Search Results (837)

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) is the only freshwater cetacean species currently found in China’s Yangtze River. To accurately evaluate its genetic diversity and provide reliable molecular markers for population genetic studies, this study developed a highly efficient and reproducible method for identifying polymorphic microsatellite loci using whole-genome sequencing data. Using this method, we identified and validated a set of highly polymorphic microsatellite markers, which were then used to analyze the genetic diversity of the YFP populations in Poyang Lake to evaluate their effectiveness. Our results demonstrated that the screening pipeline successfully identified 220 tetranucleotide repeat microsatellite loci. Based on the principle of uniform chromosomal distribution, 190 loci were randomly selected for experimental validation, of which 19 exhibited stable amplification, high polymorphism, and a low genotyping error rate. Genetic diversity analysis based on these markers revealed significant genetic variation among YFP populations in Poyang Lake, confirming the effectiveness of the developed markers. The polymorphic microsatellite molecular marker system developed in this study demonstrates high reliability and applicability for assessing YFP genetic diversity. This system provides a critical technical foundation for future research in conservation genetics, genetic resource preservation, and the development of genetic management strategies for the species. Full article

Peruvian Creole goats (PCGs) represent a unique genetic resource shaped by adaptation to diverse environments and traditional breeding practices. In this study, we performed a genomic analysis of six regional populations (Ancash, Ica, Lambayeque, Lima, Piura, and Tumbes) using high-density SNP genotype data. Principal component analysis revealed a moderate genetic structure, with the Ica population showing clear separation and northern populations exhibiting overlap. Runs of homozygosity were predominantly short, and specific regions on chromosome 6 were shared across populations. Inbreeding coefficients were generally low, with Ancash showing the highest values. Linkage disequilibrium decayed rapidly over genetic distance, especially in Piura, indicating higher genetic diversity. Estimates of effective population size revealed decreasing trends across populations, with Piura maintaining the largest recent population size. These findings offer valuable insights into the population structure of Peruvian Creole goats, providing guidance for conservation and sustainable breeding efforts. Full article

European black pine (Pinus nigra Arn. subsp. nigra) persists in scattered montane stands across Greece, where isolated populations harbour genetic variation shaped by local environments and demographic history. In this study, we assessed the genetic diversity and population structure of P. nigra using nuclear microsatellite markers (nSSRs) across four populations: Mt. Athos, Sithonia, Thassos, and Perama. A total of 67 individuals were genotyped, and seven high-quality polymorphic loci were retained after rigorous filtering. The Mt. Athos population exhibited the highest allelic richness and heterozygosity, with all loci being polymorphic and a low inbreeding coefficient after null allele correction. In contrast, the Perama population displayed reduced diversity, fewer polymorphic loci, and persistent heterozygote deficits. Principal Component Analysis (PCA) and Discriminant Analysis of Principal Components (DAPC) revealed weak overall population structure, with Perama genetically distinct from the other sites. Spatial Principal Component Analysis (sPCA) further uncovered an east–west cline within Athos and localized structure potentially shaped by both natural isolation and human influence. These findings highlight regional variation in genetic diversity within P. nigra and identify Athos as a genetically rich population of particular interest. The results provide a foundation for long-term monitoring and support informed strategies for the management and conservation of P. nigra in Greece. Full article

