Flavonoid compounds, including anthocyanins and proanthocyanidins, are significant secondary metabolites in plants and play crucial roles in various aspects of plant growth, development, and environmental stress responses. In the present study, we identified a key transcription factor from the NAC family, designated as MdNAC72-like, which had a strong correlation with the anthocyanin content during the apple fruit ripening process. Through techniques including yeast one-hybrid analysis, electrophoretic mobility shift assays, and luciferase reporter assays, we illustrated that MdNAC72-like directly interacts with the promoters of the MdMYB9, MdLAR, and MdUFGT genes. This interaction enhances their transcriptional activity, leading to a favorable impact on the biosynthesis of anthocyanins and proanthocyanidins in plants. Furthermore, utilizing yeast two-hybrid, pull-down, and bimolecular fluorescence complementation assays, we demonstrated that MdERF1B forms an interaction with MdNAC72-like, which in turn augments the transcriptional activation ability of MdNAC72-like on the downstream structural genes MdMYB9, MdLAR, and MdUFGT. In conclusion, MdNAC72-like presents significant research potential, and these results offer a theoretical framework for understanding the regulatory mechanisms governing anthocyanin and proanthocyanidin synthesis in apple.

Agropyron cristatum (2n=4x=28, PPPP), a wild perennial relative of wheat, is considered as an excellent donor for wheat improvement given its multiple florets and spikelets, broad-spectrum disease resistance, and extreme stress tolerance. In this study, we created the addition line II-24 of A. cristatum chromosome 4P, and telosomic addition lines of 4PS and 4PL by backcross of the addition line II-23 containing multiple A. cristatum chromosomes with common wheat Fukuho. Multi-year agronomic evaluations revealed that addition of 4PL in common wheat variety Fukuho resulted in a significant increase of grain number per spike (GNS) and effective tiller number (ETN) without compromising thousand-grain weight (TGW). Additionally, we developed a translocation line WAT41 (T4PL-3DS·3DL). Compared to the control, the line WAT41 simultaneously exhibited an increase of GNS (5.79%), spikelet number per spike (2.42%), kernel number per spikelet (3.52%), and spike length (4.93%) without compromising TGW. Resequencing analysis revealed that WAT41 carries a chromosomal segment from 505 to 585 Mb of 4P, harboring sixteen spike development-related genes. Furthermore, we developed two specific molecular markers from these genes to track the high-GNS chromatin segment for breeding selection. Collectively, this study provides novel germplasm resources, which is able to overcome the negative relationship between GNS and TGW and broadening the genetic base for wheat breeding.

 Iron (Fe) deficiency is a globally widespread condition in which the body lacks sufficient Fe to produce hemoglobin. However, major food crops generally have low grain Fe contents. Consequently, enhancing grain Fe concentrations is important for improving the health of populations that rely on grains as staple foods. Here, we isolated a yellow stripe leaf mutant of foxtail millet (Setaria italica), designated yellow stripe-like 1 (ysl1). This mutant exhibited typical Fe deficiency symptoms that were alleviated when grown under Fe-sufficient conditions. Compared with the wild-type, Siysl1 showed lower Fe concentrations in seedling roots, shoots, stems, elongation-stage leaves, panicles, and seeds, but a higher Fe concentration in heading-stage leaves. Using MutMap+, we identified and cloned SiYSL1 and validated its function through CRISPR/Cas9-mediated knockout experiments. SiYSL1 encodes an Fe-phytosiderophore transporter and is highly induced under Fe deficiency conditions. Histochemical staining revealed that SiYSL1 is specifically expressed in vascular bundles of roots and leaves of plants grown under Fe deficiency conditions, and in spikelets, expanding ovaries, basal endosperm, and embryo-surrounding tissues. Thus, SiYSL1 appears to regulate Fe uptake and homeostasis, and plays an essential role in Fe translocation to seeds. The overexpression of SiYSL1 in rice and foxtail millet significantly increased seed Fe contents, suggesting its value in crop breeding. Predicted transcription factor binding sites in the SiYSL1 promoter and a spikelet transcriptome analysis indicated that transcription factors regulate SiYSL1 expression. Our study provides new genetic resources for the Fe bio-enhancement of food crops and insights into the mechanisms responsible for seed Fe accumulation.

