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.

Nitrogen reduction is an effective strategy for improving nitrogen use efficiency (NUE) in crops, but it often leads to a decrease in grain number per unit area. Increasing planting density can enhance sink capacity by raising the number of grains per unit area. However, it remains unclear whether the combined strategy of reducing nitrogen input while increasing planting density can sustain or improve wheat yield, as well as the underlying source-sink regulatory mechanisms. In this study, two wheat cultivars with contrasting sink characteristics were selected: the multi-spike cultivar XN20 (Xinong 20) and the large-spike cultivar LKAZ8 (Lankaoaizao 8). A split-plot experimental design was adopted, involving three nitrogen levels and two planting densities. The results showed that the combined strategy of reducing nitrogen and increasing density significantly enhanced aboveground dry matter, grain yield, and NUE. While nitrogen reduction decreased the leaf area index (LAI) by 1.61–22.39%, increased planting density raised LAI by 2.99–14.13%, sink capacity by 3.08–27.58%, and improved the grain-to-leaf area ratio (GN-LAR). GN-LAR was significantly positively correlated with post-anthesis dry matter accumulation and nitrogen remobilization. Compared with conventional nitrogen and density management, the integrated strategy enhanced source supply, improved the source-sink relationship by increasing sink capacity and optimizing GN-LAR, and thereby promoted post-anthesis dry matter accumulation and nitrogen remobilization, strengthening the coordination between source supply and sink demand. These findings provide new insights into the regulatory mechanisms of the source-sink relationship in wheat under conditions of reduced nitrogen and increased planting density, offering a scientific basis for achieving a balance between high yield and high NUE in wheat production.

Agriculture is the foundation of global food security and quality of life, with staple crops such as rice, wheat, and maize meeting the dietary needs of the majority of the world's population. These crops are susceptible to diseases that can lead to significant yield losses; for example, wheat rust disease causes annual losses that exceed $2.9 billion. Accurate captioning of the phenotypic characteristics of plant diseases plays a crucial role in supporting diagnosis, which is essential for ensuring food security. Existing methods in agriculture struggle to adequately address the heterogeneity in visual phenotypes and disease descriptions, which leads to inadequate focus on key disease characteristics. To address this issue, we propose a zero-shot image captioning framework named PDPC. PDPC employs an extensive descriptive corpus, syntactic analysis, and optimization of semantic structures to significantly improve the quality and generalization of disease descriptions. Additionally, we construct a dataset comprising 20,943 image captions that describe the characteristics of plant diseases in more than 60 plant species and 300 diseases. Experimental results demonstrate that the PDPC framework outperforms existing models in accurately describing the characteristics of plant disease. The introduction of this innovative framework enhances the accuracy of disease descriptions and provides robust support for the intelligent diagnosis and management of plant diseases, ultimately paving the way for better plant health and higher agricultural yields. 

Crop models have been widely used to optimize nitrogen (N) applications for agronomic decision-making, but uncertainties in model calibration under varying N levels, particularly the effects of phenology choice for calibration, remain underexplored. This study employed the ORYZA v3 model, coupled with a global optimization algorithm, to assess how different calibration strategies affected predictions of leaf area index (LAI) and biomass in two rice varieties under four N levels (0, 90, 180, and 270 kg ha^-1). The results indicate when the model is calibrated separately for each N level, predictive accuracy varies considerably for both LAI and biomass, reflecting the difference in crop response to N availability. When calibrating the model simultaneously with multiple N levels from a single phenology phase, variability from different selected phenology phases becomes the dominant source of model uncertainty, rather than N levels. Specifically, calibrations using measured data from the stem elongation to anthesis (SA) and anthesis to maturity (AM) phases across N levels provide the most accurate predictions for LAI (RMSE: 0.51–1.92 m⊃2; m^-⊃2;; R⊃2;≥0.88) and biomass (RMSE: 551–2619 kg ha^-1; R⊃2;≥0.96), respectively. In contrast, calibrations using measured data from early-season (transplanting to stem elongation) result in the least reliable predictions. Combined-phase calibrations using SA and AM phases result in the best predictions for both LAI and biomass, owing to their balanced representation of pre- and post-anthesis growth dynamics. This approach significantly reduces uncertainty from phase selection. However, variability in N application rates emerges as the primary uncertainty source in model simulations, emphasizing the importance of careful selection of N levels in calibration datasets, particularly when measured data span two-thirds of the growing season. These findings offer valuable insights into improved calibration practice for precise N management, highlighting the critical role of both phenology phase and N treatment selection.

Insects depend on sophisticated olfactory systems for essential behaviors, with odorant receptors (ORs) lying at the core of odor detection. Spodoptera frugiperda is a major global agricultural pest, but the response profiles of its ORs remain largely unresolved. Here we focused on the functional characterization of SfruOR37 in S. frugiperda, an ortholog of Helicoverpa armigera HarmOR50 – which responds to (±)-camphor, an important plant volatile. Tissue expression analysis showed that SfruOR37 is specific expressed in the antennae of both sexes. Using Xenopus laevis oocytes, we functionally screened candidate ligands and identified linalyl acetate as the most potent activator of SfruOR37. To elucidate the binding mechanism between this receptor and its ligand, we performed molecular docking and dynamics simulations, which highlighted several non-conserved residues (notably S151, Y155, and Y325) likely shaping the SfruOR37 binding pocket and mediating the binding affinity to linalyl acetate. Electroantennogram (EAG) recordings demonstrated that linalyl acetate effectively elicits significant electrophysiological responses in adult antennae. In behavioral assays, linalyl acetate elicited a pronounced repellent effect on adult S. frugiperda. Together, our results illuminate how conserved ORs can diverge functionally within Lepidoptera and how such divergence contributes to ecologically relevant olfactory coding. Finally, by establishing linalyl acetate as a behaviorally active repellent for S. frugiperda, this study provides a theoretical basis for developing odorant-based, eco-friendly pest control strategies.

