Search Results (534)

The wet gluten content (WGC) of wheat is a key indicator of wheat-processing quality, and its genetic basis is extremely critical in breeding. This study evaluated the WGC of 207 wheat accessions under three growing seasons from a natural population. Nine quantitative trait loci (QTLs) explained 7.61–15.18% of phenotypic variation in a genome-wide association study (GWAS) using a 660K SNP array. Among them, qWGC6B.2 on chromosome 6BL was consistently detected across multiple environments, accounting for 10.08–12.27% of variation. Incorporating grain transcriptome data led to the identification of TaWGC6B.1 (TraesCS6B02G386700), which is highly expressed in developing endosperm and strongly correlated with WGC. A competitive allele specific PCR (KASP) marker development and validation indicated that the Whaas68366_GG allele significantly enhanced gene expression and WGC. This study identified key genes and molecular markers, providing theoretical and technical support for WGC genetic improvement in wheat (Triticum aestivum L.). Full article

Signal transducer and activator of transcription 2 (STAT2) is a key component of the type I interferon (IFN-I/III) signaling pathway, which is pivotal in host defense against cancer and viral infections and in shaping immune responses. Building on our previously reported conditional Stat2 knockout (KO) mouse, we expand its utility by validating additional tissue-specific models and exploring novel functional contexts. Mice carrying loxP-flanked Stat2 alleles were crossed with CMV-Cre, Cdx2-Cre or CD11c-Cre mice. Deletion of STAT2 was validated by PCR genotyping and western blotting in the relevant tissues. To confirm defective IFN-I signaling with STAT2 deletion, IFN-β stimulation of splenocytes from CMV-Cre Stat2 KO mice showed a lack of induction of canonical IFN-I target genes, confirming functional disruption of the pathway. In vivo, global Stat2 deletion significantly impaired the antitumor efficacy of IFN-β treatment. Similarly, lung fibroblasts isolated from globally deleted Stat2 KO mice showed defective antiviral responses to IFN-β. Tissue-specific Cre models demonstrated selective ablation of STAT2 in target compartments without affecting its expression in non-target tissues. Together, these studies expand our published conditional Stat2 KO findings and highlight the value of this model as a versatile platform for dissecting STAT2-dependent signaling pathways in a tissue- and disease-specific manner. Full article

Background/Objectives: Changes in the physiological activity of transforming growth factor-beta (TGF-β) family caused by genetic variability may significantly affect the phenotype of the musculoskeletal system and, consequently, the risk of sports injuries. This study aimed to investigate whether the TGFBI (rs1442), TGFBR3 (rs1805113 and rs1805117), and MSTN (rs11333758) polymorphisms, either individually or in combination, were associated with susceptibility to muscle injury, anterior cruciate ligament (ACL) rupture, and other injuries. Methods: The study group included 202 physically active Caucasians with reported sport injuries and 133 healthy controls. All the samples were genotyped using real-time polymerase chain reaction (real-time PCR). Results: The results revealed that (1) the TGFBR3 rs1805117 TC genotype was nominally associated with increased ACL injury risk; (2) the MSTN rs11333758 heterozygotes was more frequent in the one injury group (vs controls) and in the ACL group, whereas in the multiple vs. one comparison the over-dominant model suggested lower odds for heterozygotes; and (3) the TGFBI rs1442 CG genotype was nominally associated with lower odds of fractures, dislocations or sprains. In addition, simultaneous analysis of chosen SNPs revealed interactions between TGFBR3 rs1805117 and rs1805113, with a nominal association of the rs1805113 G allele with increased injury risk, as did rs11333758 and rs1805113, with a potential effect of rs11333758 on injury status. However, haplotype analysis of the TGFBR3 SNPs revealed no significant associations. After Bonferroni correction, none of the associations remained statistically significant. Conclusions: The results suggested that carrying specific TGFBI, TGFBR3, and MSTN genotypes may be potentially associated with susceptibility to musculoskeletal injuries in a physically active Caucasians. Full article