Under saline-alkali conditions, crops experience the dual stresses of high salinity and high pH. However, over the past few decades, the majority of researches focused primarily on plant responses to salt stress alone, leaving a limited understanding of how crops respond to combined saline-alkali stress and the underlying resistance mechanisms. In this study, we conducted large-scale screening of 458 accessions from a foxtail millet (Setaria italica) mini-core germplasm collection under mixed sodium saline-alkali stress and identified extreme tolerant and sensitive lines. Compared to sensitive varieties, saline-alkali-tolerant accessions accumulated higher levels of lignin, soluble sugars, and proline, but lower levels of malondialdehyde (MDA). These adaptive adjustments thus enable salt-tolerant varieties to undergo minimal transcriptomic reprogramming under stress. Furthermore, enhanced lignin deposition, triggered by SAPK10 overexpression, contributed substantially to plant resistance to saline-alkali stress. Collectively, our study identified promising germplasm and pinpointed lignin-mediated physical defense as a key strategy for saline-alkali tolerance in foxtail millet.

盐碱环境下，作物往往同时面临高盐和高 pH 的双重胁迫。然而，过去几十年的研究大多集中于植物对单一盐胁迫的响应，对作物应对复合盐碱胁迫的方式及其抗性机制仍缺乏系统认识。本研究在混合钠盐型盐碱胁迫条件下，对458份谷子（Setaria italica）微核心种质进行了大规模筛选，鉴定出极端耐盐碱和极端敏感材料。与敏感材料相比，耐盐碱材料中木质素、可溶性糖和脯氨酸含量更高，而丙二醛（MDA）含量较低。上述生理调节使耐盐碱材料在胁迫条件下仅需较小幅度的转录组重塑即可维持适应性。进一步研究发现，SAPK10 过表达诱导的木质素沉积增加可显著增强植株对盐碱胁迫的抗性。综上，本研究筛选出具有潜在利用价值的优异谷子种质，并揭示木质素介导的物理防御是谷子耐盐碱的重要机制。

Alternate wetting and drying irrigation (WD) is an effective water-saving practice for rice production but often increases nitrous oxide (N₂O) emissions. Plant growth-promoting bacteria such as Bacillus subtilis (BS) can enhance crop growth; however, the combined effects of WD and BS on rice yield and N₂O emissions remain unclear. A 3-year field experiment using two japonica rice cultivars was conducted to evaluate the effects of two irrigation regimes (continuous flooding (CF) and WD) and Bacillus subtilis (BS) application (without BS, -BS; and with BS, +BS) on rice yield and N₂O emissions. Results showed that BS application significantly increased rice yield under both irrigation regimes. Compared with CF-BS, CF+BS and WD+BS increased yield by 3.4-6.0% and 5.8-12.7%, respectively, mainly due to a higher total spikelet number. CF+BS had no significant effect on N₂O emissions, whereas WD-BS markedly increased cumulative N₂O emissions, while WD+BS reduced emissions by 30.0-41.0% compared with WD-BS. The WD+BS treatment enhanced root oxidation activity and increased root surface area and volume density in the 20–40 cm soil layer. It also decreased soil NO₃⁻-N content, raised the NH₄⁺/NO₃⁻ ratio, and enhanced urease and sucrase activities, thereby promoting the accumulation of dissolved organic carbon (DOC) and microbial biomass nitrogen (MBN), along with a higher abundance of the nitrous oxide reductase gene (nosZ) associated with N₂O reduction. Overall, integrating WD with BS increased rice yield while mitigating N₂O emissions. Enhanced root function, and aboveground agronomic traits, improved soil enzyme activity, and optimized nitrogen transformation and microbial processes were the key mechanisms achieving high yield with reduced environmental impact.

