Search Results (8,223)

Senecavirus A (SVA) has rapidly emerged as a globally distributed swine pathogen, with clinical signs mimicking vesicular diseases such as Foot-and-Mouth Disease, posing challenges for timely detection and control. Here, we analyzed 329 complete SVA genomes spanning multiple continents to provide a comprehensive view of its evolutionary dynamics, recombination patterns, haplotype diversity, and global dissemination. Phylogenetic analyses revealed two major lineages: Lineage 1, consisting mainly of early strains from the United States before 2007, and Lineage 2, which emerged post-2007 and subsequently spread across the Americas and East Asia. Recombination was confined to Lineage 2 and concentrated in nonstructural regions, particularly 2C, highlighting intra-lineage genetic exchange as a driver of recent diversification. Haplotype analysis of the 3AB gene identified 170 distinct haplotypes, revealing a star-like network structure consistent with rapid population expansion from a central ancestral variant, while secondary branches reflect ongoing regional diversification. Despite this high genetic variation, genome-wide dN/dS ratios remained below one, and purifying selection was strongest in the N-terminal domains of structural and nonstructural proteins, indicating functional constraints that maintain viral fitness. Time-scaled phylogenetic reconstruction and Bayesian Skyline analysis revealed rapid lineage diversification and a marked increase in effective population size in the early 2010s. Phylogeographic inference further identified repeated introductions from the Americas into East Asia, likely facilitated by swine trade and other anthropogenic factors. Collectively, SVA evolution is driven by frequent mutation and intra-lineage recombination yet constrained by pervasive purifying selection, generating extensive genetic diversity while maintaining functional integrity, with implications for genomic surveillance and targeted control. Full article

Understanding the factors that determine the success of lichen translocations is critical for effective conservation of lichen biodiversity. Both physiological acclimation and the genetic structure of source populations can influence conservation outcomes. This study examined seasonal variation in physiological parameters (specific thallus mass—STM, chlorophyll a fluorescence—F_V/F_M, and chlorophyll content) of Lobaria pulmonaria (L.) Hoffm. across one year, selecting three source populations along a latitudinal gradient in Mediterranean forests in Italy. Genetic structure of their mycobiont and photobiont were also characterized. STM differed significantly among populations and seasons, with consistent increases from March to September. In contrast, F_V/F_M remained relatively stable, while chlorophyll content showed the highest values in December. Genetic analyses revealed clear differentiation among populations for both symbionts. These results suggest that L. pulmonaria can acclimate physiologically to seasonal environmental changes and highlight the importance of considering local genetic structure when selecting source populations for translocation. Integrating physiological and genetic information provides a robust framework for improving conservation strategies for this species. Full article

Desiccation tolerance is a critical adaptive trait that enables plants to survive extreme water loss, yet its physiological basis in tomato and its wild relatives remains poorly understood. In this study, chlorophyll a fluorescence imaging was used as a reliable tool to evaluate photosystem II (PSII) response to progressive desiccation. The analysis was conducted in cultivated tomato (Solanum lycopersicum) and five wild relatives (Solanum chilense, Solanum habrochaites, Solanum peruvianum, Solanum pimpinellifolium, and Solanum pennellii). Detached leaves were subjected to controlled desiccation for up to 50 h. During this period, tissue moisture content (TMC), relative water content (RWC), PSII photochemical efficiency [Fv/Fm; maximum quantum yield (QY_max)], minimal fluorescence (F0), maximal fluorescence (Fm), and variable fluorescence (Fv) were monitored to assess changes in photosynthetic performance. Desiccation caused a significant, moisture-dependent decline in PSII efficiency across all species, with QY_max showing a strong linear relationship with RWC (R² = 0.80–0.90). Interspecific variation was evident as S. chilense, S. habrochaites, S. peruvianum, and S. pimpinellifolium exhibited rapid PSII impairment, while S. lycopersicum showed moderate tolerance. In contrast, S. pennellii maintained higher PSII stability, with 50% loss of efficiency occurring only at lower RWC (30–35%). Overall, chlorophyll fluorescence imaging effectively captured functional diversity in desiccation tolerance, highlighting S. pennellii as a valuable genetic resource for improving drought resilience in tomato. Full article