Bacterial pathogens harbor numerous two-component systems (TCSs) in their genomes, which enable rapid sensing and response to environmental fluctuations, thereby facilitating dynamic adaptation to diverse ecological niches. Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of kiwifruit bacterial canker (KBC), a devastating disease threatening global kiwifruit production. However, the biological function of the metal-responsive TCS CzcSR in Psa remains largely uncharacterized. In this study, we demonstrated that CzcSR plays a crucial role in regulating Psa pathogenicity in the host plant and the hypersensitive response (HR) in the non-host plant. Under zinc ion (Zn²⁺) stress, Psa exhibited suppressed motility and enhanced oxidative stress tolerance; notably, this phenotype depends on the Zn²⁺-binding sites of CzcS and the phosphorylation status of CzcR. However, the key virulence factor type III secretion system (T3SS) of Psa is unaffected by Zn²⁺ stress, and CzcSR-mediated regulation of the T3SS is independent of both the Zn²⁺-binding sites of CzcS and the phosphorylation status of CzcR. Instead, CzcR controls T3SS expression by binding to the promoter region of hrpR and modulates the c-di-GMP level via interacting with diguanylate cyclase (DGC) PSA_4781. Collectively, our findings expand CzcSR’s functional repertoire, highlight TCS complexity, and deepen understanding of TCS versatility—CzcSR integrates Zn²⁺ signals for canonical regulation of phenotypes (e.g., motility, antioxidant defense) while using a signal-independent mechanism for T3SS control.

小麦是人类饮食中约20%蛋白质和热量的重要来源。禾本科杂草对小麦生长与产量危害极大，其有效防控一直是麦田管理的难点，在制种田中尤为突出。本研究鉴定获得10个抗精喹禾灵（quizalofop-p-ethyl, QPE）小麦突变体，其中9个为乙酰辅酶 A 羧化酶（ACCase/ACC1）已知的A1992V位点突变，另1个为全新的 G2084S 位点突变。通过聚合不同亚基因组的突变位点，显著提升了中国小麦品种对精喹禾灵的抗性。本研究建立了高效的麦田杂草防控技术路径，为构建非转基因小麦可持续生产体系提供了重要支撑。

Early leaf spot (ELS) is one of peanut’s prominent and widespread foliar fungal diseases, causing severe yield losses and forage quality deterioration in South China. Discovery of the genomic region and the underlying candidate gene controlling ELS resistance will promote progress in resistance breeding and facilitate uncovering its genetic basis. In this study, a major genomic region, qELSB02.1, was identified using a bulked segregant RNA-Seq (BSR-seq) approach in a RIL population derived from a cross between a susceptible cultivar ZH10 and a resistant line ICG12625. It was further confirmed via simple sequence repeat genetic map-based linkage analysis, explaining 20.13-35.27% of the phenotypic variation. Using a partial genetic map and a segregation mapping population, qELSB02.1 was fine-mapped into a 465 kb genomic region by linkage analysis and substitution mapping. Furthermore, an NB-ARC-LRR gene (Arahy.V6I7WA) was identified as the most probable candidate gene for qELSB02.1 and was named Arachis hypogaea ELS resistance 1 (AhELSR1) based on functional annotation, sequence variation analysis, expression profiling, and protein structure prediction. Allelic variation analysis using 244 global peanut germplasm accessions identified four haplotypes, providing valuable clues for understanding ELS resistance evolution mediated by AhELSR1. Five SNPs, located in the first exon of AhELSR1, altering four encoding amino acids, were used to develop a diagnostic marker. The marker was further validated using diverse peanut germplasm and through introgression of AhELSR1 into a susceptible cultivar. Our results provide new insights into the genetic basis of ELS resistance regulation and benefit the breeding efforts for developing improved cultivars with enhanced ELS resistance. 

Leaf angle critically influences maize canopy structure and yield. NAC transcription factors regulate various developmental processes, yet their role in maize leaf angle remains poorly understood. In this study, we demonstrate that modulating the expression level of ZmNF-YC13 significantly alters the expression of ZmNAC118, suggesting that these two genes likely function within a common regulatory pathway. ZmNAC118 shows preferential expression in leaf tissues and encodes a nuclear-localized protein capable of transcriptional activation. Phenotypic analyses demonstrated that overexpression of ZmNAC118 leads to a pronounced reduction in auricle size and leaf angle. Transcriptomic profiling further revealed that ZmNAC118 modulates the expression of CYP450 genes associated with brassinosteroid (BR) and auxin (IAA) metabolic pathways. These CYP450 genes clustered into hormone-related phylogenetic clades, with a subset overlapping targets of ZmNF-YC13, indicating co-regulation within a shared pathway. Our study identifies ZmNAC118 as a key regulator of leaf angle and a promising candidate for maize architectural improvement.

