Search Results (17,352)

This study sought to evaluate the genetic variations of the ovocalyxin-32 gene and its association with egg quality traits in indigenous chicken populations, focusing on exons 1 and 6. Genotype frequencies of SNPs (G/T and A/G) within these exons were assessed for their conformity to the Hardy–Weinberg equilibrium (HWE) across several strains. While most strains exhibited close adherence to HWE expectations, some like light-brown and gray strains indicated substantial discrepancies, particularly for the TT genotype, which points towards the possible effects of genetic drift as well as selection pressures. This study also analyzed the influence of such SNPs on egg quality parameters. A thinner eggshell, reduced shell weight, and decreased breaking strength were associated with the G/T SNP in exon 1, suggesting a likely negative effect on egg quality in T allele carriers. Conversely, the AG genotype displayed better performance in shell thickness, weight and egg weight in the A/G SNP in exon 1, whilst yolk height was best improved by the AA genotype compared to breaking strength. For instance, in exon 6, the A/G SNP enhanced the shell and yolk quality among AG genotypes, while the CC genotype resulted in better eggshell characteristics with enlarged yolks because the C/T SNP was linked. Nonetheless, there were no significant deviations from the HWE despite these associations, which suggested that most breeds had a stable genetic background. Further, considering SNPs’ additive and dominant effects in this research, it was indicated that additive effects account for phenotypic expressions given by the G/T SNP located at exon 1. In contrast, significant additive and dominant effects were observed under the A/G SNP situated at the exon. Generally, it therefore could be concluded from this study that specific SNPs within the ovocalyxin-32 gene may act as good markers for marker-assisted selection (MAS) that can improve desired characteristics—such as those of egg quality—in indigenous chicken breeds. This study demonstrated that both additive and dominance effects must be taken into account when performing genetic analyses, thereby emphasizing the complexity of phenotypic variation caused by genetic mechanisms in native chicken races. Full article

This study investigated the potential role of specific single-nucleotide polymorphisms (SNPs) in the genes Astrotactin 1 (ASTN1), EBF Transcription Factor 1 (EBF1), Eukaryotic Elongation Factor, Selenocysteine-tRNA Specific (EEFSEC), Microtubule-Associated Serine/Threonine Kinase 1 (MAST1), and Tumor Necrosis Factor Alpha (TNF-α) to assess whether these genetic variants contribute to the risk of spontaneous preterm birth (sPTB). A case-control study was conducted involving 573 women from Croatia and Slovenia: 248 with sporadic sPTB (positive personal and negative family history of sPTB before 37 weeks’ gestation), 44 with familial sPTB (positive personal and family history of sPTB before 37 weeks’ gestation), and 281 control women. The analysis of ASTN1 rs146756455, EBF1 rs2963463, EBF1 rs2946169, EEFSEC rs201450565, MAST1 rs188343966, and TNF-α rs1800629 SNPs was performed using TaqMan real-time PCR. p-values were Bonferroni-adjusted for multiple comparisons. EBF1 SNP rs2963463 was significantly associated with sPTB (p adj = 0.03). Women carrying the CC genotype had a 3–4-times lower risk of sPTB (p adj < 0.0001). In addition, a significant difference in the frequency of the minor C allele was observed when comparing familial sPTB cases with controls (p adj < 0.0001). All other associations were based on unadjusted p-values. The minor T allele of EBF1 SNP rs2946169 was more frequent in sPTB cases overall than in controls, especially in sporadic sPTB (p = 0.045). Similarly, the CC genotype of ASTN1 SNP rs146756455 was more frequent in sporadic sPTB cases compared to controls (p = 0.019). Finally, the TNF-α SNP rs1800629 minor A allele and AA genotype were more common in the familial sPTB group compared to sporadic sPTB and controls (p < 0.05). The EBF1 SNP rs2963463 polymorphism showed a protective effect in the pathogenesis of sPTB, particularly in women carrying the CC genotype. Moreover, EBF1 SNP rs2946169 and ASTN1 SNP rs146756455, as well as TNF-α SNP rs1800629, were associated with an increased risk of sPTB, representing suggestive potential risk factors for sporadic and familial sPTB, respectively. Full article