Wheat (Triticum aestivum L.) is one of the most important staple crops in the world. Iron (Fe) plays a vital role in the growth and development of wheat as an essential nutrient. Meanwhile, Fe is closely associated with human health, as Fe deficiency anemia can cause fatigue, weakness, heart problems, and so on. In this study, quantitative trait loci (QTLs) for grain Fe content (GFeC) were detected in two populations: a recombinant inbred line (RIL) population with 175 lines derived from a cross between Avocet and Huites (AH population) genotyped with diversity array technology (DArT) and a natural population of 243 varieties (CH population) genotyped by using the 660K single-nucleotide polymorphism (SNP). Three stable QTLs (QGFe.haust-AH-5B, QGFe.haust-AH-6A, and QGFe.haust-AH-7A.2) were identified through QTL mapping with phenotypic variations of 11.55–13.63%, 3.58–9.89%, and 4.81–11.12% in the AH population in four environments. Genetic effects of QGFe.haust-AH-5B, QGFe.haust-AH-6A, and QGFe.haust-AH-7A.2 were shown to significantly increase GFeC by 8.11%, 14.05%, and 5.25%, respectively. One hundred and thirty-three significant SNPs were identified (p < 0.001) through a genome-wide association study (GWAS) for GFeC on chromosomes 1B, 2B, 3A, 3B, 5D, and 7A with phenotypic variations of 5.26–9.88% in the CH population. A novel locus was co-located within the physical interval 689.86 Mb-690.01 Mb in five environments through QTL mapping and GWAS, with one high-confidence gene, TraesCS7A02G499500, which was temporarily designated as TaqFe-7A, involved in GFeC regulation. A Kompetitive allele-specific PCR, KAFe-7A-2, was developed, which was validated in 181 natural populations. Genetic effect analysis revealed that favorable haplotype AA significantly increased GFeC by 4.64% compared to an unfavorable haplotype (p < 0.05). Therefore, this study provides the theoretical basis for cloning the GFeC gene and nutritional fortification breeding. Full article

Background/Objectives: This study evaluates the relationship between UGT1A9 polymorphisms, cardiac biomarker patterns, and clinical presentations in patients admitted to the Pamukkale University Emergency Department with cardiac symptoms. Methods: A total of 207 consecutive patients presenting with chest pain, dyspnea, palpitations, or other cardiac complaints were initially enrolled. Patients with incomplete clinical data or unsuccessful genotyping were excluded prior to analysis, and all remaining samples were included in the final evaluation. UGT1A9 *1, *2, and *3 alleles were genotyped using allele-specific PCR and TaqMan^® assays. Patients were classified into wt/wt, wt/*3, and *3/*3 groups. Statistical analyses included Kruskal–Wallis, Mann–Whitney U, and chi-square tests. Results: Genotype distribution was 64% wt/wt, 32% wt/*3, and 4% *3/*3. CK-MB levels differed significantly across genotypes (p = 0.006), with the highest in wt/*3 carriers. Troponin I levels showed no genotypic differences (p = 0.533). UGT1A9*3 carriers exhibited elevated CK-MB with relatively low Troponin I, suggesting possible statin-associated muscle injury rather than true myocardial necrosis. Conclusions: UGT1A9 polymorphisms, particularly UGT1A9*3, influence CK-MB variability and may confound the assessment of myocardial injury. Troponin I remains unaffected by genotype. Incorporating UGT1A9 pharmacogenetic testing may contribute to a better understanding of biomarker variability and support future research toward personalized therapeutic strategies. Full article

The ε4 allele of the apolipoprotein E (APOE) gene strongly increases Alzheimer’s disease (AD) risk, though its molecular mechanisms remain unclear. AD-associated genetic signals also extend to neighboring genes TOMM40 and APOC1, suggesting a complex cis-regulatory landscape. To investigate chromatin architecture and its impact on gene regulation across this region, we performed chromosome conformation capture in human cell lines and postmortem brain tissues, consistently identifying TOMM40–APOE and APOE–APOC1 interactions. We further developed a digital PCR assay to quantify APOE–APOC1 interaction strength and measured APOC1 mRNA via RT-qPCR. Enhanced chromatin interaction correlated with elevated APOC1 transcription in AD specimens. Genotypic analysis showed that ε3/ε4 carriers had strong chromatin interaction and transcriptional activation, whereas ε4/ε4 homozygotes exhibited minimal chromatin remodeling despite similar APOC1 expression, suggesting a decoupling of chromatin architecture and transcriptional output. These findings underscore the interplay of AD status, APOE genotype, and locus-specific chromatin dynamics in disease susceptibility. Integration of 3D genome topology with transcriptomic profiling offers a framework to study APOE-related disorders and supports broader application across neurodegenerative loci for genotype-guided therapy development. Full article