由于全球人口的持续增长、气候变化的加剧和农业用地面积的持续减少，提高作物产量已成为一项紧迫任务。谷子作为一种起源于中国的古老作物，与主要粮食作物相比，其产量仍有较大的提升空间。但目前关于调控谷子花序发育相关基因的研究仍较为有限。本研究结果表明，过表达SiYABBY1显著抑制了谷子的发育；而敲除该基因则可影响浆片大小，使72.8%的小穗表现为闭花授粉，同时引起穗部形态变化，最终使粒长增加11.27%–14.02%，小穗粒数增加31.16%–33.67%。本研究不仅为SiYABBY1在谷子花序发育中的作用提供了新的见解，也为优化谷子产量性状的遗传改良策略提供了重要的理论依据。

Metabolite–microbe interactions are pivotal hubs for maintaining crop productivity under abiotic stress, and silicon (Si) fertilization has been widely recognized for enhancing plant stress tolerance. However, the mechanisms by which Si mediates rhizosphere metabolic reprogramming and microbial regulation to synergistically improve crop drought resilience remain unclear. Here, a two-year field experiment (2023–2024) was conducted using upland rice cultivar “Hanyou 73”. Treatments included well-watered conditions (CK), drought stress (D), and four Si application rates under drought (DS1-DS4, 25, 50, 75, and 100 kg ha^-1, respectively). We systematically investigated the coupled effects of Si on rhizosphere metabolites, microbial communities, and plant stress responses. Drought stress disrupted oxidative homeostasis, reduced photosynthetic capacity, and inhibited carbon and nitrogen metabolism, resulting in yield reductions of 27.96 and 20.37% in 2023 and 2024, respectively. Compared with D, DS3 significantly increased the levels of rhizosphere N- and sugar-related metabolites and enhanced soil microbial diversity, thereby stabilizing soil nitrogen cycling and enriching beneficial taxa (g_Bacillus). Consequently, nitrogen use efficiency increased by 26.21%, leaf superoxide dismutase (SOD) activity increased by 40.31%, and grain yield increased by 22.98 and 20.90% across the two years. Validation experiments further demonstrated that the combined application of Si and N/sugar-related metabolites (Ethanamine, Tagatose, Urea, Sorbose, and Fumaric acid) significantly promoted upland rice growth and soil nutrient accumulation, stimulated the proliferation of strain BT021, strengthened soil N cycling, increased soil N-related enzyme activities, and enhanced plant growth and antioxidant capacity. Structural equation modeling (SEM) revealed that Si directly regulated yield variation under drought through metabolite–microbiome coupling–driven nutrient cycling. Overall, Si fertilization reshapes rhizosphere processes via metabolite–microbe synergy, improves soil N cycling and rhizosphere environmental quality under drought, promotes plant nutrient transport, and stabilizes yield, providing new mechanistic insights and an applicable paradigm for green, stress-resilient yield improvement in upland agriculture.

Accurate and nondestructive prediction of crop yield and yield categories are crucial for advancing precision. This study presented an integrated framework combining unmanned aerial vehicle (UAV) based hyperspectral imaging and machine learning to predict the early yield and yield categories of faba bean. Field experiments were conducted across three key growth stages—branching, early budding and mid budding—using high-resolution hyperspectral data. Full-band reflectance (FBR) and texture features (TF) were extracted and fused to enhance model sensitivity to canopy spectral-structural variations. The results revealed that FBR achieved higher coefficients of determination (R²>0.60) and lower root mean square errors (RMSE<0.93 t ha^-1) across all stages than vegetation indices (VIs), indicating its superior capacity to capture subtle physiological dynamics. The integration of TF with FBR further improved model accuracy, especially based on deep neural network in the mid budding stage (R²=0.8254, RMSE=0.4732 t ha^-1). Compared with the traditional method, the R² was increased by about 15-27%, and the RMSE was reduced by 38-49%, which highlighted the synergistic effect of spectral-spatial fusion. For predicting the yield categories, the XGBoost algorithm presented outstanding performance (F1-score>0.86). Spatial analyses confirmed strong consistency between measured and predicted distributions of yield and yield categories, validating the robustness of the proposed approach. In this study, the hyperspectral and machine learning prediction models were developed for early prediction of faba bean yield and yield categories, which provided a scalable data-driven tool for high-throughput phenotypic analysis and sustainable crop management.

Efficient genetic transformation technologies are crucial for exploring plant gene functions and promoting molecular breeding. However, the widely used genetic transformation technology mediated by Agrobacterium tumefaciens is time-consuming and genotype-dependent, which limits the high-throughput functional characterization of cotton genes. The transformation system mediated by Agrobacterium rhizogenes (ARM) presents a rapid and effective alternative, but previous ARM techniques in cotton suffered from low efficiency and complicated operation. Here, we optimized the traditional ARM method suitable for nonsterile environments. The two-step ARM technology we used effectively enhanced the transformation efficiency within the upland cotton. The entire process only takes one month, and this system is applicable to various upland cotton varieties, with a maximum transformation efficiency of up to 100%. Results have shown that the ARM method only produces transgenic roots rather than whole transgenic plants. The obtained transgenic hairy roots can be employed to endogenous gene silencing and gene overexpression, enabling subcellular localization analysis and in-depth exploration of gene functions. In summary, we have first described a rapid, universal, efficient, and nonsterile ARM system in cotton, offering a reliable foundation for the cotton gene functional study and the advancement of genetic improvement breeding.

Rice-fish coculture (RFC) is widely recognized for increasing soil fertility and crop yield. However, the introduction of fish in double-season rice planting areas of South China to balance relationship between rice yield, soil function and ecosystem services, and to develop an optimal model between RFC and minimal tillage/no-tillage (NT) practices in a complementary form need to be further investigated. Hence, we conducted a two-year field experiment through a combination between RFC and several tillage types including CT (conventional tillage), NT (no-tillage), Minimal tillage (e.g. ECT+LNT. ECT refers CT used in early rice phase; LNT refers NT used in late rice phase following the ECT of early rice phase) to evaluate soil nutrients, rice yields, carbon (C) components and C-related enzymes activities. Our study found that RFC significantly increased contents of available phosphorus (P) by 9.52-11.42%, nitrate nitrogen (N) by 11.90-12.82%, and rice yield by 3.25-10.13%, while NT significantly increased contents of available P by 26.96-35.64%, ammonium N by 9.40-12.33%, and organic C by 10.26-15.08%. We also found that the interaction between RFC and NT significantly took effect on rice yield and C process. Also, available N and P contributed to improve rice yield, while available P, partial organic C, pH, dissolved organic C and bulk density drove C process. Moreover, LNT treatment significantly improved rice yield than that of CT treatment. These findings suggest that rice-fish coculture combining with minimal tillage/no-tillage is a promising eco-farming model to improve nutrient availability and carbon sequestration, and maintain rice yield. 

