Global population pressures have necessitated increased focus on protecting and developing resilient plant species that can maintain productivity despite environmental challenges. Environmental degradation, driven by climate change and anthropogenic activities, poses significant threats to global food security through various forms of physical stress. Major environmental constraints affecting agricultural yields worldwide include salinity, water scarcity, nutritional imbalances (encompassing mineral toxicity and deficiencies), and extreme temperatures. Crop yield is influenced by multiple abiotic factors, including agronomic conditions, climatic variables, and soil nutrient availability. Plants develop various survival mechanisms at molecular, cellular, and physiological levels in response to stress. Abiotic stress, whether occurring individually or in combination, significantly impacts crop growth and productivity. For instance, drought stress reduces leaf area, plant height, and overall crop development. Cold stress inhibits plant development and crop efficiency, leading to diminished productivity. Salinity stress not only induces water stress in plants but also negatively affects cytosolic metabolism, cell development, membrane function, and increases reactive oxygen species (ROS) production. Elevated CO₂ concentrations may enhance global precipitation patterns, potentially resulting in increased rainfall that can adversely affect crop development. Plants under excessive water stress exhibit reduced amylose content but increased crude protein levels. This affects both quality and quantity of crop production by inhibiting seed germination and causing growth impairment through combined effects of elevated osmotic potential and ion toxicity. Plants have evolved various escape-avoidance and tolerance mechanisms in response to abiotic stress, including physiological adaptations and integrated cellular or molecular responses. This review paper examines the impact of abiotic stress on morpho-physiological, biochemical, and molecular activities across various crops. Additionally, it analyzes crop interactions with abiotic stress regarding response and adaptation mechanisms, providing a fundamental framework for species selection and development of stress-tolerant varieties in the future.

The interplay between gut microbiota and host health has attracted significant interest in the animal science community. Maintaining gut microbiota homeostasis by supplementing probiotics to treat clinical conditions like calf diarrhea is an emerging area of research nowadays because of increased concerns regarding antimicrobial resistance (AMR) and drug residues in animal products. Probiotics reduce the incidence of calf diarrhea by increasing the gut microbiota diversity and richness with more commensal bacteria such as Lactobacillus and Bifidobacterium that produce antimicrobial compounds, as well as modulating the immune response by increasing cytokines, Interleukin-2 (IL-2), IL-4, IL-6, IL-10, and reducing tumor necrosis factor-α (TNF-α), by increasing production of antibodies, especially immunoglobulin E (IgE), also IgG, differentiating naïve Th lymphocytes (Tho) into Th1, hence stimulate innate immunity and prime the adaptive immune response. Specific probiotic strains of bacteria and yeast (Saccharomyces cerevisiae) derived probiotics maintain the integrity of the intestinal barrier. In this review, data are being organized to address the role of probiotics in treating calf diarrhea by modulating gut microbiota and stimulating an immune response against notorious pathogens, to present animal and veterinary scientists and nutritionists with a new concept to treat infectious diseases from the perspective of the gut microbiota, increasing animal health, performance, and welfare. In conclusion, health status and gut microbiome are strongly interlinked. Research data indicated a significant reduction in the incidence of diarrhea after probiotic administration. If interrelations between probiotics and existing gut microbiota are explored more quantitatively, novel antibiotic substitutes can emerge in the future.

Thinopyrumponticum(2n=10×=70), a wild relative of common wheat (TriticumaestivumL.), is considered an invaluable genetic resource for wheat improvement due to its abundance of genes conferring resistance to biotic and abiotic stresses. This study focused on the CH97 line, derived from the BC₁F₇progeny of a cross between wheat cv. 7182 and Th. ponticum. Cytological evidence showed that CH97 has 42 chromosomes, forming 21 bivalents at meiotic metaphase I, with the bivalents subsequently separating and moving to opposite poles during meiotic anaphase I. Through a combination of fluorescence insituhybridization (FISH), genomic insituhybridization (GISH), multicolor GISH (mc-GISH), and liquid array analysis, it was determined that CH97 comprises 40 wheat chromosomes and two alien chromosomes from the E^egenome of Th. ponticum, featuring the absence of a pair of 5D chromosomes and variations in 1B, 6B, and 7B chromosomes. These findings confirm that CH97 is a stable wheat-Th. ponticum5E (5D) alien disomic substitution line. Inoculation experiments revealed that CH97 exhibits high resistance to wheat powdery mildew and stripe rust throughout the growth period, in contrast to the highly susceptible common wheat parent 7182. Compared to 7182, CH97 displayed improvements in thousand-kernel weight and kernel length. Additionally, utilizing specific-locus amplified fragment sequencing (SLAF-seq) technology, chromosome 5E-specific molecular markers were developed and validated, achieving a 33.3% success rate, facilitating marker-assisted selection for disease resistance in wheat. Overall, the CH97 substitution line, with its resistance to diseases and improved agronomic traits, represents valuablenew germplasm for wheat chromosome engineering and breeding.

