Advanced Online Publication

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 Synergistic optimization of mulching types and planting patterns: enhancing sustainable maize productivity via soil quality regulation in rainfed agricultural systems Zeyin Jiang, Xiaoling Wang, Wei Wang, Yafang Han, Muhammad Shoaib Asad, Wenbo Lü, Enke Liu, Xining Zhao, Xiaoli Chen, Peng Zhang, Tiening Liu, Zhikuan Jia, Xiaolong Ren DOI: 10.1016/j.jia.2026.03.044 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       Optimized planting patterns and mulching practices are recognized as robust strategies for enhancing productivity in rainfed agriculture. However, the regulatory mechanisms of crop yield and soil microenvironment in dryland farming under different planting patterns combined with mulch types remain unclear due to a lack of long-term field experiments. In this study, a seven-years field experiment was conducted with two planting methods (R, ridge-furrow planting; C, conventional flat planting) and three mulch types (S, straw; B, biodegradable film; W, without mulch) to investigate the comprehensive effects of different treatments on the soil-crop system. Ridge-furrow planting pattern significantly increased soil water storage within the 0–200 cm profile by 2.02–9.63%, while straw mulching enhanced soil organic matter content. The RS (ridge-furrow planting combined with straw mulch) demonstrated higher soil microecological functioning as compared to CW (flat planting without mulch), microbial Shannon and Richness indices increased by 148.50–203.64, and 15.49–50.29%, respectively, while carbon source metabolic efficiency improved by 99.58–236.17%. In addition, the RS treatment achieved the highest yield. Partial least squares path modeling (PLS-PM) revealed that the integration of planting with mulching primarily enhanced crop yield indirectly by improving the soil quality index (R2=0.98; path coefficient (pc)=0.70). Multi-objective decision analysis confirmed that RS represents the optimal strategy for concurrently maintaining soil health, improving resource use efficiency, and increasing crop yields. This study provides a novel strategy for optimizing spring maize cropping systems in the drylands of northern China and effectively promoting the sustainability of the soil-crop system. Reference | Related Articles | Metrics Select Auxin stabilizes soybean seed development under post-flowering high-temperature stress and enhances plant tolerance Fang Li, Yutong Zhou, Yikang Jiao, Xin Liu, Xintong Shi, Yaxuan Chen, Xin Wang, Shunli Zhou DOI: 10.1016/j.jia.2026.03.043 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       Asynchronous seed development complicates soybean response to post-flowering high-temperature (HT) stress. To elucidate the mechanisms underlying HT-induced yield reduction after flowering, soybean plants were subjected to a six-day HT treatment in a greenhouse beginning at the opening of the first flower. HT reduced seed number and impaired pod and seed development at the initial flowering nodes, as evidenced by the decline in size and fresh weight. HT downregulated genes related to DNA replication, cell division, lipid metabolism, and secondary metabolism. Notably, auxin signaling and cell cycle factors emerged as central regulatory networks governing seed development. HT downregulated the expression of critical cell cycle components, including cyclins, kinesins, MAD2, and RAD, the latter two containing auxin-responsive elements. Moreover, HT reduced auxin levels in fertilized ovaries, while exogenous auxin (0.1 nM 1-Naphthaleneacetic acid) treatment alleviated HT-induced seed developmental restriction, mainly by increasing cell number and size. Auxin treatment further improved pod set, pod and seed number, and grain weight under HT stress. These results suggest that the cell cycle suppression is determinant for growth retardation in synergy with reduced auxin levels in soybean seeds, and auxin supplementation could enhance soybean adaptation to post-flowering HT stress.  Reference | Related Articles | Metrics Select Mutation in CmPPR confers a yellow-leaf phenotype and chloroplast defects in melon (Cucumis melo L.) Jiajian Cao, Qin Shao, Yi Cheng, Feidie Ye, Xingwen Chai, Chunhua Wang, Tao Wu DOI: 10.1016/j.jia.2026.03.042 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       Leaf color variation in melon (Cucumis melo L.) serves as a valuable model for investigating chlorophyll biosynthesis, chloroplast development and photosynthesis owing to its obvious morphological differences. In this study, a stable yellow-leaf mutant Cmyl-1 was characterized, exhibiting reduced chlorophyll and carotenoid contents, impaired chloroplast ultrastructure, and retarded plant growth. Genetic segregation analysis