Premature leaf senescence significantly impacts tomato yield and quality. Understanding the molecular mechanisms underlying tomato leaf senescence holds important theoretical and practical significance for extending tomato fertility and improving yield and quality. This study identified CSAPlike, a DUF1997 protein, as playing a crucial role in regulating leaf senescence. Overexpression of CSAPlike accelerated senescence, while knockout of CSAPlike delayed the senescence process. CSAPlike-OE plants exhibited reduced chlorophyll content, increased reactive oxygen species (ROS) accumulation, and enhanced antioxidant enzyme activity, accompanied by ultrastructural degradation of chloroplasts including thylakoid disassembly and starch granule reduction. Transcriptome analysis revealed that CSAPlike may regulate the premature senescence process through a non-canonical mechanism independent of transcriptional regulation. Further screening and validation demonstrated that CSAPlike interacts with phosphoglucomutase (PGM), leading to impaired starch biosynthesis in CSAPlike-OE plants, which triggers energy deficiency and accelerates chloroplast degradation, ultimately resulting in premature leaf senescence. This study reveals a novel mechanism by which CSAPlike affects chloroplast stability and senescence progression through regulating PGM-mediated starch metabolism, providing new insights into the molecular mechanisms of leaf senescence and offering potential genetic targets for improving tomato yield by delaying senescence.

Large-scale global soybean trade raises concerns about emissions and transfers of greenhouse gas (GHG) while meeting the demand of importing countries. In this study, we calculate GHG emissions embodied in global soybean trade from 2001 to 2022 by using life cycle assessment (LCA), and assess the impact of global soybean trade on reducing GHG emissions by employing counterfactual analysis. The results show that the expansion of international soybean consumption has driven a more than threefold increase in the GHG emissions. Due to large differences in emission factors from cultivation and relevant land-use change (LUC) across countries, global soybean trade has contributed to a reduction of 272.79 Mt CO₂-eq in global GHG emissions in 2022 compared to the scenario of no trade. Since 2017, the GHG reduction contribution of global soybean trade presents an alarming trend of fluctuating or even deterioration influenced by factors such as geopolitical competition. Importing countries, represented by China, and exporting countries, represented by Brazil, have contributed to reduce GHG emissions by respectively mitigating domestic GHG emissions from agriculture and producing low-carbon products with comparative advantages. The study provides new evidence for the role of globalization in reducing GHG emissions. Additionally, it deepens the study and understanding of the environmental impact of agricultural trade by incorporating LUC emissions and assessing the overall impact.

Drought imposes a severe impediment to plant growth and development, cause yield and quality to decline. Xyloglucan endotransglucosylase/hydrolase (XTH) is a kind of cell wall-modifying protein, and contributes to cell wall assembly. However, whether XTHs are involved in the drought stress of tomato (Solanum lycopersicum L.), and its mechanism and upstream regulatory factors remain unclear. Here, SlXTH23 is identified to negatively respond to drought stress in tomato. SlXTH23 knockout tomato plants increase the content of cellulose and hemicellulose, as well as the thickness of secondary cell wall in roots, and enhance drought tolerance. In contrast, SlXTH23 overexpressed transgenic tomato plants are sensitive to drought stress. Two basic helix-loop-helix transcription factors, SlbHLH086 and SlbHLH096, are identified to directly bind and regulate SlXTH23. Silencing SlbHLH086 alone or in combination with SlbHLH096 enhances drought tolerance by stimulating the expression of SlXTH23 and promoting the thickness of secondary cell wall in tomato roots. Silencing SlbHLH096 renders plants sensitive to drought stress. In addition, SlbHLH086 interacts with SlbHLH096, and SlbHLH086 prevents the inhibitory effect of SlbHLH096 on the expression of SlXTH23. In summary, this study revealed the molecular mechanism that SlbHLH086/SlbHLH096-SlXTH23 module regulates the drought tolerance of tomato by altering cell wall components and thickness, providing a novel mechanistic insight for breeding drought tolerant tomato cultivars.

MET1 encodes DNA methyltransferase 1, which is increasingly being identified as a major regulator of abiotic stress responses and adaptation. To explore the function of DNA methyltransferase 1 in salt stress, we cloned a grape (Vitis vinifera L.) MET1 subfamily gene, VvMET2b, and overexpressed it into A. thaliana. The phenotypic analysis of transgenic Arabidopsis revealed that VvMET2b improved seed germination and seedling survival under NaCl treatment. Detailed methylome analysis revealed that VvMET2b increased the global methylation level of transgenic plants and altered the quantity of differentially methylated regions (DMRs) and DNA methylation types. Comprehensive transcriptome analyses indicated that many transcription factors, such as NACs, MYBs, and WRKYs were differentially expressed in VvMET2bOE plants under salt stress. VvMET2b overexpression induced the expression of cytokinin negative regulator type-A ARRs, the transmembrane transporter KAT1, inhibited the expression of MYB6, and the up-regulated expression of auxin-related genes Aux/IAAs and down-regulated expression of GH3s, expansin EXPA17 and tonoplast aquaporin TIP2 were mitigated. VvMET2b altered DNA methylation level of MYB6, TIP2 and EXPA17 and thereby may regulate the expression of these genes. Taken together, VvMET2b may regulate seed salt tolerance through DNA methylation changes and certain key gene expression. 