Optimizing plant density through modeling strategies is essential for improving resource-use efficiency and productivity in modern maize production systems. Functional–structural plant models (FSPMs) such as GreenLab provide a powerful framework for simulating crop growth and yield formation, yet their ability to represent interplant competition under high-density conditions remains limited, largely due to the oversimplified treatment of specific leaf area (SLA). To address this gap, a two-year field experiment (2022–2023) composed of four maize plant densities (3, 6, 9 and 12 plants m⁻⊃2;, denoted as PD3, PD6, PD9, and PD12, respectively), was conducted to examine density-driven changes in leaf structural and functional traits and to evaluate the role of SLA plasticity in regulating canopy light and nitrogen use efficiency. Increased plant density substantially reshaped canopy architecture and resource distribution. Compared to PD3, higher densities (PD6, PD9, and PD12) increased leaf orientation value, SLA, photosynthetic nitrogen-use efficiency (PNUE), radiation-use efficiency (RUE) and crop growth rate (CGR), while reducing individual leaf area (LA), specific leaf nitrogen content (SLN) and light-saturated photosynthetic rate (A_max). Further analyses showed that density-induced SLA plasticity enhanced PNUE and adjusted the ratio of nitrogen to light extinction coefficients (K_N/K_L), thereby partially compensating for the decline in leaf photosynthetic capacity caused by reduced SLN. At the canopy scale, SLA was strongly and positively associated with RUE, highlighting its role in enhancing canopy photosynthesis under interplant competition. Subsequently, the observed SLA responses to plant density were parameterized and incorporated into the GreenLab-Maize model. Compared to the standard model, the revised model markedly improved predictions of LA, leaf area index, RUE and accumulated biomass under high-density conditions. Overall, this study establishes SLA plasticity as a key adaptive trait for resource optimization in dense stands and provide a validated method to enhance the realism of competition simulations in FSPMs.

Adjusting soil pH and supplementing calcium (Ca) are widely adopted agronomic practices for peanut cultivation in acidic soils, but their role in modulating cadmium (Cd) accumulation remains poorly clarified. Therefore, pot and hydroponic experiments were both conducted to assess the impacts of lime application (at a rate of 0.7%) and Ca application in the form of Ca(NO₃)₂ at varying levels (0.01, 0.02, and 0.04%) on Cd bioavailability in an acidic soil and its uptake by peanut. Results demonstrated that lime and Ca(NO₃)₂ individually reduced seed Cd concentrations by 15.7 and 30.4%, respectively, while their combined application increased peanut yield and reduced Cd concentration in seeds. Lime predominantly reduced Cd accumulation by limiting its uptake through root; while Ca(NO₃)₂ increased Cd in the soil solution but promoted Cd sequestration in shoot cell wall, ultimately restricting Cd translocation to pods. Additionally, hydroponic experiments under acidic to near-neutral conditions revealed a parabolic response of Cd uptake to the changes in pH and Ca concentration. The maximum Cd uptake was noticed at pH 6.0 with 1 mmol L^-1 Ca application (Ca/Cd=2,000). The notable decrease of Cd uptake were observed at higher pH 7.5 and Ca>1 mmol L^-1, but it also cause the reduction of plant biomass. These findings demonstrate that the optimization of pH and Ca⊃2;⁺ levels is necessary to enhance peanut yield and minimize Cd translocation to edible seeds. 

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.

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. 

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.

每穗颖花数是决定水稻产量的关键性状，其形成受穗形态建成的调控——这是一个多基因协同控制的生物学过程，并与营养生长期植株地上部生物量的积累密切相关。本研究提出水稻颖花生产效率（spikelet production efficiency, SPE）的概念，将其定义为每穗分化的颖花数与颖花分化期单茎营养器官干物重的比值。通过对不同SPE的水稻品种进行比较分析发现，在高产群体条件下，SPE高的品种不仅能显著增强光合产物的生产供应，还能有效促进花后茎秆贮藏的非结构性碳水化合物向籽粒再转运。这种光合生产与物质转运的协同提升，促进了籽粒产量和收获指数的协同提高。本研究结果揭示，提高SPE对于进一步释放水稻产量潜力具有重要作用，尤其在高产群体条件下，可成为提高收获指数的有效途径。因此，提高SPE不仅可作为超级稻育种的关键指标，也为实现水稻高产高效的协同提供了新的调控策略。

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.

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.

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.

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.

在长期自然选择与人工选择双重压力下，不同绵羊群体表现出脂尾、瘦尾和脂臀等三类主要尾型特征。然而，目前关于尾型遗传机制研究多集中于单一基因或单一性状维度，缺乏系统性解析。本研究基于高深度全基因组重测序数据，对中国绵羊23个群体从尾的有无、尾长变异与尾脂沉积三个角度开展针对性分析，通过整合全基因组选择信号分析、精准定位以及扩群验证，鉴定到与尾形成相关TBXT（C/A）、与尾长调控相关 HOXB13（C/G），以及与尾部脂肪沉积相关 PDGFD（G/A）的非同义突变，这些位点的优势单倍型组合C-G-G、C-C-G、A-A、C-G-A 和 C-C-A分别在长细尾、短细尾、脂臀、长脂尾和短脂尾群体中显著富集。此外，功能验证结果表明，PDGFD基因在调控细胞增殖与脂肪分化平衡过程中发挥重要作用。这些结果加深了我们对多基因协同调控绵羊尾型变异遗传机制的理解，并为绵羊尾型遗传改良和分子设计育种提供关键靶点。

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.