indicated that the yellow-leaf trait was regulated by a single recessive gene, and the green leaf showed complete dominance over the yellow leaf. Genetic mapping confined the Cmyl-1 locus to a 78.45-kb region between the CAPS markers 1-CAPS and 21-CAPS on chromosome 11. Genomic and sequencing results revealed a 12-bp insertion in the promoter and a single C to T transition in the exon of MELO3C021959 in Cmyl-1; the latter caused a Pro-to-Leu amino acid change. MELO3C021959 is presumed to be the candidate gene, encoding a P-type PPR protein (CmPPR), which localizes to the cytoplasm and chloroplasts, and possibly to the cell membrane. Silencing of CmPPR in cucumber via VIGS further confirmed its role as the causal gene for the Cmyl-1 phenotype. RNA-seq analysis further demonstrated significant downregulation of chloroplast-associated genes in the Cmyl-1 mutant. The results found in this study will not only contribute to melon genetic breeding, but also provide a useful insight into the molecular understanding of leaf color development in Cucurbitaceae crops. Reference | Related Articles | Metrics Select Improving spikelet production efficiency is crucial for further unleashing yield potential in rice Weiyang Zhang, Meijie Jia, Shengkai Yang, Xiaohan Zhong, Haotian Chen, Ying Liu, Zhiqing Wang, Jianhua Zhang, Jianchang Yang DOI: 10.1016/j.jia.2026.03.041 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       Reference | Related Articles | Metrics Select System-level optimization of cultivar, sowing, and water–nitrogen management enhances cotton yield and resource efficiency under future warming in Xinjiang, China Hongqin Wang, Lei Li, Jiaxue Li, Yong He DOI: 10.1016/j.jia.2026.03.040 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       Cotton production in Xinjiang’s irrigated arid regions faces growing challenges from climate-induced alterations in hydrothermal conditions, necessitating adjustments in cultivar selection, sowing time, and water–nitrogen management. However, most studies have focused on individual factors, with limited evaluation of integrated cultivar–sowing–water–nitrogen management. To assess the combined effects of irrigation and nitrogen management under future climates, a locally calibrated APSIM-Cotton model was driven by two CMIP6 scenarios (SSP2-4.5, SSP5-8.5) at two representative irrigated sites, Aral and Shihezi. The design included five maturity types, eight sowing dates (31 March–5 May), five irrigation thresholds (55–75% of field capacity, FC), and five fertigation levels (10–18 kg N ha-1 per irrigation). Multi-objective NSGA-III optimization identified optimal combinations for yield, water use efficiency (WUE), and nitrogen use efficiency (NUE), which were then extended to the regional scale across Xinjiang. Optimal strategies consistently converged on late-maturity cultivars with early-April sowing, high irrigation thresholds (0.65–0.75 FC), and relatively high per-event fertigation (14–18 kg N ha-1), a pattern robust across periods and both scenarios. Under the baseline climate, these optimal combinations increased yield by >32%, WUE by >21%, and NUE by >38% relative to conventional water–nitrogen management reported in previous field studies. Relative to the baseline (1981–2010) climate period, these strategies increased yield by >10%, WUE by >14%, and NUE by >21% under future scenarios. Regional simulations further revealed that southern Xinjiang holds greater potential for improving WUE, while northern Xinjiang is more advantageous in enhancing NUE. These findings highlight the synergistic effects between sowing time and water–nitrogen management, representing a key pathway to stabilizing yields and improving resource-use efficiency under future climate conditions, informing development of high-yield and efficient cotton systems in Xinjiang and offering insights for climate-adaptive management in similar arid regions worldwide. Reference | Related Articles | Metrics Select Dual-action biocontrol of Fusarium in wheat by Clonostachys: Perithecia suppression and systemic defense priming Xin Zhang, Xinyuan Ding, Yuanzhe Li, Yixi Zhu, Yuying Wei, Ming Xu, Guanghui Wang, Huiquan Liu DOI: 10.1016/j.jia.2026.03.039 Online: 19 March 2026 Abstract （1）      PDF in ScienceDirect       Fusarium head blight (FHB) and crown rot (FCR) threaten global wheat production, demanding sustainable biocontrol solutions. We isolated 50 indigenous Clonostachys strains (C. chloroleuca, C. rosea, C. rogersoniana) from Chinese agroecosystems and identified key biocontrol traits. Critically, sporulation rate—not mycelial growth—correlates with Fusarium suppression efficacy, revolutionizing agent selection criteria. Five elite strains completely prevented perithecia formation on crop residues. Microscopy revealed