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.

Skeletal muscle cellular heterogeneity and molecular regulation are fundamental to understanding exercise physiology in Equus species. However, these mechanisms remain incompletely characterized in donkeys (Equus asinus) and horses (Equus caballus). Here, we integrated single-nucleus transcriptomics and metabolomics to systematically compare the longissimus dorsi muscle across developmental stages in both species. We identified nine and twelve distinct skeletal muscle cell types in donkeys and horses, respectively. Muscle fiber composition exhibited species-specific age-related changes: in adult horses, the proportion of both type I and II fibers increased; in adult donkeys, by contrast, the proportion of type I fibers decreased while that of type II fibers increased. The predominance of type II fibers in horses likely reflects a species-specific adaptation to high-intensity locomotor demands. Pseudotime analysis delineated muscle fiber trajectories and revealed dynamic gene expression profiles along these paths. Subpopulation analysis of immune cells revealed the activation of pro-inflammatory signaling pathways (TNF and NOD-like receptor pathways) in adult groups, coupled with diminished anti-inflammatory capacity in dendritic cells, collectively indicating an age-associated pro-inflammatory shift. Intercellular communication analysis further indicated age-related dysregulation in key signaling pathways, including BMP (adipogenic differentiation), Notch (immune regulation), and IGF (tissue repair), which may contribute to impaired muscle metabolism and regenerative capacity. Cross-species comparison revealed that skeletal muscle transcriptomes of donkeys and horses are highly conserved (Pearson correlation coefficient 0.87), although species-specific marker gene expression, such as SLC29A1 in endothelial cells, was observed. Metabolomic profiling identified distinct differences in overall metabolite category composition and revealed significantly divergent gene-metabolite networks between the two species. Together, these findings comprehensively illuminate the cellular dynamics, metabolic remodeling, and evolutionary conservation of skeletal muscle development in Equus species, providing valuable insights into mammalian muscle adaptation and identifying potential targets for enhancing locomotor performance or managing myopathies in equids.

Saliva plays a crucial role in mediating plant-insect interactions, yet the functional diversity of salivary proteins remains poorly understood. Here, we identify NlSP6935, a salivary gland-specific protein conserved among rice planthoppers but absent in bamboo-feeding relatives. Silencing NlSP6935 causes severe lethality, feeding impairment, and infertility in Nilaparvata lugens, independent of host plant resistance. Transient expression assays reveal that NlSP6935 suppresses H₂O₂ accumulation in plants, while overexpression in rice downregulates terpenoid biosynthesis and enhances host attractiveness. However, transgenic NlSP6935 plants only weakly rescue RNAi-induced lethality, demonstrating its dual role in insect physiology and plant defense suppression. Our findings reveal a novel effector essential for both planthopper survival and host adaptation, providing new insights into pest control strategies.

DNA methylation is a stable epigenetic modification with essential roles in plant drought response. It is known that methyltransferase mutant is necessary for the regulation of methylation variations, but this epigenetic molecular mechanism based on methyltransferase mutant in responding to drought stress was still unclear in cotton. In this study, we aim to decipher the epigenetic code of drought response regulated by methyltransferase gene GhDMT9 in cotton, providing valuable information for the molecular research of drought resistance in cotton. We successfully created the first cotton methyltransferase mutant ghdmt9 using CRISPR/Cas9 method and performed methylation variations analysis with whole-genome bisulfite sequencing (WGBS) and transcriptome analysis based on ghdmt9 mutant. In addition, specific antibody of methyltransferase GhDMT9 was prepared and used for Chromatin Immunoprecipitation (ChIP-seq) analysis. The results indicated that ghdmt9 mutant interpreted approximately 2.06% methylation variations under drought stress. Demethylation variations, mainly derived from the CHG and CHH contexts, were closely correlated with drought response. Whether at normal growth stage or under drought stress, the number of up-regulated genes induced by demethylation variations was apparently higher than the number of down-regulated genes, especially genes regulating lipids and lipid-like molecules and hormone-related genes. In addition, fiber quality of ghdmt9 mutant was obviously better than that of wild type (WT). Interestingly, a transcription factor lsh (lysine-specific histone) was found to interact with methyltransferase gene GhDMT9 to activate its hyper-methylation function of target genomic regions by ChIP-seq analysis. Overall, our results extend our understanding of the epigenetic regulation of methyltransferase GhDMT9 in drought response and contribute to further investigations of the epigenetic mechanisms underlying abiotic stresses in cotton. 

