Search Results (5,461)

Background: The UCP1 A-3826G polymorphism, located in the gene’s regulatory region, is associated with obesity and altered fat metabolism. Because UCP1 plays a central role in thermogenesis, variation in its expression may influence metabolic efficiency and dietary fat preference. Methods: We examined associations between the A-3826G polymorphism and food preferences in healthy young Japanese adults (50 males, 48 females). Preferences for high-fat and basic-taste foods were assessed using a self-administered questionnaire, with sweet foods classified as low- or high-fat. Genotypes (AA, AG, GG) were analyzed using a two-way mixed-design ANOVA to evaluate genotype × fat level interactions. Results: Preference scores for basic tastes did not differ significantly among genotypes in either sex (except for sour taste in males). In males, no significant genotype × fat level interaction was observed, although AA carriers preferred high-fat to low-fat sweet foods (p < 0.05). In females, a significant genotype × fat level interaction was detected (p < 0.01), with AG carriers showing lower preference for high-fat sweet foods. Conclusions: These findings indicate that the UCP1 A-3826G polymorphism may modulate preference for high-fat sweet foods in a sex-dependent manner, suggesting a link between thermogenic genetic variation and dietary fat preference relevant to obesity prevention. Full article

Camellia oleifera Abel, recognized as a woody oil-producing tree species, possesses considerable economic significance. To improve the breeding efficiency of C. oleifera, it is crucial to elucidate the genetic foundation underlying the mechanisms regulating fruit traits. In this study, a total of 6,252,197 high-quality single-nucleotide polymorphisms (SNPs) were identified from 109 germplasm accessions. Through genetic structure analysis, these accessions were categorized into two distinct populations. The average fixation index (Fst) was found to be 0.0153, indicating weak population differentiation. The genome-wide association analysis (GWAS) identified 157 significant loci. From these loci, 110 candidate genes were selected, which were associated with disease resistance, reproduction, development, and RNA biosynthesis. Twenty-three genes were involved in metabolic pathways, including genetic information-processing protein families, metabolic protein families, terpenoids, and polyketides. The identification of gene loci closely related to fruit traits not only provides genetic data for studying the molecular mechanisms of fruit traits but also offers new research avenues for molecular breeding of C. oleifera. Full article

Winter survival in barley depends on freezing tolerance and de-acclimation tolerance, yet their genetic determinants under increasingly unstable winters remain poorly understood. Here, 188 Polish barley accessions were evaluated over two consecutive growing seasons (2021–2022) using genome-wide association studies (GWAS) with a mixed-linear model (MLM) and high-density single nucleotide polymorphism (SNP) and diversity arrays technology sequencing (DArTseq) markers. Freezing and de-acclimation tolerance were quantified by 16 chlorophyll fluorescence parameters and post-freezing survival rates in plants subjected to 21 days of cold acclimation (4 °C/2 °C, day/night) and 7 days of de-acclimation (12 °C/5 °C, day/night). The results showed that freezing and de-acclimation tolerance are related but genetically distinct. The cold-acclimated (CA) state exhibited significant marker–trait associations on chromosomes 2H and 6H, whereas the de-acclimated (DA) state displayed a broader, more complex genetic architecture, particularly on chromosomes 2H and 7H. F_v/F_m showed the strongest associations for both SNP and DArTseq markers in both states. PI_(csm), followed by PI_(cs0) and PI_(total), showed high SNP associations in the DA state, indicating a strong relationship between photosynthetic performance and freezing tolerance after de-acclimation. Notably, the DArTseq marker 11400277 on chromosome 7H showed multiple marker–trait associations across both states. These findings provide a genomic basis for marker-assisted selection of climate-resilient winter barley cultivars. Full article

