Search Results (4,881)

Background: Smith–Lemli–Opitz syndrome (SLOS) is an inborn error of cholesterol biosynthesis, caused by biallelic mutations in the DHCR7 gene. Genotype–phenotype correlations regarding DHCR7 variants could explain the variation in severity, ranging from in utero demise or severe SLOS to a mild phenotype. Clinical recognition can be challenging. This study aimed to determine the frequency of SLOS carriers in the Central European population, as well as the mutational spectrum of DHCR7 in these carriers. Methods: A retrospective analysis of DHCR7 variants was conducted using next-generation sequencing data from 55,289 individuals in Czech and Hungarian genetic laboratories. Results: The SLOS carrier frequency and the mutational spectrum of the DHCR7 gene in its carriers were established in the Czech and Hungarian sub-cohorts. In the combined dataset, we identified causative DHCR7 variants on 1567 alleles among 55,289 tested individuals, contributing to an SLOS carrier frequency of 2.83%. Of the 31 DHCR7 variants detected, the c.452G>A variant was the most prevalent, accounting for 1.8% of all detected alleles in our cohorts. In contrast, the c.964-1G>C variant was more frequent in non-Finnish Europeans, as indicated by the gnomAD 4.1.0 database. The DHCR7 mutational spectra of patients and carriers were comparable in terms of the most common variants. Conclusions: The high SLOS carrier frequency (2.83%) underscores the importance of SLOS carrier screening in Central European populations. The prevalent DHCR7 null mutations and their potential combinations may explain the lower-than-expected prevalence of SLOS, whilst Central and Eastern European populations remain likely underrepresented in the current gnomAD database. Full article

Rhizoctonia solani anastomosis group (AG)-2-2IIIB and AG-4HGI are the main pathogens causing sugar beet seedling damping-off and crown and root rot disease. In this study, 1232 loci of simple sequence repeats (SSRs) were obtained via transcriptome sequencing, with 592 from AG-2-2IIIB and 640 from AG-4HGI. Fourteen and twenty loci of SSRs were selected for studying the genetic structure of the AG-2-2IIIB and AG-4HGI populations, respectively. A population of 134 strains of AG-2-2IIIB and 145 strains of AG-4HGI, sampled from three geographic regions in China, indicated that both AG-2-2IIIB and AG-4HGI had a high level of genetic diversity, and that the selected SSR markers could reliably capture the genetic variation. Genetic analysis indicated that the individual strains of AG-2-2IIIB and AG-4HGI randomly mated within their respective population, and that a considerable degree of inbreeding was present among the populations. High to moderate gene flow and low to moderate population subdivision were detected among the populations of AG-2-2IIIB and AG-4HGI, which indicated that weak differentiation existed in these two subgroups. In addition, a founder effect (genetic drift) or a bottleneck effect was inferred to have occurred in the AG-4HGI population. This study provides the first analysis of the population genetic structure of AG-2-2IIIB and AG-4HGI associated with sugar beet seedling damping-off and crown and root rot disease, and the present results offer useful guidance for developing effective integrated disease management. Full article

Sugarcane (Saccharum spp. L.) is a globally vital sugar and energy crop whose genetic improvement has been constrained by its complex polyploid–allopolyploid genome. To address this limitation, we developed a practical, high-throughput single-nucleotide polymorphism (SNP) genotyping system. Using specific-locus amplified fragment sequencing (SLAF-seq) on 107 diverse accessions, we identified 2,420,550 high-quality SNPs anchored to the Saccharum officinarum LA-Purple genome. Stringent filtering yielded 55,750 SNPs for population analysis, which revealed three distinct genetic groups consistent with breeding history and adaptation. From these resources, 329 SNPs were converted into PCR-based ligase detection reaction (PCR-LDR) markers, resulting in a validated panel of 177 highly reliable SNPs (151 core and 26 extended) organized into an efficient multiplex typing system. The panel exhibited exceptional discriminatory power, successfully distinguishing all 303 tested sugarcane varieties and clearly resolving 186 individuals from three segregated hybrid populations. Compared to existing SSR and SNaPshot platforms, this SNP system offers superior experimental reproducibility, enhanced varietal clustering, and broader genome coverage. This work provides a robust, efficient genotyping tool to advance sugarcane variety identification, germplasm management, pedigree analysis, and marker-assisted breeding, with potential applicability to other complex polyploid crops. Full article

