Search Results (2,559)

Plant genomes exhibit extensive structural diversity generated by large-scale genomic alterations, collectively known as structural variations (SVs). Unlike single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), SVs can reshape genome architecture through changes in sequence content, gene dosage, regulatory landscapes, and chromosome organization. Recent advances in long-read sequencing (LRS), pan-genome construction, and multi-omics technologies have greatly expanded our ability to identify and interpret SVs across plant species. In this review, we summarize recent progress in understanding the formation mechanisms, classification, and functional consequences of plant SVs. We discuss major sources of SV generation, including transposable element activity, non-allelic homologous recombination (NAHR), horizontal gene transfer (HGT), and genome restructuring following polyploidization. We further highlight how LRS and graph-based pan-genomes overcome limitations of traditional linear reference genomes and enable more comprehensive characterization of genetic diversity. Beyond variant discovery, we emphasize the importance of integrating genomic, transcriptomic, epigenomic, proteomic, metabolomic, and spatial omics datasets to decipher how SVs influence gene regulation and complex agronomic traits. We also discuss current challenges, including repetitive genomes, polyploidy, computational complexity, and translation of SV knowledge into practical breeding applications. Together, these advances establish SV-centered genomics as a critical framework for understanding plant genome evolution and accelerating precision crop improvement. Full article

β-D-Xylosidases (BXLs) are members of glycoside hydrolase family 3. They play essential roles in cell wall remodeling, plant development, and abiotic stress responses. BXL gene families have been systematically characterized in several crop species. However, a comprehensive analysis of BXL genes in cotton (Gossypium hirsutum), a globally important fiber and oilseed crop, is still lacking. In this study, we performed a genome-wide identification of BXL genes in allotetraploid cotton. A total of 25 GhBXL genes were identified and classified into six phylogenetic clades. Gene structure and conserved domain analyses showed that all GhBXL proteins possess the characteristic tripartite GH3 domain architecture. Chromosomal distribution and synteny analyses indicated that the expansion of the cotton BXL family may be associated with whole-genome duplication and allopolyploidization. Promoter cis-element analysis detected stress-responsive regulatory motifs in the GhBXL promoters, including STRE, W-box, DRE core, and as-1 elements. Under PEG-simulated drought and salt stress, expression profiling, independently confirmed by qRT-PCR, showed distinct temporal response patterns among GhBXL members. Weighted gene co-expression network analysis (WGCNA) further identified GhBXL-8, GhBXL-9, and GhBXL-20 as hub genes in stress-responsive modules. Their co-expressed partners were enriched in transcription factors, kinases, and stress-related proteins. These findings provide a systematic foundation for understanding the evolutionary dynamics and functional roles of BXL genes in cotton. They also highlight candidate genes for future functional investigation. Full article

Organic fertilization is a key strategy for improving soil structure and fertility in China’s Vertisols, yet the trade-offs among soil quality enhancement, grain yield performance, and nutrient use efficiency under different organic amendment regimes remain insufficiently elucidated. Based on a unique 43-year field fertilization experiment, this study systematically evaluated the effects of long-term chemical fertilization (NPK) alone, low-dose (NPKLS) and high-dose straw incorporation (NPKHS), combined chemical fertilizer with cattle manure (NPKCM), and pig manure (NPKPM) fertilization on soil physical, chemical properties, crop yields and plant nutrient utilization efficiency. The results showed that NPKCM and NPKPM significantly improved soil physical properties by reducing soil bulk density, improving soil pore structure, and enhancing soil water retention capacity and saturated hydraulic conductivity. Although long-term manure application led to slight soil salt accumulation, the rate of accumulation remained substantially lower than that associated with commercial organic fertilizers and did not approach the crop salinity damage threshold, suggesting low ecological risk. Compared with NPK treatment, manure amendment effectively counteracted soil acidification induced by prolonged chemical fertilization, while also significantly increasing soil total phosphorus and available phosphorus content, and elevated the proportion of active phosphorus (PAC). The improved soil phosphorus activation capacity and comprehensive soil quality further contributed to substantial increases in wheat grain yield under NPKCM and NPKPM treatments. Despite these agronomic benefits, the additional nitrogen and phosphorus inputs from manure resulted in soil nutrient surpluses, which considerably reduced nitrogen and phosphorus partial factor productivity as well as agronomic efficiency. In contrast, straw incorporation treatments (NPKLS, NPKHS) sustained stable crop yield without notable declines in nutrient efficiency, positioning them as a greener and more sustainable approach to balancing grain production with resource use efficiency. These findings highlight the need to integrate nutrient credits from manure into fertilization program. Given the 43-year evidence, fertilization strategy should consider not only the nutrients supplied by manure but also the quantities exported through harvested products, with adjustments based on annual soil fertility analyses. Such nutrient budgeting is essential to maximize fertilizer use efficiency, prevent excessive phosphorus accumulation, and maintain balanced soil fertility over time. Full article