Carbohydrate partitioning from source to sink tissues is essential for plant growth and development. However, in maize (ZeamaysL.), the molecular mechanisms by which callose synthase genes regulate this process remain largely unexplored. This study demonstrates that mutation of maize callosesynthase12(ZmCals12) results in increased carbohydrate accumulation in photosynthetic leaves but decreased carbohydrate content in sink tissues, leading to plant dwarfing and male sterility. Histochemical β-glucuronidase (GUS) activity assay and mRNA insituhybridization (ISH) revealed that ZmCals12expression mainly occurs in the vascular transport system. ZmCals12 loss-of-function decreased callose synthase activity and callose deposition in plasmodesmatas (PDs) and surrounding phloem cells (PCs) of the vascular bundle. The drop-and-see (DANS) assay indicated reduced PD permeability in photosynthetic cells and diminished transport competence of leaf veins in Zmcals12mutants, resulting in decreased symplastic transport. Paraffin section analysis revealed that less-developed vascular cells (VCs) in Zmcals12mutants likely disrupted sugar transport, contributing to the pleiotropic phenotype. Furthermore, impaired sugar transport inhibited internode development by suppressing auxin (IAA) biosynthesis and signaling in Zmcals12mutant. These findings elucidate the mechanism by which ZmCals12-mediated callose deposition and symplastic transport regulate maize growth and development

The pathogenesis-related protein PR10 plays a vital role in plant growth, development, and stress responses. This study systematically identified and analyzed PR10genes in cultivated peanut (ArachishypogaeaL.), examining their phylogenetic relationships, conserved motifs, gene structures, and syntenic relationships. The analysis identified 54 AhPR10genes, which were classified into eight groups based on phylogenetic relationships, supported by gene structure and conserved motif characterization. Analysis of chromosomal distribution and synteny demonstrated that segmental duplications played a crucial role in the expansion of the AhPR10gene family. The identified AhPR10genes exhibited both constitutive and inducible expression patterns. Significantly, AhPR10-7, AhPR10-33, and AhPR10-41demonstrated potential importance in peanut resistance to Aspergillus flavus. Invitrofungistatic experiments demonstrated that recombinant AhPR10-33 effectively inhibited A.flavusmycelial growth. These findings provide valuable insights for future investigations into AhPR10 functions in protecting peanut from A.flavusinfection.

Alternate wetting and drying irrigation (AWD) significantly influences the cooking and eating quality of rice (Oryza sativa L.). However, the mechanisms by which AWD affects rice cooking and eating quality remain unclear. Lipid and free fatty acid contents in grains correlate positively with cooking and eating quality of rice. This study examined Yangdao 6 (YD6, a conventional taste indica inbred) and Nanjing 9108 (NJ9108, a superior taste japonica inbred) cultivated under conventional irrigation (CI), alternate wetting and moderate drying irrigation (AWMD), and alternate wetting and severe drying irrigation (AWSD) from 10 days after transplanting to maturity. The research investigated the relationship between lipid and free fatty acid biosynthesis in grains and the cooking and eating quality of rice. Compared to CI treatment, AWMD significantly enhanced the contents of lipid, total free fatty acids (TFFAs), free unsaturated fatty acids (FUFAs), linoleic acid, and oleic acid in milled rice by increasing activities of enzymes associated with lipid synthesis, while AWSD produced opposite effects. Correlation analysis revealed that elevated levels of lipid, TFFAs, FUFAs, linoleic acid, and oleic acid contribute to improved rice cooking and eating quality. The findings demonstrate that AWMD enhances cooking and eating quality of milled rice through optimization of lipid and fatty acid synthesis in rice grains.

Coordinating light and nitrogen (N) distribution within a canopy is essential for improving rice yield and resource use efficiency. However, limited research has examined light and N distribution in response to planting density and N rate, and their relationships with grain yield, radiation use efficiency (RUE), and N use efficiency for grain production (NUEg) in rice. A two-year field experiment was conducted with two hybrid varieties under three N levels, 0 kg ha^–1(N1), 90 kg ha^–1(N2) and 180 kg ha^–1(N3), and two planting densities, 22.2 hills m^–2(D1) and 33.3 hills m^–2(D2). Results showed 3.4% higher yield and 4.4% higher NUEg under N2D2 compared with N3D1. The extinction coefficient for N (K_N) and light (K_L) and their ratio (K_N/K_L) at heading stage were significantly influenced by N rate, planting density, and their interaction. K_Ndecreased with the increase of N input or planting density. Compared to N1, K_Ndecreased by 43.5 and 58.8% under N2 and N3, respectively, while K_Nunder D2 decreased by 16.0% compared to D1. Higher K_Land K_N/K_Lvalues occurred under low N rates, with opposite trends under high N rates. Increased planting density led to decreased K_Land K_N/K_Lvalues. N2D2 demonstrated higher K_Land K_N, and thus comparable K_N/K_L, compared to N3D1. Correlation analysis revealed K_Lnegatively correlated with RUE, while K_Nand K_N/K_Lpositively correlated with NUEg. These findings indicate that increasing planting density under reduced N input could maintain rice yield while enhancing resource use efficiency through regulation of canopy light and N distribution.

Persistent overcast rain was an essential limiting factor for summer maize production, of which immediate impact was the dual pressure of waterlogging and shading. However, the mechanisms underlying independent and combined effects of waterlogging and shading on maize yield losses remain understudied, particularly across different growth stages. Denghai 605 (DH605) was selected tobe subjected shading, waterlogging, and their combined stress at the 3rd leaf stage (V3), the 6th leaf stage (V6), and tasseling stage (VT). Results showed that shading, waterlogging and their combination significantly restricted leaf areaexpansion, reduced leaf net photosynthetic rate (P_n) and net assimilation rate (NAR), thereby decreasing the crop growth rate (CGR) and biomass accumulation. Additionally, compared to control, the process of lignin synthesiswas inhibited under stressed treatment, resulting in diminished stem mechanical strength and impaired vascular systemdevelopment, which substantially reduced assimilate remobilizationefficiency to the ear and ultimate grain yield. Waterlogging and combined stresses exhibited maximum impact atthe V3 stage, followed by V6 and VT stages, while shading effects were most pronounced atthe VT stage, followed by V6 and V3 stages. Moreover,the compound stress exacerbated the damage brought about by a single stress. As climate change is projected to increase the frequency of multiple abiotic stress occurrences, these findings provide valuable insights for future summer maize breeding research under persistent rainfall conditions.