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.

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. 

Peanut (Arachis hypogaea L.) is a globally recognized crop with a pivotal role in the agricultural and economic sectors worldwide. Low temperature during the flowering stage is a major constraint for peanut yield in high-altitude and high-latitude regions. Despite extensive progress in understanding vegetative low temperature responses, the molecular mechanisms governing reproductive-stage low temperature sensitivity remain largely unexplored. To clarify how low temperature disrupts anther function and pollen fertility, a comparative study was conducted between a low temperature-tolerant genotype (NH5) and a low temperature-sensitive genotype (NH9) under controlled low temperature conditions. Low temperature markedly impaired peanut reproductive development by reducing peg and pod formation, altering floral organ morphology, and decreasing pollen viability, while tolerant genotype NH5 exhibited milder yield and pollen damage than sensitive NH9, indicating that low temperature primarily affects peanut yield through pollen quality deterioration. Furthermore, multi-omics profiling identified 20,928 differentially expressed genes and 1,613 metabolites, showing significant enrichment in carbohydrate metabolism, glycolysis, and tricarboxylic acid (TCA) cycle pathways, thereby highlighting severe metabolic reprogramming in low temperature-sensitive anthers. Importantly, low temperature stress triggered a pronounced accumulation of abscisic acid (ABA) in sensitive genotypes, which in turn suppressed key sugar-metabolizing enzymes activities (BAM, INV, HXK, PK, and CS) and restricted hexose availability to developing pollen. Consistently, exogenous ABA application exacerbated pollen sterility, whereas chemical inhibition of ABA biosynthesis restored fertility and reactivated carbon metabolism under low temperature conditions. Together, these findings demonstrate that ABA acts as a pivotal negative regulator of reproductive low temperature tolerance by constraining sugar utilization in peanut anthers. This study thus provides new mechanistic insight into ABA–sugar metabolism coordination during floral low temperature adaptation and offer a theoretical basis for breeding peanut varieties with enhanced low temperature resilience.

The fungal pathogen Ustilaginoidea virens, which causes the devastating rice false smut disease, relies on scavenging host nutrients for infection, yet the identity and exploitation mechanisms of these nutrients remain unclear. This study reveals a previously unrecognized virulence strategy in which U. virens hijacks host-derived trehalose, a disaccharide linked to plant stress responses, by enhancing its trehalose catabolic capacity. Central to this process are two functionally distinct trehalases, UvNTH (neutral trehalase) and UvATH (acid trehalase), which exhibit a clear division of labor. UvNTH drives extracellular trehalose utilization, vegetative growth, and asexual sporulation, while UvATH specifically regulated aerial hyphal development. Strikingly, the ΔUvNTH mutant colonizes host tissues normally but completely fails to produce mature false smut balls, uncoupling colonization from symptom formation and identifying UvNTH as a dedicated virulence switch essential for pathogenicity. In addition, UvNTH plays a critical regulatory role in the germination process of chlamydospores, the primary inoculum of the pathogen. Collectively, these findings demonstrate that UvNTH functions not only as a metabolic enzyme but also as a dual-functional regulator that coordinates virulence and the propagation of primary infection sources, thereby providing an ideal target for the sustainable management of rice false smut.

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.

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.

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.

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.

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. 

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.

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 (∆H_gel), 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 ∆H_gel 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.

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.