direct mycoparasitism through perithecial wall adhesion and enzymatic destruction of asci/ascospores. Transcriptomics of parasitized perithecia showed Fusarium stress responses including ABC transporter induction, membrane remodeling, and DNA repair activation, confirming membrane damage and genotoxic stress. Strain Cc878 exhibited dual-mode protection: suppressing residue-borne inoculum while establishing root endophytism via seed treatment. This protected against multiple soilborne diseases (FCR, common root rot, take-all) without yield penalties and primed systemic immunity through MAPK/phenylpropanoid pathways. Genome analysis revealed extensive secretomes, CAZymes, and secondary metabolite clusters underpinning biocontrol mechanisms. This integrated strategy combining inoculum reduction with immunity priming provides a sustainable alternative to chemical fungicides for managing devastating Fusarium diseases in wheat production systems. Reference | Related Articles | Metrics Select Elucidating functional partitioning and inhibitory regulation of ammonia oxidizers in agricultural ecosystems under long-term fertilization regimes Beibei Zhang, Manman Chen, Meng Wei, Yanhong Lou, Haojie Feng, Hui Wang, Quangang Yang, Hongjie Di, Yuping Zhuge, Hong Pan DOI: 10.1016/j.jia.2026.03.038 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       Ammonia-oxidizing microorganisms (AOMs) mediate a pivotal yet poorly understood step in agricultural nitrogen cycling under long-term fertilization. To identify the key microbial drivers of ammonia oxidation, two DNA stable isotope probing (DNA-SIP) experiments were conducted on soils under long-term fertilization regimes. Through integrated DNA-SIP and targeted inhibition approaches (C2H2, simvastatin, C8H14), we intended to resolve functional partitioning among ammonia-oxidizing archaea (AOA), bacteria (AOB), and comammox Nitrospira in soils subjected to multi-decadal fertilization regimes. SIP revealed the exclusive functional dominance of AOB (primarily Nitrosospira cluster 3a), which drove over 85% of autotrophic nitrification in fertilized soils. In contrast, AOA activity was significant only in non-fertilized (CK) and mineral N-only (N) soils. Notably, comammox Nitrospira showed negligible functional engagement, with no labeled DNA detected. The inhibitor 1-octyne (C8H14) broadly suppressed both AOB (by 61.9–88.9%) and, unexpectedly, AOA (by up to 42.7%), challenging its specificity. Simvastatin preferentially inhibited comammox Nitrospira clade B. High-throughput sequencing confirmed Nitrososphaera (AOA) and Nitrosospira 3a as keystone nitrifiers, with no active comammox phylotypes detected. These findings challenge assumptions of comammox metabolic prominence in agroecosystems, demonstrating that long-term fertilization restructures nitrification networks through species sorting driven by high ammonium availability, leading to the competitive dominance of AOB. Our work establishes AOB as primary nitrogen cycle engineers in intensively managed soils, providing a molecular blueprint for precision nitrogen management to mitigate environmental impacts. Reference | Related Articles | Metrics Select Root-derived brassinosteroids coordinate high rice yield and methane mitigation under wetting alternating with mild drying management Weiyang Zhang, Wei Cai, Haotian Chen, Meijie Jia, Ying Liu, Kuanyu Zhu, Hao Zhang, Junfei Gu, Zhiqin Wang, Zujian Zhang, Lijun Liu, Jianhua Zhang DOI: 10.1016/j.jia.2026.03.037 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       This study explored the effects of a wetting alternating with mild drying (WMD) management strategy, on rice productivity and methane (CH4) emissions, and its underlying mechanisms. A high-yielding hybrid rice cultivar was grown in field trials under either conventional irrigation (CI) or the WMD regimen from transplanting to maturity. Results revealed that the WMD approach significantly boosted grain yield while simultaneously reducing CH4 emissions. It was accompanied by a slight increase in nitrous oxide (N2O) emissions versus CI. However, the mitigation benefits of decreased CH4 emissions in lowering global warming potential (GWP) and greenhouse-gas intensity (GHGI) outweighed the adverse contributions of elevated N2O emissions. Elevated BR levels in roots enhanced antioxidant defense through the ascorbate-glutathione cycle pathway, which reduced ROS accumulation, thereby not only maintaining root activity but also suppressing root aerenchyma formation—ultimately restricting CH4 transport pathways under WMD regime. Furthermore, the increased root BR levels suppressed CH4 production by directly or indirectly inhibiting the mcrA gene abundance, while promoting CH4 oxidation through rhizosphere exudates enriched with specific