Elevated CO₂(eCO₂) may mitigate stress-induced damage to cotton (Gossypiumspp.) growth and development.However, understanding the early-stage responses of cotton to multiple abiotic stressors at eCO₂ levels has been limited. This study quantified the impacts of chilling (CS, 22/14°C, day/night temperature), heat (HS, 38/30°C), drought (DS, 50% irrigation of the control), and salt (SS, 8 dSm^–1) stresses on pigments, physiology, growth, and development of 14 upland cotton cultivars under ambient CO₂(aCO₂, 420 ppm; current) and eCO₂(700 ppm; future) levels during the vegetative stage. The eCO₂partially negated the effects of all stresses by improving one or more of the pigments, physiological, growth, and development traits, except CS. For instance, HS at aCO₂significantly increased stomatal conductance by 36% compared with non-stressed plants at aCO₂. However, HS at eCO₂significantly decreased stomatal conductance by 18% compared with HS at aCO₂.The first squaring was delayed by one day under SS at aCO₂but two days earlier under SS at eCO₂than non-stressed plants at aCO₂.Root and shoot dry mass and the total leaf area were significantly higher under all stresses, except for CS, at the eCO₂compared with similar stresses at theaCO₂. Most growth and development traits, including plant height, leaf area, and shoot dry mass, displayed a mirroring response pattern between aCO₂and eCO₂ under all environments except CS.Cultivars exhibited significant interaction with stressed environments. Further, results revealed differential sensitivity and adaptation potential of cultivars to stress environments at varying CO₂levels. This study highlights the need to consider eCO₂in designing breeding programs to develop stress-tolerant varieties for future cotton-growing environments.

Flower and fruit abscission reduce crop yield, so decreasing abscission is a significant agricultural issue. HAESA (HAE) and HAESA-like2 (HSL2) kinases and their ligand, INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide, have been confirmed to be the core elements regulating floral organ abscission in Arabidopsis thaliana. Our earlier research revealed that SlIDL6, a homolog of IDA in tomato, functions similarly to AtIDA, regulating the abscission of tomato flower organs. Here, we further isolated three HAESA-like homologs, SlHSL1/2/3, which are involved in tomato flower abscission. SlHSL1/2/3are highly expressed in the abscission zone (AZ). The knockout mutant lines of Slhsl1, Slhsl2, and Slhsl3 showedlower flower pedicel abscission than wild type (WT). The double mutant of Slhsl1Slhsl2, Slhsl1Slhsl3, and Slhsl2Slhsl3 further depressed abscission than each of the single mutant lines, while triple mutants Slhsl1Slhsl2Slhsl3exhibited the lowest abscission, indicating that SlHSL1/2/3 mediated abscission is non-redundancy, at least partially. Treating tomato pedicel explants with SlIDL6 peptide significantly accelerated pedicel abscission in WT. However, it had little effect on the abscission rate of SlHSL1/2/3 knockout lines, indicating that SlHSL1/2/3 are the receptors of SlIDL6 in pedicel abscission. Ethylene action inhibitor 1-methylcyclopropene (1-MCP) can significantly depress the expression of SlHSL1/2/3. Ethylene can significantly accelerate the abscission of WT, while less abscission was found in SlHSL1/2/3knockout lines. Our findings indicate that SlHSL1/2/3 can act as receptors for SlIDL6 to positively regulate tomato pedicel abscission, and the abscission regulated by SlHSL1/2/3 was partially dependent on ethylene

Xyloglucan represents the primary hemicellulose component in higher plant cell walls, providing mechanical support. The XTH gene family encodes xyloglucan endotransferase/hydrolase, a crucial enzyme in cell wall remodeling. Studies examining XTH family-related genes in apples remain limited. This studyinvestigated the MdXTH30gene, isolated from apple (Malus×domestica), which demonstrated responsiveness to abscisic acid, NaCl, and polyethylene glycol (PEG) 6000, with cytoplasmic localization confirmed through subcellular mapping. To elucidate the role of MdXTH30in stress response, transgenic MdXTH30apple calli were generated andthe gene was heterologously expressed in ArabidopsisviaAgrobacterium-mediated transformation. The findings revealed that MdXTH30enhanced resistance to drought, salt stress, and pathogens through regulation of relevant genes inboth apple calli and Arabidopsis. These results identify potentially significant candidate genes for improving biotic and abiotic stress resistance at the cell wall level.

Osmanthusfragransis most famous for its strong aroma, and different varieties have different degrees of fragrance and color. Fragrance and color are important factors affecting the ornamental quality of O.fragrans. Terpenoids are important secondary metabolites in plants, with β-carotene (C40) being the major pigment substance and linalool (C10) being the key aromatic component in O.fragrans. The geranylgeranyl pyrophosphate synthase genes (GGPPSs) play important roles in secondary metabolism in plants. However, the functions of the GGPPS family in floral color and fragrance formation has rarely been reported in O.fragrans. In this study, 24 OfGGPPSgenes were identified and classified into two subfamilies. The OfGGPPSsshowed tissue-specific expression and OfGGPPS13had highest expression in flowers. The OfGGPPS13 protein was localized to chloroplasts. The transcriptome data of OfGGPPS13was verified by qRT-PCR and the expression level in ‘Wanyingui’ with strong aroma was higher than that in ‘Zhuangyuanhong’ with deep color at different flower development stages. Transient overexpression of OfGGPPS13in O.fragranspetals showed that OfGGPPS13increased the β-carotene content, the main color substance of O.fragrans, but decreased the linalool content, the main volatile organic compound (VOC) in the floral aroma of O.fragrans. OfGGPPS13was indicated as the critical gene related to terpenoid synthesis in the floral aroma and color formation in O.fragrans. Our findings provide gene resources on the GGPPS gene family for further revealing the molecular regulation mechanism of the floral color and aroma formation in O.fragrans.