Background/Objectives: Pygmy rabbits (Brachylagus idahoensis) are closely associated with sagebrush steppe habitat across the western United States, and loss and fragmentation of this habitat has contributed to the near extirpation of the Columbia Basin population in Washington state (CB). The CB pygmy rabbit was listed under the Endangered Species Act in 2003, and recovery efforts have included captive breeding, reintroduction, and genetic rescue with the translocation of rabbits from populations across the species range. Methods: We used restriction site-associated DNA sequencing (RADseq) on samples from across the species range, including CB pygmy rabbits captured prior to genetic rescue and admixture. We determined population genetic structure across the pygmy rabbit range, tested for genomic signatures of adaptive divergence among populations, assessed the genetic distinctiveness of the ancestral CB population, and identified loci useful for monitoring ancestry in the current admixed CB population. Results: Our dataset included 9794 single-nucleotide polymorphisms (SNPs) across 123 individuals. We identified four distinct genetic groups, including the central portion of the species range and three peripheral populations: CB, northern Utah/Wyoming, and southern Utah. The ancestral CB population showed the highest degree of genetic distinctiveness using multiple clustering, ordination, and genetic differentiation analyses. We identified evidence for putatively adaptive variation among populations, but no significant gene ontology associated with local adaptation. Conclusions: Our results highlight the long-term isolation of the ancestral CB population as well as historical isolation of other peripheral populations. Our results also provide SNP loci for monitoring the consequences of genetic rescue efforts in the current admixed CB population. Full article

In this study, the phenotypic consequences of naturally occurring single nucleotide polymorphisms (SNPs) in the Middle East respiratory syndrome coronavirus (MERS-CoV) Spike protein were investigated. The impact of Spike mutations on the syncytia formation and neutralisation of contemporary MERS-CoV strains is not currently well understood. Mutations were identified by aligning 584 MERS-CoV Spike sequences from either human clinical isolates collected between 2012 and 2024 or from a clinical isolate that had been passaged in human cells. Fifteen SNPs of interest occurring in the N-terminal domain (NTD), receptor binding domain (RBD) and adjacent to the S1/S2 cleavage site were selected for further characterisation based on their location in the Spike protein, frequency and identification in previous studies. A contemporary clade B, lineage 5 wildtype Spike sequence, obtained from a human MERS-CoV clinical isolate, was used as the backbone in this study. The mutations of interest were introduced to the wildtype backbone to generate Spike variants. Spike variants were characterised via cell–cell fusion assays, and a lentiviral pseudotyping system was used to investigate the impact of these Spike mutations on neutralisation. The I529T, E536K and L745F mutations were shown to increase fusion and syncytia formation. The L411F, T424I, L506F, L745F and T746K mutations were found to increase resistance to neutralisation by pooled patient sera. This study has identified novel naturally occurring Spike mutations that resulted in phenotypic differences in the syncytia formation and neutralisation of contemporary MERS-CoV strains. Continued investigation of the phenotypic consequences of MERS-CoV Spike mutations is essential for assessing the risk to public health, especially given the pandemic potential of this virus. Full article

Influenza viruses remain a major health threat, causing significant illness, death, and high healthcare costs worldwide, despite ongoing research and prevention efforts. A complex interaction between host and viral factors greatly influences the outcomes of influenza infection. Early research mainly focused on the influenza virus’s characteristics, but gaining an in-depth understanding of host factors involved in infection helps identify those that may influence disease severity. Notably, as the number of people with one or more comorbidities—that is, conditions that increase the risk of severe influenza—continues to rise, it becomes even more important to investigate the role of host factors. Recognizing host risk factors associated with severe outcomes, mainly caused by excessive inflammatory responses and disruption of epithelial barrier function, is crucial in identifying predictive markers and developing host-based prevention and treatment strategies, especially during pandemics. Moreover, early identification of host risk factors can help reduce severe outcomes and healthcare costs due to hospitalization. To achieve this, detailed analyses of the molecular signature of the host response to influenza virus infection are essential. This review highlights key host factors involved in severe influenza, allowing a better understanding of their roles, especially at the cellular level. Full article