organic acids that stimulated the pmoA gene abundance in paddy soil. Under the WMD regime, BR-induced enhancement of root activity significantly boosted photosynthetic capacity, establishing a positive feedback loop that promoted assimilate accumulation. Concurrently, WMD facilitated photosynthate allocation from vegetative tissues to grains, collectively improving rice yield. Collectively, our data suggest that the WMD practices can effectively reduce CH4 emissions, GWP, and GHGI in rice paddies while maintaining high grain yield by stimulating root-derived BR biosynthesis. Reference | Related Articles | Metrics Select Candidate functional variants in TBXT, HOXB13, and PDGFD associated with tail morphology in Chinese sheep for marker-assisted selection Sha Zeng, Benmeng Liang, Wanmei Luo, Yuhetian Zhao, Sijia Ma, Yabin Pu, Yuehui Ma, Jiangang Han, Lin Jiang DOI: 10.1016/j.jia.2026.03.036 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       Reference | Related Articles | Metrics Select Ultrasound-Assisted Extraction Modifies the Structural Characteristics and Enhances the Prebiotic Potential of Large Yellow Tea Polysaccharides Bayarsaikhan Tsevelsuren, Zhiliang Jiang, Xiaobo Wu, Yuexin Liu, Fuqing Bai, Yiang Chen, Qianfen Liu, Minhao Xie, Daxiang Li, Guijie Chen, Huimei Cai DOI: 10.1016/j.jia.2026.03.047 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       Large yellow tea polysaccharides (LYPS) have demonstrated various bioactivities, including antioxidant, lipid metabolism regulation, and hypoglycemic effects. However, their gastrointestinal digestibility and potential prebiotic functions remain largely unknown. This study aimed to compare the structural characteristics and in vitro fermentation behaviors of LYPS using traditional hot water extraction (LYPS-W) and ultrasound-assisted extraction (LYPS-U), with a focus on their potential prebiotic effects. Ultrasonic extraction significantly modified the structural features of LYPS, yielding a lower molecular weight and higher contents of galacturonic acid, along with more uniform particle morphology. Both LYPS-W and LYPS-U resisted upper gastrointestinal digestion but were readily fermented by gut microbiota. LYPS-U exhibited superior fermentability, producing significantly higher levels of short-chain fatty acids (SCFAs), particularly acetic and propionic acids, compared with LYPS-W. Microbial analysis revealed that both polysaccharides promoted the growth of beneficial SCFAs-producing bacteria, such as Bacteroides, Prevotellaceae_UCG-001, and Phascolarctobacterium, and suppressed potential pathogens such as Pseudomonas. Thus, ultrasound-assisted extraction enhances the structural accessibility and biological functionality of LYPS, improving their microbial fermentability and prebiotic potential. These findings provide a theoretical foundation for the application of ultrasonic processing in the development of gut-targeted functional foods based on tea-derived polysaccharides. Reference | Related Articles | Metrics Select Breaking data barriers with homomorphic encryption: The HEGS platform for secure joint genomic selection in animal breeding Jiamin Gu, Wei Zhao, Zhenyang Zhang, He Han, Yongqi He, Xiaoliang Hou, Jianlan Wang, Yan Fu, Qishan Wang, Yuchun Pan, Zhen Wang, Zhe Zhang DOI: 10.1016/j.jia.2026.03.046 Online: 19 March 2026 Abstract （0）      PDF in ScienceDirect       Genomic selection (GS) is one of the most effective approaches for accelerating genetic improvement in animals and plants, but its efficiency largely depends on the size of the training population. However, establishing a large training population is often time-consuming and costly. An alternative strategy is to combine multiple populations distributed across different breeding farms or companies for joint GS, but this is greatly constrained by data-security concerns and the lack of a public platform for secure collaborative analysis. In this study, we developed HEGS (Homomorphic Encryption Genomic Selection), an open-source platform for privacy-preserving joint GS across institutions, which is in principle applicable to diploid species. HEGS uses homomorphic encryption to perform genomic analyses directly on encrypted data without revealing raw information, and extends the encrypted analysis framework from the initial genomic best linear unbiased prediction (GBLUP) model to include both conventional best linear unbiased prediction (BLUP) and single-step GBLUP (ssGBLUP), thereby broadening its applicability in breeding evaluation. To demonstrate the utility of the platform, we constructed a large encrypted pig dataset comprising four breeds (Duroc, Yorkshire, Landrace, and Pietrain), 36 economically important traits, 180 pre-encrypted datasets, and more than 580,000 phenotypic