Search Results (3,534)

Dengue virus (DENV) poses a growing risk in Tanzania, yet its genetic diversity in mosquito populations remains poorly understood. Using Nanopore sequencing, we recovered full coding sequences from six DENV-2 positive mosquito pools collected in Dar es Salaam outside recognized outbreak periods. Phylogenetic analysis placed these sequences in a distinct monophyletic clade within genotype II, separate from strains linked to Tanzania’s 2014 outbreak. Instead, they clustered with Asian lineages and showed the closest relatedness to DENV-2 strains from Kenya (2013) and India (2014), with divergence estimated to have occurred around 2010. Variant profiling identified 212 low-frequency intra-pool variants, predominantly non-synonymous changes in the NS3, NS4B, and NS5 coding regions. These results suggest a previously unrecognized introduction of genotype II that is now circulating silently within local mosquito populations. Our findings highlight the value of genomic surveillance in mosquito vectors for early detection of arboviral threats, even in the absence of reported human cases. Full article

Background/Objectives: Amyotrophic Lateral Sclerosis (ALS) is a rare, neurodegenerative disease with complex genetic and environmental determinants. The MTHFR C677T (rs1801133) variant, known for reducing enzymatic activity in the folate cycle, has been implicated in ALS risk, though findings remain inconsistent across diverse populations. Methods: A population-based case–control study was conducted in 248 age-matched individuals to investigate the MTHFR C677T (rs1801133) and ALS susceptibility. Molecular analysis was performed using the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP). Genetic associations were evaluated under multiple inheritance models, while survival analysis utilized the Kaplan–Meier method to assess the relationship between MTHFR genotypes and patient prognosis. Results: The C677T variant showed a significant association under the codominant and recessive models, suggesting involvement in ALS risk (OR = 4.63; p = 0.01 and OR = 3.92; p = 0.02), respectively. However, stratification by sex demonstrated an association predominantly in women (OR = 7.10, p = 0.02; OR = 5.87, p = 0.04). Additionally, Kaplan–Meier analysis revealed a numerically shorter mean survival time for the mutant genotype compared with wild-type and heterozygous carriers, without statistical significance. Conclusions: Notably, we identified a significant association between the MTHFR C677T (rs1801133) variant and ALS risk, particularly among women. These findings suggest that the mutant (T/T) genotype showed a stronger association, potentially reflecting postmenopausal hormonal influences on one-carbon metabolism and related susceptibility pathways. Full article

Staphylococcus aureus nasal carriage contributes to asymptomatic transmission in both community and healthcare settings. This study aimed to characterize S. aureus strains isolated from students of the Pomeranian Medical University in Szczecin, Poland, using phenotypic and genotypic methods. A total of 175 S. aureus strains were isolated from the nasal vestibules of 800 students between 2014 and 2015. Species identification and antimicrobial susceptibility testing were performed using standard microbiological methods, while virulence-associated genes and agr groups were analyzed using Single-PCR and Multiplex-PCR assays. Genotypic diversity was assessed by pulsed-field gel electrophoresis (PFGE). The prevalence of S. aureus nasal carriage among students was 21.9% and did not differ according to faculty or year of study. Most isolates (84.0%) were susceptible to all tested antibiotics, and no methicillin-resistant S. aureus (MRSA) strains were detected. All strains carried the hla gene, whereas hld and hlg were identified in 93.7% and 93.1% of isolates, respectively. In addition, the tst gene was detected in 22.3% of strains, while the lukS-PV/lukF-PV genes were identified in only one isolate (0.6%). The most prevalent enterotoxin genes were sep (17.1%) and sea (13.7%), whereas genes of the egc cluster, including seg, sei, and seo, were detected in 53.7% of isolates. Significant associations were observed between specific egc gene combinations and superantigen gene profiles, including increased frequencies of sec, sel, and tst genes (p < 0.001). The predominant agr type was agr-1 (49.7%), followed by agr-3 (28.6%) and agr-2 (20.0%). Strains carrying agr-1 more frequently harbored the g i m n o cluster as well as the sec, sel, and sep genes, whereas agr-3-positive isolates were significantly associated with the g i m o u and g i o u clusters and with the presence of tst, sea, and seh genes (p < 0.05). PFGE analysis demonstrated substantial genetic heterogeneity among the isolates, with no evidence of a predominant clonal lineage. These findings indicate a heterogeneous, non-epidemic population structure of S. aureus strains circulating among university students and highlight the considerable diversity and interrelationships of virulence-associated genetic profiles within this population. Full article