Background: Compensatory mutations offer clues in deciphering the role of a particular protein in cellular processes. Here, we investigate an unknown compensatory mutation, present in the BEAF^NP6377 fly line, that provides sufficient rescue of the defective ovary phenotype caused by null BEAF alleles to allow the maintenance of fly stocks lacking the chromatin domain insulator proteins Boundary Element-Associated Factors BEAF-32A and BEAF-32B. We call this dominant mutation Tofu. Methods: We employ both classical genetics and genomic sequencing to attempt to identify the mutation. Results: We find evidence that points to a mutation in a predicted Polycomb response element (PRE) upstream of the ribbon transcription factor gene. This may lead to aberrant rib expression, which is otherwise not expressed in adult ovaries. BEAF and Rib colocalize to a set of promoters, suggesting overlap in gene regulation. Conclusions: Tofu could be a PRE mutation leading to the aberrant activation of rib in the ovaries. This could allow Rib to compensate for a lack of BEAF to activate one or more coregulated genes necessary for egg production in flies. Full article

As an elite indigenous poultry breed under national protection in China, the Xupu goose is renowned for its large body size, superior fatty liver production, premium meat quality, and high tolerance to roughage. To elucidate its genomic architecture, genetic diversity, and evolutionary selection signatures, we conducted whole-genome resequencing on 15 purposively selected, unrelated male Xupu geese. An average of 6.79 Gb of high-quality sequence data was generated per individual, yielding approximately 4.27 million single-nucleotide polymorphisms (SNPs) with a transition/transversion (Ti/Tv) ratio of 2.49. Population genomic analyses revealed that while the population retains a moderate genetic reservoir (H_E = 0.298), it exhibits a distinct heterozygote deficit (H_O = 0.217) and a moderate genomic inbreeding coefficient F_ROH = 0.204). This structural pattern underscores the genetic impact of historical ex situ closed-flock conservation and the consequent formation of cryptic family lineages. Furthermore, genome-wide integrated haplotype score (iHS) scans detected distinct regions under recent positive selection. Functional annotation of these regions highlighted candidate genes tightly associated with the breed’s hallmark traits, specifically lipid metabolism and hepatic fat deposition (ACSS2, ACSS3, PECR), alongside muscle development (CMYA5, MTPN, LEPR). Conclusively, this study delineates a comprehensive genomic landscape of the Xupu goose, providing a robust foundational resource for future germplasm conservation, molecular marker development, and precision breeding programs. Full article

Background/Objectives: We analyzed the whole-genome sequences of ciprofloxacin-resistant (CIP-R) enteropathogenic Escherichia coli (EPEC) ST752 isolates in South Korea to characterize their molecular epidemiology. This lineage has emerged as the predominant CIP-R EPEC clone in South Korea, accounting for 28.8% of human clinical isolates and circulating within the One Health interface. Methods: We performed whole-genome sequencing (WGS) and reference-based core-genome single-nucleotide polymorphism (SNP) analysis on 26 CIP-R EPEC ST752 isolates (19 human clinical and 7 poultry-derived isolates). To elucidate their evolutionary history and transmission dynamics, Bayesian phylodynamic and phylogeographic reconstructions were implemented by integrating domestic isolates with a global genome dataset (n = 508). Results: Isolates from human and poultry sources clustered together with an identical virulence profile and minimal genetic distance. The Bayesian molecular clock analysis estimated that the time to the most recent common ancestor of the South Korean clade was 2000.65. Moreover, the phylogeographic analysis supported statistical evidence (Bayes factor 32.16) for the introduction of this lineage into South Korea from Denmark and revealed a strongly supported host transition from humans to poultry (Bayes factor > 10,000), although this requires cautious interpretation due to limited temporal sampling of poultry isolates. Conclusions: Continued integrated One Health surveillance across human, animal, and environmental reservoirs is needed to monitor and prevent the spread of high-risk antimicrobial-resistant clones. Full article