Brucellosis, caused primarily by Brucella abortus, Brucella melitensis, and Brucella suis, remains a critical global public health challenge, particularly in regions where these pathogens persist in livestock and wildlife reservoirs. Despite decades of control measures-including vaccination, test-and-removal programs, and biosecurity protocols-persistent human and animal cases highlight the limitations of existing diagnostic and intervention strategies. CRISPR-based diagnostics have emerged as a transformative tool, offering rapid, ultrasensitive, and field-deployable pathogen detection. Here, we present BOVDS (Brucella melitensis/abortus/suis-other pathogens-vaccine detection and differentiation system), an innovative CRISPR/Cas13a-based platform that integrates ultrahigh sensitivity (10 copies/µL), screening for 10 major abortifacient pathogens, and precise strain differentiation-overcoming key challenges in Brucella diagnostics. By incorporating mismatched spacer designs, BOVDS achieves robust discrimination between B. melitensis, B. abortus, and B. suis despite their high genomic conservation. Additionally, the platform enables differentiation between vaccine and wild-type strains, addressing critical gaps in vaccination monitoring and epidemiological surveillance. Uniting laboratory-level accuracy with on-farm practicality, BOVDS facilitates real-time outbreak management, targeted culling, and environmental decontamination, advancing One Health initiatives toward sustainable brucellosis prevention and control. This system sets a new benchmark for next-generation zoonotic disease diagnostics, with broad applicability in global public and veterinary health.

Under accelerating climate change, elevated atmospheric CO₂ (e[CO₂]) presents a substantial challenge to nitrogen (N) cycling in agricultural systems. This study elucidated the mechanistic role of biochar in regulating soil N transformations and plant N acquisition under e[CO₂] conditions through a three-year pot experiment (2019-2022) with wheat. Using ¹⁵N isotope tracing combined with metagenomic sequencing, we examined the interactions between two CO₂ concentrations (a[CO₂] 400 μmol mol⁻¹ vs. e[CO₂] 600 μmol mol⁻¹) and 2% (w/w) biochar amendment. Our results demonstrated that under e[CO₂], biochar application reduced the incorporation of fertilizer-derived N into the recalcitrant heavy fraction organic N (HFON) by 39.4%, while enhancing the content of native soil-derived N in the light fraction N (LFON) by 34.0%. Concurrently, biochar promoted the formation of micro-aggregates (<0.25 mm) and particulate organic N (PON) by 37.3 and 13.2%, respectively. Metagenomic analysis revealed that biochar under e[CO₂] suppressed the relative abundance of key N-cycling genes (involved in assimilation, nitrification, and nitrate reduction) that were upregulated under a[CO₂] condition. These physicochemical processes, coupled with microbial modulation, resulted in a 52.6% reduction in soil NO₃^--N accumulation and a significant increase in aboveground N uptake. Structural equation modeling indicated that biochar counteracted the adverse effects of e[CO₂] on micro-aggregate stability and N-cycling gene abundance. Synergistically, biochar enhanced the uptake of fertilizer-N and native soil-N by 30.8% and 111.4%, respectively, under e[CO₂], leading to a 55.4% increase in grain N accumulation. Our findings demonstrate that biochar is an effective amendment for mitigating e[CO₂]-induced N limitation by redistributing N from recalcitrant to labile pools, enhancing N bioavailability, and ultimately supporting crop productivity in future CO₂-enriched agroecosystems.

Gossypium hirsutum L. is a globally important economic, oil and forage crop, and its yield stability is facing severe challenges. Improving photosynthetic efficiency is a core scientific problem urgently to be solved in the field of cotton genetic improvement and high-yield cultivation. In this study, a brassinosteroid (BR)-responsive basic helix-loop-helix (bHLH) transcription factor GhPAS1 was identified, and two independent overexpression lines (OE-1, OE-2) and wild-type ZM24 were used as materials to carry out gene function identification. A two-year field experiment showed that the effects of GhPAS1 overexpression were stable and consistent across the two growing seasons: the stomatal density (SD) of overexpression lines was increased by 27.9-67.6% and the stomatal size (SS) was decreased by 9.1-26.7% compared with the wild type, and the optimized stomatal structure significantly increased the net photosynthetic rate (A_N) of leaves in overexpression lines by 13.1-28.0%. Meanwhile, the leaf area index (LAI), canopy light interception efficiency (FIPAR) and canopy photosynthetic rate (CAP) of overexpression lines were increased by 36.5-78.8%, 5.8-9.5% and 24.1-38.5%, respectively, thereby promoting the aboveground biomass and yield to increase by 50.1-78.8% and 21.6-53.6% compared with the wild type. Molecular mechanism analysis showed that GhPAS1 interacted with BR signaling components (BA13, BRI1) and light-responsive factor PRE6, integrating signals to regulate stomatal development and canopy architecture. In conclusion, GhPAS1 stably regulates stomatal and canopy traits, improves photosynthetic efficiency, and promotes yield formation, making it a key functional gene for the improvement of photosynthesis and yield in cotton.

