, Steve Wylie, Hong Cai, Xiaojiao Chen, Pingxiu Lan, Fan Li DOI: 10.1016/j.jia.2026.02.018 Online: 11 February 2026 Abstract （3）      PDF in ScienceDirect       Pea (Pisum sativum) and broad bean (Vicia faba) are important legume crops grown worldwide. Viral diseases pose a significant threat to these crops in China, particularly in Yunnan Province, where the year-round mild climate and continuous cropping systems create favorable conditions for virus infection and spread. From 2020 to 2022, a survey of viral diseases was conducted in pea and broad bean fields across six major regions of Yunnan Province, namely Kunming, Yuxi, Baoshan, Chuxiong, Dali, and Honghe. High-throughput sequencing (HTS) combined with RT-PCR was used to detect and identify viruses in 261 pea and 164 broad bean samples. Seventeen distinct viruses, including a new species, were identified in both pea and broad bean samples, whereas turnip yellows virus (TuYV) was detected only in pea samples. A novel virus, tentatively designated pea enamovirus 3 (PEnV-3), was identified based on the complete genome sequence of isolate YWD and phylogenetic analyses. Accordingly, we propose the species name Enamovirus pisi. Pea enation mosaic virus 1 (PEMV-1) and bean yellow mosaic virus (BYMV) were the most prevalent viruses detected in pea and broad bean crops, with detection rates of 54.02% and 81.10%, respectively. Co-infections with multiple viruses were common in both pea and broad bean samples, with 148 and 97 co-infected samples identified, respectively. The geographic distribution of the viruses varied considerably across the six sampling regions. PEMV-1, pea seed-borne mosaic virus (PSbMV), BYMV, Brassica yellows virus (BrYV), and chickpea chlorotic stunt virus (CpCSV) were the most widespread, occurring in all regions. In contrast, Vicia cryptic virus (VCV) was found only in pea samples from Dali, while PEnV-3 and clover yellow vein virus (ClYVV) were unique to pea samples from Kunming. In broad bean samples, BYMV and PSbMV were also the most prevalent, detected in five regions, whereas PEnV-3 was again confined to samples from Kunming. Regarding virus detection across crops and regions, Kunming exhibited the highest viral diversity in pea crops, with 15 different viruses identified, whereas Honghe had the lowest (9 viruses). Dali displayed the greatest viral diversity in broad bean crops (15 viruses), while Honghe showed the least, with BrYV as the sole virus detected. This study reveals several novel virus-host associations and previously unreported occurrences of viruses in specific region. To our knowledge, this study represents the first report of pea infection by BrYV, tomato yellow mottle-associated virus (TYMaV), Bidens mottle virus (BiMoV) and VCV. Additionally, its also documents the first report of TuYV in pea in China, as well as the first identification of ClYVV in pea in Yunnan Province. Similarly, infections of broad beans by BrYV and TYMaV are reported here for the first time. Furthermore, this study presents the first detection of BiMoV in China, and the first detections of VCV and ClYVV in Yunnan Province.  Reference | Related Articles | Metrics Select Dissection of genetic loci modulating heading date in common wheat Yueting Zheng, Zhenhai Jing, Haolong Feng, Yifei Yang, Jareer Abdullah, Chunyi Liu, Bangcai Zhao, Qianhui Xi, Fangyu Xiang, Qingmiao Yin, Ya Wang, Jiangmin Xing, Ge Kong, Lei Zhao, Xiaodong Yu, Congwei Sun, Feng Chen DOI: 10.1016/j.jia.2026.02.017 Online: 11 February 2026 Abstract （0）      PDF in ScienceDirect       Heading date is one of the most important indicators to evaluate adaptation in wheat. In this study, we used three association panels to construct a genome-wide recombination landscape consisting of 97 recombination hotspots regions (RHR) in wheat. We further identified 1,043 RHR in six bi-parental populations, and 88 recombination hotspots overlapped with association panels. We next identified 2223 significant SNPs forming 55 clusters for heading date by phenotype-based genome-wide association studies (pGWAS), and 53 stable SNPs associated with 13 candidate genes were detected in at least two environments. Twenty-one QTLs were mapped in bi-parental populations and five QTL intervals overlapped RHR. By integration of collinearity analysis, recombination hotspots, and haplotype analysis, five homoeologous interval pairs were discovered, of which 7D_Hap1 advanced heading by 8.7 days. Further analysis showed that heading date-network genes were involved into transcription regulation and post-translational modification (PTM). Meanwhile, expression GWAS (eGWAS) on heading date