Cowpea (Vigna unguiculata (L.) Walp.) is a globally cultivated leguminous crop, but an efficient and stable genetic transformation system for cowpea is lacking. Thus, in this study, using different cowpea accessions, the main factors (genotype, explant, Agrobacterium strain for infection, and vector) affecting genetic transformation efficiency were systematically screened. Among the 43 cowpea accessions, two accessions (JD-0212 and A132) whose in vitro regeneration frequencies were high (propagation coefficient > 0.8 and adventitious bud induction index > 0.7) were identified. A system with a high infection rate for the two cowpea accessions was subsequently constructed, including cotyledonary nodes with cotyledons as the optimal explants, the Agrobacterium rhizogenes strain K599 and the rbcs-RUBY vector. Next, the system was optimized for its transformation conditions, such as infection duration, vacuum infiltration parameters and cocultivation time. The maximum transformation efficiency of genotype JD-0212 reached 82.79% under the optimal transformation conditions: 60 min of infection combined with 30 s of vacuum infiltration (−0.08 MPa), followed by four days of cocultivation. Furthermore, the transformation efficiency was validated in 86 cowpea accessions using two distinct vectors (rbcs-RUBY and bs-EGFP), indicating an average transformation efficiency of 42.09% (ranging between 4.04% and 82.79%). An efficient hairy root genetic transformation system for cowpea was established in this study. Full article

This review provides a comprehensive overview of the genetic diversity and epidemiological potential of Yersinia pestis in Kazakhstan’s natural plague foci, emphasizing the link between genotypic variation and outbreak capacity. Integrating historical epidemiological records with contemporary microbiological and genomic data (including PCR, VNTR/MLVA, SNP analysis, and whole-genome sequencing), we evaluate core and accessory genome variations. The data reveal substantial regional heterogeneity. High-risk desert foci (Caspian and Aral regions) are dominated by the Medievalis biovar, including atypical genovariants lacking canonical markers. Conversely, high-mountain foci (Sarydzhaz, Talas) harbor the Antiqua and Talas biovars, primarily linked to enzootic circulation. Notably, the Ili River focus exhibits extreme genomic variability, featuring strains with plesiomorphic traits. Furthermore, the widespread distribution of mobile elements like the cryptic plasmid pCKF suggests significant horizontal transfer contributing to pathogen adaptation. Ultimately, Central Asian plague dynamics are driven by complex evolutionary and ecological interactions. Given climate change and expanding human–wildlife interfaces, continuous genomic and ecological surveillance is essential for the early detection of high-risk Y. pestis genovariants and improving public health preparedness. Full article

Myrtus communis L. (common myrtle) is an economically valuable Mediterranean shrub with diverse applications in food, pharmaceutical, and ornamental sectors. However, the biochemical diversity of myrtle genotypes from Mediterranean environments remains insufficiently characterized, particularly regarding the relationship between primary and secondary metabolism and stress adaptation. This study investigated the biochemical and aroma profiles of six myrtle genotypes selected from natural populations in Antalya, Turkey, to identify chemotypic diversity and elucidate metabolic diversity observed in Mediterranean genotypes. Volatile compounds were analyzed using HS-SPME/GC-MS, while sugars and organic acids were quantified by HPLC. Multivariate statistical analyses (PCA, hierarchical clustering) were employed to evaluate metabolic relationships and genotype classification. Descriptive analysis suggested three potential chemotypic patterns: (i) 1,8-cineole-type (G34, G36) with G29 showing a transitional profile, (ii) α-Pinene-type (G15, G37), and (iii) Ester-aldehyde type (G9). These groupings are based on single volatile measurements and should be considered preliminary patterns pending validation through replicate analyses. Significant genotypic variation was observed for primary metabolites (sugars and organic acids) (p < 0.001, η² > 0.90), as evaluated by ANOVA with triplicate biological replicates. Volatile compound differences were evaluated as descriptive exploratory patterns only. Hierarchical clustering revealed three metabolic strategies: balanced metabolism integrating diverse volatile and primary metabolite profiles (Cluster 1: G9, G15, G37), terpene-rich volatile defense with enhanced organic acid metabolism (Cluster 2: G29, G36), and specialized 1,8-cineole-dominant biosynthesis (Cluster 3: G34). These findings highlight substantial metabolic diversity and provide a basis for germplasm evaluation and selection and potential applications. Full article