Glaciers have been proposed as evolutionary hotspots for microbial evolution; however, direct evidence for glacial microbial population formation and genomic loci undergoing selective sweeps remains limited. To address this knowledge gap, we investigated the genomic diversity, evolutionary pressures, and adaptive strategies of Cryobacterium, a representative genus of glacier environments. Based on recent gene flow analysis, 18 distinct populations of Cryobacterium were identified, each exhibiting clear discontinuities in gene flow and genetic boundaries. Selective pressure analyses revealed purifying selection within populations, maintaining genetic stability, and positive selection between populations, suggesting adaptive divergence from environmental differences. Notably, half of the populations spanned geographically distant glaciers, suggesting widespread dispersal mechanisms such as atmospheric circulation or glacial fauna migrations. We identified 17 genes under strong selective sweeps, involved in metabolic enzymes, transporters, and gene regulation. Based on the reverse ecology principles, these genes (e.g., glucose-6-phosphate dehydrogenase assembly and RNA polymerase-binding gene), are likely to be critical for cold adaptation. This study provided clear genomic evidence of glacial microbial population formation driven by recent gene flow, significantly enhanced our understanding of microbial adaptation in extreme cold ecosystems, and emphasized the importance of deep genomic sequencing in ecological and evolutionary research. Full article

Insect infestation poses a significant threat to global agriculture by impairing plant growth and reducing crop yields. The western flower thrip (WFT) causes substantial damage through both direct feeding and transmission of plant viruses. Although the jasmonic acid (JA) signaling pathway is known to participate in plant defense against WFTs, the underlying molecular mechanisms in non-model crops such as peppers, remain largely elusive. This study investigates the role of suppressor of prosystemin-mediated responses2 (Spr2) within JA-mediated defense against WFTs in pepper. Through an integrated approach employing virus-induced gene silencing (VIGS), transcription analysis, phytohormone quantification, insect behavior assays and life history investigations, we demonstrated that silencing CaSpr2 significantly reduced JA and JA-Ile accumulation, and led to a strong feeding preference of WFTs for CaSpr2-silenced plants. Furthermore, the adult lifespan, survival rate, female fecundity, oviposition rate, and population parameters of WFTs were significantly improved on CaSpr2-silenced plants. Spr2 functions as an essential component within the JA signaling pathway, thereby playing a critical role in conferring resistance to WFTs in cultivated pepper. These findings provide profound insights and practical implications for breeding thrips-resistant cultivars in non-model plants, through genetic manipulation of JA signaling, offering a promising avenue for sustainable agricultural pest management. Full article

To address the issue of traditional Particle Swarm Optimization (PSO) being prone to local optima and insufficient global search capability in sparse phased array optimization, a hybrid optimization algorithm integrating PSO with a Genetic Algorithm (GA) is proposed. Within the PSO framework, the proposed algorithm incorporates the adaptive crossover and mutation operations of the GA to enhance population diversity. It combines an adaptive weighting factor and a constriction factor to balance global exploration and local exploitation capabilities. Furthermore, a density-weighted method is employed to generate a high-quality initial population, thereby accelerating convergence. The proposed algorithm is applied to an 8 × 8 planar sparse array. On the E-plane (φ = 0°) and H-plane (φ = 90°), simulation results indicate that the achieved normalized maximum sidelobe level is −23.14 dB, which is significantly superior to those obtained by standalone PSO and GA. Based on these simulation results, microstrip patch antennas are introduced for array constitution and analysis. Full-wave electromagnetic simulation proves that the proposed sparse array has the ability of wide-angle scanning and low sidelobe. Our work demonstrates that the PSO-GA hybrid algorithm effectively enhances search capability and convergence performance, providing a reliable solution for sparse array design. Full article