regulatory core module identified 307 potential novel genes acting in heading date regulatory network. These findings provide new insights into wheat phenological adaptation and developed resources for developing climate-resilient wheat cultivars. Reference | Related Articles | Metrics Select Co-applying mild alternate wetting and drying with biochar synergistically improves rice yield and quality Haotian Chen, Yunyi Gu, Shengkai Yang, Xiaohan Zhong, Meijie Jia, Wei Cai, Kuanyu Zhu, Junfei Gu, Kaifeng Huang, Hao Zhang, Zhiqin Wang, Zujian Zhang, Lijun Liu, Jianhua Zhang, Weiyang Zhang DOI: 10.1016/j.jia.2026.02.015 Online: 11 February 2026 Abstract （0）      PDF in ScienceDirect       To address the dual challenges of water scarcity and rising demand for premium rice, this study investigated the synergistic effects of mild alternate wetting and drying (Mild AWD) irrigation combined with wheat straw biochar application on rice yield and grain quality. A two-year field experiment (2023–2024) was conducted with the hybrid rice cultivar Yongyou 2640, with two irrigation regimes: continuous flooding (CF) and Mild AWD (re-irrigation at a soil water potential of −10 to −15 kPa at 15–20 cm depth), with or without a one-time biochar application (10 t ha-1). The results showed that co-application of Mild AWD and biochar significantly increased grain yield by 18.7% in 2023 and 13.4% in 2024 compared to CF alone. It also comprehensively improved grain quality: milling quality (head rice rate increased by 23.1–24.6%), appearance quality (chalkiness reduced by 36.4–38.2%), cooking and eating quality (higher peak viscosity, lower gelatinization temperature and enthalpy), and nutritional quality (increased glutelin and decreased prolamin content and starch digestion). These improvements were attributed to enhanced root activity alongside leaf photosynthetic rate, which promotes the accumulation of photoassimilates in vegetative organs and their translocation to grains. Moreover, elevated activities of key starch synthases further enhanced starch biosynthesis and accumulation, which underpinned the improved yield and superior quality. We also identified that a minimum soil water potential of −10 to −15 kPa at a depth of 15–20 cm represents the optimal threshold for mild AWD in rice production. This research provides a cultivation approach for synergistically producing high-yield, high-quality rice, which shows promising potential for scalable implementation. Reference | Related Articles | Metrics Select Single-nucleus RNA sequencing and metabolomics reveal evolutionary divergence in muscle fiber programming between Equus caballus and Equus asinus Cong Li , Xuyong Qin, Jiale Han, Na Li, Zhaofei Wang, Qiwen Yang, Halima Jafari, Chuzhao Lei, Ruihua Dang DOI: 10.1016/j.jia.2026.02.014 Online: 11 February 2026 Abstract （0）      PDF in ScienceDirect       Skeletal muscle cellular heterogeneity and molecular regulation are fundamental to understanding exercise physiology in Equus species. However, these mechanisms remain incompletely characterized in donkeys (Equus asinus) and horses (Equus caballus). Here, we integrated single-nucleus transcriptomics and metabolomics to systematically compare the longissimus dorsi muscle across developmental stages in both species. We identified nine and twelve distinct skeletal muscle cell types in donkeys and horses, respectively. Muscle fiber composition exhibited species-specific age-related changes: in adult horses, the proportion of both type I and II fibers increased; in adult donkeys, by contrast, the proportion of type I fibers decreased while that of type II fibers increased. The predominance of type II fibers in horses likely reflects a species-specific adaptation to high-intensity locomotor demands. Pseudotime analysis delineated muscle fiber trajectories and revealed dynamic gene expression profiles along these paths. Subpopulation analysis of immune cells revealed the activation of pro-inflammatory signaling pathways (TNF and NOD-like receptor pathways) in adult groups, coupled with diminished anti-inflammatory capacity in dendritic cells, collectively indicating an age-associated pro-inflammatory shift. Intercellular communication analysis further indicated age-related dysregulation in key signaling pathways, including BMP (adipogenic differentiation), Notch (immune regulation), and IGF (tissue repair), which may contribute to impaired muscle metabolism and regenerative capacity. Cross-species comparison revealed that skeletal muscle transcriptomes of donkeys and horses are highly conserved (Pearson correlation coefficient 0.87), although species-specific