Wheat (Triticum aestivum L.) is one of the most cultivated crops in the world, but production is often affected by drought. The wheat chromosome 4A contains several quantitative trait loci (QTL) associated with drought tolerance and yield-related traits, making it a valuable target for genetic improvement. In this study, we developed near-isogenic lines (NILs) carrying qDT.4A.1, a major QTL for yield using a fast generation cycling system (FGCS) and characterized these NILs for grain yield and thousand-grain weight (TGW) under drought stress and control conditions. We identified a single nucleotide polymorphism (SNP) marker Kukri_c27037_112, which showed a consistent genotype–phenotype associations across two NIL pairs. This marker is linked to four candidate genes encoding a RING-finger E3 ubiquitin ligase, a receptor kinase, and a protein kinase family protein involved in drought stress response and pathways. In silico expression analyses revealed upregulation of these genes in grain tissue under drought conditions, supporting their potential role in grain development and yield formation during drought stress conditions. The identified SNP marker and its associated candidate genes are potential resources in marker-assisted selection and fine mapping pending further validation and functional studies. Our results provide valuable genomic resources, laying the foundation for the development of drought-tolerant wheat varieties and highlighting chromosome 4A as a key region governing drought tolerance. Full article

Background: Clinical outcomes for multiple myeloma are highly variable. Inherited genetic variants of immune regulatory genes can modulate disease susceptibility and clinical outcomes. The germline variant CTLA4 rs231775 polymorphism may alter T-cell function and affect clinical outcomes. Methods: We conducted a retrospective single-center study including 156 consecutive myeloma patients who underwent first-line ASCT. The patients were stratified according to the CTLA4 rs231775 genotype and disease stage (ISS I–III). Results: The CTLA4 rs231775 AA genotype was associated with inferior PFS in ISS I–II and superior PFS in ISS III. In the multivariate analysis, the CTLA4 rs231775 AA genotype emerged as a potential risk factor in ISS I-II and a potential protective factor in ISS III. Conclusions: This germline CTLA4 polymorphism may serve as biomarker to refine post-transplant risk stratification and enable personalized treatment management. Full article

Single nucleotide polymorphisms (SNPs), as common genetic variations, can influence biological processes. Identifying these variations is crucial for recognizing high-risk subgroups, guiding preventive strategies, and enabling personalized management. Objective: This study aimed to determine the relationship between SNPs and survival, thereby identifying genetic profiles associated with increased risk. Methods: We included seropositive patients with Chagas disease who had a disease duration of >20 years and no comorbidities. DNA was extracted. A SNP panel focusing on genes involved in cardiac structure was created from the GnomAD database. Patients were followed for 8 years to assess survival. The association between SNPs and survival was evaluated, and a genetic risk score was generated. Univariate and multivariate Cox regression models assessed the association between SNPs (coded as ordinal variables) and survival time. SNPs with p < 0.05 were selected to construct a risk score, which was then assessed using Kaplan–Meier curves and median survival times. Results: A total of 182 patients were included, with 96.7% completing follow-up for a median of 5.1 years (interquartile range: 3.4–6.5). The median age was 62 years; 39.6% of patients were male, and 31% had reduced left ventricular ejection fraction. Univariate analysis showed that 3 of the 68 SNPs studied were associated with survival. Variant rs3755863 (PPARGC1A gene) was significantly associated with an increased risk of death (hazard ratio, HR = 1.94; p = 0.022). Conversely, two variants, rs7310615 (SH2B3 gene) and rs7405731 (JUP gene), showed a protective effect with significantly reduced mortality risk (HR = 0.45; p = 0.006 and HR = 0.48; p = 0.006, respectively). In multivariate analysis, rs7310615 and rs7405731 remained significantly associated with survival. A genetic risk score was constructed, assigning 0 points for homozygous wild-type, 1 point for heterozygotes, and 2 points for homozygous alternative alleles. Individual scores were calculated, and survival was estimated for each score category using Kaplan–Meier analysis and median survival times. Conclusions: Two SNPs were identified as significantly associated with survival. These findings require confirmation in larger and more diverse populations. Their validation could enable the identification of a subgroup of patients at particularly high risk. Full article