Although best known as a major parasite of sheep and goats, the blood-feeding abomasal nematode Haemonchus contortus can also infect cattle and buffaloes under the mixed-grazing Mediterranean conditions prevalent in Greece. The objectives of this study were as follows: (i) to determine the prevalence of H. contortus infections in dairy and beef cattle and buffaloes in Greece through an abattoir survey, (ii) to evaluate potential host- and farm-related risk factors including age, sex, management system, cattle productive orientation, and the co-existence of cattle and buffaloes on the occurrence of haemonchosis, and (iii) to assess the likelihood of detecting homozygous benzimidazole (BZ)-resistant H. contortus in large ruminant populations in relation to these determinants. A total of 213 abomasa (115, 55, and 43 from dairy, beef cattle, and buffaloes, respectively) were examined. A structured questionnaire provided additional animal- and farm-level information. Haemonchus-like helminths were collected and molecularly identified at the species level by amplifying a 321 bp fragment of the internal transcribed spacer 2 region of nuclear DNA. An allele-specific multiplex PCR, targeting codon 200 of the β-tubulin gene, was applied to detect BZ-resistant alleles. The prevalence of H. contortus infection was 21.2% in cattle and 69.8% in buffaloes. In cattle, multivariable analysis revealed that mixed-species farming (i.e., farms where cattle were the primary species and buffaloes were kept in smaller numbers), productive orientation, and slaughter age were significant predictors of increased H. contortus infection. Controversially, none of these factors were significantly associated with infection in buffaloes. Finally, multivariable modelling suggested that resistance patterns varied by host species, being more prevalent in intensively managed, older cattle, yet less common among older buffaloes and in herds where both species coexisted. Full article

Background: Urothelial bladder carcinoma (UBC) is a disease that lacks robust non-invasive laboratory biomarkers. Recently, urine liquid biopsy has emerged as a promising tool for diagnosis and surveillance of patients with these tumors. The aim of this study was to evaluate the diagnostic potential of a urinary tumor DNA detection panel, which included eight common point mutations in TERT, GPR126, FGFR3, and PIK3CA genes, in UBC. Methods: The study included patients with histologically confirmed UBC (n = 88) and patients with cystitis, bladder leiomyomas, or other non-malignant conditions (control group; n = 72). DNA was extracted from whole urine specimens. ddPCR analysis was performed using the Bio-Rad QX200 AutoDG ddPCR system. Results: Urinary tumor DNA detection panel demonstrated a sensitivity of 78.4% and a specificity of 100% (AUC−ROC = 0.892). Detection rates for the analyzed mutations were the following: 54.5%, 37.5%, 28.4%, and 38.6% for TERT, GPR126, FGFR3, and PIK3CA, respectively. Pairwise comparisons of mutant allele fractions (MAFs) for samples simultaneously positive for ≥2 mutations revealed an absence of significant differences (p > 0.05), except for the pair of FGFR3 vs. PIK3CA (p = 0.03). MAFs were not associated with any clinical and demographic features (p > 0.05), with the only exception being the tumor size: patients with tumors larger than 2.16 cm³ had higher MAFs than the rest (23.4 [1.8; 46.3] vs. 1.6 [0; 24.6] %, respectively, p = 0.02). Conclusions: Upon further validation, the presented tumor DNA detection panel for ddPCR might become a useful tool for diagnostic purposes in UBC. Full article