Objectives: To facilitate the innovation and efficient utilization of specialty maize germplasm, this study aimed to systematically evaluate a panel of 222 inbred lines. The objective was to comprehensively characterize phenotypic variation, genetic diversity, and genotype–phenotype associations to screen for representative germplasm resources. Methods: We integrated Best Linear Unbiased Prediction (BLUP) values derived from multi-environment field trials with high-density whole-genome single-nucleotide polymorphism (SNP) data. Population structure and genetic diversity were analyzed, Mantel tests were conducted to assess genotype–phenotype correspondence, and a genome-wide association study (GWAS) was performed to identify significant loci. Results: The population exhibited substantial phenotypic variation, particularly in plant height and tassel traits, with distinct morphological differentiations among specialty types. Genetic diversity analyses revealed varying diversity levels among subpopulations. While Mantel tests indicated a weak overall genotype–phenotype correspondence, specific traits showed significant associations with genetic distance. GWAS successfully identified significant loci associated with plant height and tassel traits. Furthermore, population structure analysis revealed distinct genetic stratification corresponding to specialty types, albeit with a certain degree of admixture. Conclusions: By integrating multi-dimensional phenotypic and genomic profiles, a panel of highly diverse and representative candidate germplasm was identified. These findings provide a crucial theoretical basis for specialty maize breeding and the optimized utilization of germplasm resources. Full article

Tomato brown rugose fruit virus (ToBRFV) poses a major threat to global tomato (Solanum lycopersicum) production, as it can overcome conventional resistance genes that are effective against tobamoviruses. In this study, a multiplex CRISPR/Cas9 system was developed to target the SlTOM1 susceptibility gene family (SlTOM1a–d), which encodes host factors essential for tobamovirus replication. Six guide RNAs (gRNAs), designed following 12 off-target analyses, were assembled into a multiplex CRISPR/Cas9 construct using a Golden Gate cloning strategy and introduced into tomato genotypes through an Agrobacterium-based tissue culture transformation procedure. Although primary T₀ transformants exhibited chimeric mutation patterns, stable inheritance and segregation of edited alleles were confirmed in the T₁ generation. Sequence analyses identified diverse indel mutations across target loci, with SlTOM1d exhibiting the highest editing efficiency. Multiplex genome editing successfully generated single-, double-, and triple-mutant combinations, with higher-order mutants displaying the strongest tolerance phenotypes. Following mechanical ToBRFV inoculation, edited T₁ plants exhibited markedly reduced symptom severity, low viral accumulation, and improved fruit health compared to wild-type controls. RT-qPCR analysis further confirmed significantly reduced viral RNA levels, supporting a host-factor-mediated tolerance mechanism. Importantly, edited lines maintained normal growth and agronomic performance. Collectively, these findings demonstrate that multiplex CRISPR/Cas9-mediated targeting of SlTOM1 homologs represents a promising and practical strategy for improving ToBRFV tolerance in tomato breeding programs. Full article

Lactococcosis has emerged as an economically and ecologically significant disease in aquatic animals worldwide. This study employed multilocus sequence typing (MLST) to investigate the genetic diversity of Lactococcus spp. strains from Brazilian fish species and evaluate their phylogenetic relationships with global isolates to elucidate potential epidemiological connections involving multiple host species and distinct geographic regions. A total of 55 isolates from different laboratories had their DNA extracted, followed by the amplification and sequencing of the internal fragments of seven housekeeping genes (als, atpA, tuf, gapC, gyrB, rpoC and galP). Sequence types (STs) and clonal complexes (CCs) were defined. An unrooted neighbor-joining phylogenetic tree was generated using allele profiles from this study and those previously reported from other aquatic animal species. The isolates comprised 29 STs (11 previously reported, 18 novel ones), which were grouped into species-specific CCs: CC5 (L. formosensis); CC4, CC17, CC62 (L. garvieae); CC24, CC29, CC97 (L. petauri). Considerable genetic divergence was observed, with L. formosensis and L. garvieae forming heterogeneous populations, while L. petauri was more homogeneous. These findings describe the MLST structure of the sampled isolates and should be interpreted as hypothesis-generating rather than population-level estimates of genotype prevalence. Phylogenetics confirmed groupings within the CCs and revealed additional phylogenetic clustering patterns. In conclusion, the Brazilian Lactococcus spp. strains analyzed in this study constitute a genetically diverse population based on their STs. MLST and phylogenetic analysis demonstrated genetic relatedness between the L. garvieae and L. formosensis isolates from this study and those from other aquatic animal species. In contrast, all the STs identified for L. petauri in this study were unrelated to the MLST lineages responsible for outbreaks in Brazilian Nile tilapia (Oreochromis niloticus) and North American rainbow trout (Oncorhynchus mykiss). This suggests that piscine L. petauri populations in the Americas evolved from distinct ancestral origins. Full article