本研究选取了来自不同群系的20份苦荞种质，并系统评估了其未成熟合子胚的原胚细胞复合体（PECCs）诱导和增殖能力，从而筛选出了具有卓越的PECCs诱导和增殖能力的种质G253。基于G253的形态发生愈伤（MC），成功建立了一个稳定的农杆菌介导的遗传转化平台，获得的愈伤转化系中T-DNA整合的阳性率超过90%，并通过PECCs再生体系获得了转基因植株。此外，还基于苦荞MC开发了一个高效的原生质体瞬时转化系统。本研究为克服苦荞遗传转化的瓶颈、加速其分子育种进程提供了关键的种质资源和技术平台。

Melanins are a class of dark pigments widely distributed among living organisms. In cereal crops, the black husk-pericarp trait arises from melanin accumulation. The durum wheat (Triticum turgidum L. var. durum Desf.) cultivar Ofanto (Oft) exhibits black awns beginning at the soft dough stage. To identify the genetic loci associated with awn color, we analyzed an F₂ population derived from a cross between Oft (black awn) and Langdon (LDN, yellow awn). Genetic mapping revealed a single dominant black awn gene, TdBa, located within an approximately 4.38 Mb interval on the short arm of chromosome 1AS. Among the 34 annotated genes located within this interval, TRITD1Av1G000090, which encodes amino acid transporters homologous to the rice black hull gene OsBh4 and barley black husk/pericarp gene HvBlp, was identified as a candidate gene based on sequence, expression, and gene function prediction analyses. In contrast to its homologous genes OsBh4 and HvBlp, TdBa causes only black awn in wheat. The role of TRITD1Av1G000090 in awn coloration was subsequently confirmed through transgenic assays.

Understanding the relative contributions of climatic and non-climatic factors to cotton yield variability is essential for developing climate-resilient production systems. Using county-level yield records from 1990 to 2024 together with gridded climate data, this study quantified the impacts of climate variability on cotton yield across Xinjiang, China, and assessed future yield responses under two CMIP6 scenarios (SSP2-4.5 and SSP5-8.5). Random forest models and a panel regression approach were applied to disentangle climatic and non-climatic yield components and to capture nonlinear climate–yield relationships. The results show that climate variability accounts, on average, for approximately one-third of the interannual yield variation across Xinjiang, while non-climatic factors dominate long-term yield growth. Pronounced spatial heterogeneity is observed in climate impacts: warming conditions are projected to benefit cotton production in southern and eastern Xinjiang, whereas about one-third of cotton-growing counties, predominantly situated in northern Xinjiang and high-altitude regions, are projected to experience negative climate impacts. At the regional scale, the net effect of climate change on cotton yield is projected to remain positive, with stronger yield enhancement under SSP5-8.5, although this overall gain masks substantial county-level disparities. Assuming constant planting areas, adverse climate impacts are projected to result in total production losses of approximately 2.4–3.2×10⁵ t by mid-century and 2.8–3.0×10⁵ t by the end of the century across negatively affected counties. These findings highlight the critical role of non-climatic drivers, including agronomic innovations and irrigation management, in sustaining yield growth and buffering adverse climate effects. From a policy perspective, the results underscore the need for region-specific adaptation strategies that enhance climate resilience in major production zones while guiding the spatial optimization of cotton production under future climate change.

高效、省力的制种生产对杂交水稻至关重要。在制种过程中，需要割除剑叶以消除授粉障碍并提高水稻种子产量。然而，这一过程对劳动强度和操作技能要求极高，且不可避免地会对稻穗造成一定损伤。本研究通过对籼稻品系93-11进行⁶⁰Co-_γ辐射处理，创制出一个新型小剑叶突变体ym66。图位克隆分析表明，该现象是由GATA型转录因子OsGATA15中的插入突变所致。我们将ym66突变体与籼稻品系YHSM杂交，培育出优良的小剑叶恢复系NP27。在制种过程中，NP27在不割除剑叶的情况下，其种子产量并未降低。此外，其F₁代在株型和稻米品质方面均表现出优良性状。这些结果表明，这种OsGATA15基因的新型小剑叶等位变异能够有效简化水稻制种流程，在杂交水稻中具有良好的应用潜力。