Improving cropland carbon performance while maintaining food security is central to China’s agricultural transition and climate goals This study examines low-carbon cropland use performance (PCLU) and its model-implied interprovincial association network across 31 Chinese provinces from 2010 to 2023. A global super-efficiency slacks-based measure model estimated PCLU by incorporating agricultural output, carbon emissions, nonpoint-source pollution, and crop sequestration; annual directed networks were constructed with a modified gravity model and analyzed using social network analysis, a temporal exponential random graph model (TERGM), and complementary quadratic-assignment analyses. Mean PCLU increased from 0.524 to 0.861, while the interquartile range widened from 0.146 to 0.310; network density declined before partially recovering as hierarchy increased, indicating improvement without provincial convergence and reconnection within a more differentiated multi-hub structure. Persistence (β = 4.510) and reciprocity (β = 2.376) dominated network evolution, whereas shared partners produced neither additional triadic closure nor expanding open chains; similarities in urbanization and planting structure favored ties, while rural-income differences reflected socioeconomic complementarity. External validation showed moderate overall correspondence with green-technology patent collaboration (mean annual QAP r = 0.335) but limited overlap among the strongest dyads. Overall, China’s low-carbon cropland transition combined rising but increasingly uneven performance with a path-dependent and selective interprovincial structure, providing an empirical basis for differentiated coordination based on provincial performance and network position. Full article

Cereal production is increasingly constrained by soil degradation, water scarcity, climate variability, and rising disease and weed pressure. This review synthesizes current knowledge on the role of regenerative agronomic practices in cereal production, with particular emphasis on soil health, plant disease management, water-use efficiency, and yield stability. Available evidence consistently indicates that the greatest benefits arise not from individual practices but from integrated systems combining reduced tillage, crop residue retention, diversified crop rotations including legumes, cover crops, organic fertilization, and biologically based pest management. Such practices can increase soil biological activity and its ability to limit disease by enriching functionally beneficial microbial communities and limiting pathogens through competition for resources and niches, antibiosis, hyperparasitism, and the induction of plant resistance. They can also improve soil structure, water infiltration, water retention, and crop resilience to drought stress and, under certain conditions, reduce erosion, nutrient losses, and yield variability. However, the effects of regenerative practices are strongly dependent on soil type, climate, nitrogen balance, pest pressure, and the extent of adoption of regenerative practices. Risks may arise during the transition period, including yield declines, nitrogen immobilization, weed infestation, and increased disease pressure. Evaluation of these systems should encompass not only yield but also the grain quality and phytosanitary status, soil organic carbon stocks throughout the soil profile, N₂O emissions, and production profitability. The review covers cereal systems from temperate, humid, arid and semi-arid zones, and the results were interpreted considering climate, soil quality, water availability, and agronomic practices, as the same practice can produce different effects in different agroecological zones. Further research should prioritize long-term, multifactorial experiments conducted across diverse agroecological environments that integrate agronomic performance, environmental sustainability, and crop quality. Full article