Yellow fever virus (YFV) is divided into seven genotypes, including West Africa II (WAII) and South America I (SAI). The first wild-type YFVs isolated, Asibi (Ghana/1927) and French Viscerotropic virus ([FVV] Senegal/1927), are members of WAII. The first YFV strain isolated in South America, JSS (Brazil/1935), was associated with the last outbreak of urban YF in Brazil and has been insufficiently studied. We utilized Next Generation Sequencing to compare JSS with Asibi, FVV, and other South American YFV strains. SAI strains, including JSS, had higher genetic diversity than WAII strains. Phylogenetic and phylogeographic studies of YFV in South America have revealed the circulation of five lineages within Brazil, termed 1A-1E. JSS was found to be distinct from the five genetic lineages currently recognized in Brazil, and so we termed JSS as the currently sole member of Brazilian linage 1F. a comparison of JSS with all other Brazilian genomes of YFV suggests that lineage 1F appears to have become extinct. Full article

Genetic diversity within maize inbred populations is essential for sustaining genetic gain in breeding programmes. This study evaluated 280 maize inbred lines with two checks using an augmented block design (22 × 14). At harvest, 271 lines and two checks were analysed, with nine entries excluded due to poor survival. Using both descriptive (24) and quantitative (19) traits, significant variations were observed across many traits. Descriptive traits varied among the genotypes, as revealed by graphical analysis and correlation heatmaps. The likelihood ratio test (LRT) for lines showed significant differences for several quantitative traits with moderate–high heritability, while anthesis–silking interval, tassel length, ear position, ear aspect, bad husk cover, number of plants, and number of ears per plant exhibited low heritability. High genetic advance as a percentage of the mean was observed for grain yield, plant height, grain texture, number of plants, number of kernels, and grain weight per plant. Positive associations were observed among genotypic coefficient of variation, genetic advance, and heritability. Grain yield showed significant positive correlations with yield-related traits and morphological traits, but negative correlations with flowering traits. The first 10 principal components explained 86.17% of total variation, with flowering traits contributing most to variability in PC 1. Cluster analysis grouped genotypes into 10 clusters, with substantial genetic divergence within and between cluster groups. In conclusion, the study revealed considerable genetic diversity, supporting the selection of superior parents in breeding programmes and developing improved maize varieties to enhance productivity. Full article

Background: Locally adapted goat populations represent important reservoirs of genetic diversity and play a crucial role in the sustainability of livestock production systems, particularly in marginal environments. However, many of these populations are currently threatened by genetic erosion caused by crossbreeding with highly specialized commercial breeds. Although previous studies have described the genetic diversity of several goat populations from South America and the Iberian Peninsula, the influence of geographic factors on the genetic structure of these populations remains insufficiently understood. In this study, we investigated the influence of geographic distance and spatial factors on the genetic diversity, population structure, and relationships among locally adapted goat populations from Brazil, Spain, and Ecuador. Methods: A total of 561 goats representing 15 populations were genotyped using a panel of 23 microsatellite markers. The dataset included six locally adapted Brazilian breeds, three Spanish breeds, one Ecuadorian population (Chusca Lojana), four exotic breeds, and one undefined genotype group. Genetic diversity parameters, population structure, genetic relationships, and spatial genetic patterns were evaluated through a combination of population genetic and spatial analyses. Results: The locally adapted populations showed considerable levels of genetic diversity, with the Spanish (H_o = 0.629; H_e = 0.685) and Ecuadorian (H_o = 0.628; H_e = 0.704) populations displaying higher diversity than the Brazilian populations (H_o = 0.583; H_e = 0.628). Significant genetic differentiation was observed among geographic groups. A strong and significant correlation between genetic and geographic distances was detected when all local populations were considered (r = 0.77; R² = 0.59; p < 0.001), as well as when only Brazilian populations were analyzed (r = 0.65; R² = 0.43; p = 0.0075). Spatial analyses further identified potential genetic barriers that may restrict gene flow among certain populations. Conclusions: These findings suggest that geographic isolation plays an important role in shaping the genetic structure of locally adapted goat populations, while historical connections among Iberian and South American populations may also contribute to the observed genetic relationships. The integration of genetic and spatial information provides valuable insights for understanding the evolutionary dynamics of these populations and supports the development of more effective strategies for the conservation and sustainable management of goat genetic resources. Full article