Heterosis is a highly effective strategy for increasing yield and quality of pepper (Capsicum annuum L.). Although genic male sterile (GMS) lines offer advantages for seed production by avoiding the limitations associated with cytoplasmic male sterile lines, their use typically requires the labor-intensive removal of 50% of fertile plants during seed production. To address this challenge, we identified an anthocyanidin-absent (aa) mutant characterized by green hypocotyls at the seedling stage and yellow anthers. We identified dihydroflavonol 4-reductase (CaDFR) as a key gene regulating anthocyanin biosynthesis in pepper through fine mapping and virus-induced gene silencing. Genetic segregation analysis revealed that CaDFR and CaDYT1 (a GMS gene) were closely linked. Based on this finding, we developed an efficient hybrid seed production strategy for screening sterile plants at the seedling-stage by combining the green hypocotyl morphological marker from the aa mutant with the male sterile line gms1 (CaDYT1 locus). In conclusion, we successfully cloned CaDFR, a key gene controlling hypocotyl and anther color in pepper. In addition, we proposed an efficient seed propagation strategy to accelerate hybrid seed production and facilitate the utilization of heterosis. This study not only deepens our understanding of the genetic regulation of pepper pigmentation but also establishes a practical framework for optimizing hybrid breeding protocols, thereby simplifying the pepper breeding process.

Chlorophyll degradation occurs during mango fruit ripening, contributing to the color and commercial value of the fruit. Ethylene response factors (ERFs) are recognized as important regulators of chlorophyll degradation. This study investigated the regulatory effects of MiERF023 on mango coloration through ethylene (ETH) and 1-methylcyclopropene (1-MCP) treatments. ETH treatment increased the activities of chlorophyll degradation-related enzymes (Chlase, MDCase, PPH, and PAO), activated the expression of chlorophyll catabolism genes (MiPPH and MiPAO), accelerated chlorophyll degradation, and promoted coloration of mango. In contrast, the opposite effects were observed after 1-MCP treatment. Meanwhile, the expression of MiERF023 was greatly induced by ethylene and inhibited by 1-MCP, then MiERF023 was isolated and characterized. Yeast one-hybrid (Y1H) and dual luciferase reporter (DLR) assays demonstrated that MiERF023 binds to the promoters of MiPPH and MiPAO, upregulating their transcript levels. Transient overexpression of MiERF023 in tomato and mango fruits increased the transcript levels of MiPPH and MiPAO, accelerating chlorophyll degradation and promoting peel coloration. Collectively, these findings reveal a novel regulatory mechanism by which MiERF023 modulates ethylene-mediated pigment metabolism，offering potential targets for improving sensory quality in postharvest mango fruits. 

The tubers of potato (Solanum tuberosum L.) exhibit diverse colors, primarily resulting from different levels of anthocyanin pigments. While the loci regulating the accumulation of red and purple pigments have been reported, the regulatory mechanism underlying the biosynthesis of pink anthocyanins in potato remains unclear. In this study, we identified the pink tuber skin locus Pink through a bulked-segregant analysis sequencing approach using a BC₁S₁ population segregating for tubers with red, pink, or yellow skin. We narrowed down the location of Pink to a 265-kb interval on chromosome 3. Metabolomic and transcriptomic analyses revealed the anthocyanin biosynthesis gene Flavonoid 3'-hydroxylase (StF3'H) as the candidate gene. Genetic transformation assays demonstrated that StF3'H is essential for the production of tubers with pink skin. Furthermore, we showed that the red tuber skin locus (R) is epistatic to Pink. These findings provide a new theoretical basis for the development of colored potatoes through molecular breeding and offer an important reference for exploring the complex regulatory mechanisms of anthocyanin biosynthesis in potatoes.

Gibberellin 2-oxidases (GA2ox) play an important role in regulating the balance of bioactive gibberellins in plants, while the role in the drought response mechanism of grapes remains unclear. In this study, the subcellular localization analysis revealed that VvGA2ox5 was predominantly expressed in the cytoplasm and nucleus. Transient transformation experiment on ‘Pinot noir’ grape leaves showed that overexpression of VvGA2ox5 reduced relative electrical conductivity (REC) and malondialdehyde (MDA) levels and increased proline content, antioxidant enzyme activity, and expression of drought-responsive genes. In contrast, virus-induced gene silencing (VIGS) silenced strains showed the opposite results. Additionally, the overexpression of VvGA2ox5 in ‘Pinot noir’ grape callus and Arabidopsis thaliana (Arabidopsis) further validated its positive function. In the CRISPR-Cas9 grape callus, the experimental results were in contrast to the overexpression lines. Meanwhile, the yeast two-hybrid (Y2H) assay screened a drought-responsive protein, VvDEH (Dehydration-induced 19 homolog 3). RNA-seq analyses showed that overexpression of VvGA2ox5 significantly participates in the hormone signaling pathway. Accordingly, VvGA2ox5 is a crucial regulation gene in enhancing drought tolerance in grapes and serves as a potential candidate gene for improving drought tolerance in plants. This finding offers significant theoretical support for drought tolerance breeding in grapes.