Salt stress is a major limiting factor for global wheat production, especially during the germination stage. Traditional methods for evaluating salt resistance at the germination stage are limited by low throughput and their inability to capture dynamic phenotypic changes. In this study, a low-cost and high-throughput seed germination phenotyping platform was developed by integrating side-view RGB imaging with image analysis algorithms. Organ segmentation and germination related traits extraction processes was built via a deep learning pipeline for comprehensive phenotyping of the germination process of diverse varieties under different salt levels. Organ-level segmentation achieved a mean precision of 89.08%, a mean recall of 91.65%, a pixel accuracy of 91.65%, and a mean intersection over union of 83.20%. The 13 image-derived traits were highly consistent with manual measurements. Salt stress significantly inhibited the growth of roots and seedlings, with inhibitory effects intensifying as salt concentration increased. Further analysis revealed seed size shows no correlation with germination capacity and radicle growth rate significantly surpasses that of the coleoptile. Clustering analysis based on dynamic image-derived indices classified the 210 wheat materials into two groups with significantly different salt tolerance. GWAS identified 429 loci associated with salt stress response during germination, including one potential candidate gene, TraesCS7A03G007080, known to play a role in salt tolerance mechanisms. This study provides important genetic materials for the evaluation of salt-tolerant wheat varieties at the germination stage and offers a low-cost, high-throughput, and reliable technical approach for dissecting the genetic basis of salt tolerance during wheat germination.

Within the context of modern cotton cultivation, which emphasizes cost savings and efficiency improvements, drip application of 1,1-dimethyl piperidinium chloride (DPC) provides potential advantage such as reducing the labour and mechanical costs associated with the chemical regulation of conventional DPC foliar spraying in arid cotton-growing areas. However, the appropriate drip DPC dose and its regulatory effects on cotton growth and yield, and particularly the responses to cultivars with different sensitivities to DPC, remain uncertain. A two-year (2023–2024) field experiment was conducted to evaluate the influences of various cultivars and drip DPC doses on cotton phenology, agronomic traits, canopy development, defoliation, boll opening, yield and residual DPC levels. The cultivars Huiyuan 720 (H₇₂₀, DPC-sensitive) and Xinluzao 74 (L₇₄, DPC-insensitive) were chosen, the D₀ (no DPC) and S₁ (DPC foliar spraying at 330 g ha⁻¹ in 2023 and 375 g ha⁻¹ in 2024) treatments were used as controls, and the drip DPC doses were D₁ (the same dose as that in S₁), D₄ (four times the dose in S₁) and D₆ (six times the dose in S₁). The results indicated that compared with those in D₀, the growth periods of H₇₂₀ in D₄ and L₇₄ in decreased by 9 days; in particular, the number of growth days from the peak flowering stage to the late peak bolling stage decreased by 6 days. The plant height, the height of the first fruiting branch, and plant width decreased significantly, by 10.1–19.1%. The diffuse non-interceptance and canopy light transmittance in the middle and upper parts from the peak squaring stage to the boll opening stage increased by 7.9–55.9% and 0.4–7.0%, respectively. The defoliation and boll opening rates increased by 1.5–3.4%. The boll numbers in the middle part increased by 16.7–36.4%, and the yield increased by 4.9–7.6%. Compared with those in S₁, the yields of H₇₂₀ in D₄ and of L₇₄ in D₆ were comparable but the levels of DPC residues in the cotton plants significantly decreased by 36.3–71.0%. Moreover, the levels of DPC residues in D₆ were minimal in soil. These results indicated that an appropriate drip DPC dose can optimize cotton growth and development and reduce the levels of DPC residues based on the cultivar characteristics. This study provides valuable practical insights into the potential of a drip DPC regulation system to replace the foliar spraying method and to advance light and simplified cotton cultivation.