Husk tomato (Physalis ixocarpa Brot.) is a crop of major economic, cultural, and nutritional importance in Mexico and exhibits substantial genetic and morphological diversity. Characterizing this variability is essential for both germplasm conservation and breeding programs. During the spring–summer 2024 growing season, 28 husk tomato populations were evaluated at the Bajío Experimental Station (INIFAP), Guanajuato, Mexico, using a completely randomized design with 12 replications. Forty-one traits were assessed following UPOV and IPGRI descriptors. Cluster analysis, canonical discriminant analysis, and the ESIM selection index were applied. A total of 77 morphotypes were identified, exhibiting variation in 33 of the 41 evaluated traits, mainly related to growth habit, leaf morphology, fruit traits, and calyx attributes. Correspondence analysis revealed a close relationship between vegetative growth and fruit size. Cluster analysis clustered the morphotypes into six clusters with no clear geographic structure, suggesting extensive gene flow. Canonical discriminant analysis explained 94.65% of the total variation, identifying seed size, leaf dimensions, and number of anthers as key discriminant traits. The ESIM index highlighted six morphotypes with favorable agronomic and morphological combinations. These results provide a practical basis for the selection of parental materials in husk tomato breeding programs under diverse agroecological conditions. Full article

Background: Piper is one of the largest genera in the family Piperaceae, with approximately 2100 species. Most Piper species are used as spices or as medicinal plants. Piper methysticum G. Forst., popularly known as kava-kava (or kava), is widely used to treat anxiety disorders. Due to similar morphological features, P. auritum Kunth (known as “false kava”) is sometimes mistakenly or intentionally used as an alternative botanical source for “kava” extracts. The false kava extracts do not contain active kavalactones but contain safrole, which is hepatotoxic. It is important to verify the component botanical materials in order to evaluate the quality and safety attributes of a potential botanical drug. Some studies have evaluated genetic variation in Piper sp. using the chloroplast regions matK, rbcL, rpoC1 and trnH-psbA and the nuclear ITS2 markers. However, none has focused on the identification of P. methysticum using DNA barcodes. In the present investigation, the ITS2 DNA barcode region from the nuclear genome was tested to confirm the identification and authentication of kava-kava samples. Methods: Seven P. methysticum samples were collected from three different geographic lo-cations and two P. auritum samples were collected and the ITS2 region from the nuclear genome, was amplified, sequenced and aligned to determine their genetic distances. Results: The ITS2 locus showed high amplification and sequence output with a discriminating barcode gap. A distance-based phylogenetic tree and BLAST confirmation (using blastn) revealed the ITS2 locus as a diagnostic DNA barcode for the accurate identification of kava-kava species. Discussion: In conclusion, the ITS2 region proves to be an effective and reliable DNA barcode for distinguishing P. methysticum from closely related species such as P. auritum. Its application can significantly improve the safety, quality, and traceability of kava-containing products, addressing a critical need in the standardization of botanical drugs. Full article

Background: Blood flow restriction training (BFRT) is a low-load resistance training modality capable of inducing muscle hypertrophy and strength adaptations that are comparable to traditional high-load resistance training. Beyond athletic performance settings, BFRT has growing relevance for musculoskeletal health, rehabilitation and populations unable to tolerate high mechanical loads. However, substantial inter-individual variability in adaptive responses has been reported. Genetic and molecular factors may partly contribute to this variability and inform more individualised exercise strategies. Other intrinsic and extrinsic factors, including age, sex, training status, nutrition, and protocol-related differences, may also influence adaptive responses. Objective: This scoping review aimed to map available evidence on molecular modulators of adaptation to BFRT and to identify gaps in the literature regarding genetic influences on BFRT responses. Methods: A structured search of PubMed, Web of Science and Google Scholar was conducted till 1 February 2026. Experimental and quasi-experimental studies examining BFRT in relation to genetic polymorphisms, gene expression, and molecular signalling pathways associated with strength and hypertrophy outcomes were included. Primary outcomes were genetic and molecular factors relevant to BFRT adaptation, including genetic polymorphisms, gene expression, and molecular signalling markers. Secondary outcomes included muscle strength, hypertrophy, vascular responses, and related functional outcomes where reported. Study selection and data extraction were conducted according to PRISMA-ScR guidelines. The methodological quality of randomised controlled trials was assessed using the PEDro scale. This scoping review was registered retrospectively in the Open Science Framework on 17 March 2026, after completion of the literature search. Results: From an initial 47 records, only three studies (n = 3) met the inclusion criteria. The included studies reported molecular responses associated with BFRT, including downregulation of proteolytic genes, suppression of myostatin expression, and upregulation of angiogenic markers. Notably, no studies directly examined genetic polymorphism or genotype–BFRT interactions, highlighting a clear need for these studies in this field. Conclusions: This scoping review therefore identifies a critical evidence gap, with genotype-informed BFRT prescription remaining unsupported by the current literature. Limited evidence supports the possible role of BFRT in molecular responses associated with muscle adaptation. Future research should prioritise well-designed studies integrating both genetic and molecular analyses to better understand inter-individual variability in BFRT adaptations. Full article