To analyze intra-household nutrition allocation, we examine the differences in expenditure elasticities among demographic groups within rural households, employing an asymmetric model along with data from the China Health and Nutrition Survey (CHNS) from 2004 to 2011. Our analysis reveals significant heterogeneity in household nutrient allocation: during periods of expenditure expansion, households prioritize the nutritional improvement of vulnerable members, specifically children and the elderly, with a notable bias toward girls, often at the expense of prime-age adults, particularly women. Conversely, during expenditure contraction, households shift strategies to protect the nutritional intake of prime-age adults. This asymmetry underscores the complexity of intra-household distribution and provides critical insights for designing nutrition security policies that account for economic volatility.

Non-heading Chinese cabbage (NHCC, Brassica campestris [syn. Brassica rapa] ssp. chinensis) is one of the most important leafy vegetables in China. As soil salinization becomes increasingly serious, salt stress limits the growth and development of NHCC, reducing its yield and quality. Previous studies have shown that histone modifications play an important role in plant salt-stress responses by regulating the expression of key genes, but little is known about such modifications in NHCC. Here, we used CUT&Tag-seq and RNA-seq to profile genome-wide H3K27ac and H3K27me3 modifications and transcriptome changes in NHCC root tips subjected to salt stress at 12 and 24 hours. Genome-wide levels of the repressive chromatin mark H3K27me3 increased under salt stress, whereas those of the active chromatin mark H3K27ac decreased. Genes whose H3K27ac and H3K27me3 levels responded to salt stress were associated with processes such as trehalose synthesis, transcription, membrane transport, defense responses, and cell wall structure. Among the cell wall-related genes with increased H3K27ac levels and expression under salt stress, there is a homologous gene of Arabidopsis pectin methylesterase inhibitor 4 (BcPMEI4). The virus-induced gene silencing (VIGS) assay confirmed that silencing BcPMEI4 significantly reduced the salt tolerance of NHCC, as reflected by decreased leaf area, reduced root area, and increased hydrogen peroxide levels. This suggests that the H3K27ac-mediated transcriptional activation of BcPMEI4 may enhance salt tolerance by regulating the cell wall pathway. In summary, our findings provide the comprehensive picture of changes in active and repressive chromatin marks in NHCC under salt stress, offering insight into epigenetic mechanisms of salt-stress response in NHCC and other Brassica crops.

Plant viral diseases pose a persistent threat to global agriculture, requiring efficient platforms for antiviral agent screening to ensure sustainable crop protection. Here, we developed a simplified mini-replicon reverse genetics (RG) system for tomato spotted wilt virus (TSWV) based on co-expression of SR_(+)eGFP replicon and L_(+)opt genome in the absence of viral suppressors of RNA silencing (VSRs). Using this system, we demonstrated that the movement protein NSm and M_(-)opt genome significantly enhance both the replication and cell-to-cell movement of the TSWV mini-replicon. We further constructed a tandem expression vector (SR_(+)eGFP-M_(-)opt), and established a novel dual-vector-driven TSWV RG system. Notably, this system achieved 100% systemic infection efficiency without requiring any VSR. This is unprecedented for plant negative-strand RNA virus reverse genetics. This optimized system enabled the screening of antiviral agents, among which ribavirin, ningnanmycin, chitooligosaccharide, cellobiose, azadirachtin, and copper sulfate (CuSO₄) potently inhibited TSWV infection. Our study provides a new RG manipulation tool for functional genomics of plant negative-strand RNA viruses (NSVs) and a powerful platform for high-throughput antiviral agents discovery.

Fusarium crown rot (FCR), a major soil-borne disease caused by Fusarium species, threatens global wheat production. This study identified quantitative trait locus (QTL) for FCR resistance in wheat using genome-wide association study (GWAS) on a panel of 299 wheat cultivars/lines and bulked segregant exome sequencing (BSE-Seq) on a recombinant inbred line (RIL) population. Phenotypic evaluation revealed five wheat accessions with resistance levels comparable to the resistant control Sunco. Fourteen putative QTLs were mapped on chromosomes B, 2B, 2D, 4A, 5D, 6D, 7A, 7B, and 7D by GWAS, with the phenotypic variation explained by 3.73-6.64%. A major QTL (Qfcr.caas.7A-2) on chromosome 7A was consistently detected across all replications. BSE-Seq analysis confirmed enrichment of associated polymorphisms on chromosome 7A, encompassing the Qfcr.caas.7A-2 interval. Within this region, TraesCS7A02G53500. (encoding an RGA5-like protein) was prioritized as a candidate gene based on expression and phylogenetic analysis. Two kompetitive allele-specific PCR (KASP) markers KASP-7079 and KASP-3538 were successfully developed and validated for Qfcr.caas.7A-2. These findings offer valuable insights into the genetic mechanisms underlying FCR resistance and provide valuable resistance resources and molecular markers for FCR resistance breeding. 

Endophytes are prevalent in plants and significantly contribute to plant growth and development. In the present study, Epichloë bromicola endophyte strain WBE1 was artificially inoculated into wild barley (Hordeum brevisubulatum, natural host) and cultivated barley (Hordeum vulgare, novel host) to obtain endophyte-barley symbionts. Physiological traits, such as callus formation, lignin content, cell mortality, early signaling molecules, second messenger endogenous signaling molecules, and the expression patterns of differential genes at different time periods were studied. The colonization rate of E. bromicola was 54.21% in wild barley and 9.91% in cultivated barley. Artificial endophytic infection enhanced callus growth, lignin content, and cell mortality in both hosts, with cultivated barley showing stronger resistance than wild barley. The infection induced the expression of early signaling molecules, and the O₂^- production rate as well as H₂O₂ and NO contents were increased in both hosts. During the early infection stage, mitogen-activated protein kinase (MAPK) activity in cultivated barley increased by 12.24% and 54.60% compared with wild barley at 2 and 4 days post-infection, respectively. Transcriptomic analysis revealed that cultivated barley triggered an earlier and targeted defense response than wild barley, characterized by the stage-specific upregulation of genes involved in resistance-related secondary metabolite biosynthesis and key signaling molecules. Expression patterns showed upregulation of signaling molecules alongside downregulation of genes associated to oxylipin biosynthesis, lipid oxidation, cellular responses to environmental stimuli, oxidoreductase activity, and heme binding. These findings indicated that E. bromicola infection effectively triggered an enhanced and timely defense response in cultivated barley. 