The accuracy of genomic annotation is crucial for subsequent functional investigations; however, computational protocols used in high-throughput annotation of open reading frames (ORFs) can introduce inconsistencies. These inconsistencies, which lead to non-uniform extension or truncation of sequence ends, pose challenges for downstream analyses. Existing strategies to rectify these inconsistencies are time-consuming and labor-intensive, lacking specific approaches. To address this gap, we developed toGC, a tool that integrates genomic annotation with RNA-seq datasets to rectify annotation inconsistencies. Using toGC, we achieved an accuracy of nearly 100% accuracy in correcting inconsistencies in published PhytophthorasojaeORFs. We applied this innovative pipeline to the GPCR-bigrams gene family, which was predicted to have 42 members in the P.sojaegenome but lacked experimental validation. By employing toGC, we identified 32 GPCR-bigram ORFs with inconsistencies between previous annotations and toGC-corrected sequences. Notably, among these were 5 genes (GPCR-TKL9, GPCR-TKL15, GPCR-PDE3, GPCR-AC3, and GPCR-AC4) showed substantial inconsistencies. Experimental gene annotation confirmed the effectiveness of toGC, as sequences obtained through cloning matched those annotated by toGC. Importantly, we discovered two novel GPCRs (GPCR-AC3and GPCR-AC4), which were previously mispredicted as a single gene. CRISPR/Cas9-mediated knockout experiments revealed the involvement of GPCR-AC4but not GPCR-AC3in oospore production, further confirming their status as two separate genes. In addition to P.sojae, the reliability of the toGC pipeline in Phytophthoracapsiciand Pythiumultimumfurther emphasizes the robustness of this pipeline. Our findings highlight the utility of toGC for reliable gene model correction, facilitating investigations into biological functions and offering potential applications in diverse species analyses.

In recent years, an unusual wilt disease affecting Pyruspyrifoliahas been observed in various regions of Jiangsu, China. This disease originates from the roots and progresses with distinctive browning patterns along vascular tissues, even extending over two meters above the ground. These symptoms set it apart from recognized pear diseases and typically lead to the death of affected trees within the same or the following year. Furthermore, this disease exhibits a tendency to spread to neighboring trees even after the removal of affected trees, presenting a substantial threat to pear production. To ascertain the causative agent, the present study encompassed pathogen isolation, morphological and molecular identification, as well as validation experiments adhering to Koch’s postulates. The fungal isolates obtained were identified as Fusariumcugenangensebased on characteristics of the colonies and conidia, in addition to a phylogenetic analysis using DNA sequences of the translation elongation factor 1-alpha (tef1), calmodulin (CaM), and RNA polymerase second largest subunit (rpb2) genes. Pathogenicity of the isolated F.cugenangenseon pear was confirmed by artificial inoculation. By introducing GFP-labeled pathogens into the roots, colonization in stem and leaf tissues was observed viafluorescence microscopy and transmission electron microscopy. Furthermore, these pathogens were successfully reisolated from stems and foliage, conclusively providing evidence of systemic infection within the pear plants. To the best of our knowledge, this is the first report of F.cugenangensecausing pear wilt disease in China.

The plant pathogenic fungus Sclerotiniasclerotiorumis the causative agent of Sclerotinia stem rot (SSR) disease in most dicotyledons. Among the various proteins involved in drug efflux or substance transport, ATP-binding cassette (ABC) transporters constitute a superfamily of membrane-bound proteins that may play a crucial role in the survival of S.sclerotiorum. However, the expression patterns and functions of ABC transporter genes in S.sclerotiorumremain largely uncharacterized. This study characterized a highly expressed S.sclerotiorumABC transporter gene during inoculation on host plants, SsBMR1. Silencing SsBMR1resulted in a significant reduction in hyphal growth, infection cushion development, sclerotia formation, and virulence. Moreover, host-induced gene silencing (HIGS) of SsBMR1significantly enhanced plant resistance. Transcriptome and metabolomics analyses suggested that SsBMR1is involved in antioxidant and toxin transport, thereby influencing fungal defense and cell rescue mechanisms. In comparison to the wild-type strain, SsBMR1gene-silenced transformants exhibited a diminished response to extracellar oxidative stress and a decreased exporting of antioxidant glutathione. Tolerance assays further demonstrated the crucial role of SsBMR1in conferring resistance to the plant antifungal substances, camalexin and brassinin, as well as certain fungicides. Furthermore, SsBMR1gene-silenced transformants showed enhanced repression on virulence when sprayed with camalexin and brassinin on the leaves. Thus, SsBMR1likely contributes to virulence by facilitating the export of antioxidant and providing resistance against antifungal agents. The findings of this study provide valuable insights that could contribute to the development of novel management techniques for SSR.

The native thelytokous (TH) and arrhenotokous (AR) strains of Neochrysocharisformosa(Westwood) (Hymenoptera: Eulophidae) are promising biocontrol agents against the invasive tomato pest Tutaabsoluta(Meyrick) (Lepidoptera: Gelechiidae). This study assessed the performance and preferences of these strains in choice experiments involving five host instar ratios and evaluated their functional responses to seven densities of 1st instar larvae (5 to 40 hosts). In host-attacking behavior assays, an increasing proportion of 1st instar larvae led to a significant rise in host mortality rates for both strains. Both strains exhibited strong preferences for parasitizing and attacking 1st instar larvae over later instars, with the TH strain demonstrating significantly greater host-killing efficacy than the AR strain. Functional response experiments revealed that the attack rates of both strains were positively correlated with host density. Parasitism by both strains and host-stinging behavior by the TH strain showed type III functional responses, while host-feeding by both strains and host-stinging by the AR strain followed type II functional responses. Early establishment of the TH strain in tomato agroecosystems could enhance the management of T.absoluta. These findings provide critical insights into the functional dynamics of the TH and AR strains of N.formosathat can inform the development of effective biocontrol programs for this globally significant pest.