marker gene expression, such as SLC29A1 in endothelial cells, was observed. Metabolomic profiling identified distinct differences in overall metabolite category composition and revealed significantly divergent gene-metabolite networks between the two species. Together, these findings comprehensively illuminate the cellular dynamics, metabolic remodeling, and evolutionary conservation of skeletal muscle development in Equus species, providing valuable insights into mammalian muscle adaptation and identifying potential targets for enhancing locomotor performance or managing myopathies in equids. Reference | Related Articles | Metrics Select Salivary protein NlSP6935 that restricted to rice planthoppers is critical for insect survival and host defense regulation Zelong Zhang, Xiaojing Wang, Xinye Xu, Tangbin Hu, Chuanxi Zhang, Haijian Huang DOI: 10.1016/j.jia.2026.02.013 Online: 11 February 2026 Abstract （0）      PDF in ScienceDirect       Saliva plays a crucial role in mediating plant-insect interactions, yet the functional diversity of salivary proteins remains poorly understood. Here, we identify NlSP6935, a salivary gland-specific protein conserved among rice planthoppers but absent in bamboo-feeding relatives. Silencing NlSP6935 causes severe lethality, feeding impairment, and infertility in Nilaparvata lugens, independent of host plant resistance. Transient expression assays reveal that NlSP6935 suppresses H2O2 accumulation in plants, while overexpression in rice downregulates terpenoid biosynthesis and enhances host attractiveness. However, transgenic NlSP6935 plants only weakly rescue RNAi-induced lethality, demonstrating its dual role in insect physiology and plant defense suppression. Our findings reveal a novel effector essential for both planthopper survival and host adaptation, providing new insights into pest control strategies. Reference | Related Articles | Metrics Select Methylation dynamics modified by GhDMT9, playing an vital role in drought response of cotton Xuke Lu, Junjuan Wang, Shuai Wang, Xiugui Chen, Delong Wang, Zujun Yin, Lanjie Zhao, Lixue Guo, Waqar Afzal Malik, Maohua Dai, Wuwei Ye DOI: 10.1016/j.jia.2026.02.011 Online: 07 February 2026 Abstract （12）      PDF in ScienceDirect       DNA methylation is a stable epigenetic modification with essential roles in plant drought response. It is known that methyltransferase mutant is necessary for the regulation of methylation variations, but this epigenetic molecular mechanism based on methyltransferase mutant in responding to drought stress was still unclear in cotton. In this study, we aim to decipher the epigenetic code of drought response regulated by methyltransferase gene GhDMT9 in cotton, providing valuable information for the molecular research of drought resistance in cotton. We successfully created the first cotton methyltransferase mutant ghdmt9 using CRISPR/Cas9 method and performed methylation variations analysis with whole-genome bisulfite sequencing (WGBS) and transcriptome analysis based on ghdmt9 mutant. In addition, specific antibody of methyltransferase GhDMT9 was prepared and used for Chromatin Immunoprecipitation (ChIP-seq) analysis. The results indicated that ghdmt9 mutant interpreted approximately 2.06% methylation variations under drought stress. Demethylation variations, mainly derived from the CHG and CHH contexts, were closely correlated with drought response. Whether at normal growth stage or under drought stress, the number of up-regulated genes induced by demethylation variations was apparently higher than the number of down-regulated genes, especially genes regulating lipids and lipid-like molecules and hormone-related genes. In addition, fiber quality of ghdmt9 mutant was obviously better than that of wild type (WT). Interestingly, a transcription factor lsh (lysine-specific histone) was found to interact with methyltransferase gene GhDMT9 to activate its hyper-methylation function of target genomic regions by ChIP-seq analysis. Overall, our results extend our understanding of the epigenetic regulation of methyltransferase GhDMT9 in drought response and contribute to further investigations of the epigenetic mechanisms underlying abiotic stresses in cotton.  