Kiwifruit bacterial canker (KBC), caused by Pseudomonas syringae pv. actinidiae (Psa), severely threatens the kiwifruit industry. The type III secretion system (T3SS) is a key virulence factor in Psa, but the regulatory mechanisms remain poorly understood. Polymyxin B1, the main component of polymyxin B, inhibits T3SS gene expression in Psa, yet its underlying mechanism is unclear. Cyclic diguanosine monophosphate (c-di-GMP), a crucial bacterial second messenger, is synthesized by diguanylate cyclases (DGCs) containing a GGDEF domain. In this study, we identified and characterized PSA_1379 (WspR), a GGDEF domain-containing protein in Psa. Biochemical assays demonstrated that WspR exhibits DGC activity. Virulence assays showed that WspR negatively regulates Psa virulence. RT-qPCR analyses revealed that polymyxin B induces wspR expression. Additionally, polymyxin B upregulates intracellular c-di-GMP levels and inhibits the expression of T3SS genes through WspR. Bacterial two-hybrid and GST pull-down assays confirmed that WspR interacts with the transcription factor PsrA. Both WspR and c-di-GMP inhibit the binding of PsrA to the promoter of the T3SS master regulator hrpL, thereby suppressing PsrA-mediated transcriptional activation of hrpL and ultimately repressing T3SS gene expression. This study provides new insights into Psa virulence regulation and suggests potential targets for KBC control through the WspR-c-di-GMP pathway.

Land application of manure containing antibiotic residues poses significant environmental risks, primarily via leaching of these emerging contaminants into water resources. Despite extensive attention to antibiotic pollution, the mechanisms by which manure-derived dissolved organic matter (MDOM) influences their transport remain poorly understood. Using integrated techniques including fluorescence quenching and density functional theory (DFT) calculations, this study investigated molecular-scale interactions between eight typical antibiotics from five categories and four DOM species (humic acid, L-tryptophan, chicken MDOM and pig MDOM). These molecular interactions were linked to field-relevant conditions via soil column experiments and hydraulic modeling. Results demonstrated that the extent of antibiotic-DOM binding was determined by molecular HOMO-LUMO energy gaps (ΔE), following the order: quinolones (QLs)>tetracyclines (TCs)>macrolides (MLs)>sulfonamides (SAs)>chloramphenicols (CAPs). Protein-like species exhibited stronger antibiotic affinity than humic acid (HA), with chicken MDOM showing higher reactivity than pig MDOM. MDOM impact on antibiotic leaching strongly depended on their molecular binding strength, governing soil-water interface behavior. MDOM acted as a mobile carrier for weakly-bound antibiotics, facilitating transport via competitive adsorption, whereas it enhanced the retention of strongly-bound antibiotics through co-adsorption. These findings bridge molecular interactions and macroscopic leaching behavior in soil, providing a scientific basis for improving risk assessment and sustainable manure management in agricultural systems.

水稻是我国重要的粮食作物，病害是威胁其稳产高产的主要因素之一。近年来，泛菌属的Pantoea ananatis（Pa）在我国多地被发现可引起水稻细菌性病害，其寄主范围广，潜在威胁大。本研究于2023年6月在江苏省徐州市的水稻育苗田中发现一种导致水稻叶片叶脉枯死的新症状，其特征为茎基部及中下部叶脉褐变，叶片上部枯萎，呈自下而上的侵染模式。通过组织分离，获得了纯化的细菌分离物。经显微形态观察、16S rRNA和gyrB基因序列分析，鉴定该病原菌为Pantoea ananatis。通过针刺接种法进行柯赫氏法则验证，证实该菌可导致接种水稻重现叶脉枯死症状，并从发病组织中重新分离到相同病原菌。该病原菌可在苗期侵染水稻，造成显著危害。据我们所知，这是Pantoea ananatis在中国江苏省引起水稻细菌性叶脉枯死症状的首次报道，其扩散对当地水稻生产构成潜在风险，需引起重视。

Intensive swine production causes nutrient losses and enhanced gaseous emissions during manure management, which disrupts nutrient cycling within agricultural systems and threatens agroecosystem sustainability. Prior research has typically examined feeding and manure management as isolated processes, failing to integrate these two components to improve system performance, and this gap limits the design of integrated agricultural systems. Here, we implemented a low-protein balanced diet (LPBD) system and compared it with a high-protein traditional diet (HPTD) to evaluate impacts on swine growth performance and nutrient-use efficiency, followed by sawdust co-composting of the resulting manures. System responses were quantified through integrated monitoring of nutrient excretion, compost physicochemical properties, and gaseous emissions, together with metagenomic profiling of microbial communities and functional genes and subsequent path modeling to resolve key interaction pathways across the feed–compost agricultural system. We found that LPBD improved C/N digestion synchronization, reduced protein/energy excretion, and maintained swine productivity, while markedly decreased CO₂, CH₄, N₂O and NH₃ emissions during composting. Metagenomics indicated that LPBD enriched N-cycling genes (nirK, nosZ, nifH) and restructured CAZyme repertoires and microbial communities, patterns consistent with lower NH₃ emissions and enhanced carbon cycling. Path modeling further indicated that diet-driven shifts in compost composition altered environmental factors and indirectly regulated gas emissions via enzymatic and genetic pathways. Overall, this integrated feed–compost strategy links livestock nutrition with environmental management, enhances nutrient cycling efficiency at the agroecosystem level, and provides a basis for sustainable, low-emission circular livestock systems.