油菜素内酯（brassinosteroids，BRs）是调控水稻株型建成、发育进程和产量形成的重要植物激素。尽管同属粳稻亚种，中花11（Zhonghua 11，ZH11）与台中65（Taichung 65，TC65）在BR相关性状上仍存在明显差异，这与其遗传背景及育种历程的分化密切相关。由于株型紧凑、抽穗期短、遗传转化效率高，并拥有完整的T2T基因组序列，ZH11已成为当前水稻功能基因组研究的重要模式材料。然而，ZH11中缺乏诸如OsBRI1等关键BR信号通路突变体，在一定程度上制约了BR相关研究的开展。本研究从形态、生理和分子层面系统比较了ZH11与TC65对外源BR处理的响应差异，揭示了两种材料在BR敏感性上的显著分化。基于此，我们通过连续回交并结合分子标记辅助选择，将TC65背景的弱等位d61-1突变导入ZH11背景，成功构建了近等基因系d61-zh11。该材料表现出适度的BR不敏感性和紧凑株型，遗传稳定，同时避免了强突变体常见的严重多效性缺陷。作为一种非转基因突变体，d61-zh11为在现代遗传背景下精细解析BR信号通路提供了理想平台，也可作为正向和反向遗传筛选的重要研究资源。本研究实现了经典激素遗传学与现代功能基因组学的有效衔接，为水稻BR相关基础研究和育种应用提供了重要的遗传材料。

Sclerotinia stem rot (SSR) is caused by the necrotrophic fungus Sclerotinia sclerotiorum and threatens global oilseed rape (Brassica napus) production. Moreover, researchers have not yet identified a gene that confers complete resistance. Here, we developed a multi-target RNA interference (RNAi) strategy to enhance plant resistance by simultaneously silencing eight fungal genes involved in development (SsChsI–VII, SsGas1) and two involved in pathogenicity (SsPG1, SsOAH1) of S. sclerotiorum. Accordingly, we designed a 1,250-bp chimeric double-stranded RNA (dsRNA) consisting of ten 125-bp fragments each targeting a different gene, and evaluated its effectiveness using spray-induced gene silencing (SIGS) and host-induced gene silencing (HIGS) via stable transformation. In vitro application of the chimeric dsRNA resulted in >50% downregulation of nine target genes, indicating efficient uptake and processing by S. sclerotiorum. Both lesion area and fungal biomass were significantly lower in Nicotiana benthamiana and oilseed rape plants following SIGS. Moreover, stable transgenic plants for HIGS effectively generated gene-specific short interfering RNAs and exhibited an increase in resistance from the T₂ to T₅ generations, with lesions that were 38.9–59.1% smaller in leaves and 43.2–65.8% smaller in stems in the T₅ generation compared with the control plants. Gene silencing resulted in lower oxalic acid accumulation, decreased polygalacturonase activity, and impaired hyphal development, suggesting interference with multiple fungal infection pathways. Notably, HIGS conferred stable, heritable resistance without yield penalty, whereas SIGS provided rapid, nontransgenic protection. This study demonstrates the effectiveness of long chimeric dsRNAs for multi-target gene silencing and highlights a promising RNAi-based strategy for improving disease resistance in oilseed rape, possibly in combination with natural quantitative resistance loci.

Compact maize architecture is crucial for high planting densities and yields, which is a key breeding objective. In this study, a maize T-DNA insertion mutant with compact plant architecture (cpa) was identified, showing reduced leaf curling, drooping angle, plant and ear height, leaf dimensions, internode and tassel length, tassel branch number, and yield compared to WT. Paraffin section analysis showed reduced vein cross-sectional area, epidermal cell width, and increased vein density in the cpa mutant. Genetic analysis revealed that T-DNA was inserted into the first exon of a gene encoding TATA-box binding protein-associated factor (TAF) in the cpa mutant, which was named ZmTAF11. ZmTAF11 exhibited ubiquitous expression across various tissues and nuclear localization. Loss-of-function Zmtaf11 mutants generated by CRISPR/Cas9 exhibited the characteristic compact phenotype, which was consistent with that of the cpa mutant. ZmTAF11 directly binds to the promoters of leaf morphogenesis-related genes ZmAXL and ZmBOB1, thereby promoting their transcription. Furthermore, four SNPs in ZmTAF11 were significantly associated with ear height index (EHI), and the AGTG haplotype showed a lower EHI. This haplotype was predominantly found in temperate maize lines and geographically distributed across North America. These findings reveal the role of ZmTAF11 in regulating maize architecture and its potential application in high-density maize breeding. 