Copper (Cu) contamination poses severe threats to agricultural productivity and food safety, particularly affecting economically important crops such as rapeseed (Brassica napus L.). This study investigated the protective effects of selenium nanoparticles (SeNPs) against Cu toxicity in four B. napus cultivars. Exposure to Cu (200 μM) caused severe reductions in growth and photosynthetic efficiency while significantly elevating oxidative stress markers across all cultivars. Application of SeNPs (25 μM) effectively mitigated these adverse effects, improving biomass, restoring chlorophyll content, and enhancing photosynthetic performance compared to Cu-stressed plants. SeNP treatment significantly enhanced antioxidant enzyme activities, with corresponding upregulation of antioxidant gene expression. Secondary metabolite profiling revealed cultivar-specific responses, with sensitive cultivar Zheda 622 exhibiting metabolic adaptation and higher volatile organic compound (VOC) accumulation, while tolerant cultivar Zheda 635 maintained metabolic stability. PCA analysis demonstrated distinct metabolic clustering patterns, reflecting differential stress-responsive strategies. The study demonstrates that SeNPs attenuate Cu-induced toxicity through integrated mechanisms encompassing diminished Cu acquisition, augmented antioxidant defense systems, and comprehensive metabolic reprogramming. Cultivar-specific responses highlighted substantial genetic variation in tolerance mechanisms across B. napus genotypes. These findings substantiate SeNPs as a viable and efficacious nanomaterial for sustainable agronomic management in Cu-contaminated edaphic environments. The approach offers dual benefits of improved crop productivity and reduced Cu accumulation, ensuring enhanced food safety. Full article

GDSL esterase/lipase (GELP) proteins constitute an evolutionarily conserved yet functionally diversified hydrolase family in land plants. They participate in cuticle and secondary cell wall biosynthesis, seed lipid remobilization, reproductive development, and hormone-mediated responses to biotic and abiotic stresses. Despite extensive genome-wide and comparative genomic studies that have categorized large GELPs across numerous crops and model species, only a fraction of members have been functionally characterized in plants, and their catalytic mechanisms and regulatory architectures remain poorly understood. Recent population genomics and cross-species orthogroup analyses in 46 angiosperms have uncovered substantial natural variation within GELP coding sequences and regulatory regions, providing a powerful framework to link allelic diversity to evolutionary trajectories and physiological functions. This review synthesizes current knowledge on GELP evolution, biochemical properties, and roles in development and stress adaptation, and critically evaluates how these insights can be translated into biotechnology and molecular breeding strategies. It highlights emerging resources and concepts from orthogroup-based classification and multi-species datasets that enable systematic discovery of GELP alleles affecting agronomic traits. It further outlines research exploiting GELPs in crop improvement, emphasizing the integration of reverse and forward genetics with multi-omics profiling, biochemical and structural characterization, and gene regulatory network reconstruction. Systematic assessment of the phenotypic impacts of single and combinatorial GELP perturbations on yield, quality, and stress resilience is proposed as a key step toward translating basic insights into breeding and engineering strategies. Full article

Starch synthesis is critical for crop yield and quality and is regulated and coordinated by a series of key enzymes encoded by starch synthesis-related genes (SSRGs). Although this process is well characterized in many crops, the genomic location and expression patterns of SSRGs in wheat remain unclear. Here, we performed a genome-wide analysis and identified 78 SSRGs in wheat, classified into the AGPase, SSS, GBSS, SBE, and DBE subfamilies. SSRGs within each subfamily showed conserved motifs and domain organization. RNA-seq analysis indicated that most SSRGs are expressed during early grain development. We further examined genetic variation in SSRGs across wheat and its progenitors using re-sequencing data. Diploid wheat showed greater genetic differentiation and diversity than tetraploid and hexaploid wheat. Five SSRGs exhibited significant haplotype differences between emmer wheat and common wheat; emmer wheat displayed diverse haplotypes, whereas common wheat showed a single dominant haplotype. Finally, starch characteristics differed between emmer wheat and common wheat in amylose content and thermodynamic properties, while viscosity, crystal structure, and morphology were largely similar. Overall, this study systematically characterizes SSRGs in wheat and provides insights for improving starch quality. Full article