Camellia oleifera Abel., an economically significant oil-producing crop widely cultivated in southern China, is renowned for its high-quality edible oil and diverse pharmacological activities. The plant is rich in terpenoids, particularly triterpenoid saponins, which contribute to its health-promoting properties. However, a comprehensive review summarizing the diversity, biological activities, biosynthesis, and regulatory mechanisms of terpenoids in C. oleifera is lacking. This review systematically categorizes terpenoids identified from different parts of C. oleifera, elucidates their structural features, and infers their biosynthetic pathways. The biological activities of terpenoid-rich extracts and individual compounds, including antioxidant, anti-inflammatory, anticancer, antimicrobial, and hypoglycemic effects, are discussed. Furthermore, the potential applications of C. oleifera terpenoids in functional foods, pharmaceuticals, and agriculture are explored. This review aims to provide a valuable reference for future research and utilization of C. oleifera terpenoids. Full article

Agronomic modulation of secondary metabolism may influence not only crop resilience but also the biological activity of fruit-derived phytochemicals. In this study, we evaluated the impact of exogenous methyl jasmonate (MeJA) application under contrasting water regimes on the selected phenolic compounds and vascular bioactivity of Vaccinium corymbosum L. cv. Legacy. Antioxidant capacity was assessed by FRAP and DPPH assays, phytochemical composition was characterized by HPLC-DAD, and antiplatelet activity was evaluated through inhibition of TRAP-6–induced P-selectin (CD62P) expression in human platelets. Selected phenolic constituents were further examined using molecular docking and molecular dynamics simulations against a platelet receptor model. Although MeJA treatment altered the abundance of selected phenolic compounds identified by HPLC-DAD, total antioxidant capacity remained largely unchanged. Blueberry extracts significantly inhibited platelet activation in a concentration-dependent manner without cytotoxic effects, and antiplatelet potency was not strictly related to global antioxidant indices. Computational analyses revealed stable ligand–receptor interactions and favorable binding free energies for selected phenolics, providing a structural explanation for receptor-level modulation. These findings suggest that elicitor-driven responses in blueberries can influence platelet functional responses and highlight the importance of qualitative phytochemical composition in determining vascular bioactivity. This multiscale approach connects plant stress physiology, natural product chemistry, and human platelet biology, underscoring the translational relevance of agronomic strategies for nutraceutical functionality. Full article

Photosynthesis is the fundamental biological process underlying plant growth, crop productivity, and global food security. However, its efficiency is highly vulnerable to abiotic stresses, which disrupt chlorophyll biosynthesis, electron transport, carbon assimilation, stomatal regulation, and photoprotective mechanisms, ultimately reducing crop yield. Improving photosynthetic resilience under adverse environments has therefore become a major objective of modern crop improvement. Recent advances in phenomics and high-throughput phenotyping (HTP) have transformed the evaluation of photosynthesis-related traits by enabling rapid, non-destructive, and large-scale assessment across diverse environments, while facilitating quantitative characterization of structural, physiological, biochemical, and thermal responses to abiotic stress. Technologies including chlorophyll fluorescence, gas-exchange analysis, thermal imaging, hyperspectral imaging, LiDAR, and UAV-based sensing provide comprehensive insights into plant physiological responses and stress adaptation. Integration of these phenomic approaches with genomic information and artificial intelligence (AI)-driven analytical frameworks has strengthened genomic and phenomic prediction, enabling more accurate identification of candidate genes, selection of superior genotypes, and accelerated genetic gain. This review critically synthesizes recent advances in photosynthesis-related traits, phenomics, HTP technologies, and their integration with genomics and AI-assisted breeding, highlighting current challenges, knowledge gaps, and future opportunities for developing climate-resilient wheat and rice cultivars and promoting sustainable crop production. Full article