Gray mold, caused by Botrytis cinerea, is a devastating disease of strawberry, with petal abscission rate (PAR) being a critical disease-avoidance trait. Rapid petal abscission removes a key infection site for the pathogen, thereby reducing disease incidence. To dissect the genetic basis of PAR, a segregating F₁ population was constructed from a cross between ‘Benihoppe’ (rapid abscission) and ‘Sweet Charlie’ (slow abscission). Utilizing BSR-Seq analysis of extreme bulks, five high-confidence quantitative trait loci (QTLs) were identified on chromosomes Fvb2-2, Fvb4-4, and Fvb6-3. These QTLs encompassed 672 candidate genes, with enrichment in “Plant hormone signal transduction” pathway. Integrated analysis of gene expression and SNPs identified 16 candidate genes, including those involved in flowering time (e.g., ELF3, HUA2 and AGL62) and plant hormone (e.g., ANT, RTE (ethylene), NDL2, FPF1 (auxin), and CYP707A7, ABF2 (abscisic acid) signaling, as well as calcium transport (ACA1, ECA3). Fourteen Kompetitive Allele-Specific PCR (KASP) markers were developed from candidate genes, with four markers showing significant correlations with PAR. This study provides the first genetic mapping of PAR in strawberry, revealing candidate genes and molecular markers that will facilitate the breeding of cultivars with improved gray mold resistance through enhanced petal abscission. Full article

Background: Colorectal cancer is a major public health burden in Hungary, with one of the highest incidence and mortality rates in Europe. Long non-coding RNAs (lncRNAs) have emerged as key regulators in tumorigenesis, but population-specific genetic associations remain understudied. This study aimed to investigate whether single-nucleotide polymorphisms (SNPs) in lncRNA genes are associated with colorectal cancer susceptibility, with attention to tumor site- and sex-specific effects. Methods: We conducted an exploratory case–control study involving 91 Hungarian participants (38 patients with colorectal lesions and 53 controls). Genotyping of six SNPs located in HOTAIR, PTCSC3, H19, CCAT1, and CCAT2 was performed using TaqMan-based qPCR. Associations were tested using allele frequency analysis, different genotype models (dominant, recessive, additive), and binary logistic regression, including stratified analyses by tumor subtype and sex. Results: While no significant associations were found in the unadjusted overall case–control comparisons, logistic regression including sex revealed that HOTAIR rs12826786 and rs7958904 were significantly associated with a reduced risk of colorectal lesions, particularly in females (p = 0.022 and p = 0.043). Analyses by tumor localization revealed that H19 rs2839698 and PTCSC3 rs944289 were more frequent in colon than in rectal tumors (p = 0.017 and p = 0.035) and were associated with a reduced risk of rectal tumors (OR = 0.18 and OR = 0.20), suggesting that these variants may influence tumor site rather than overall susceptibility. None of the results remained significant after Bonferroni correction. Conclusions: Our findings suggest that these selected lncRNA-related SNPs may contribute to colorectal cancer risk in a sex- and site-specific manner. These preliminary results warrant further validation in larger, independent cohorts and functional studies. Full article