Maize (Zea mays L.) is an important food crop worldwide. Understanding yield-limiting factors is essential for optimizing maize productivity under varying agroclimatic conditions. In this study, the relative contributions of climate, soil, and management factors to yield variation in spring and summer maize across 34 sites in China during 2017-2020 were assessed. Random forest (RF) models explained more than 80% of the yield variation, and SHapley Additive exPlanations (SHAP) and Accumulated Local Effects (ALE) were employed to interpret the effects of key variables. Climate emerged as the dominant driver, accounting for nearly 50% of the total feature importance. For spring maize, solar radiation during the establishment stage (ES) had a strong positive effect, whereas the minimum temperature during the grain-filling stage (GFS) had a negative effect. In contrast, summer maize yield was constrained by elevated nighttime temperatures during ES but benefited from increased growing degree days (GDD) during GFS. Among all the variables, planting density (PD) was consistently important across both systems, and increasing PD represented a direct and effective pathway to enhance yield. The results of the yield component analysis further revealed that the significantly higher kernel number per ear (on average 68 kernels more than summer maize) was the main contributor to the superior performance of spring maize. Climate scenario simulations indicated that, without adaptive management, future warming could reduce spring and summer maize yields by 6.1–11.8% and 5.5–9.1%, respectively. These findings underscore the stage-specific climate sensitivity of maize and support the development of targeted adaptation strategies to sustain yields under future climate change.

Pod constriction (PC) is a key morphological trait determining both commercial values and yield of in-shell peanuts. Conventional phenotyping metrics (visual scores and pod waist length derived descriptors) suffer from low precision or limited applicability, especially for atypical pod shapes, which have constrained discovery of underlying genes. To address these limitations, this study introduced two novel image descriptors: front and back constriction depth indices (Front_DI and Back_DI). These indices enable accurate and robust evaluation of PC across diverse pod morphologies. Additionally, a Python script employing the deep learning technology was developed to efficiently and precisely extract these metrics. By applying both novel and conventional phenotyping methods to a recombinant inbred line population (Luhua 11×06B16), this study identified four quantitative trait loci (QTLs) for Front_DI, four for Back_DI, three for visual score, and two for a pod waist length-based descriptor across three environments. A major and co-localized QTL region was consistently detected on chromosome 2. Meta-analysis further refined this region to a 728-kb consensus interval. Within this interval, an InDel was identified in the coding region of Arahy.X14VTN between the two parental lines, resulting in a frameshift mutation and a predicted alteration in protein structure. Diagnostic markers were developed for this candidate gene, confirming the genetic effect on PC variation. The novel image descriptors and genetic loci presented here improve our understanding of the genetic basis of PC in peanut and offer practical tools for molecular breeding aimed at trait improvement.

Accurate monitoring of rice growth status is essential for scientific water and fertilizer management in paddy fields. Using remote sensing data combined with radiative transfer models and artificial intelligence algorithms can realize the semi-mechanism inversion. However, the commonly used hybrid inversion models have difficulties in adapting to paddy field scenarios covered with water layers. In addition, the data simulation methods often ignore the correlations between parameters, leading to distortion of the simulated data. To address these challenges, by developing the PROSAIL-Dw model considering the influence of the underlying surface moisture state on the canopy reflectance and proposing a multivariable joint prior knowledge data simulation method based on C-Vine Copula, this study proposed a novel hybrid framework based on Stacking model for retrieving rice growth parameters from multispectral imagery. The results indicated that, by introducing two parameters reflecting the presence and depth of the water layer, the PROSAIL-Dw model can more accurately simulate the NIR reflectance with water layer coverage (with R⊃2; increased by 0.42 for low nitrogen treatment). The growth parameters simulated by the C-Vine Copula method could retain the correlations, thus effectively improving the accuracy of the Stacking model compared with conventional methods (with rRMSE decreased by 5.81%-15.00%, and R⊃2; increased by 0.19-0.30). The hybrid inversion framework constructed in this study has further improved the accuracy and reliability of rice growth parameter inversion, and has important practical value for the scientific management of water and fertilizer in early-stage paddy fields.

Accurate estimation of Leaf Area Index (LAI) in multi-variety rice using optical remote sensing remains challenging due to spectral saturation under dense canopy conditions and inter-varietal physiological differences. To address this, we developed a multimodal data fusion framework integrating RGB and multispectral imagery acquired by unmanned aerial vehicles (UAVs), combined with features derived from Digital Surface Models (DSM), vegetation indices (VIs), texture, and depth representations. Using field data collected across 60 rice varieties, four machine learning models were evaluated for LAI estimation. Our results demonstrate that multimodal fusion substantially outperforms conventional VI-based approaches. Among them, the Random Forest Regression (RFR) model achieved optimal performance (R⊃2;=0.76, RMSE=0.57), representing a 26–58% improvement in R⊃2; over baseline models. SHAP-based feature importance analysis identified DSM feature, height-stratified vegetation indices, and depth features as key contributors to model accuracy. This study establishes that incorporating canopy structural information and deep features mitigates saturation effects and enhances generalizability across varieties. The proposed approach offers a robust and efficient solution for high-throughput LAI estimation, supporting applications in precision agriculture and rice breeding programs.