Crop straw is an abundant lignocellulosic resource, but its efficient bioconversion is hindered by the recalcitrant structure of plant cell walls. This study integrated degradation phenotyping, enzyme activity assays, whole-genome analysis, and comparative transcriptomics to link the wheat-straw degradation performance of strain XH2 with its enzymatic and molecular responses. Strain XH2 was isolated from fully decomposed compost collected in Anhui Province, China, selected based on the formation of a distinct hydrolysis halo on CMC-Congo red agar, and deposited in the China Center for Type Culture Collection (CCTCC) under accession number CCTCC M 2025519. Morphological, cultural, phylogenetic, and genomic analyses identified strain XH2 as Streptomyces thermocarboxydus. Its degradation capacity was evaluated during 28 days of cultivation by measuring straw degradation, lignocellulosic components, scanning electron microscopy (SEM), and extracellular enzyme activities. S. thermocarboxydus XH2 caused marked disruption of the wheat-straw surface and achieved a degradation rate of 31.45%. Cellulose and hemicellulose contents decreased from 41.10% to 28.87% and from 30.72% to 16.85%, respectively, whereas lignin decreased from 8.28% to 6.30%. Endoglucanase activity, filter paper activity (FPase, an indicator of total cellulase activity), and xylanase activity peaked on day 7, reaching 35.99, 17.68, and 37.01 U/mL, respectively. Genome analysis revealed multiple genes encoding cellulases and hemicellulases. Comparative transcriptomic analysis after 72 h of cultivation in wheat-straw medium identified 1614 differentially expressed genes relative to Gause No. 1 medium, with major enrichment in ABC transporters and fructose and mannose metabolism. Most genes associated with polysaccharide degradation were upregulated. These findings link the degradation phenotype of S. thermocarboxydus XH2 to its enzymatic and molecular responses and support its further evaluation as a candidate for wheat-straw bioconversion under greenhouse and field conditions. Full article

Immune-mediated inflammatory diseases (IMIDs) arise from interactions among genetic susceptibility, epithelial barrier function, microbiota, diet, and other environmental exposures. Modern diets influence mucosal immunity not only through fibre intake, food processing, and microbiota composition, but also through a less explored exposure layer: plant-derived molecules with potential immune activity. Crop breeding, intensive agriculture, global trade, gluten-free substitutes, and plant-based food technologies have changed the spectrum, dose, concentration, and matrix in which plant defence proteins, antinutritional factors, endogenous toxicants, and novel plant antigens reach the intestinal surface. In this structured, hypothesis-generating narrative review, we propose dietary adjuvanticity as a mechanistic framework for considering how selected food-derived molecules may amplify mucosal immune responsiveness, modify antigen presentation, disturb barrier function, or lower tolerance thresholds without necessarily acting as classical autoantigens. The framework differs from general food-derived immunomodulation, nutritional exposomics, and diet-microbiota-host interaction models by focusing specifically on adjuvant-like immune amplification at the intestinal mucosa. The ASIA concept is used only in Shoenfeld’s functional sense, as an analogy for exogenous immune amplification through innate activation, danger signalling, bystander activation, epitope spreading, and loss of tolerance in susceptible hosts; it is not applied as a dietary diagnosis. Wheat amylase-trypsin inhibitors, gluten epitopes, lectins, potato glycoalkaloids, saponins, quinoa prolamins, emerging legume proteins, L-canavanine, and tolerance-promoting plant substrates are discussed with explicit separation of established clinical evidence, strong mechanistic evidence, preclinical/ex vivo evidence, and speculative disease-modifier hypotheses. Overall, plant-derived exposures are best interpreted as potential modifiers within the IMID exposome, not as primary causes of autoimmunity. Testing this model will require defined exposures, food-matrix and processing studies, biomarkers of barrier and immune activation, patient stratification, and controlled human studies. Full article