The red imported fire ant, SolenopsisinvictaBuren, is a highly invasive eusocial insect pest that threatens native biodiversity, agriculture, and human health. The innate immune system and intricate social immune responses of S.invictapose challenges to the development of effective control strategies. MicroRNAs (miRNAs) play critical roles in the post-transcriptional regulation of gene expression, which influences various biological processes, including immunity and host-pathogen interactions. While the miRNA-mediated response of insects to pathogens has been extensively studied in solitary insects, little is known about the innate immune responses of individual members within a colony. To address this gap, we constructed small RNA libraries from Metarhiziumanisopliae-infected S.invictaworkers and investigated the temporal dynamics of miRNA-mediated immune responses to the entomopathogen. Several differentially expressed miRNAs were identified, and they were found to regulate genes involved in the Toll, IMD, and melanization immune pathways. Quantitative real-time PCR (qRT-PCR) was employed to analyze the spatiotemporal dynamics of key miRNAs/target genes, specifically miR-71/ModSP1-Relishand miR-7/Lysozyme2-Serineprotease7. A dual luciferase assay (invitro) was performed to validate the interactions between miRNAs and their target genes. Overexpression of miR-71 and miR-7 (viamiRNA mimics) efficiently suppressed their target genes, impaired the antifungal immune response of S.invictaand increased the susceptibility to M.anisopliaeinfection compared to controls. Furthermore, RNA interference-based gene silencing elucidated the roles of these immune genes in regulating fungal susceptibility, thus providing vital clues for developing virulent and effective mycoinsecticides using modern genetic engineering tools.

The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology, contractility, cell proliferation, differentiation, interactions, migration, and death. The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes. The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages. Hi-C was used to build chromatin architectures during four representative stages. ChIP-seq was conducted to identify enhancers and promoters in these four stages, which are occupied by histone H3K27ac and H3K4me3 peaks. Results show that large-scale genome architecture changes are mostly unidirectional, and coupled by complex on/off dynamic patterns of gene expression. Specifically, we observed 258.30Mb of the genome undergoing A/B compartment switching. Notable alterations (316.57Mb) of interaction frequencies within TADs were observed. Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development. Some muscle-related gene promoters that interacted with active enhancers during development, and some myopathy/aging-associated genes that were activated in aging muscle were founded. These results provide key insights into skeletal muscle development in vivo, and offer a valuable resource that allows in-depth functional characterization of candidate genes.

Primordial germ cells (PGCs) are the stem-cell population of adult animal gametes, which develop into sperm or eggs. It can be propagatedin vitroand injected into the host chicken for genome editing to obtain germline chimeric chicken. However, it has the limitation that the host embryo contains endogenous PGCs, which raises complications, resultantly donor PGCs fail to compete, and transmission efficiency reduced. Therefore, to increase the transmission efficiency, we generated a novel sterile chicken with the inducible elimination of endogenous PGCs in the host. This is the first study that applied the herpes simplex virus thymidine kinase (HSV-TK) cell ablation system in avian. CRISPR/Cas9-mediated homology-directed repair was performed to localize the HSV-TKsuicide gene to the last exon of the deleted in azoospermia-like (DAZL) gene, and ganciclovir (GCV) was added to induce the apoptosis in the germ cells of the host embryo. The sterilized host embryo introduced genome-edited PGCs to produce chimeric chicken carrying exogenous germ cells only. It was observed that the germline transmission efficiency was 100% achieved, and the obtained chicks were purely from donor breeds. The technologies established in the current study have important applications in germplasm conservation and gene editing in chicken.

NADC34-like porcine reproductive and respiratory syndrome virus (PRRSV), which first appeared in China in 2017, is currently one of the main epidemic strains in China. In this study, we found that a new variant of NADC34-like PRRSV evolved, named the L1A variant. The phylogenetics, epidemic status, and pathogenicity of the LA variants were subsequently comprehensively evaluated. Based on the results of the ORF5 phylogenetic analysis, the L1A variants were classified as NADC34-like PPRSV. All the strains had the same discontinuous 131-aa deletion in the NSP2 region (similar to that in the NADC30). Recombination analysis revealed that the L1A variants were recombinant viruses that contained an NADC30-like PRRSV skeleton, a nonstructural protein-encoding gene region obtained in part from JXA1-like PRRSV and a ORF2-ORF6 gene region partly obtained from NADC34-like PRRSV and that exhibited similar recombination patterns. We successfully isolated the L1A variant TZJ2756 from PAMs and Marc-145 cells. In animal experiments, TZJ2756 exhibited moderate pathogenicity in piglets, causing obvious clinical symptoms, namely, persistent fever, significantly reduced body weight, interstitial edema and severe interstitial pneumonia in the lungs, and prolonged high-load viremia. L1A variants have been detected in at least 12 provinces in China and share many similar epidemiological characteristics with the American L1C variant. This research will enhance our understanding of the prevalence of L1A variants and furnish valuable data for the ongoing monitoring of NADC34-like PRRSV in China.