Reference | Related Articles | Metrics Select Combining cost-effective germination imaging and genome-wide association study to unravel genetic variation of temporal salinity responses in wheat Qing Li, Zhuangzhuang Sun, Xiaofang Li, Zihan Jing, Xiaomiao Tian, Yinchen Zhang, Yingyin Yao, Zhen Zhang, Meng Wang, Xiao Wang, Qin Zhou, Jian Cai, Yingxin Zhong, Mei Huang, Wenliang Wan, Jiawei Chen, Dong Jiang DOI: 10.1016/j.jia.2026.02.010 Online: 07 February 2026 Abstract （7）      PDF in ScienceDirect       Salt stress is a major limiting factor for global wheat production, especially during the germination stage. Traditional methods for evaluating salt resistance at the germination stage are limited by low throughput and their inability to capture dynamic phenotypic changes. In this study, a low-cost and high-throughput seed germination phenotyping platform was developed by integrating side-view RGB imaging with image analysis algorithms. Organ segmentation and germination related traits extraction processes was built via a deep learning pipeline for comprehensive phenotyping of the germination process of diverse varieties under different salt levels. Organ-level segmentation achieved a mean precision of 89.08%, a mean recall of 91.65%, a pixel accuracy of 91.65%, and a mean intersection over union of 83.20%. The 13 image-derived traits were highly consistent with manual measurements. Salt stress significantly inhibited the growth of roots and seedlings, with inhibitory effects intensifying as salt concentration increased. Further analysis revealed seed size shows no correlation with germination capacity and radicle growth rate significantly surpasses that of the coleoptile. Clustering analysis based on dynamic image-derived indices classified the 210 wheat materials into two groups with significantly different salt tolerance. GWAS identified 429 loci associated with salt stress response during germination, including one potential candidate gene, TraesCS7A03G007080, known to play a role in salt tolerance mechanisms. This study provides important genetic materials for the evaluation of salt-tolerant wheat varieties at the germination stage and offers a low-cost, high-throughput, and reliable technical approach for dissecting the genetic basis of salt tolerance during wheat germination. Reference | Related Articles | Metrics Select Proactive optimization of drip-applied DPC based on cultivar sensitivity: Increasing machine-harvested cotton yield and reducing DPC residues Feng Shi, Yu Tian, Xiaojuan Shi, Liwen Tian, Xianzhe Hao, Nannan Li, Hongxia Zhang, Humei Zhang, Houxiu Zhao, Shijie Deng, Xuan Liu, Guoxing Ma, Jing Li, Jun Wang, Honghai Luo DOI: 10.1016/j.jia.2026.02.009 Online: 07 February 2026 Abstract （4）      PDF in ScienceDirect       Within the context of modern cotton cultivation, which emphasizes cost savings and efficiency improvements, drip application of 1,1-dimethyl piperidinium chloride (DPC) provides potential advantage such as reducing the labour and mechanical costs associated with the chemical regulation of conventional DPC foliar spraying in arid cotton-growing areas. However, the appropriate drip DPC dose and its regulatory effects on cotton growth and yield, and particularly the responses to cultivars with different sensitivities to DPC, remain uncertain. A two-year (2023–2024) field experiment was conducted to evaluate the influences of various cultivars and drip DPC doses on cotton phenology, agronomic traits, canopy development, defoliation, boll opening, yield and residual DPC levels. The cultivars Huiyuan 720 (H720, DPC-sensitive) and Xinluzao 74 (L74, DPC-insensitive) were chosen, the D0 (no DPC) and S1 (DPC foliar spraying at 330 g ha−1 in 2023 and 375 g ha−1 in 2024) treatments were used as controls, and the drip DPC doses were D1 (the same dose as that in S1), D4 (four times the dose in S1) and D6 (six times the dose in S1). The results indicated that compared with those in D0, the growth periods of H720 in D4 and L74 in decreased by 9 days; in particular, the number of growth days from the peak flowering stage to the late peak bolling stage decreased by 6 days. The plant height, the height of the first fruiting branch, and plant width decreased significantly, by 10.1–19.1%. The diffuse non-interceptance and canopy light transmittance in the middle and upper parts from the peak squaring stage to the boll opening stage increased by 7.9–55.9% and 0.4–7.0%, respectively. The defoliation and boll opening rates increased by 1.5–3.4%. The boll numbers in the middle part increased by 16.7–36.4%, and the yield increased by 4.9–7.6%. Compared with those in S1, the yields of H720 in D4 and of L74 in D6 were comparable but the levels of DPC residues in the cotton plants significantly decreased by 36.3–71.0%. Moreover, the levels of DPC residues in D6 were minimal in soil. These results indicated that an appropriate drip DPC dose can optimize cotton growth and development and reduce the levels of DPC residues based on the cultivar characteristics. This study provides valuable practical insights