Newcastle disease (ND) is a highly contagious and economically significant viral infection that affects poultry globally, with recurrent outbreaks occurring even among vaccinated flocks in Egypt. Caused by the Newcastle disease virus (NDV), the disease results in substantial losses due to high mortality rates, decreased productivity, and the imposition of trade restrictions. This study aimed to develop a rapid, sensitive, and field-deployable diagnostic assay based on real-time reverse transcription recombinase-aided amplification (RT-RAA) for the detection of all NDV genotypes in clinical avian specimens. Primers and an exo-probe were designed based on the most conserved region of the NDV matrix gene. After testing ten primer combinations, the pair NDV RAA-F1 and RAA-R5 demonstrated the highest sensitivity, detecting as low as 6.89 EID₅₀/mL (95% CI). The RT-RAA assay showed excellent clinical sensitivity and specificity, with no cross-reactivity to other common respiratory pathogens such as avian influenza virus, infectious bronchitis virus, Mycoplasma gallisepticum or infectious laryngotracheitis virus. All 25 field samples that were tested positive by real-time RT-PCR, including those with high CT values (~35), were detected by RT-RAA in 2–11 min, indicating superior sensitivity and speed. The assay requires only basic equipment and can be performed under isothermal conditions, making it highly suitable for on-site detection in resource-limited or rural settings. The successful implementation of RT-RAA can improve NDV outbreak response, support timely vaccination strategies, and enhance disease control efforts. Overall, the assay presents a promising alternative to conventional diagnostic methods, contributing to the sustainability and productivity of the poultry sector in endemic regions. Full article

Background/Objectives: African swine fever (ASF) is a disease of domestic pigs and wild boar caused by African swine fever virus (ASFV), in which infection often leads to high morbidity and mortality. Although subunit and mRNA vaccines based on protective antigens have been explored for ASFV, their protective efficacy remains insufficient for practical ASF control, highlighting the need to identify new potential antigens capable of inducing more potent and broadly protective immune responses. Previously, we found that the antibodies against the ASFV E120R protein (pE120R) could significantly inhibit virus replication in primary porcine alveolar macrophages (PAMs). However, it is not yet known whether anti-pE120R antibodies can induce antibody-dependent cellular cytotoxicity (ADCC). Methods: In this study, we analyzed the conservation and immunogenic features of pE120R and established an HEK293T cell line with stable expression of pE120R as target cells (HEK293T-pE120R). Additionally, a co-culture system comprising target cells and peripheral blood mononuclear cells (PBMCs) was established to evaluate the ability of the anti-pE120R antibodies to induce ADCC as measured by lactate dehydrogenase (LDH) release assays. Results: The results showed that pE120R is highly conserved among different ASFV genotypes and contains multiple B-cell and T-cell epitopes. Importantly, LDH release assays demonstrated that anti-pE120R antibodies triggered NK cell-mediated ADCC. Notably, ASFV replication in HEK293T-pE120R cells was not promoted. Conclusions: In summary, pE120R was associated with antibody production in a cytotoxicity assay. The ability of this antigen to induce protective immunity, if any, requires further evaluation in vivo. Full article

Background and Clinical Significance: Arterial and venous thromboses are typically distinct clinical entities, each governed by unique pathophysiological mechanisms. The concurrent manifestation of both, particularly in the setting of massive pulmonary embolism (PE), is exceptionally rare and poses significant diagnostic and therapeutic challenges. Case Presentation: This report describes a 61-year-old male with well-controlled hypertension and type 2 diabetes who developed extensive thromboses involving deep vein thrombosis (DVT) of the right popliteal vein, arterial thrombosis of the left iliac artery, and massive PE. The patient was initially managed conservatively, in accordance with the European Society of Cardiology (ESC) 2019 Guidelines for Acute PE, using unfractionated heparin (UFH), low-molecular-weight heparin, a direct oral anticoagulant (DOAC), and adjunctive therapy. This approach was chosen due to the absence of hemodynamic instability. However, given failed percutaneous revascularization and persistent arterial occlusion, surgical thromboendarterectomy (TEA) was ultimately required. Post hoc genetic testing was prompted by the complex presentation in the absence of classical provoking factors—such as trauma, surgery, malignancy, or antiphospholipid syndrome—consistent with recommendations for selective thrombophilia testing in atypical or severe cases. The analysis revealed four thrombophilia-associated polymorphisms: heterozygous Factor V Leiden (FVL; R506Q genotype), Plasminogen Activator Inhibitor-1 (PAI-1; 4G/5G genotype), Methylenetetrahydrofolate reductase (MTHFR; c.677C > T genotype), and homozygous Angiotensin-Converting Enzyme Insertion/Deletion (ACE I/D; DD genotype). Conclusions: While each variant has been individually associated with thrombotic risk, their co-occurrence in a single patient with simultaneous arterial and venous thromboses has not, to our knowledge, been previously documented. This case underscores the potential for gene–gene interactions to amplify thrombotic risk, even in the presence of variants traditionally considered to confer only modest to moderate risk. It highlights the need for a multidisciplinary approach and raises questions regarding pharmacogenetics, anticoagulation, and future research into cumulative genetic risk in complex thrombotic phenotypes. Full article