Background: Congenital anomalies are influenced by genetic and environmental factors. While interventions including folic acid supplementation have reduced neural tube defects, data on modifiable socio-demographic risk factors remain limited. Aim: This study aimed to assess variation in the prevalence of selected congenital anomalies across the United States according to socio-demographic factors. Methods: A population-based analysis was conducted using CDC-WONDER natality data from 2016 to 2023. Included anomalies were anencephaly, spina bifida, cyanotic heart disease, diaphragmatic hernia, omphalocele, gastroschisis, limb reduction, cleft lip/palate, Down syndrome, chromosomal disorders, and hypospadias. Associations with maternal age, BMI, race, tobacco use, diabetes, and fertility treatments were analyzed. Prevalence rates were calculated per 1000 live births. Relative risks (RRs) and 95% confidence intervals (CIs) were estimated. Joinpoint regression was used to assess annual percent changes (APCs), with p < 0.05 considered significant. Results: Among 3,482,944 singleton live births in 2023, the overall prevalence of the selected congenital anomalies was 3.3 per 1000. Compared to Caucasian mothers, risk was lower in Asian (RR 0.57; 95% CI: 0.52–0.63) and Black (RR 0.81; 95% CI: 0.76–0.85) infants and higher in American Indian/Alaska Native infants. Significant risk factors included pre-pregnancy diabetes (RR 2.41; 95% CI: 2.16–2.69), maternal age > 45 (RR 2.95; 95% CI: 2.36–3.69), and tobacco use (RR 1.78; 95% CI: 1.64–1.94). A significant decline in prevalence was observed from 2016 to 2023 (APC: –0.6%; 95% CI: –1.1 to –0.2; p = 0.006). Conclusions: Significant disparities and modifiable maternal risk factors were associated with the prevalence of selected congenital anomalies in the U.S. from 2016 to 2023. A modest statistically significant decline in overall prevalence was observed during the study period, supporting the importance of continued national surveillance and targeted preconception and prenatal interventions to reduce risk and address inequities. Full article

Influenza D virus (IDV) and co-circulating respiratory pathogens were investigated using RT-qPCR in 316 samples collected from 210 Spanish cattle farms with bovine respiratory disease (BRD) outbreaks between July 2023 and September 2024. Thirty-eight IDV-positive samples, from 30 farms across 15 provinces throughout Spain, were identified. IDV was significantly more frequent in bronchoalveolar lavage samples (22.1%) and nasal swabs (13.5%) compared to lung tissues (5%) and other sample mixtures (5%). All IDV-positive specimens exhibited co-infections, with most (94.7%) harboring three to seven viral and/or bacterial pathogens, highlighting the complexity of BRD outbreaks. Cramer’s V analysis revealed moderate IDV association with Mycoplasma bovis (V = 0.255) and Pasteurella multocida (V = 0.223), and a weaker IDV-bovine coronavirus association (V = 0.202), while IDV association with Histophilus somni (V = 0.025) and bovine herpesvirus 1 (V = 0.000) was negligible. Partial sequences of the hemagglutinin-esterase (HEF) gene from a subset of 13 IDV-positive samples (Ct < 32) were obtained. This confirmed the presence of the two major genetic lineages detected among cattle in Europe, D/OK and D/660, with D/660 exhibiting higher genetic diversity, as determined by DNAsp 6.12 software. This is the first report of IDV infection in Spanish cattle, confirming the circulation of the D/OK and D/660 lineages within the cattle population. Full article

The Cladia aggregata group of lichen-forming fungi comprises multiple species that are difficult to differentiate based on phenotypic characters. It has a wide distribution across several continents, but is most diverse in Australasia. We aimed to delimit the species complex further, investigate the relatedness of the lineages, and examine their distributional ranges and phenotypic traits. We used Restriction Site Associated DNA Sequencing (RAD-seq) to compare thousands of loci across 91 individuals from the Americas, Asia, and Australasia. All Asian samples formed a distinct, monophyletic clade in all phylogenetic trees, while the American samples divided into two clades, one comprising South American samples and another comprising Caribbean samples, with the latter representing C. aggregata sensu stricto, as the type specimen was collected in Jamaica. Further population-genomic analyses support the conclusion that the Asian samples are genetically distinct and are here described as a new species. The new species, Cladia asiatica, accommodates the Asian samples previously included in C. aggregata. Our analysis highlights the potential of next-generation sequencing to reveal hidden diversity and resolve the phylogeny of this species complex and lichen-forming fungi in general. Full article