into the potential of a drip DPC regulation system to replace the foliar spraying method and to advance light and simplified cotton cultivation. Reference | Related Articles | Metrics Select A weak OsBRI1 allele in Zhonghua 11 as a genetic tool for brassinosteroid signaling research in rice Yanzhao Feng, Qingfeng Zhu, Qiuyue Yuan, Pei Chen, Xielian Tan, Ning Huang, Jiao Xue, Yang Yu DOI: 10.1016/j.jia.2026.02.008 Online: 07 February 2026 Abstract （6）      PDF in ScienceDirect       Reference | Related Articles | Metrics Select Simultaneous silencing of ten essential Sclerotinia sclerotiorum genes via spray- and host-induced gene silencing enhances against Sclerotinia stem rot resistance in oilseed rape Sichao Ren, Ying Zhang, Yi Ye, Wenjing Huang, Wenxin Liu, Shengliang Yin, Yang Yang, Yu Liu, Jialin Fan, Yumei Wang, Youping Wang, Li Lin, Jian Wu DOI: 10.1016/j.jia.2026.02.007 Online: 07 February 2026 Abstract （9）      PDF in ScienceDirect       Sclerotinia stem rot (SSR) is caused by the necrotrophic fungus Sclerotinia sclerotiorum and threatens global oilseed rape (Brassica napus) production. Moreover, researchers have not yet identified a gene that confers complete resistance. Here, we developed a multi-target RNA interference (RNAi) strategy to enhance plant resistance by simultaneously silencing eight fungal genes involved in development (SsChsI–VII, SsGas1) and two involved in pathogenicity (SsPG1, SsOAH1) of S. sclerotiorum. Accordingly, we designed a 1,250-bp chimeric double-stranded RNA (dsRNA) consisting of ten 125-bp fragments each targeting a different gene, and evaluated its effectiveness using spray-induced gene silencing (SIGS) and host-induced gene silencing (HIGS) via stable transformation. In vitro application of the chimeric dsRNA resulted in >50% downregulation of nine target genes, indicating efficient uptake and processing by S. sclerotiorum. Both lesion area and fungal biomass were significantly lower in Nicotiana benthamiana and oilseed rape plants following SIGS. Moreover, stable transgenic plants for HIGS effectively generated gene-specific short interfering RNAs and exhibited an increase in resistance from the T2 to T5 generations, with lesions that were 38.9–59.1% smaller in leaves and 43.2–65.8% smaller in stems in the T5 generation compared with the control plants. Gene silencing resulted in lower oxalic acid accumulation, decreased polygalacturonase activity, and impaired hyphal development, suggesting interference with multiple fungal infection pathways. Notably, HIGS conferred stable, heritable resistance without yield penalty, whereas SIGS provided rapid, nontransgenic protection. This study demonstrates the effectiveness of long chimeric dsRNAs for multi-target gene silencing and highlights a promising RNAi-based strategy for improving disease resistance in oilseed rape, possibly in combination with natural quantitative resistance loci. Reference | Related Articles | Metrics Select The TATA-box binding protein-associated factor ZmTAF11 regulates plant architecture in maize Fengzhong Lu, You Zhou, Yajie Liu, Xin Zhang, Tao Wan, Jingtao Qu, Wanchen Li, Fengling Fu, Wei Guo, Haijian Lin, Jianfeng Hu, Jie Xu, Guangchao Sun, Yao Wang, Yanli Lu, Haoqiang Yu DOI: 10.1016/j.jia.2026.02.006 Online: 07 February 2026 Abstract （3）      PDF in ScienceDirect       Compact maize architecture is crucial for high planting densities and yields, which is a key breeding objective. In this study, a maize T-DNA insertion mutant with compact plant architecture (cpa) was identified, showing reduced leaf curling, drooping angle, plant and ear height, leaf dimensions, internode and tassel length, tassel branch number, and yield compared to WT. Paraffin section analysis showed reduced vein cross-sectional area, epidermal cell width, and increased vein density in the cpa mutant. Genetic analysis revealed that T-DNA was inserted into the first exon of a gene encoding TATA-box binding protein-associated factor (TAF) in the cpa mutant, which was named ZmTAF11. ZmTAF11 exhibited ubiquitous expression across various tissues and nuclear localization. Loss-of-function Zmtaf11 mutants generated by CRISPR/Cas9 exhibited the characteristic compact phenotype, which was consistent with that of the cpa mutant. ZmTAF11 directly binds to the promoters of leaf morphogenesis-related genes ZmAXL and ZmBOB1, thereby promoting their transcription. Furthermore, four SNPs in ZmTAF11 were significantly associated with ear height index (EHI), and the AGTG haplotype showed a lower EHI. This haplotype was predominantly found in temperate maize lines and geographically distributed across North America. These findings reveal the role of ZmTAF11 in regulating maize architecture and its potential application in high-density maize breeding.  