Improving radiation use efficiency (RUE) is critical for increasing wheat yield; however, the influence of plant architectural traits on RUE under low-light conditions is poorly understood. In this study, the effects of the architectural traits of wheat plants on RUE under low-light conditions were assessed. Four wheat varieties with distinct canopy architectures were examined: CM88 (erect and involute flag leaves, high spike density), SM1963 (semierect flag leaves, high spike density), SM1868 (drooping flag leaves, small spike size), and SM830 (prostrate flag leaves, large spike size). Their influence on RUE was evaluated via processes of light interception, photosynthetic capacity, and assimilate utilization. The canopy light distribution uniformity decreased progressively: CM88>SM1963 and SM1868>SM830. In contrast, the radiation interception rate in the middle and lower layers was highest in SM1963, followed by CM88/SM1868, and then SM830. CM88 exhibited the highest stomatal area, stomatal conductance (g_s), and net photosynthetic rate (P_n), indicating superior photosynthetic capacity. SM1963 and SM1868 showed intermediate g_s and P_n (moderate photosynthetic capacity), while SM830 exhibited the lowest g_s and P_n (weakest photosynthetic capacity). The key processes governing assimilate utilization—peak activities of sucrose phosphate synthase and sucrose synthase, and the consequent grain filling rate—were highest in SM1963 and SM830. CM88 displayed intermediate levels for these parameters, whereas SM1868 showed the lowest level. Integrating these processes, CM88 and SM1963 achieved the highest overall RUE. This high performance was driven by divergent strengths: CM88 excelled in light interception and photosynthetic capacity with moderate assimilate utilization performance, whereas SM1963 exhibited superior interception and assimilate utilization with moderate photosynthetic capacity. Importantly, light interception contributed the largest share to both RUE and yield, significantly exceeding the contributions from photosynthetic capacity and assimilate utilization, with specific proportions of 51.4 and 74.2%, respectively. This well-coordinated balance among processes, free of any major bottleneck, enabled CM88 and SM1963 to achieve the highest RUE and yield. In conclusion, under low-light conditions, an optimal wheat architecture for high RUE combines erect or semi-erect flag leaves (to optimize light interception) with high spike density (to ensure strong sink capacity).

Overapplication of nitrogen (N) is an important limiting factor in sustainable agricultural development. Breeding N-efficient genotypes is an effective approach to reduce crop N input, increase N-efficiency, and improve crop productive. However, the molecular mechanisms underlying low-N adaptations in peanut (Arachis hypogaea L.) roots are unknown. Herein, we compared root adaptation mechanisms to low-N stress between the N-efficient genotype JH15 (JH) and the N-inefficient genotype HY20 (HY), focusing on N metabolism and antioxidant capacity. Under N deficiency, JH exhibited a more developed root architecture, higher antioxidant activity, and higher N-metabolic enzyme levels under N deficiency. The expression of both high- and low-affinity nitrate transporter proteins (NRT2.5, NRT1.6), and the chloride channel protein CLC was upregulated in JH, with higher expression of genes encoding glutamine synthetase and asparagine synthase. However, only the low-affinity N transporters (NPF5.2, NPF7.3) were upregulated in HY. Flavonoid and isoflavonoid biosynthesis were the main metabolic pathways underlying the differences between the two genotypes under low-N treatment. The results of weighted gene co-expression network analysis and correlation network analysis revealed that differential expression of the key genes encoding caffeoyl-CoA O-methyltransferase, chalcone synthase, 2'-hydroxyisoflavone reductase, and shikimate hydroxycinnamoyl-CoA transferase affected key metabolites levels (epicatechin, kaempferol, calycosin, and biochanin A). We also found that WRKY40 and MYB30, MYB4, and bHLH35 may regulate flavonoids accumulation as positive and negative regulators, respectively. In summary, enhanced N uptake and assimilation and flavonoid accumulation in JH enhanced N metabolism and antioxidant capacity, improving N-efficiency.