Background/Objectives: Emerging evidence suggests that enlarged perivascular spaces (EPVS), which play a significant role in brain fluid exchange and waste removal, may be involved in the pathogenesis of amyotrophic lateral sclerosis (ALS). In this study, we aimed to explore the shared genetic link and causal effect between EPVS and ALS. Methods: This study used publicly available summary data from the largest and most recent genome-wide association studies (GWAS) on EPVS (n = 40,095) and ALS (n = 138,086) in European populations. EPVS were assessed in the hippocampus (EPVS-HIP), basal ganglia (EPVS-BG), and white matter (EPVS-WM). We used linkage disequilibrium score regression (LDSC) to investigate the genetic correlation. Multi-trait analysis of GWAS (MTAG), Cross-Phenotype Association (CPASSOC) analysis, and genetic colocalization analysis were performed to identify shared risk loci. Bidirectional Mendelian randomization analysis was used to investigate the causal relationship. Results: A negative genetic correlation was observed between EPVS-WM and ALS after Bonferroni correction (rg = −0.24, p < 0.01). No significant correlations were observed between ALS and EPVS-HIP (rg = −0.03, p = 0.79) or EPVS-BG (rg = 0.01, p = 0.91). Four significant loci including rs113247976 in KIF5A and rs118082508 in SDR9C7 were identified as potential pleiotropic loci of the relationship. None of these loci demonstrated evidence of genetic colocalization. Furthermore, Mendelian randomization analysis revealed no causative effect in either direction. Conclusions: EPVS-WM and ALS may share part of their genetic architecture, but no evidence for a causal relationship was observed. Future research is needed to further refine these relationships. Full article

Background: We describe the post-mortem analysis of a CARD11 variant allele, p.Ser995Leu, identified in fraternal twins who died in early infancy with no identifiable cause of death. CARD11 variants through varied inheritance models can alter immune function through loss- or gain-of-function mechanisms, involving distinct protein domains; yet the significance of GUK domain variants remains poorly characterized. Twin autopsies showed non-specific findings, such as pulmonary macrophage accumulation and splenic white pulp expansion, but without infection or structural abnormalities. Methods: Whole-exome sequencing, performed as part of molecular autopsies, identified the shared CARD11 p.Ser995Leu variant, previously classified as a variant of uncertain significance (VUS). We assessed evolutionary conservation across CARD family proteins and species and predicted functional impact using in silico tools, which estimate the likelihood that a variant is deleterious. AlphaFold-based structural modeling emphasized qualitative biophysical assessment. Using epidemiological data, population allele frequency, and Bayesian ACMG variant classification, we assessed competing hypotheses under an autosomal dominant model. Results: The p.Ser995Leu substitution affects a conserved, surface-exposed β-sheet within the GUK domain. While CADD scores exceeded 20, other predictive algorithms offered only partial support of pathogenicity. Structural modeling suggested a potential GUK domain destabilization. Integrating genetic, pathologic, immunologic, and probabilistic modeling, we propose a biologically plausible model in which the variant, like other GUK variants, may alter NF-κB or other signaling pathways and is likely pathogenic. Conclusions: While the CARD11 p.Ser995Leu variant’s contribution to disease is uncertain without functional validation or parental testing, and phenotypic findings are non-specific, the presence of an ultra-rare GUK domain variant in both twins, combined with in silico and statistical modeling, supports its interpretation as likely pathogenic or high risk. The results highlight the challenges of data-limited post-mortem variant interpretation. Full article

Background/objectives: Knowledge of the genetic background of evaluated traits has been the basis for genetic progress in every horse-breeding population and is essential for precise breeding and up-to-date decision-making. The study aimed to estimate the heritability coefficients for field performance traits in mares. Methods: The research was based on 1408 evaluations of mares conducted during the years 2002–2021 in 51 training centers in Poland. The preliminary analyses of the effects, significant for the investigated traits, were obtained using analysis of variance, and these additional data are also presented (SAS program, GLM and Mixed procedures). The final statistical model for the AI-REML procedure of the DMU program included a fixed effect of the training center-season-year of evaluation, a random effect of the animal, and a regression on age in years. Results: The heritability coefficients of the performance traits were moderate to high (0.32–0.60) with the SE within the range of 0.06–0.08. The highest heritability was estimated for the free jumping, trot, and overall results. The lowest heritability was achieved for the rideability. Conclusions: The level of heritability estimations allowed for the population progress in the evaluated traits. Full article