Reference | Related Articles | Metrics Select Identifying limiting factors for maize yield in China’s major maize-producing regions using random forest Liangbing Rong, Qianlan Jia, Kaiyuan Gong, Fengying Duan, Xia Li, Congfeng Li, Peng Liu, Dalei Lu, Gang Zhao, Ning Yao, Yi Li, Hao Feng, Jianqiang He, Qiang Yu, Wenbin Zhou DOI: 10.1016/j.jia.2026.02.005 Online: 07 February 2026 Abstract （6）      PDF in ScienceDirect       Maize (Zea mays L.) is an important food crop worldwide. Understanding yield-limiting factors is essential for optimizing maize productivity under varying agroclimatic conditions. In this study, the relative contributions of climate, soil, and management factors to yield variation in spring and summer maize across 34 sites in China during 2017-2020 were assessed. Random forest (RF) models explained more than 80% of the yield variation, and SHapley Additive exPlanations (SHAP) and Accumulated Local Effects (ALE) were employed to interpret the effects of key variables. Climate emerged as the dominant driver, accounting for nearly 50% of the total feature importance. For spring maize, solar radiation during the establishment stage (ES) had a strong positive effect, whereas the minimum temperature during the grain-filling stage (GFS) had a negative effect. In contrast, summer maize yield was constrained by elevated nighttime temperatures during ES but benefited from increased growing degree days (GDD) during GFS. Among all the variables, planting density (PD) was consistently important across both systems, and increasing PD represented a direct and effective pathway to enhance yield. The results of the yield component analysis further revealed that the significantly higher kernel number per ear (on average 68 kernels more than summer maize) was the main contributor to the superior performance of spring maize. Climate scenario simulations indicated that, without adaptive management, future warming could reduce spring and summer maize yields by 6.1–11.8% and 5.5–9.1%, respectively. These findings underscore the stage-specific climate sensitivity of maize and support the development of targeted adaptation strategies to sustain yields under future climate change. Reference | Related Articles | Metrics Select Development of innovative image descriptors for phenotyping peanut pod constriction and discovery of QTLs underlying this trait Shengzhong Zhang, Feifei Wang, Xiaohui Hu, Huarong Miao, Jun Hong, Shihua Shan, Xiaoyuan Chi, Jing Chen, Xinyou Zhang, Shengzhong Zhang, Feifei Wang, Xiaohui Hu, Huarong Miao, Jun Hong, Shihua Shan, Xiaoyuan Chi, Jing Chen, Xinyou Zhang DOI: 10.1016/j.jia.2026.02.004 Online: 07 February 2026 Abstract （6）      PDF in ScienceDirect       Pod constriction (PC) is a key morphological trait determining both commercial values and yield of in-shell peanuts. Conventional phenotyping metrics (visual scores and pod waist length derived descriptors) suffer from low precision or limited applicability, especially for atypical pod shapes, which have constrained discovery of underlying genes. To address these limitations, this study introduced two novel image descriptors: front and back constriction depth indices (Front_DI and Back_DI). These indices enable accurate and robust evaluation of PC across diverse pod morphologies. Additionally, a Python script employing the deep learning technology was developed to efficiently and precisely extract these metrics. By applying both novel and conventional phenotyping methods to a recombinant inbred line population (Luhua 11×06B16), this study identified four quantitative trait loci (QTLs) for Front_DI, four for Back_DI, three for visual score, and two for a pod waist length-based descriptor across three environments. A major and co-localized QTL region was consistently detected on chromosome 2. Meta-analysis further refined this region to a 728-kb consensus interval. Within this interval, an InDel was identified in the coding region of Arahy.X14VTN between the two parental lines, resulting in a frameshift mutation and a predicted alteration in protein structure. Diagnostic markers were developed for this candidate gene, confirming the genetic effect on PC variation. The novel image descriptors and genetic loci presented here improve our understanding of the genetic basis of PC in peanut and offer practical tools for molecular breeding aimed at trait improvement. Reference | Related Articles | Metrics page Page 1 of 21 Total 402 records First page Prev page Next page Last page