records, enabling immediate joint analyses without exposing raw data. Using both simulated and real datasets, we demonstrated the feasibility and effectiveness of GS under homomorphic encryption. After model fitting, HEGS outputs genomic estimated breeding values (GEBVs) for genotyped candidates without phenotypic records, facilitating selection without additional phenotyping. Overall, HEGS provides a deployable and scalable open-source solution for privacy-preserving cross-institutional collaboration in animal breeding. Reference | Related Articles | Metrics Select Phenotype-driven machine learning models for predicting average daily gain in Yorkshire pigs with SHAP interpretation Shan Jiang, Jiahao Chen, Yifan Han, Haoyu Pei, Jiakai Tang, Chuxiong Zhang, Miaomiao Qin, Fei Cheng, Lijing Bai, Jiangwei Wu DOI: 10.1016/j.jia.2026.03.045 Online: 19 March 2026 Abstract （4）      PDF in ScienceDirect       Average daily gain (ADG) is a key indicator of growth performance in swine production. Although genomic prediction tools such as genomic best linear unbiased prediction (GBLUP) and single-step genomic best linear unbiased prediction (ssGBLUP) are widely used in breeding programs, their application may be limited by cost and data availability. To provide a practical and cost-effective complement to genomic evaluation, we developed a machine learning–based phenotypic prediction framework for estimating ADG in Yorkshire pigs using routinely recorded early-life variables. Production records from 12,079 pigs raised under standardized conditions between February 2020 and April 2024 were curated, and after data cleaning, fifteen regression algorithms were trained and evaluated using the root mean squared error (RMSE), mean absolute error (MAE), mean absolute percentage error (MAPE), and the coefficient of determination (R2). Model interpretability was assessed using SHapley Additive exPlanations (SHAP), and an independent external cohort was used for validation. Results indicated that CatBoost delivered the highest predictive accuracy and demonstrated strong generalization in both internal and external validations. SHAP analysis identified biologically meaningful early-life predictors contributing to ADG variation. To promote practical adoption, we developed a user-friendly web application that enables real-time prediction and interpretation of ADG outcomes. Overall, this study demonstrates that routinely collected phenotypic and management data can effectively support accurate ADG prediction through machine learning, offering a data-driven tool to enhance decision-making and production efficiency in swine systems.  Reference | Related Articles | Metrics Select SbGBST47K: A high-resolution genotyping-by-target-sequencing liquid chip in sorghum Qiaoling Zhang, Yanqing Ding, Yinlin Wang, Jianxia Xu, Feng Jiang, Ning Cao, Fan Yang, Liyi Zhang DOI: 10.1016/j.jia.2026.03.031 Online: 17 March 2026 Abstract （1）      PDF in ScienceDirect       Sorghum (Sorghum bicolor L. Moench) is essential for global food security, yet its genetic improvement has been hindered by the limited exploitation of genomic resources. To address this gap, we developed the SbGBST47K liquid chip, a high-throughput genotyping-by-target-sequencing (GBTS) platform with 47,040 SNPs, using whole-genome resequencing data from 1,025 diverse accessions. This chip integrates 45,506 genome-wide background SNPs, 1,278 liquor-sorghum diagnostic markers, and 268 trait-associated loci, enabling cost-effective, high-resolution genotyping. Validation across 434 accessions revealed a distinct population structure comprising four genetic groups (Foreign, Chinese north, Chinese south, and Chinese southwest). Genome-wide association studies (GWAS) detected 160 significant SNPs for eight agronomic traits, highlighting chromosomes 1, and 2 (pigmentation, tannin content), 7 (plant height), and 10 (starch metabolism) as genomic hotspots. Haplotype analysis of Wx and Tan2 revealed that their population distribution reflects regional preferences in sorghum usage. Furthermore, a important candidate gene for grain pigmentation was predicated at the major locus on chromosome 4. The SbGBST47K platform bridges functional genomics and precision breeding, accelerating the development of multi-purpose sorghum varieties. Reference | Related Articles | Metrics Select Genetic dissection of spike morphology in Australian barley panel: Insights from a multi-model GWAS and haplotype analysis Shunlin Zhang, Tianhua He, Yong Han, Gaofeng Zhou, Bettina Berger, Baojin Guo, Chengdao Li DOI: 10.1016/j.jia.2026.03.030 Online: 17 March 2026 Abstract （2）      PDF in ScienceDirect       Barley (Hordeum vulgare L.) is a globally important cereal crop increasingly challenged by climate variability and shifting agronomic