Soft tissue sarcomas are rare malignant mesenchymal tumors for which accurate diagnosis, prognostic stratification, and therapeutic decision-making remain challenging. Although histopathology and immunohistochemistry are essential diagnostic tools, they frequently fail to capture the molecular complexity underlying tumor aggressiveness and treatment resistance. In this study, we evaluated the utility of RNA-based next-generation sequencing for the molecular characterization of STS and for elucidating transcriptomic mechanisms associated with aggressive tumor behavior. An observational cohort of 24 patients with histologically confirmed soft tissue sarcomas was analyzed, using adipose and skeletal muscle tissue as controls. RNA was extracted from tumor samples, libraries were prepared with a targeted pan-cancer panel, and sequencing was performed on the Illumina platform, followed by bioinformatic analysis using DRAGEN pipelines and DESeq2. RNA-NGS identified a predominance of single-nucleotide polymorphisms and significant differential gene expression, with overexpression of proliferation-related genes (TOP2A, MKI67, BUB1B), extracellular matrix and microenvironment-associated genes (COL11A1, SPP1), and developmental regulators (HOXD13, MELK). Subgroup analysis revealed a distinct transcriptomic profile in leiomyosarcoma, while gene fusion analysis detected clinically relevant alterations. These findings demonstrate that RNA-NGS provides biologically and clinically meaningful insights into the molecular landscape of soft tissue sarcomas and supports its integration into precision medicine-oriented diagnostic workflows. Full article

Genomic improvement and sustainable breeding of Mediterranean buffalo are hampered by the lack of breed-specific genomic resources compared with bovine. To address this gap, we aimed to identify a comprehensive set of high-confidence single-nucleotide polymorphisms (SNPs) in Mediterranean buffalo and evaluate their informativeness across other buffalo populations. A total of 58 whole-genome sequencing samples, from three different sets, were merged through the integration of short- and long-read sequencing technologies. Variants, both unique and shared among datasets, were identified using a combination of bioinformatic tools to increase the reliability of the dataset. From these, over 11 million high-confidence biallelic SNPs were identified in the Mediterranean breed. The same SNPs were also tested in additional populations (other rivers and swamps) to evaluate their polymorphism and missingness. These results provide a robust genomic resource for Mediterranean buffalo, overcoming the limitations of bovine-derived genotyping tools available today. The identified SNPs dataset lays the basis for the development of a breed-specific SNP array, providing a dense and informative set of markers that could support cost-effective SNP chip development compared with existing arrays and sequencing technologies. This resource will facilitate more accurate genomic selection, precision breeding, and the conservation of genetic diversity in the Mediterranean buffalo population. Full article

Phascolosoma esculenta is an economic species endemic in China and a highly prized delicacy along the country’s southeastern coast. This study focused on five P. esculenta populations and investigated their genetic diversity, population structure, and historical population dynamics. These populations were sampled from five locations, namely Beihai (BH) and Fangchenggang (FCG), in Guangxi; Putian, in Fujian (FJ); Danzhou, in Hainan (HN); and Zhanjiang (ZJ), in Guangdong. Genomic data were obtained through restriction site-associated DNA sequencing (RAD-seq) of 100 individuals. After quality filtering, a panel of 158,264 high-quality single nucleotide polymorphism (SNP) markers was established for subsequent analysis. The results revealed that the observed heterozygosity (Ho = 0.1872–0.2065) was lower than the expected heterozygosity (He = 0.2304–0.2382), with inbreeding coefficients (Fis) ranging from 0.1114 to 0.1592, indicating heterozygote deficiency and moderate inbreeding. Genetic diversity was moderate across all populations, as reflected in the values I (0.5220–0.5530), π (0.2415–0.2478), and PIC (0.1914–0.1982). Low genetic differentiation was observed among populations (Fst: 0.0339–0.0509) accompanied by high gene flow (Nm = 4.6658–7.1192), suggesting ongoing genetic exchange between populations. Analysis of Molecular Variance (AMOVA) indicated that most genetic variation occurred within populations. Genetic distance and genetic similarity ranged from 0.0345 to 0.0522 and 0.9491 to 0.9661, respectively, with no significant isolation by distance (Mantel test, R = 0.0793, p = 0.4307). Analysis of the species’ historical population dynamics suggests that P. esculenta may have experienced a substantial population contraction beginning approximately 300 years ago. Overall, the five populations exhibit moderate genetic diversity, though signs of inbreeding and recent population decline may indicate early stages of germplasm degradation. These findings provide important insights for the conservation and sustainable aquaculture of this species. Full article