This study aimed to characterize variation in the storage tolerance of eating and cooking quality (ECQ) among rice varieties from Southern China and to establish a quantitative evaluation framework. Indica, japonica, and indica–japonica hybrid rice varieties were subjected to accelerated aging under high-temperature and high-humidity conditions (35°C, 75% RH) for 90 days. Nineteen indices encompassing ECQ traits, chemical composition, pasting properties, amylase activity, lipoxygenase (LOX) activity, and antioxidant enzyme activities were determined before and after storage. The storage variation coefficient of individual indices (SVCI) and a newly developed paddy rice storage tolerance index (PRSI) were used for integrated evaluation. Principal component analysis, grey relational analysis, and stepwise regression analysis were applied to identify key indicators and construct a predictive model. ECQ deteriorated significantly after storage, with pronounced changes (mean SVCI>0.2) observed in fatty acid value (FAV), cooked rice appearance (CRA), cooked rice texture (CRT), comprehensive taste value (CTV), and antioxidant enzyme activities. PRSI values ranged from 0.257 to 0.609, with higher PRSI values indicating more rapid ECQ deterioration during storage. Cluster analysis classified the varieties into storage-tolerant, moderately storage-tolerant, and storage-sensitive groups. Compared with storage-sensitive varieties, storage-tolerant varieties showed markedly smaller declines in CRA, CRT, and CTV (mean reductions lower by 45.8, 40.9, and 49.3%, respectively), a weaker increase in FAV (mean lower by 28.3%), and consistently higher antioxidant enzyme activities, with SOD and POD activities exceeding those of storage-sensitive varieties by 19.7 and 10.0%, respectively, in both fresh and stored samples. These results demonstrate that PRSI is an effective index for evaluating ECQ storage tolerance. The SVCIs of CTV, FAV, and POD activity were identified as key predictors of PRSI. This work provides a robust methodological basis for breeding storage-tolerant rice varieties and for developing quality-preserving storage strategies in southern rice-growing regions. 

Although jasmonate (JA) signaling participates in heat stress (HS) responses, the mechanism by which it balances spikelet development and yield stability via the OsCOI1 gene remains unclear, particularly under HS during the panicle differentiation stage (PDS). This study comprehensively examined the influence of HS on panicle architecture, carbon (C) and nitrogen (N) metabolism, accumulation and allocation, root oxidative activity, antioxidant enzyme activity, JA and methyl jasmonate (MeJA) contents, yield and yield components using wild-type rice (WT, Nipponbare) and the coi1-18 mutant (OsCOI1 knockdown mutant, blocked JA signaling). The results demonstrated that under normal temperature (NT) conditions, the coi1-18 mutant exhibited significantly higher grain number per panicle, grain setting rate, and 1000-grain weight relative to the WT, collectively increasing grain yield by 23.2%. Conversely, under HS, reduced JA and MeJA contents in the coi1-18 mutant resulted in enhanced heat sensitivity, diminished antioxidant capacity, and dysregulated C-N metabolism. These effects markedly suppressed spikelet differentiation, thereby causing a yield reduction in the coi1-18 mutant that was 16.1 percentage points greater than in WT. Exogenous MeJA application effectively mitigated HS-induced suppression of spikelets differentiation in WT but failed to significantly rescue the phenotype in the coi1-18 mutant. This study reveals OsCOI1 as a context-dependent regulator: knockdown of OsCOI1 enhances yield under NT but impairs HS tolerance during PDS. This indicates a breeding-relevant trade-off and suggests that modulating JA signaling could balance yield under NT with panicle protection under HS.

 Mechanized seed production with a large restorer-to-sterile parental row ratio is a developmental trend; however, the effects of different parental row ratios on spikelet pollination effectiveness and seed-setting rates remain unclear. In this study, a single-factor randomized block experiment was conducted in Sichuan, China, to evaluate the influence of parental row ratio designs on spikelet pollination effectiveness and seed-setting rate in sterile lines under unmanned aerial vehicle-assisted pollination conditions. In 2021 and 2022, R2 treatment significantly reduced the number of pollen grains and pollen grain number per spikelet position in the middle (M) and far (F) rows of the plot. However, this treatment yielded a significantly higher pollination rate of exposed stigma florets at each spikelet position in the near (N) and middle rows when compared to the results of the R1 and R3 treatments, resulting in a greater seed-setting rate. The number of pollen grains per stigma (1–3) did not significantly differ among the R1, R2, and R3 patterns in 2022. Over 50% of successfully pollinated florets had pollen loaded on a single stigma. In the C1 combination, the seed-setting rate of R2 increased by 43.07% (vs. R1) and 34.23% (vs. R3), with yield increases of 42.35% (vs. R1) and 18.53% (vs. R3). In the C2 combination, R2 seed-setting rate increased by 13.75% (vs. R1) and 34.62% (vs. R3), with final yield increases by 14.87% (vs. R1) and 29.80% (vs. R3). The R2 pattern reduced pollen loss by optimizing the matching degree between pollination wind field and parental strip width, providing a stable pollen supply for the sterile lines (N, M). This supply enhanced stigma pollen capture, thereby significantly increasing floret pollination rates, seed-setting rates, and yield. This study provides a theoretical basis and practical guidance for pollination strategies and optimization of parental row ratios in mechanized seed production.