demands. Spike morphology is pivotal in determining yield potential, but its genetic underpinnings remain only partially understood. Here, we leveraged the OzBarley panel with 214 elite Australian barley accessions, integrating high-density markers (65,465 SNPs) with multi-environment phenotyping to dissect the genetic architecture of six spike traits: awn length (AL), grain number per spike (GNS), spike density (SD), spike length (SL), spikelet number per spike (SNS), and seed setting rate (SSR). Genome-wide association studies identified 27 stable quantitative trait loci (QTLs) distributed across six chromosomes, explaining up to 22.52% of phenotypic variance. High heritability estimates (49.02-93.54%) and strong inter-trait correlations (r=0.33-0.89, P<0.001) underscore the stable genetic control. Haplotype-based dissection prioritized two major loci: QAL.Murdoch.7H.1, and QGNS/SD/SNS.Murdoch.4H.1. A missense SNP (Lys372Asn) in HORVU.MOREX.r3.7HG0720710 was implicated in the suppression of awn length at QAL.Murdoch.7H.1, while a nonsynonymous mutation (Ala127Thr) in HORVU.MOREX.r3.4HG0336810 at QGNS/SD/SNS.Murdoch.4H.1 was associated with increased spikelet and grain number. Longitudinal analysis revealed directional selection for favourable haplotypes, QGNS/SD/SNS.Murdoch.4H.1-Hap002 and QAL.Murdoch.7H.1-Hap004, with frequencies increasing significantly in recent Australian cultivars. Conversely, unfavourable haplotypes introduced during the 1990s were later counter-selected, highlighting refined breeding strategies. Our findings offer critical insights into the genetic regulation of barley spike morphology, thereby linking genomic discoveries to breeding applications. The OzBarley panel serves as a valuable genomic resource for accelerating marker-assisted selection, facilitating the development of high-yielding barley cultivars tailored to meet future agricultural demands. Reference | Related Articles | Metrics Select VvCRY2 mediates blue light signaling to regulate grape anthocyanin biosynthesis via the VvCOP1-VvHY5 signaling cascade Tianyu Dong, Shaonan Li, Yanhua Ren, Peian Zhang, Zhenyu Sun, Tianyi Hao, Jinggui Fang DOI: 10.1016/j.jia.2026.03.029 Online: 17 March 2026 Abstract （0）      PDF in ScienceDirect       Blue light enhances anthocyanin accumulation in grape berries, yet the molecular mechanisms underlying this photoreceptor-mediated process remain partially elucidated. ‘Kyoho’ grapevines were subjected to various light treatments, including monochromatic blue and red light (blue, red, or white) and mixed red-blue light treatments before fruit coloration. Anthocyanin content, transcriptome profiles, and gene expression were analyzed. Blue light most effectively promoted anthocyanin biosynthesis and upregulated structural genes (VvCHS, VvUFGT, VvANS) and the photoreceptor gene (VvCRY2) expression, whose expression was strongly correlated with anthocyanin accumulation. VvCRY2 physically interacts with the E3 ubiquitin ligase VvCOP1, repressing its activity under blue light. VvCOP1 interacts with transcription factors VvHY5 and VvMYBA1 in darkness, suppressing anthocyanin synthesis. Overexpression of VvCRY2 or VvHY5 enhanced anthocyanin accumulation in transgenic grape calli and strawberry fruits under blue light. VvHY5 directly binds to G-box elements in promoters of VvMYBA1, VvCHS, VvUFGT and VvANS, activating their expression via dual-luciferase assay. We propose a mechanistic model wherein blue light-activated VvCRY2 inhibits VvCOP1, releasing VvHY5 to transcriptionally activate anthocyanin biosynthesis genes. This study elucidates the VvCRY2-VvCOP1-VvHY5 module as a central regulatory axis for light-quality-mediated fruit coloration in grape. Reference | Related Articles | Metrics Select PbTCP2–PbTCP4 protein complex promotes pear flowering by suppressing transcription of the flowering-inhibition gene PbSVP Hongjuan Zhang, Jingjing Cheng, Kaile Liu, Hongbo Xia, Yutong Wang, Zesheng Wang, Jingjing Miao, Guangya Sha, Rui Zhai, Chengquan Yang, Zhigang Wang, Lingfei Xu DOI: 10.1016/j.jia.2026.03.028 Online: 17 March 2026 Abstract （0）            Members of the TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family are plant-specific transcription factors regulating numerous growth and developmental processes, including the flowering transition. However, the roles of TCP genes in regulating the flowering of pear remain unknown. Here, we identified PbTCP2 as a transcription factor associated with flowering. PbTCP2 was identified as a typical nucleus-located transcription factor without self-activation activity. The biofunction of PbTCP2 in promoting flowering was verified by heterologously expressing it in Arabidopsis. Compared with wild-type lines, the transcription levels of flowering activators in PbTCP2-overexpressing