Pea (Pisum sativum) and broad bean (Vicia faba) are important legume crops grown worldwide. Viral diseases pose a significant threat to these crops in China, particularly in Yunnan Province, where the year-round mild climate and continuous cropping systems create favorable conditions for virus infection and spread. From 2020 to 2022, a survey of viral diseases was conducted in pea and broad bean fields across six major regions of Yunnan Province, namely Kunming, Yuxi, Baoshan, Chuxiong, Dali, and Honghe. High-throughput sequencing (HTS) combined with RT-PCR was used to detect and identify viruses in 261 pea and 164 broad bean samples. Seventeen distinct viruses, including a new species, were identified in both pea and broad bean samples, whereas turnip yellows virus (TuYV) was detected only in pea samples. A novel virus, tentatively designated pea enamovirus 3 (PEnV-3), was identified based on the complete genome sequence of isolate YWD and phylogenetic analyses. Accordingly, we propose the species name Enamovirus pisi. Pea enation mosaic virus 1 (PEMV-1) and bean yellow mosaic virus (BYMV) were the most prevalent viruses detected in pea and broad bean crops, with detection rates of 54.02% and 81.10%, respectively. Co-infections with multiple viruses were common in both pea and broad bean samples, with 148 and 97 co-infected samples identified, respectively. The geographic distribution of the viruses varied considerably across the six sampling regions. PEMV-1, pea seed-borne mosaic virus (PSbMV), BYMV, Brassica yellows virus (BrYV), and chickpea chlorotic stunt virus (CpCSV) were the most widespread, occurring in all regions. In contrast, Vicia cryptic virus (VCV) was found only in pea samples from Dali, while PEnV-3 and clover yellow vein virus (ClYVV) were unique to pea samples from Kunming. In broad bean samples, BYMV and PSbMV were also the most prevalent, detected in five regions, whereas PEnV-3 was again confined to samples from Kunming. Regarding virus detection across crops and regions, Kunming exhibited the highest viral diversity in pea crops, with 15 different viruses identified, whereas Honghe had the lowest (9 viruses). Dali displayed the greatest viral diversity in broad bean crops (15 viruses), while Honghe showed the least, with BrYV as the sole virus detected. This study reveals several novel virus-host associations and previously unreported occurrences of viruses in specific region. To our knowledge, this study represents the first report of pea infection by BrYV, tomato yellow mottle-associated virus (TYMaV), Bidens mottle virus (BiMoV) and VCV. Additionally, its also documents the first report of TuYV in pea in China, as well as the first identification of ClYVV in pea in Yunnan Province. Similarly, infections of broad beans by BrYV and TYMaV are reported here for the first time. Furthermore, this study presents the first detection of BiMoV in China, and the first detections of VCV and ClYVV in Yunnan Province. 

Heading date is one of the most important indicators to evaluate adaptation in wheat. In this study, we used three association panels to construct a genome-wide recombination landscape consisting of 97 recombination hotspots regions (RHR) in wheat. We further identified 1,043 RHR in six bi-parental populations, and 88 recombination hotspots overlapped with association panels. We next identified 2223 significant SNPs forming 55 clusters for heading date by phenotype-based genome-wide association studies (pGWAS), and 53 stable SNPs associated with 13 candidate genes were detected in at least two environments. Twenty-one QTLs were mapped in bi-parental populations and five QTL intervals overlapped RHR. By integration of collinearity analysis, recombination hotspots, and haplotype analysis, five homoeologous interval pairs were discovered, of which 7D_Hap1 advanced heading by 8.7 days. Further analysis showed that heading date-network genes were involved into transcription regulation and post-translational modification (PTM). Meanwhile, expression GWAS (eGWAS) on heading date regulatory core module identified 307 potential novel genes acting in heading date regulatory network. These findings provide new insights into wheat phenological adaptation and developed resources for developing climate-resilient wheat cultivars.

To address the dual challenges of water scarcity and rising demand for premium rice, this study investigated the synergistic effects of mild alternate wetting and drying (Mild AWD) irrigation combined with wheat straw biochar application on rice yield and grain quality. A two-year field experiment (2023–2024) was conducted with the hybrid rice cultivar Yongyou 2640, with two irrigation regimes: continuous flooding (CF) and Mild AWD (re-irrigation at a soil water potential of −10 to −15 kPa at 15–20 cm depth), with or without a one-time biochar application (10 t ha^-1). The results showed that co-application of Mild AWD and biochar significantly increased grain yield by 18.7% in 2023 and 13.4% in 2024 compared to CF alone. It also comprehensively improved grain quality: milling quality (head rice rate increased by 23.1–24.6%), appearance quality (chalkiness reduced by 36.4–38.2%), cooking and eating quality (higher peak viscosity, lower gelatinization temperature and enthalpy), and nutritional quality (increased glutelin and decreased prolamin content and starch digestion). These improvements were attributed to enhanced root activity alongside leaf photosynthetic rate, which promotes the accumulation of photoassimilates in vegetative organs and their translocation to grains. Moreover, elevated activities of key starch synthases further enhanced starch biosynthesis and accumulation, which underpinned the improved yield and superior quality. We also identified that a minimum soil water potential of −10 to −15 kPa at a depth of 15–20 cm represents the optimal threshold for mild AWD in rice production. This research provides a cultivation approach for synergistically producing high-yield, high-quality rice, which shows promising potential for scalable implementation.