Background: Celiac disease (CD) is a multifactorial autoimmune disorder strongly associated with specific HLA class II molecules, particularly HLA-DQ–encoding haplotypes. Although the genetic contribution of these loci is well established, the structural features accompanying allele-specific disease susceptibility remain incompletely explored. Methods: In this study, molecular HLA typing was integrated with in silico secondary structure analysis to examine the relationship between genetic predisposition and structural organization of HLA class II molecules in a Sardinian population. A total of 100 patients with CD and 100 healthy controls were genotyped for HLA-DR and HLA-DQ alleles, and allelic and haplotypic distributions were compared between groups. Secondary structure predictions were performed using PSIPRED on selected HLA class II alleles, focusing on groove-forming domains of HLA-DRB1 and HLA-DQA1. Results: CD patients showed a marked enrichment of the DR3–DQ2.5 haplotype, together with a population-specific predominance of DQ2.5 and a reduced contribution of DQ8. Secondary structure analysis of the HLA-DRB1 β1 domain revealed a largely conserved organization, with only modest allele-dependent variations. In contrast, comparative analysis of HLA-DQA1 identified localized differences within the α1 domain, with the DQ2.5 molecule displaying a more coherent secondary structure organization compared with the lower-risk DQ2.2 variant. Conclusions: By integrating genetic and in silico structural analyses, this study highlights that HLA-associated susceptibility to celiac disease reflects not only allele and haplotype distribution but also subtle, allele-specific features in the structural organization of peptide-binding regions. These findings provide a refined framework for interpreting HLA-DQ–mediated genetic risk and support the relevance of structural coherence as a complementary dimension in the assessment of disease susceptibility. Full article

Fruit size and pungency are key yield and quality traits in chili. This study combines high-throughput genotyping with bulk segregant analysis (BSA) to identify candidate SNPs and quantitative trait loci (QTLs) by analyzing extreme phenotypes from a Ghotki × Chakwal-4 F2 population. The traits were fruit length, diameter, length-to-diameter ratio, and weight, along with capsaicin content. Significant correlations were observed among length, diameter, and length-to-diameter ratio. A total of 534 single nucleotide polymorphisms (SNP) markers were used to develop genetic maps from 4315 to 6607 cM long. The SNP frequency data was pooled for the 25% of individuals showing extreme values for each measured trait, and bulk segregant analysis (BSA) was performed. BSA identified high-scoring SNPs associated with pungency (SNP 1_41308232; SNP 12_104377148), fruit length (SNP 1_92509300; SNP 6_218780813), and fruit weight (SNP 6_100989762 and SNP 6_138660974). Genetic mapping identified twelve pungency QTLs, three for fruit length, two for fruit diameter, two for the length-to-diameter ratio, and thirteen for fruit weight. Overlapping QTL regions on chromosome 6 influence fruit length, fruit width, and capsaicin content, indicating potential pleiotropy and offering promising targets for multi-trait selection in chili breeding. The study identifies key SNPs and QTLs that simultaneously influence chili fruit size and pungency, providing valuable targets for multi-trait breeding. Full article

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne zoonotic pathogen of significant public health concern in South Korea, where human cases continue to occur at high levels; however, information on the molecular epidemiology and genotype diversity of SFTSV in goats—an increasingly important livestock species—remains limited. In this study, blood samples were collected from 750 clinically healthy goats during nationwide surveillance in 2024. Viral RNA was detected by RT-PCR targeting the S and M genomic segments. Epidemiological characteristics were analyzed according to season, region, farm size, breed, and sex. Positive samples were subjected to sequencing and phylogenetic analysis to determine SFTSV genotypes. SFTSV RNA was detected in 10 of 750 goats (1.3%), with significantly higher detection rates in autumn compared with summer, in southern regions compared with northern regions, and in female goats compared with males, while no significant association was observed with farm size or breed. Phylogenetic analysis showed that goat-derived SFTSV strains belonged to genotypes B2, D, and F; notably, genotypes D and F were identified in goats for the first time in South Korea. These findings indicate that goats are exposed to genetically diverse SFTSV strains circulating in tick populations and exhibit epidemiological patterns consistent with tick ecology and human SFTS incidence, supporting the role of goats as incidental or sentinel hosts. Continuous molecular surveillance of goats, integrated with vector monitoring programs, may enhance understanding of regional SFTSV transmission dynamics and facilitate early detection of emerging genotypes with public health implication. Full article