Crataegus harbisonii Beadle (Harbison’s or Harbison hawthorn) is a Tennessee (USA) endemic tree of the Rosaceae family, currently considered “critically imperiled” at the state, national, and global levels. It is known from only two extant wild locations, one in Davidson County, Tennessee consisting of a single living individual and a population of less than 100 individuals in Obion County, Tennessee. Key ex situ conservation efforts undertaken over the last three years with this critically imperiled species are reported here. The Obion County population was intensively surveyed and all C. harbisonii individuals documented. Over three seasons, seeds were collected and propagated, and clones were generated via chip-budding and grafting. Conservation seed orchards were planned and established to provide a stable, long-term source of genetically robust seed for reforestation and research. To date, 19 sources from the Obion County location as well as the single Davidson County genotype have been successfully preserved through clonal propagation, and open-pollinated seedlings produced from 12 unique mother trees. Additional material is being added annually. We report lessons learned as well as key future research directions, now enabled through the establishment of germplasm resources. Full article

The population size of black poplar (Populus nigra L.), once an important part of floodplain forests in the Czech Republic, has greatly declined due to human activity. In this study, we applied microsatellite (SSR) markers to identify species and assess genetic diversity, with the aim of supporting conservation of this endangered species. A total of 378 poplar trees were analyzed following field surveys. Five diagnostic SSR markers with species-specific alleles for P. deltoides Bartr. ex Marsh. enabled the identification of 39 interspecific hybrids, which were distinguished from native P. nigra. Thirteen SSR loci were used to evaluate genetic diversity among confirmed P. nigra individuals. The results revealed high genetic variation, with 66% of pairwise genotype comparisons differing at all loci. After excluding 45 genetically similar individuals, 292 genetically verified and polymorphic P. nigra trees were selected as potential sources of reproductive material. Genetic differentiation (Fst) was highest between P. nigra and P. deltoides (0.27), and lowest between reference Populus ×euroamericana clones and detected hybrid poplars (0.05) from natural localities. Distinct genetic structures were identified among P. nigra, P. deltoides, and hybrid individuals. These findings provide essential data for the protection, reproduction, and planting of black poplar. Full article

To explore the phenotypic diversity of jujube germplasm resources and identify superior genotypes, this study systematically evaluated 150 jujube accessions. Multiple organ-related traits—including branches, thorns, bearing shoots, leaves, flowers, and fruits—were investigated. A comprehensive, multidimensional analysis was conducted to assess phenotypic variation and diversity. The results provide valuable insights for germplasm conservation and the selection of elite jujube varieties. The results showed that the variation coefficient of 18 quantitative traits ranged from 5.07% to 21.43%; the variation coefficient of fruit quality traits ranged from 4.25% to 13.48%; and the results of the cluster analysis showed that the germplasm resources were classified into three categories according to the quantitative traits and four categories according to the fruit quality traits. Principal component analysis extracted six significant components for fruit quality traits, accounting for 86.88% of the total variance. Based on the comprehensive evaluation of factor analysis, Sanlengzao, Linyilajiaozao, Zan 2, Jinmanguo, and Jing 39 performed well and ranked high in the comprehensive ranking, which can be used as an important reference for the evaluation of jujube germplasm resources and the selection and breeding of good varieties. Full article