Arabidopsis were increased, while the transcription levels of flowering repressors, including PbSVP (SHORT VEGETATIVE PHASE), were significantly decreased. Yeast one-hybrid and electrophoretic mobility shift assays indicated that TCP2 protein directly binds to the promoter of PbSVP. The transcriptional repression activity of PbTCP2 on PbSVP was further confirmed by dual-luciferase assays. We further show that PbTCP4 interacts with PbTCP2, as evidenced by yeast two-hybrid, bimolecular fluorescence complementation, and pull-down assays. Notably, forming a complex with PbTCP2, PbTCP4 synergistically enhances this repression, a conclusion supported by dual-luciferase and GUS staining assays. Overexpression of PbTCP4 also promoted flowering in Arabidopsis. Collectively, these findings confirm a PbSVP-controlled flowering mechanism regulated by the TCP4–TCP2 complex in pear, shedding light on the molecular mechanisms underlying flowering regulation in perennial crops. Reference | Related Articles | Metrics Select Classification of fruit shape based on decision tree model and identification of QTLs and genes controlling fruit shape in eggplant Qiang Li, Shuangxia Luo, Huimin Du, Chive Paradowski, Jingjian Ma, Liying Zhang, Xupeng Jia, Ruoxuan Zhao, Dongfang Zhang, Wei Yan, Jianan Liu, Lijun Song, Esther van der Knaap, Sofia Visa, Xueping Chen DOI: 10.1016/j.jia.2026.03.027 Online: 17 March 2026 Abstract （0）      PDF in ScienceDirect       Eggplant (Solanum melongena L.) shows remarkable diversity in fruit shape, making it an excellent model for studying shape variation. Eggplant fruit shape influences consumer preference and plays an important role in the classification of commercial varieties and germplasm. Despite its importance, existing classification systems are limited to description without quantitative criteria, differ by country or region and fail to fully capture the diversity of eggplant fruit shapes. In the present study, thirteen shape categories were identified using a decision tree model with Gini index-based variable selection. Ten key attributes that largely determine fruit shape were identified and high accuracy (92.59%) classification rules were generated. Five other methods, including random forest, XGBoost, SVM, K-means and GMM, were also applied to fruit shape classification, but they proved less robust for classification compared to the decision tree. The shape modeling informed the key attribute selection for the QTL-seq and GWAS analyses. Four QTLs controlling Fruit Shape Index (FSI) and Proximal Angle Micro (PAMi) were detected using GWAS and QTL-seq. The candidate gene SmFSI3.1/SmFL, a member of the SUN/IQD family, was over-expressed in tomato and resulted in elongated fruits, indicating the positive roles of this gene in regulating fruit elongation in eggplant. In summary, we developed an accurate and reproducible model for classifying eggplant fruit shapes, which is of significance for eggplant breeding and variety classification. Moreover, we verified the function of the causal gene responsible for fsi3.1/fl3.1 locus, providing a foundation for understanding the genetic regulation of fruit shape in eggplant.  Reference | Related Articles | Metrics Select Leveraging disease-resistant gene mining to enhance genomic predictability for southern leaf blight in maize Youyu Zhao, Sen Xie, Guanhua He, Dengfeng Zhang, Zhenju Li, Chunhui Li, Yu Li, Tianyu Wang, Xuyang Liu, Yuncai Lu, Yongxiang Li DOI: 10.1016/j.jia.2026.03.026 Online: 17 March 2026 Abstract （1）      PDF in ScienceDirect       Southern leaf blight (SLB) is a significant and persistent threat to global maize production. While genomic selection (GS) offers promise for improving complex traits, strategies leveraging functionally informed SNPs with reduced marker sets can enhance model efficiency, cost-effectiveness, and biological interpretability. Here, we established a large association panel comprising 2,108 diverse inbred lines and employed a multi-model genome-wide association study (GWAS) framework. Through this approach, we identified 325 quantitative trait nucleotides (QTNs) and resolved 83 candidate genes. These candidate genes were functionally enriched in plant immune responses and included known disease resistance gene ChSK1 and ZmMM1. Haplotype analysis revealed that favorable alleles of novel candidate genes including ZmCNGC2 and ZmAGC1.8 are predominantly enriched in specific subgroups such as tropical lines but remain underutilized in other modern breeding materials, indicating significant potential for genetic improvement. Leveraging these genetic insights, we developed a compact set of 83 GWAS Tag-SNPs. This compact marker set achieved genomic prediction accuracy comparable to a full genome-wide markers while reducing