A microbial strain designated BacilluslicheniformisQX928 was screened from hot springs in Sichuan Province, China, and a compound generated in the culture of this strain clearly inhibited PseudomonasaeruginosaATCC27853. The measured minimum inhibitory and lowest bactericidal concentrations were (13±0.17) and (22±0.72) mg L^–1, respectively. The compound was identified as 3-isopropylhexahydro-4H-pyrido[1,2-α]pyrazine-1,4(6H)-dione (IPHPPD). A SciFinder search revealed that IPHPPD could be the first compound synthesized by microorganisms that had both antibacterial and anti-quorum sensing properties. At low concentrations, IPHPPD interfered with the signaling factors and population effects of P.aeruginosa, thereby altering the biofilm morphology and structure. IPHPPD more strongly inhibited P.aeruginosaat high concentrations, primarily by reducing its virulence factors, cell membrane permeability and energy metabolism. A transcriptome analysis highlighted the role of IPHPPD in the transcriptional regulation of cellular metabolism and quorum sensing. Thus, the results of this study provide critical evidence that IPHPPD is a potential target for drug development to prevent and treat diseases in animals.

Long-term manure application has the potential to alleviate soil acidification, and increase carbon sequestration and nutrient availability, thus improving cropland fertility. However, the mechanisms behind greenhouse gas N₂O emissions from acidic soil mediated by long-term manure application remain poorly understood. Herein, we investigated N₂O emission and its linkage with gross N mineralization and nitrification rates, as well as nitrifying and denitrifying microbes in an acidic upland soil subjected to 36-year fertilization treatments, including an unfertilized control (CK), inorganic fertilizer (F), 2× rate of inorganic fertilizer (2F), manure (M), and the combination of inorganic fertilizer and manure (FM) treatments. Compared to the CK treatment (1.34 μg N kg^–1d^–1), fertilization strongly increased N₂O emissions by 34-fold on average, with more pronounced increases in the manure-amendment (10.6–169 μg N kg^–1d^–1) than those in the inorganic fertilizer treatments (3.26–5.51 μg N kg^–1d^–1). The manure amendment-stimulated N₂O emissions were highly associated with increased soil pH, mean weight diameter of soil aggregates, substrate availability (e.g., particulate organic carbon, NO₃⁻and available phosphorus), gross N mineralization rates, denitrifier abundances and the (nirK+nirS)/nosZratio. These findings suggest that the increased N₂O emissions primarily resulted from alleviated acidification, increased substrate availability and improved soil structure, thus enhancing microbial N mineralization and favoring N₂O-producing denitrifiers over N₂O consumers. Moreover, ammonia-oxidizing bacteria (AOB) rather than ammonia-oxidizing archaea (AOA) positively correlated with soil NO₃⁻concentration and N₂O emissions, indicating that nitrification indirectly contributed to N₂O production by supplying NO₃⁻for denitrification. Collectively, manure amendment potentially stimulates N₂O emissions, primarily resulting from alleviated soil acidification and increased substrate availability, thus enhancing N mineralization and denitrifier-mediated N₂O production. Our findings suggest that consideration should be given to the greenhouse gas budgets of agricultural ecosystems when applying manure for managing the pH and fertility of acidic soils.

As the global leader in rice production, China’s paddy fields contribute substantially to greenhouse gas emissions through methane (CH₄) and nitrous oxide (N₂O) releases. Aromatic rice cultivation practices have been optimized to enhance the aroma, so the relationship between its cultivation and greenhouse gas emissions from paddy fields is unclear. To investigate how aroma-enhancing cultivation practices drive microbial community dynamics in aromatic rice paddies and their implications for greenhouse gas emissions, a two-year experiment in five ecological locations (Xingning, Nanxiong, Conghua, Luoding, and Zengcheng) compared two farming practices: partial organic substitution for inorganic fertilizers combined with water-saving irrigation (IOF+W) and traditional cultivation (CK). The CH₄and N₂O emissions, soil microbial composition and function, global warming potential (GWP), nitrogen use efficiency, yield, and the content of 2-acetyl-1-pyrroline (2-AP) were measured and analyzed. The main purpose was to investigate the impact of IOF+W on CH₄and N₂O emissions and their relationship with soil microorganisms. The results showed that IOF+W significantly reduced CH₄emission fluxes and totals (36.95%) and GWP (31.29%), while significantly increasing N₂O emission fluxes and totals (14.82%). The soil microbial community structure was reshaped by the IOF+W treatment, which suppressed methanogens but enhanced the abundances of nitrifying and denitrifying bacteria. Key enzymatic activities involved in CH₄production, such as methyl-coenzyme M reductase, formylmethanofuran dehydrogenase, and methyltransferase, decreased. In contrast, the activity of the key CH₄-oxidizing enzyme methanol dehydrogenase increased.This shift led to an overall attenuation of the CH₄production metabolism while enhancing the CH₄oxidation metabolism. In addition, the activities of pivotal enzymes involved in denitrification and nitrification were improved, thus enhancing nitrogen nitrification and denitrification metabolism. Moreover, the IOF+W treatment significantly increased nitrogen use efficiency (47.83%), yield (14.77%), and 2-AP content (13.78%). Therefore, the IOF+W treatment demonstrated good efficacy as a sustainable strategy for achieving productive, green, resource-efficient, and premium-quality aromatic rice cultivation in South China.