Chilo suppressalis is a major pest in rice-producing regions, posing serious threats to rice yield and quality. Existing pest prediction research generally ignore the stage-specific heterogeneity in population dynamics and neglect the synergistic effects among meteorological, soil, and rice physiological information. This makes it challenging to accurately characterize the complete dynamic changes in pest populations. In this study, we explicitly highlight three methodological innovations: (1) the use of a LOESS-based curve fitting and slope-change detection framework to objectively partition C. suppressalis population dynamics into three stages—population establishment, expansion, and outbreak; and (2) the integration of multi-source data, including trap monitoring, rice physiological indices derived from remote sensing, and ERA5 meteorological and soil variables, to construct stage-specific prediction models.; and (3) building upon this stage-based framework, we designed a targeted sensitivity-parameter screening scheme and developed daily dynamic prediction models using the Random Forest (RF) algorithm, which incorporate meteorological, soil, and crop physiological indicators. The results demonstrate that the proposed stage-specific prediction model achieves excellent performance. During the outbreak stage, the R² for all three experimental fields exceeds 0.9, with MAE below 23.16 and RMSE under 32.86. In the Jiulong field, stage-specific predictions show R² values above 0.89. Compared with Long Short Term Memory (LSTM) and Prophet models, RF exhibits superior stability and generalization, with test set R⊃2; consistently above 0.69, highlighting its robustness and reliability for stage-specific prediction of C. suppressalis population dynamics. These findings highlight the practical value of our approach for enhancing comprehensive pest forecasting and supporting targeted pest management.

Strip configurations play a crucial role in mediating crop productivity and resource utilization in intercropping systems. However, there remains a substantial knowledge gap concerning the mechanization-adaptive strip widths for cotton-soybean intercropping systems. Specifically, understanding how these strip widths can enhance synergies in crop productivity and land use efficiency is imperative. This study evaluated the impact of row ratio (strip) configurations on crop growth, physiology, productivity and land use efficiency in intercropped and monoculture systems. Treatments included two intercropping treatments (two rows of cotton plants alternating with three rows of soybean plants (2C3S), and three rows of cotton alternating with five rows of soybean (3C5S)), and two monoculture controls (monoculture cotton (MC), and monoculture soybean (MS)). Compared with monoculture cotton, the 3C5S system significantly increased both years averaged based chlorophyll content (SPAD value) by 6.64% at the peak boll-setting stage with increased leaf area index (LAI) and canopy photosynthetically active radiation interception ratio (In) during the early flowering stage. Furthermore, at the boll-opening stage, this system further enhanced boll and total plant nitrogen uptake. Intercropping significantly increased cotton boll density by enhancing dry matter translocation to reproductive organs with high lint yield. The 3C5S configuration outperformed 2C3S, increased the land equivalent ratio by 9.2% and net revenue by 15.87% over both years. The PCA results showed stronger relationships between cotton harvest index and other physiological parameters in 3C5S. The Mantel test indicates that yield of cotton-soybean intercropping was closely associated with cotton leaf area index and soybean aboveground biomass. Structural equation modeling identified nitrogen uptake as the key driver of yield in 3C5S. Overall, 3C5S improved crop productivity and land use efficiency compared to both 2C3S and monoculture systems, representing the optimal cotton-soybean intercropping strategy. The 2C3S and 3C5S intercropping systems were designed with a standard 2:1 row spacing (76 cm for cotton and 38 cm for soybean), compatible with mainstream agricultural machinery in China. A 55 cm operational clearance was maintained between crop strips to support fully mechanized sowing and harvesting, thereby reducing labor cost with high production revenue.