Competition is a fundamental driver of evolution, shaping species' adaptive trajectories and ecological dynamics, where interspecific competition influences community structure and niche differentiation, while intraspecific competition plays a critical role in functional development and adaptive evolution, particularly in agroecosystems where competition among pathogen genotypes, combined with host-pathogen interactions, significantly impacts the evolution of virulence. Through laboratory experiments involving single and mixed inoculations, this study investigates intraspecific competition in Phytophthora infestans, the causal agent of late blight in potatoes and tomatoes, to understand the impact of genotype frequency, genetic relatedness, and genetic variation on transmission and pathogenicity. Results revealed that strains with higher field frequencies exhibited greater competitive ability, while increased genotypic complexity and genetic distance between coinfecting strains enhanced disease severity and reduced incubation periods, highlighting the role of intraspecific competition in shaping pathogen evolution and virulence, with implications for disease management. Strategies such as crop diversification, biocontrol agents and microbiome applications are proposed to mitigate the evolution of highly virulent strains and promote sustainable agricultural practices. This study bridges theoretical and empirical insights into competitive interactions, offering a deeper understanding of the mechanisms driving pathogen evolution and their ecological consequences.

The continuous rise in global temperatures and the increasing frequency of extreme heat events pose severe challenges to rice production due to heat stress. Exploring heat tolerance genes and developing heat-tolerant rice varieties represent effective strategies to address this issue. In this study, we identified a novel heat tolerance gene, OsClpI3, through analysis of the Caseinolytic proteases (Clp) ATPase gene family. OsClpI3 is predominantly expressed in leaves, encodes a chloroplast-localized protein, and positively regulates heat tolerance during both the seedling and heading stages. OsClpI3 exhibits ATPase activity, which is markedly reduced in mutant lines. Integrated transcriptomic and metabolomic analyses revealed that OsClpI3 contributes to rice thermotolerance by maintaining photosynthetic electron transport efficiency and overall photosynthetic performance under high-temperature conditions. Furthermore, natural variation in OsClpI3 affects heat tolerance, and haplotype analysis revealed a superior haplotype, Type4. These findings provide new insights into the molecular mechanisms underlying heat tolerance in rice and offer valuable genetic resources for breeding heat-tolerant rice varieties.

Mammalian orthoreoviruses (MRVs) have been identified in various mammalian species, including humans. Although there have been numerous reports on the cross-species transmission and genetic reassortment of MRVs among humans, livestock and wildlife, the prevalence and pathogenicity of MRVs on swine herds in China remain largely unknown. In this study, a novel MRV type 3 (MRV3) HN2019-01 strain was isolated on Vero cells from a clinical porcine epidemic diarrhea virus-positive intestinal content of a diarrheic piglet, and was identified using the small RNA deep sequencing, electron microscopic observation and the immunofluorescence assays. This isolated strain was able to replicate in multiple cell lines and showed the best replicative efficiency on Vero cells. Genetic analysis revealed that MRV HN2019-01 was a recombinant strain with gene segments from the swine MRV2 and MRV3, and has a close phylogenetic relationship with the MRV2/117 RNA, MRV2/CH/GX/PReoV/2435/2018, MRV3/ZJ2013 and MRV3/BM-100 strains. Subsequently, the pathogenicity of MRV HN2019-01 was evaluated in 5-day-old piglets. The results showed that the MRV HN2019-01 strain caused diarrhea and intestinal villi damage in piglets. Meanwhile, MRV HN2019-01 infection was shown to affect both the diversity and composition of the colonic microbiota in piglets, with a significant increase in Collinsella and Enterococcus and a notable decrease in Lactobacillus, Desulfovibrio and Ruminococcus. Metabolomic analysis revealed that MRV HN2019-01 infection in piglets induced alterations in multiple intestinal metabolites, including carbohydrates, bile acids, 3-hydroxy-L-tyrosine-AMP and short-chain fatty acids. KEGG pathway enrichment analysis indicated significant differences between the infected group and the control group in pathways such as thiamine metabolism, protein digestion and absorption, tyrosine metabolism and phenylalanine metabolism. This study provided important foundational data for investigating the pathogenic mechanisms and evolutionary characteristics of MRV and for the development of vaccines against MRV.This study provided important foundational data for investigating the pathogenic mechanisms of MRV and for the development of vaccines against MRV.