Myriophyllum spicatum is a globally distributed aquatic plant capable of sexual and clonal reproduction. Despite its ecological importance and biochemical potential, studies on its genetic and clonal structure in freshwater systems throughout South Korea remain limited. We investigated the genetic and clonal diversity of M. spicatum using 30 newly developed microsatellite markers across 120 individuals from six freshwater systems in South Korea. Overall, 148 alleles were identified, with an average polymorphism information content value of 0.530. Clonal diversity differed among populations, with the genotypes to individuals (G/N) ratio ranging from 0.200 to 1.000. Bottlenecks and clonal dominance were observed in riverine populations. High genetic differentiation (mean F_ST = 0.556) indicated limited gene flow, and STRUCTURE analysis revealed six distinct genetic clusters. No significant correlation was found between genetic and geographic distance, suggesting possible seed dispersal by waterfowl, particularly between adjacent populations. Genetic structure was shaped by habitat type, disturbance intensity, and reproductive strategy. Stable reservoir habitats favored sexual reproduction and higher genetic diversity, whereas disturbed river systems showed clonal dominance and reduced variation. These findings provide essential genetic insights for conservation planning and sustainable management of aquatic plant resources. Full article

The southern region of Kazakhstan represents the northernmost boundary of the natural habitat of five wild almond species, among which Amygdalus communis L. is of particular interest due to a range of favorable traits for use in breeding programs and cultivation in the region. The current distribution range of common almond growth was clarified using GPS to determine precise coordinates, and a schematic map was developed. Monitoring revealed a significant reduction in population size. In the surveyed areas, 54 trees were selected and described. Seed material was collected from 34 genotypes and characterized according to a descriptor. Genotypes A3, A8, and A15 were identified as having favorable trait combinations. To restore populations and preserve the gene pool of Amygdalus communis L., a method of clonal micropropagation was employed. The composition of the nutrient medium was optimized for establishment, multiplication, and rhizogenesis. It was determined that Murashige and Skoog (MS) medium without phytohormones is effective for in vitro establishment (70% regeneration rate). For multiplication, MS medium with 0.5 mg/L BAP (6-benzylaminopurine) was used (with a multiplication rate of 3.5 per explant). For rhizogenesis, MS medium with 0.5 mg/L BAP, 0.02 mg/L gibberellic acid (GA), and 0.1 mg/L IBA (indole-3-butyric acid) was used. A total of 340 clonal Amygdalus communis L. plants with closed root systems were grown for field collection. The research results can be applied for the restoration, propagation, and conservation of populations both in vitro and in situ, as well as for the inclusion of selected high-performing genotypes in breeding programs. Full article

The endangered Bengal slow loris (Nycticebus bengalensis) relies heavily on captive/rescue populations for conservation. This study investigated the critical link between Major Histocompatibility Complex (MHC) class II DRB1 exon 2 (DRB1e2) genetic variation and gut microbiota in 46 captive individuals, aiming to improve ex situ management. Using standardized conditions across three enclosure types, we characterized DRB1e2 polymorphism via targeted sequencing and analyzed fecal microbiota using 16S rRNA gene amplicon sequencing. Results demonstrated that high DRB1e2 polymorphism significantly reduced microbial community evenness. Specific genotypes showed distinct microbial associations: G9 strongly correlated with beneficial short-chain fatty acid producers like Fructobacillus, and G2 positively correlated with Bifidobacterium spp., while G2, G3, and G4 correlated negatively with Buchnera (a nutrient-provisioning symbiont). Genotypes and polymorphism collectively explained 9.77% of microbiota variation, exceeding the weaker (5.15%), though significant, influence of enclosure type on β-diversity. These findings reveal that host DRB1e2 variation is a primary driver shaping gut microbiota structure and taxon abundance in captive slow lorises, providing evidence for MHC-mediated host–microbe co-adaptation. This offers a genetically informed framework for optimizing conservation strategies, such as tailoring diets or probiotics to specific genotypes, to enhance gut health and population viability. Full article