DNA methylation constitutes a primary layer of epigenetic regulation in plants, operating across three sequence contexts (CG, CHG, and CHH) through distinct enzymatic pathways. Over the past fifteen years, accumulating evidence has shown that DNA methylation varies substantially among individuals and populations of wild plants, sometimes independently of underlying genetic polymorphism. This variation can influence gene expression, transposable element activity, and phenotypic traits relevant to ecological adaptation. Population epigenetics, the study of methylation variation at the population scale, has matured from initial surveys using methylation-sensitive amplified fragment length polymorphism (MS-AFLP) into a discipline increasingly reliant on reduced-representation bisulfite sequencing (epiGBS, bsRADseq), whole-genome bisulfite sequencing (WGBS), enzymatic methyl-seq (EM-seq), and direct long-read detection by nanopore sequencing. These methodological advances are opening population epigenetics to non-model organisms across the full breadth of the plant phylogeny, from angiosperms and gymnosperms to ferns and bryophytes. We cover (i) the molecular machinery underlying plant DNA methylation, including the debated status of N6-methyladenine (6mA); (ii) empirical evidence for natural epigenetic variation in plant populations, spanning clonal, invasive, and outcrossing species; (iii) the methodological toolkit available for population-scale methylation profiling, with emphasis on approaches suitable for non-model taxa; and (iv) the ecological and evolutionary significance of population epigenetic variation, including transgenerational inheritance, stress memory, epigenetic clocks, conservation applications, and the emerging integration of epigenetics into the extended evolutionary synthesis. We identify critical knowledge gaps, particularly the near-complete absence of population-level epigenetic data for bryophytes, ferns, and lycophytes, and outline priorities for future research. Full article

Quercus acorns have been part of animal or human diets; however, their nutritional potential depends on morphological and chemical characteristics highly influenced by genetic and geographical factors. Research on the Quercus genus has focused on Asian and European species overlooking the American taxa. Therefore, this study aimed to evaluate the morphological and nutritional characteristics, and the content and profile of bioactive compounds of acorns from four populations of the American species Quercus virginiana from the state of Chihuahua, Mexico. Discriminant function analysis showed a well-established group formed by the two southern populations (CH), while the two northern populations were separated into different groups (CJA and CJB). CH populations showed smaller seeds (1.4 g, 2.0 cm length) and higher starch (57–58%), oleic acid (65–70%), phenolic compounds (78–176 mg GAE/g), flavonoids (29–37 mg CE/g), and antioxidant activity (278–282 μmol TE/g). Acorns from the CJA population were the largest (2.3 g, 2.4 cm length) and displayed the highest protein content (7.0%). Acorns from the CJB population showed the highest values for ash (2.2%), sugars (13.8%), palmitic and linoleic acids (19.1%), and condensed tannins (0.26 CE/g). Fourteen polyphenolic compounds were identified: twelve hydrolysable tannins; one hydroxycinnamic acid, and one flavonol. These variations reflected the impact of local climatic and geographic conditions and may influence the potential use of Quercus acorns in sustainable agriculture and food development. Full article

Background/Objectives: Eleocharis ussuriensis Zinserl. is a perennial riparian sedge widely distributed in Northeast Asia and a dominant component of freshwater vegetation in South Korea. However, the intraspecific genetic structure of this species across contrasting hydrological habitats remains insufficiently understood. This study aimed to develop novel SSR markers from whole-genome data and investigate genetic variation and population structure among E. ussuriensis populations in South Korea. Methods: Twenty-one novel simple sequence repeat (SSR) markers were developed from whole-genome sequence data and applied to analyze genetic variation in 120 individuals from 6 populations. Genetic diversity, differentiation, and gene flow were estimated using allele-frequency-based metrics, and population genetic structure was further evaluated using spatial information derived from geographic coordinates. Results: A total of 201 alleles were detected, with a mean polymorphism information content (PIC) of 0.759, indicating high marker informativeness. Mean genetic diversity across populations showed observed heterozygosity (Ho = 0.360) and expected heterozygosity (He = 0.281), while multilocus genotype ratios (G/N) ranged from 0.30 to 1.00 among populations. Genetic differentiation was substantial (F_ST = 0.373–0.669; Jost’s D = 0.540–0.997). Mantel tests revealed that genetic differentiation was significantly correlated with geographic distance (r = 0.67, p < 0.001). Both allele-frequency-based and spatially explicit approaches suggested genetic structuring among populations. Conclusions: The results suggest spatial tendencies in genetic structure among populations, reflecting patterns of allele distribution across regions. These findings provide baseline information on genetic variation in E. ussuriensis and may contribute to a better understanding of its ecological dynamics. Full article