The continuous supply of phosphorus (P) is indispensable in crop production. However, P resources are non-renewable, and environmental concerns like eutrophication associated with its loss from agroecosystems make the sustainable management of P resources essential for ensuring global food security. This study was designed to reduce mineral P inputs through management practices. A field experiment comprising a wheat–maize rotation system was conducted in the Guanzhong Plain of Shaanxi Province, China from 2018–2023. The eight treatments included CK (without P), FP (conventional P application); RP (recommended P); RP₈₀(20% reduction in RP); SRP₈₀(20% reduction in RP with straw wrapping); ARP₈₀(20% reduction in RP with ammonium sulfate instead of urea); SARP₈₀(20% reduction in RP with straw wrapping and ammonium sulfate instead of urea); and SARP₆₀(40% reduction in RP with straw wrapping and ammonium sulfate instead of urea). Crop yield, P uptake, and P fertilizer use efficiency were measured during harvest and throughout the entire period of the study. At the end of the experiment, P fractions were estimated using the Tiessen-Moir P classification method. The results revealed that the grain yields of all the treatments except for RP₈₀were significantly increased compared to CK, with increases of 14.9–28.8%. Furthermore, agronomic efficiency, apparent P use efficiency, P recovery rate, and partial factor productivity were significantly improved for the treatments that received 20% less P with straw wrapping. Moreover, the enhancement measures significantly increased labile and moderately labile P in the soil. Therefore, straw wrapping with ammonium sulfate instead of urea is one of the most effective ways to reduce mineral P inputs while increasing the efficiency of P in wheat–maize rotation systems.

Nitrogen use efficiency in rice is lower than in upland crops, likely due to differences in soil nitrogen dynamics and crop nitrogen preferences. However, the specific nitrogen dynamics in paddy and upland systems and their impact on crop nitrogen uptake remain poorly understood. The N dynamics and impact on crop N uptake determine the downstream environmental pollution from nitrogen fertilizer. To address this poor understanding, we analyzed 2,044 observations of gross nitrogen transformation rates in soils from 136 studies to examine nitrogen dynamics in both systems and their effects on nitrogen uptake in rice and upland crops. Our findings revealed that nitrogen mineralization and autotrophic nitrification rates are lower in paddies than in upland soil, while dissimilatory nitrate reduction to ammonium is higher in paddies, these differences being driven by flooding and lower total nitrogen content in paddies. Rice exhibited higher ammonium uptake, while upland crops had over twice the nitrate uptake. Autotrophic nitrification stimulated by pH reduced rice nitrogen uptake, while heterotrophic nitrification enhanced nitrogen uptake of upland crops. Autotrophic nitrification played a key role in regulating the ammonium-to-nitrate ratio in soils, which further affected the balance of plant nitrogen uptake. These results highlight the need to align soil nitrogen dynamics with crop nitrogen preferences to maximize plant maximize productivity and reduce reactive nitrogen pollution.

Green manuring is essential for improving soil quality and nutrient uptake. With the gradual depletion of phosphorus (P) resources, more attention is being paid to the role of green manures in cultivation systems, such as maize–green manure intercropping, to find possible pathways for enhancing soil P utilization. A maize–green manure intercropping experiment was started in 2009 to investigate the effects and mechanisms for enhancing P uptake and yield in maize. Three species of green manures (hairy vetch (HV), needleleafpea (NP), sweet pea (SP)) and a sole maize treatment (CK) were used, resulting in four treatments (CK, HVT, NPT, and SPT) in the experiment. During 2020–2023, the intercropping treatments enhanced maize yields in 2020 and 2021, particularly in HVT with increases of 13.7% (1.96t ha^–1) and 13.0% (2.13t ha^–1) compared with CK, respectively. Grain P accumulation of maize was significantly higher in the intercropping treatments than CK in 2020, 2021, and 2023, and with an average increase of 10.6% over the four years (5.2% for NPT, 10.8% for SPT and 15.9% for HVT) compared with CK. Intercropping promoted maize growth with a greater root length density and a higher organic acid release rate. HVT changed the soil properties more dramatically than the other treatments, with increases in the acid phosphatase and alkaline phosphatase activities of 29.8 and 38.5%, respectively, in the topsoil (0–15cm), while the soil pH was reduced by 0.37 units compared to CK (pH=8.44). Intercropping treatments facilitated the conversion of non-labile P to mod-labile P and stimulated the growth of soil bacteria in the topsoil. Compared with CK, the relative abundance of Gemmatimonadota,known for accumulating polyphosphate, and Actinobacteriota, a prominent source of bioactive compounds, increased significantly in the intercropping treatments, especially in HVT and SPT. A PLS-PM analysis showed that intercropping promoted soil P mobilization and the enrichment of beneficial bacteria by regulating maize root morphology and physiology. Our results highlight that maize–green manure intercropping optimizes root traits, soil properties and bacterial composition, which contribute to greater maize P uptake and yield, providing an effective strategy for sustainable crop production.