Lipizzan horses, bred for over four centuries, represent a unique genetic, cultural and historic resource. This study assessed genetic diversity and population structure across seven European Lipizzan populations, with emphasis on the Bosnia and Herzegovina population. A total of 547 Lipizzan horses were genotyped using 12 microsatellite markers. The parameters of genetic variability, admixture level and migration rate were calculated. The mean number of alleles, effective number of alleles and Shannon’s information index were 5.78, 3.24 and 1.31, respectively. The average fixation indices were estimated to be F_IT = 0.05 (SE = 0.02), F_IS = −0.02 (SE = 0.01), and F_ST = 0.07 (SE = 0.01). The level of genetic diversity observed within each Lipizzan horse subpopulation shows similar fluctuations, with the lowest values observed in Bosnia and Herzegovina and the highest in the Slovak Lipizzan population. The observed heterozygosity was lower than the expected heterozygosity. The Hardy–Weinberg equilibrium was maintained in Serbia, while minor deviations occurred in other populations, most notably in Slovakia. Nei’s genetic distances were highest between Slovakia and other populations, particularly Bosnia and Herzegovina. The population structure analysis confirmed admixture involving Bosnia and Herzegovina, and the migration pattern corresponded to geographic proximity and breeding practices. These findings provide a valuable basis for developing breeding strategies to reduce inbreeding and preserve genetic diversity. Full article

Bacterial wilt (BW), caused by soil-borne bacteria of the Ralstonia solanacearum species complex (RSSC), is a serious disease affecting eggplant (Solanum melongena) in tropical and subtropical regions. Resistance to BW in eggplant has been identified in several accessions and wild relatives, but no source has shown broad and stable resistance across diverse strains and environmental conditions. In the first screening trial, six eggplant genotypes, including five previously identified as resistant to RSSC, were evaluated along with two tomato checks against eight BW strains representing two phylotypes (I and II) and three biovars (2, 3, and 4). In the second screening trial, 26 hybrids developed from seven parental eggplant genotypes (including the six evaluated genotypes in the first screening plus an additional one) were evaluated, together with the parents, against three BW strains (Pss97, Pss2016, and Pss4). The results showed that the parental line EG048 was highly susceptible, whereas EG44 was resistant to the three strains, with a disease index (DI) of ≤20%. Furthermore, fourteen hybrids were classified as resistant or moderately resistant to the three strains. Among them, hybrid EG27 was categorized as highly resistant to all three strains with a disease index of 5.6–7.3%. In addition, three hybrids (EG8, EG20, and EG29) were highly resistant or resistant to all three strains, with a disease index of 3.8–15.8%. A strong positive correlation was observed between wilting percentage and disease index in the eggplant hybrids across the tested strains. Our results provide valuable support for eggplant breeding programs aimed at developing hybrid rootstocks with broader and potentially broad-spectrum resistance to RSSC in tomato and eggplant. Full article

Cystic echinococcosis (CE) is a zoonotic disease caused by the larval stage of the Echinococcus granulosus sensu lato (s.l.) complex. The disease is globally distributed, with particularly high prevalence in Central Asian countries, including Kazakhstan. Despite its significant impact on public health and livestock production, data on CE in sheep in Kazakhstan remain limited. This study investigated the prevalence and genetic diversity of Echinococcus granulosus sensu stricto (s.s.) in sheep across Kazakhstan, addressing an important zoonotic disease affecting both livestock and human health. Over the course of one year, a total of 31,389 sheep were examined, and cystic echinococcosis cysts were collected from the livers and lungs of 550 infected sheep across 14 regions of Kazakhstan. Molecular analyses targeting mitochondrial genes (nad1, cox1) were performed to determine genetic diversity. The results revealed a higher occurrence of CE in the southern regions of the country. Among the genotyped isolates (57), genotype G1 was dominant, accounting for 84.2% (48) of the samples, whereas genotype G3 (9) was detected at a lower frequency in three regions. A total of 11 distinct haplotypes were identified, indicating considerable genetic diversity among the isolates. Haplotype network analysis suggested gene flow among populations and revealed the widespread presence of the most common haplotype (EgKZ-2) across multiple regions. These findings highlight the need for continuous monitoring and targeted control strategies for cystic echinococcosis, emphasizing the importance of understanding parasite genetic diversity for public health interventions and livestock management in endemic areas. Overall, this study contributes to the understanding of the genetic diversity and transmission dynamics of E. granulosus s.s. in Central Asia. Full article