Background: Rapid antimicrobial susceptibility testing (RAST) allows early detection of resistance directly from positive blood cultures, potentially improving outcomes in bloodstream infections (BSIs). We evaluated the performance of EUCAST RAST for Gram-negative ESKAPEEc pathogens and characterized carbapenemase genes in carbapenem-resistant Klebsiella pneumoniae (CRKP). Methods: A total of 354 positive blood cultures were screened, including 51 monomicrobial Gram-negative ESKAPEEc isolates. RAST results at 4, 6, 8, and 16–20 h were compared with standard antimicrobial susceptibility testing (AST) obtained using the BD Phoenix™ system. Categorical agreement (CA) and error frequency were calculated. Multiplex PCR and Sanger sequencing were performed on 15 CRKP isolates to identify carbapenemase genes and allelic variants. Results: 51 Gram-negative ESKAPEEc isolates met the inclusion criteria for RAST (15 E. coli, 19 K. pneumoniae, 11 A. baumannii, and 6 P. aeruginosa). Overall performance varied markedly by species and antibiotic. E. coli showed frequent unreadable or ATU zones at early timepoints and wide CA variability (50–100%), with high very major error (VME) rates for AMP, TZP, and CAZ, particularly at 6–8 h. K. pneumoniae displayed consistently high CA (mostly 100%) for carbapenems, CAZ, and TZP. A. baumannii demonstrated excellent agreement (100% for most agents), except for GEN at 6–8 h. P. aeruginosa could be evaluated only at 16–20 h, showing high CA for AMK, CAZ, and CIP; lower CA for MEM (83%); non-calculable CA for IMI due to universal ATU readings; and a CA value of 0% for TZP due to the predominance of the ATU results. VMEs ranged from 0% to 26.1% across species and reading times, but carbapenems did not generate VMEs. Molecular analysis revealed bla_KPC in 66.7%, bla_NDM in 46.7%, and bla_OXA-48 in 33.3% of isolates, with co-occurrence in several strains. Sequencing identified bla_KPC-2 and bla_NDM-1 as the predominant variants, with one isolate harboring bla_NDM-5. Conclusions: EUCAST RAST markedly accelerates susceptibility reporting from positive blood cultures, but its accuracy is species- and time-dependent. Performance was excellent for K. pneumoniae (including CRKP) and A. baumannii and acceptable for P. aeruginosa at 16–20 h. In contrast, E. coli showed frequent ATU results at early timepoints and high ME/VME rates, making readings before 8 h unreliable for clinical decisions. Overall, RAST can effectively support rapid antimicrobial stewardship when species-specific limitations are recognized, and early-timepoint results are interpreted with caution. Full article

Background: Detecting low-frequency mutations is crucial for predicting prognosis and monitoring minimal residual disease (MRD) in acute myeloid leukemia (AML). However, the presence of abundant wild-type sequences hinders the detection of rare mutant alleles. We present a highly sensitive method called ACE (Amplifying–Cleaving–Enriching) to selectively enrich mutant sequences. Methods: ACE includes three steps: (1) initial PCR amplification using biotin-labeled primers, (2) cleavage of wild-type sequences with a specific restriction enzyme, and (3) enrichment of undigested mutant alleles via streptavidin-labeled magnetic beads. Results: Using two rounds of ACE, we achieved over 80,000-fold enrichment of mutant sequences carrying FLT3-TKD, enabling the detection of mutant alleles at levels as low as 0.0001% in AML patient blood samples. Additionally, the ACE method can be adapted to nearly any driver mutation by introducing wild-type-specific restriction sites through PCR with mismatched primers, which has been validated in the IDH1 mutation. Furthermore, the ACE method can be flexibly integrated into conventional detection techniques including Sanger sequencing, quantitative real-time PCR, allele-specific PCR, and even with advanced techniques like droplet digital PCR. Conclusions: ACE significantly enhances the sensitivity of existing techniques for rare mutation detection and holds potential for broad clinical applications. Full article

Background/Objectives: Epilepsy is characterized by recurrent, unprovoked, self-limiting seizures of genetic, acquired, or unknown origin. It affects more than 50 million people worldwide. The prevalence in Peru is 11.9–32.1 per 1000 people. Our objective was to describe the association between CYP2C9 and CYP2C19 genetic polymorphisms and adverse reactions induced by antiseizure medications among Peruvian patients with epilepsy. Methods: A descriptive observational study was conducted on Peruvian patients with epilepsy. Non-probability, non-randomized, purposive sampling was carried out through consecutive inclusion. Genomic DNA was obtained from venous blood samples. Genotypes were determined by real-time PCR using specific TaqMan probes to identify the alleles of interest. Results: In total, 89 Peruvian patients with epilepsy were recruited at the Alberto Sabogal Sologuren National Hospital-ESSALUD: 45 were male (23.6 ± 10.0 years) and 44 were female (24.0 ± 12.4 years). The observed frequencies for CYP2C9*2, CYP2C9*3, CYP2C19*2, CYP2C19*3, and CYP2C19*17 were 0.034 (T allele), 0.034 (C allele), 0.14 (A allele), 0.00 (A allele), and 0.03 (T allele), respectively. Patients with intermediate and poor metabolic phenotypes of CYP2C9 and CYP2C19 had a significantly higher risk of adverse drug reactions (ADRs) (OR = 3.75; 95%CI: 1.32–10.69; p = 0.013), compared with normal metabolizers. Polytherapy was a predictor increasing the likelihood of ADRs (OR = 4.33; 95% CI: 1.46–12.80; p = 0.008). Conclusions: In this cohort of Peruvian patients with epilepsy, the reduced-function alleles CYP2C9*2, CYP2C9*3, and CYP2C19*2, associated with decreased metabolic activity, were significantly linked to an increased risk of adverse drug reactions induced by antiseizure medications. Polytherapy further heightened this risk. Collectively, these findings highlight the clinical relevance of CYP2C9 and CYP2C19 genotyping to enhance the safety of antiseizure pharmacotherapy in Latin American settings, where pharmacogenomic evidence remains limited. Full article