Nuclear factor Y (NF-Y) constitutes a pivotal transcription factor family that modulates plant growth and development as well as abiotic stress responses. Oat (Avena sativa L.) is an economically vital cereal crop and a major livestock forage globally. Nevertheless, the NF-Y gene family has not yet been systematically characterized in the oat genome. Here, we identified 36 AsNF-Y genes in the oat genome and categorized them into three distinct subfamilies (NF-YA, NF-YB, and NF-YC). Phylogeny, gene structure, duplication, collinearity, and conserved motif analyses revealed high evolutionary conservation of this gene family. Additionally, the identification of diverse cis-acting regulatory elements in the promoters of AsNF-Y genes, combined with their differential expression profiles under multiple abiotic stress conditions, indicated that AsNF-Ys serve as crucial regulators in modulating oat abiotic stress tolerance. Furthermore, preliminary functional validation via the TRV-VIGS system confirmed that two candidate genes, AsNF-YC02 and AsNF-YC06, may positively regulate salt tolerance in oat. Collectively, our findings deepen the understanding of NF-Y genes in gramineous crops and supply promising candidates for the genetic improvement of oat stress tolerance and molecular breeding. Full article

Arbuscular mycorrhizal (AM) fungi are often considered host generalists. Although the host-mediated assembly of AM fungal communities is well documented, its functional significance remains poorly understood, particularly in organic and low-input agroecosystems, where crop–weed interactions may influence the soil AM fungal reservoir. We investigated plant and AM fungal functional traits, mycorrhizal dependency (MD), and root AM communities in three legume crops and five weed species grown in pots with the same indigenous AM fungal inoculum. AM fungal communities were characterized using SSU rRNA gene clone libraries, sequencing, and terminal restriction fragment length polymorphism (T-RFLP) analysis. Of 825 examined clones, 792 were assigned to AM fungi, representing 23 RFLP types. Plant species significantly affected the plant traits, root colonization, spore density, extraradical mycelium density, and MD. PERMANOVA revealed that plant species explained 97.3% of the variation in the AM fungal community structure, although this result should be interpreted cautiously because within-species dispersion may have contributed to the explained variance. RELATE analysis showed a significant association between the AM fungal community structure and plant–AM fungal functional traits. The specific root length, shoot and root N concentrations, AM fungal colonization, and spore abundance best explained community patterns. Legume crops supported greater AM fungal development and positive growth responses, whereas several weeds hosted diverse AM communities without showing biomass benefits. These findings highlight that weed management could indirectly influence AM fungal persistence through host-mediated community assembly, although field validation is required. Full article

Biotic stresses (pest feeding, pathogenic fungal/bacterial/viral infection) and diverse abiotic stresses (extreme temperature, drought, waterlogging, saline–alkali soil, heavy metal pollution, nutrient deficiency, UV-B, ozone) severely restrict crop growth and global agricultural yield. Lipids act as core membrane structural constituents and vital secondary signaling messengers, executing multi-layered adaptive balancing functions during cell-type interactive stress acclimation, rather than uniform whole-plant lipid responses. They sustain membrane structural integrity across distinct cell populations, serve as synthetic precursors of bioactive signaling molecules, and trigger cascaded transcriptional and metabolic reprogramming upon environmental stimuli to rebalance physiological status among different cell types. This review systematically summarizes cell-type interactive lipid-mediated plant defense and acclimation balance mechanisms across biotic and abiotic stress contexts. We elaborate the biological functions of fatty acids, phospholipids, galactolipids, sphingolipids and their derivatives (jasmonate, salicylic acid, phosphatidic acid, oxylipin) in stress signal transduction and antioxidant defense and strictly distinguish two categories of lipid changes under all stress types: active adaptive lipid remodeling and passive stress-induced lipid oxidative damage. Key contents include stress-triggered cell-type-specific membrane lipid remodeling, the hierarchical transcriptional regulatory network mediated by WRI1, LEC1, PHR, MADS and other transcription factors governing oil metabolism, as well as crosstalk between lipid metabolism and compartmentalized reactive oxygen species (reactive oxygen species (ROS)) signaling. We further compare conserved lipid-regulatory modules and species-specific divergent responses across model plants and economic oilseed crops, integrating state-of-the-art targeted/untargeted lipidomics, single-cell spatial lipidomics and multi-omics joint breeding strategies to improve multi-stress tolerance in oilseed crops. By consolidating global research progress up to 2025, including the two latest 2026 cross-species meta-analysis reviews, this review provides systematic theoretical support and operable multi-level technical frameworks for genetic engineering targeting conserved lipid pathways to breed stress-resilient high-oil crop germplasm, and highlights reliable lipid stress biomarker screening as a promising translational research direction. Full article