Background. Antimicrobial resistance (AMR) poses a significant global health threat, necessitating a deeper understanding of bacterial adaptation mechanisms. Introduction. This study investigates the genotypic and phenotypic evolutionary trajectories of Escherichia coli under meropenem and gentamicin selection, and it benchmarks these findings against florfenicol-evolved strains. Methodology. Utilizing a downsized, three-layer acrylic modified “Microbial Evolution and Growth Arena (MEGA-plate) system”—scaled to 40 × 50 cm for sterile handling and uniform 37 °C incubation—we tracked adaptation over 9–13 days, enabling real-time visualization of movement across antibiotic gradients. Results. Meropenem exposure elicited pronounced genetic heterogeneity and morphological remodeling (filamentous and circular forms), characteristic of SOS-mediated division arrest and DNA-damage response. In contrast, gentamicin exposure produced a uniform resistance gene profile and minimal shape changes, suggesting reliance on conserved defenses without major morphological adaptation. Comprehensive genomic analysis revealed a core resistome of 22 chromosomal loci shared across all three antibiotics, highlighting potential cross-resistance and the central roles of baeR, gadX, and marA in coordinating adaptive responses. Gene ontology enrichment underscored the positive regulation of gene expression and intracellular signaling as key themes in resistance evolution. Discussion. Our findings illustrate the multifaceted strategies E. coli employs—combining metabolic flexibility with sophisticated regulatory networks—to withstand diverse antibiotic pressures. This study underscores the utility of the MEGA-plate system in dissecting spatiotemporal AMR dynamics in a controlled yet ecologically relevant context. Conclusions. The divergent responses to meropenem and gentamicin highlight the complexity of resistance development and reinforce the need for integrated, One Health strategies. Targeting shared regulatory hubs may open new avenues for antimicrobial intervention and help preserve the efficacy of existing drugs. Full article

Local adaptation allows animal populations to persist in diverse and changing environments, yet its genomic underpinnings remain poorly characterized in livestock. Chinese indigenous pigs, renowned for their rich phenotypic and ecological diversity, offer a powerful model for investigating environmental adaptation. Here, we integrated whole-genome resequencing data, environmental variables, genotype–environment association (GEA) analyses, and functional annotation to explore the adaptive genomic landscape of 46 native pig breeds across China. Based on 578 individuals and 17.7 million SNPs, we performed genome-wide GEA using latent factor mixed models (LFMMs), identifying 8644 SNPs significantly associated with environmental factors, including 310 linked to precipitation in the wettest quarter (BIO16). Redundancy analysis (RDA) and gradient forest modeling identified BIO16 as a major environmental driver of genomic variation. Functional annotation of BIO16-associated SNPs revealed significant enrichment in regulatory elements and genes highly expressed in the lung, spleen, hypothalamus, and intestine, implicating immune and metabolic pathways in local adaptation. Among the candidate loci, MS4A7 exhibited strong association signals, population differentiation, and tissue-specific regulation, suggesting a role in precipitation-mediated adaptation. This work enhances our understanding of livestock adaptation and informs climate-resilient conservation and breeding strategies. Full article

Purple totomoxtle (maize husk) in native maize represents a phenotypic trait of cultural and agronomic significance within traditional Mesoamerican agroecosystems. This study evaluated the phenotypic expression of anthocyanins in vegetative and reproductive tissues of ten native maize genotypes, including inter-parental crosses derived from both pigmented and non-pigmented lines. Field trials were conducted under rainfed conditions in Chiapas, Mexico. Visual and quantitative assessments included pigmentation intensity, chlorophyll and carotenoid content, ear traits and appearance, grain health, and yield performance. Genotypes exhibiting the purple phenotype showed consistent pigment accumulation in stems, nodes, leaf sheaths, tassels, and bracts (totomoxtle), with statistically significant differences compared to non-pigmented controls. Anthocyanin content in totomoxtle increased by 30% during late developmental stages, whereas chlorophyll and carotenoid levels peaked during early vegetative growth. Pigmented materials displayed healthier grain, enhanced ear appearance, and higher yields, with the JCTM × LLMJ cross reaching 6.60 t ha⁻¹. These findings highlight the functional value of purple totomoxtle and its potential in agroecological programs aimed at resilience, genetic conservation, and integral resource utilization, providing useful criteria such as stable pigment expression and superior yield to guide sustainable reproduction strategies. Full article