Enhancing soil organic carbon (SOC) stocks is a key aspect of modern agriculture, but whether this can be achieved by incorporating legume green manure crops in cereal production to substitute synthetic N fertilizers is unknown. This study used a six-year (2017–2022) field study to explore the impacts of intercropping green manure with maize and reducing nitrogen fertilization on SOC stocks, while specifically focusing on the relationship between aggregate composition and carbon sequestration. Maize intercropped with common vetch (M/V), maize intercropped with rapeseed (M/R), and sole maize (M), were each tested at conventional (N2, 360kg ha^–1) and reduced (N1, 270kg ha^–1, 25% reduced) N application rates. Soil was sampled in 2020, 2021, and 2022. Compared with sole maize, intercropping with green manure (M/V and M/R) significantly increased SOC stocks which compensated for any negative effect due to the 25% reduction in N application. Based on 3-year averages, intercropping with M/V and M/R increased the SOC content compared to sole maize (M) by 12.1 and 9.1%, respectively, with intercropping further mitigating the negative impact of reduced nitrogen application. There was no significant difference between M/V and M/R. The SOC content at N1 was reduced by 9.3–10.5% compared to that at N2 in sole maize, but the differences in SOC stocks between N1 and N2 were not significant in the intercropping patterns (M/V and M/R). The intercropped M/V and M/R showed 20.9 and 16.3% higher SOC contents compared to sole maize at N1, with no differences at N2. Intercropping green manure led to a 5.3% greater SOC in the 0–20cm depth soil in 2022compared to that in 2020, due to the cumulative effect of two years of green manure intercropping. Intercropping green manure (M/V and M/R) increased the proportion of macroaggregates (>0.25mm) and aggregate stability while reducing the proportion of microaggregates compared to sole maize under the N1 application. Structural equation modeling indicated that cropping patterns and nitrogen application levels mainly affect SOC indirectly by regulating the composition of macroaggregates and aggregate organic carbon (AOC). Correlation analysis further revealed that the composition of macroaggregates is significantly and positively correlated with the SOC content (R²=0.64). In addition, intercropping green manure can maintain high crop yields by increasing SOC under reduced chemical nitrogen application. The results of this study show that intercropping green manure with grain crops can be a viable measure for increasing SOC sinks and maize productivity by optimizing the aggregate composition with reduced N application in the Hexi Oasis Irrigation Area.

The effect of adding hydroxycinnamic acids (caffeic acid, sinapic acid, p-coumaric acid and chlorogenic acid) in Cabernet Sauvignon dry red wine before and after fermentation was investigated, taking into account the color parameters, anthocyanin content, and overall polyphenol levels in the wine samples. The copigmentation effect of malvidin-3-O-glucoside and sinapic acid was further explored in model solution and through theoretical calculations. The results indicated that the addition of hydroxycinnamic acids significantly enhanced the wine’s color with sinapic acid (before the fermentation) showing the most pronounced color protection effect. Compared to control samples, the addition of hydroxycinnamic acids resulted in a 36% increase in total phenolic content and a 28% increase in total anthocyanin content. Thermodynamic analysis revealed that the interaction between sinapic acid and malvidin-3-O-glucoside was spontaneous and exothermic. Theoretical studies identified hydrogen bonding (HB) and dispersion forces as the main primary stabilizing forces, with the carboxyl group of sinapic acid playing a critical role while the anthocyanin backbone also influenced the interaction.

Understanding the molecular responses of tea leaves to mechanical stress is crucial for elucidating the mechanisms of post-harvest quality formation during oolong tea processing. This study employed an integrated multi-omics strategy to characterize the changes and interactions among metabolomic (MB), transcriptomic (TX), and proteomic (PT) profiles in mechanically stressed tea leaves. Mechanical stress initially activated damage-associated molecular patterns (DAMPs), including Ca²⁺signaling, jasmonic acid signaling, and glutathione metabolism pathways. These processes subsequently induced quality-related metabolic pathways (QRMPs), particularly α-linolenic acid and phenylalanine metabolism. Up-regulated expression of LOX, ADH1, and PARgenes, together with the increased abundance of their encoded proteins, respectively promoted the accumulation of jasmine lactone, benzyl alcohol, and 2-phenylethanol. These findings indicate that mechanical stress influences the metabolite biosynthesis in tea leaves through coordinated molecular responses. This study provides new insights into the molecular mechanisms underlying tea leaf responses to mechanical stress and a foundation for future investigations into how early molecular events may contribute to post-harvest metabolic changes during oolong tea processing.

In China, farmers have increasingly adopted direct-seeded rice (DSR). While various impacts of DSR have been studied, limited evidence exists regarding the effect of DSR adoption on pesticide use. This study examines the impact of DSR adoption on pesticide use utilizing data from a 2018 survey of 982 rice farmers in China’s Yangtze River Basin. The endogenous treatment-regression and switching regression models are employed to address self-selection bias. The results indicate that, after accounting for self-selection, DSR adopters spend 401.72 CNY ha–1 more on pesticides compared to non-adopters. Although DSR adoption significantly increases the use of insecticides, fungicides and herbicides, its impact is most pronounced for insecticide expenditure and least pronounced for herbicide expenditure. The findings remain robust when altering the dependent variable, truncating the research sample, and modifying the estimation method. Heterogeneous analysis reveals that DSR adoption has a stronger positive impact on pesticide expenditure among farmers below 60 years of age, with at least 6 years of education, and managing rice sown areas less than 2 ha. Based on these findings, this study recommends enhancing complementary techniques for DSR, improving the dissemination of DSR cultivation technologies, and strengthening socialized services. This research provides a comprehensive assessment of DSR’s advantages and disadvantages, particularly regarding pesticide use, offering important policy implications for pesticide reduction.

Malnutrition remains a significant global challenge, particularly in developing countries. Policymakers have increasingly focused on improving household food security and nutrition through farm production diversity (FPD). While research indicates that FPD correlates positively with reduced malnutrition, other studies emphasize the importance of market access for improved nutritional outcomes. However, this evidence varies by region and remains inconsistent. To address this knowledge gap, this study analyzed survey data from 450 smallholder farmers in Punjab, Pakistan, using regression models to examine the relationship between FPD and dietary diversity, as well as the underlying impact pathways. The findings demonstrate that FPD significantly correlates with increased household dietary diversity score (HDDS). FPD influences dietary diversification through both own-farm production and market food consumption pathways, with the own-farm production pathway showing greater impact. The increase in food expenditure through own-farm production yielded a marginal return of 8% in household dietary diversity compared to 5.3% through marketing. Gender differences emerged as significant, with male-headed households showing relatively lower dietary diversity. These findings have substantial implications for countries with smallholder farming systems, providing valuable insights for the formation of agricultural policies, resource optimization, and rural development initiatives.