Hypoxia is a critical environmental stressor in aquaculture, significantly affecting the survival and growth performance of cultured fish. To explore the genetic basis of hypoxia tolerance in grass carp (Ctenopharyngodon idella), we integrated genome-wide association analysis (GWAS) and multi-tissue transcriptome profiling. A total of 2000 grass carp were subjected to hypoxic stress, from which the 150 most hypoxia-intolerant (HI) and 150 most hypoxia-tolerant (HT) individuals were selected based on the time to loss of equilibrium (LOE). GWAS using 3,730,919 SNPs and 851,595 InDels identified 21 SNPs and 6 InDels associated with hypoxia tolerance. Two SNPs on chromosomes 10 and 13 reached genome-wide significance, accounting for 2.7% and 4.8% of the phenotypic variance explained (PVE), respectively. Validation of identified SNPs was performed using kompetitive allele-specific PCR (KASP) analysis. Candidate genes within ±50 kb of these variants were enriched in steroid biosynthesis, insulin signaling, and glycosphingolipid biosynthesis pathways. Transcriptomic analysis of six tissues (brain, gill, intestine, kidney, liver, and spleen) revealed 1620, 1221, 796, 246, 210, and 58 differentially expressed genes (DEGs) in the HT group compared to the HI group, respectively. DEGs in the brain were primarily enriched in steroid metabolic processes and angiogenesis regulation, while those in kidney and spleen DEGs were associated with oxygen transport and erythrocyte development. Integrated analysis of GWAS and transcriptome data identified 16 shared genes, including usf1 and trpv4. These findings reveal key genomic loci and molecular pathways underlying hypoxia tolerance in grass carp, providing valuable markers for future selective breeding programs. Full article

Background: Dopaminergic signaling is a key mechanism in behavioral regulation and impulse control. While DAT1 promoter methylation has been linked to behavioral dysregulation in clinical groups, its role in high-functioning populations such as elite athletes remains unclear. Objectives: To compare DAT1 promoter methylation, DAT1 VNTR genotype, and impulsivity between elite combat sport athletes and matched controls, and to assess potential gene–environment interactions. Methods: The study included 209 male participants (100 elite combat athletes, 109 controls). Methylation of 33 CpG sites within the DAT1 promoter was quantified from peripheral blood DNA. DAT1 VNTR genotypes were determined via PCR and gel electrophoresis. Impulsivity was assessed using the Barratt Impulsiveness Scale (BIS-11). Group differences and interactions were analyzed using analysis of variance (ANOVA), non-parametric tests, and post hoc comparisons. Results: Athletes displayed significantly higher overall DAT1 promoter methylation and lower impulsivity scores across all BIS-11 subscales compared with controls. A significant group × genotype interaction for methylation indicated genotype-specific epigenetic differences by athletic status. No differences in VNTR genotype or allele frequencies were observed. Conclusions: Elevated DAT1 promoter methylation in elite athletes may be associated with enhanced behavioral control, potentially reflecting neurobiological adaptations to high-intensity training. These results highlight the need to integrate genetic and epigenetic perspectives in sports science. Longitudinal and multi-omics studies are warranted to determine causal links and evaluate the potential of epigenetic markers as indicators of performance-related traits. Full article