marker density by 99.7%. In independent validation, the compact SNP set maintained robust predictive ability, which could be further enhanced by incorporating population structure as covariates. Our study provides a comprehensive dissection of the genetic architecture of SLB resistance and offers a cost-effective and biologically interpretable framework for disease resistance breeding in maize. Reference | Related Articles | Metrics Select Amino acid compound fertilizer and 24-Epibrassinolide regulate starch accumulation and flour physicochemical properties of mid-summer fresh waxy maize: A case study from the Yangtze River Basin, China Chenyang Jiang, Chao Yuan, Guoqing Chen, Jian Guo, Guanghao Li, Dalei Lu DOI: 10.1016/j.jia.2026.03.025 Online: 17 March 2026 Abstract （0）      PDF in ScienceDirect       Mid-summer fresh waxy maize often suffers concurrent high temperature and drought during kernel filling in the Yangtze River Basin, causing yield losses and quality deterioration. This study investigated the combined effects of fertilization and exogenous regulators on mid-summer fresh waxy maize yield and quality. A two-factor field experiment was conducted with two fertilization treatments (conventional compound fertilizer (CCF), and amino acid compound fertilizer (AACF)), two plant growth regulators (6-benzylaminopurine (6-BA) and 24-Epibrassinolide (BR)), and four co-treatments (CCF+6-BA, CCF+BR, AACF+6-BA, and AACF+BR). Compared with control (no fertilization and exogenous regulators), fertilization significantly increased fresh 100-kernel weight (HKW), soluble sugar content (SSC), starch content (SC), protein content (PC), and gelatinization enthalpy (∆Hgel), while it reduced average starch granule size (ASGS), relative crystallinity (RC), peak viscosity (PV), and setback viscosity (SB). AACF was more effective than CCF, increasing SC by 9.2% in SYN5 and by 13.4% in SYN11. Exogenous 6-BA and BR treatments significantly increased SSC and SC and decreased PC, ASGS, and RC. BR consistently increased ∆Hgel and reduced the retrogradation percentage (by 5.1% in SYN5 and by 9.9% in SYN11). However, the effects of 6-BA and BR on PV and breakdown viscosity depended on the variety. Principal component analysis showed that combined fertilization and regulator treatments produced greater improvements in yield and kernel quality than single-factor treatments, with AACF+BR having the strongest effect. These results demonstrated that coupling amino acid compound fertilizer with 24-Epibrassinolide was an effective strategy to stabilize quality under mid-summer climatic conditions in fresh waxy maize. Reference | Related Articles | Metrics Select Drought coupled with heat stress impairs maize silk vitality by disrupting sucrose metabolism and lignin biosynthesis Yulou Tang, Yifei Sun, Yingbo Gao, Reda M. M. Ahmed, , Meiyu Chen, Yongchao Wang, Hao Wang, Jiameng Guo, Xiuli Hu, Nasr M. Abdou, Mahmoud A. Abdelfattah, Qinghua Yang, Ruixin Shao DOI: 10.1016/j.jia.2026.03.024 Online: 17 March 2026 Abstract （0）      PDF in ScienceDirect       Under climate change, combined heat and drought stress (HD) during flowering increasingly threatens the maize production of the Huang-Huai-Hai region in China. While individual effects of heat (HS) or drought stress (DS) are well documented, their combined impacts—particularly on silk function—remain poorly understood. We conducted a two-year, temperature-controlled field experiment from the ten-leaf stage to silking to investigate the impacts of HD on silk function through physiological responses and transcriptomic pathways. The kernel setting rate under HD decreased significantly by an average of 56.7, 52.4, and 34.1% compared to non-stressed control, HS, and DS, respectively. This reduction was driven by increased floret abortion, resulting from unemerged silks and reduced vitality of emerged silks. Reactive oxygen species (ROS) accumulation impaired silk vitality. Transcriptomic analysis revealed that HD disrupted sucrose metabolism and lignin biosynthesis, leading to reduced glucose, fructose and lignin content. Peroxidase activity declined by 32.5, 38.7, and 46.1% under HS, DS, and HD conditions, respectively, while lignin content decreased by 24.4, 34.4, and 44.3%. Phenylalanine ammonia-lyase and cinnamyl alcohol dehydrogenase activities increased under stress, with the strongest upregulation observed under HD. HD synergistically suppressed the vitality of emerged silks by promoting sucrose and ROS accumulation while reducing lignin content, leading to increased floret abortion and kernel loss. These findings highlight a synergistic interaction between drought and heat stress in maize. Reference | Related Articles | Metrics page Page 1 of 22 Total 422 records First page Prev page Next page Last page