Tea [Camellia sinensis (L.) O. Kuntze] is the most widely consumed beverage worldwide and also has significant economic crop value. Understanding the genetic diversity and population structure of wild tea plants by analyzing their germplasm is essential for effective collection, management, and utilization. In this study, the genetic diversity and population structure of 283 wild tea accessions were analyzed using 16 SSR markers. A total of 81 alleles were detected, ranging from 3 to 8 alleles per marker, with an average of 5.06 alleles per locus. The average polymorphism information content (PIC) value of 0.545 indicates that the SSR marker set was, on average, highly informative. Moreover, the MSG0533 marker showed the presence of a distinct allele (350 bp) exclusively in tea accessions from the Chiang Mai province. This unique allele could be further developed into a DNA marker for accurate identification of tea sourced from this region. Based on the dendrogram, wild tea accessions were grouped into three major clusters exhibiting substantial genetic divergence. Population structure analysis showed two distinct subpopulations. Subpopulation 1 consists of 70 (24.73%) accessions from the provinces of Lampang, Mae Hong Son, Nan, and Phrae, whereas all 213 (75.27%) accessions in subpopulation 2 originate from the provinces of Chiang Mai and Chiang Rai. Analysis of molecular variance (AMOVA) identified 13% variance among and 56% variance within populations, while 31% was attributed to individuals, indicating a high gene exchange rate between the two subpopulations. These findings provide comprehensive information for future breeding and genetic studies of tea. Full article

Quorum sensing (QS) is critically involved in mediating microbial interactions and serves as a central regulatory mechanism in bacterial pathogenesis. As an emerging countermeasure, quorum quenching (QQ) suppresses QS-regulated virulence through enzymatic or chemical disruption of signal systems. N-acyl homoserine lactone (AHL), an evolutionarily conserved QS signal, coordinates the pathogenicity of multiple plant pathogens, particularly Dickeya zeae, which causes soft rot disease in various crops and leads to substantial agricultural losses. In this study, the QQ strain Acinetobacter schindleri XJ-10 was evaluated for its capacity to degrade AHL and attenuate the pathogenicity of D. zeae EC1 in host plants. Notably, strain XJ-10 exhibited efficient AHL degradation at 0.2 mmol/L within 24 h, achieving a degradation efficiency of 98.80%. Subsequently, gas chromatography–mass spectrometry (GC-MS) analysis identified N-hexanoyl-L-homoserine lactone and propanamide as key intermediates during AHL degradation, confirming complete mineralization to CO₂ and H₂O. Based on the structural characterization of AHL and its intermediates, the metabolic pathway within strain XJ-10 was proposed. The degradation pathway initiates with the hydrolysis of the ester ring of N-hexanoyl-L-homoserine lactone, generating N-hexanoyl-L-homoserine. Subsequent carbon–nitrogen bond scission is predicted to yield N-cyclohexyl-propanamide, which is further catabolized to produce hexanamide and propanamide. Furthermore, strain XJ-10 exhibited biocontrol activity against soft rot disease affecting potato (Solanum tuberosum), radish (Raphanus sativus), and Chinese cabbage (Brassica rapa subsp. pekinensis), as its crude enzyme extract effectively reduced disease incidence and severity in planta. While strain XJ-10 showed no detectable acylase activity, it exhibited significant degradation activity against AHL, suggesting a distinct QQ mechanism. Collectively, these findings broaden the scope of QQ-based biocontrol strategies and enhance mechanistic insights into managing bacterial diseases through QS modulation. Full article