Teat number is an important economic trait in pigs because it affects sow reproductive performance and piglet nursing ability, yet its genetic basis and molecular regulatory mechanisms remain incompletely understood. In this study, a combined-population genome-wide association study was performed in Canadian and French Large White pigs to identify loci associated with teat number traits. A total of 4217 pigs were genotyped, and 2,244,684 autosomal single-nucleotide polymorphisms were retained after quality control and genotype imputation. Multiple association signals for total teat number were detected, with major peaks located on chromosomes 7 and 10. Among the positional candidate genes, PROX2 was prioritized for further validation, and genotype–phenotype association analysis showed that pigs with the CC genotype at the PROX2 polymorphic locus had significantly lower total teat number than those with the CT and TT genotypes. To investigate its biological role, PROX2 was silenced in porcine mammary epithelial cells. Transcriptome analysis identified 887 differentially expressed genes after PROX2 knockdown, and functional assays showed that PROX2 silencing inhibited cell proliferation, altered cell cycle progression, and affected the expression of proliferation- and development-related genes. These findings indicate that PROX2 is an important candidate gene associated with teat number variation in pigs. Full article

Aiming at the issues of low recognition accuracy and high model computational complexity for power quality disturbances (PQDs) in strong-noise environments, this paper proposes a novel lightweight PQD-recognition method that integrates a hybrid architecture of variational mode decomposition (VMD), convolutional neural network (CNN), and transformer. Firstly, a hybrid optimization algorithm named the monkey–genetic hybrid optimization algorithm (MGHOA) is proposed to optimize VMD parameters for denoising disturbance signals, thereby enhancing recognition accuracy in noisy environments. Secondly, to fully extract disturbance signal features and reduce the computational complexity of the model, a lightweight CNN–transformer model is designed. Depthwise separable convolution (DSC) is employed to extract local features and the multi-head attention mechanism of transformer is utilized to mine the long-distance dependence and global features, thereby enhancing the feature representation. Thirdly, a multitask joint-learning method is proposed to collaboratively optimize classification accuracy and temporal localization tasks, enhancing the discrimination of similar disturbances. Additionally, a dual-pooling global feature fusion strategy is designed to further enhance the model’s ability to discriminate complex disturbances. Comparative experiments on 16 typical PQD types demonstrate that the proposed method achieves excellent performance in recognition accuracy, model robustness, and computational efficiency. The integration of the MGHOA–VMD module improves recognition accuracy by 1.08%, while the multitask joint-learning method contributes an additional 0.55% improvement. When achieving recognition accuracy comparable to complex models, the training time of the proposed method is 36.51% of that required by DeepCNN and merely 5.90% of that required by bidirectional long short-term memory (BiLSTM), with a 31.22% reduction in parameter scale. This work provides a novel solution for intelligent power quality disturbance recognition. Full article

The global demand for Salvia miltiorrhiza Bunge in the botanical medicine market is steadily increasing. However, its production has long relied on asexual root propagation, making it highly susceptible to germplasm degradation. Transitioning to seed reproduction offers the advantage of genetic renewal, yet it is constrained by unstable seed vigor and slow seedling growth. In the present study, comprehensive physiological and microbiome analyses of S. miltiorrhiza seeds from 14 regions across 7 provinces in China were conducted to elucidate the association between the seed microbiome and vigor, and to identify plant growth-promoting (PGP) strains. The results demonstrated: (1) Seed physical traits and germination characteristics varied significantly across geographic origins. Seed vigor, exhibiting the highest coefficient of variation, served as a key parameter reflecting germination quality. (2) High-vigor seeds harbored distinct microbial communities characterized by higher diversity indices, greater network complexity, and the significant enrichment of potentially beneficial bacteria (e.g., Pseudomonas). (3) Through correlation-directed screening of isolated pure cultures, Pseudomonas mendocina P-6 and Enterobacter ludwigii BM-12 were identified as exhibiting robust, multi-trait PGP capacity. In planta validation showed that these two strains significantly promoted the growth of 1-month-old S. miltiorrhiza seedlings, increasing total fresh weight by 33.9–71.3%. This study reveals the microecological drivers of seed vigor and provides candidate strains for inoculant development, thereby supporting the sustainable, seed-based propagation of S. miltiorrhiza. Full article