Background: Hereditary transthyretin-related amyloidosis is a clinically heterogeneous autosomal dominant disease caused by pathogenic variants in the TTR gene (hATTR amyloidosis). Objective: The current study describes the demographic, clinical, and genetic characteristics of patients with suspected hATTR amyloidosis. Methods: This study is part of the “Hereditary transthyretin-related amyloidosis and longitudinal monitoring of TTR-positive patients” (TRAMmoniTTR) study. This study included 3167 participants, along with their clinical details. Principal component (PC) analysis was used to analyze their clinical symptomatology. Next-generation sequencing of the TTR gene was performed and genotype–phenotype relationships were investigated. We compared the demographic and clinical characteristics using the principal components (PCs) and also compared participants with and without the TTR pathogenic variants. Results: We identified five main clinical phenotypes out of 22 single symptoms that explained 49% of the variation. The first two PCs referred to polyneuropathy and cardiomyopathy. We found significant differences between gender and PC-polyneuropathy and PC-cardiomyopathy, with male over-representation in the higher quantiles of PC-polyneuropathy and male under-representation in the lowest quantiles of PC-cardiomyopathy. We identified 92 participants with hATTR (3%), exhibiting 17 unique heterozygous TTR variants. The p.Val50Met variant was the most frequent. Furthermore, 503 participants (20%) were identified with ATTR and no relevant TTR variants (ATTRwt). We detected significant differences between the ATTRwt and hATTR groups, with male gender predominance in only the ATTRwt group and a positive family history of polyneuropathy and/or cardiomyopathy among the hATTR participants. Conclusions: The current clinical and genetic characterization of this cohort serves as a foundation for further longitudinal monitoring and assessment. Full article

Multiple repetitive sequences of authentic genes commonly exist in fungal genomes. AT-biased genotypes of Ophiocordyceps sinensis have been hypothesized as repetitive pseudogenes in the genome of Hirsutella sinensis (GC-biased Genotype #1 of O. sinensis) and are generated through repeat-induced point mutation (RIP), which is charactered by cytosine-to-thymine and guanine-to-adenine transitions, concurrent epigenetic methylation, and dysfunctionality. This multilocus study examined repetitive sequences in the H. sinensis genome and transcriptome using a bioinformatic approach and revealed that 8.2% of the authentic genes had repetitive copies, including various allelic insertions/deletions, transversions, and transitions. The transcripts for the repetitive sequences, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in the H. sinensis transcriptome, resulting in changes in the secondary protein structure and functional specification. Multiple repetitive internal transcribed spacer (ITS) copies containing multiple insertion/deletion and transversion alleles in the genome of H. sinensis were GC-biased and were theoretically not generated through RIP mutagenesis. The repetitive ITS copies were genetically and phylogenetically distinct from the AT-biased O. sinensis genotypes that possess multiple transition alleles. The sequences of Genotypes #2–17 of O. sinensis, both GC- and AT-biased, were absent from the H. sinensis genome, belong to the interindividual fungi, and differentially occur in different compartments of the natural Cordyceps sinensis insect–fungi complex, which contains >90 fungal species from >37 genera. Metatranscriptomic analyses of natural C. sinensis revealed the transcriptional silencing of 5.8S genes in all C. sinensis-colonizing fungi in natural settings, including H. sinensis and other genotypes of O. sinensis. Thus, AT-biased genotypes of O. sinensis might have evolved through advanced evolutionary mechanisms, not through RIP mutagenesis, in parallel with GC-biased Genotype #1 of H. sinensis from a common genetic ancestor over the long course of evolution. Full article

Hereditary thoracic aorta diseases (HTADs) are a heterogeneous group of rare disorders whose major manifestation is represented by aneurysm and/or dissection frequently located at the level of the ascending thoracic aorta. The diseases have an insidious evolution and can be encountered as an isolated manifestation or can also be associated with systemic, extra-aortic manifestations (syndromic HTADs). Along with the development of molecular testing technologies, important progress has been made in deciphering the heterogeneous etiology of HTADs. The aim of this study is to identify the genetic variants associated with a group of patients who presented clinical signs suggestive of a syndromic form of HTAD. Genetic testing based on next-generation sequencing (NGS) technology was performed using a gene panel (Illumina TruSight Cardio Sequencing Panel) or whole exome sequencing (WES). In the majority of cases (8/10), de novo mutations in the FBN1 gene were detected and correlated with the Marfan syndrome phenotype. In another case, a known mutation in the TGFBR2 gene associated with Loeys–Dietz syndrome was detected. Two other pathogenic heterozygous variants (one de novo and the other a known mutation) in the SLC2A10 gene (compound heterozygous genotype) were identified in a patient diagnosed with arterial tortuosity syndrome (ATORS). We presented the genotype–phenotype correlations, especially related to the clinical evolution, highlighting the particularities of each patient in a family context. We also emphasized the importance of genetic testing and patient monitoring to avoid acute aortic events. Full article

Introduction: Obesity is characterized by low-grade chronic inflammation, which can be modulated by lipid mediators derived from omega-3 (n-3) polyunsaturated fatty acids (PUFA). Obesity is a multifactorial disease, where genetic and environmental factors strongly interact to increase its development. In this context, the FADS1 gene encodes the delta-5 desaturase protein, which catalyzes the desaturation of PUFA. The rs174547 genetic variant of FADS1 has been associated with alterations in lipid metabolism, particularly with decreases in eicosapentaenoic acid (EPA) and arachidonic acid (AA) concentrations. Objective: To analyze the effect of an n-3-supplemented diet on the fatty acid profile and composition in red blood cells (RBCs) of obese subjects carrying the rs174547 variant of the FADS1 gene. Methodology: Seventy-six subjects with obesity were divided into two groups: omega-3 (1.5 g of n-3/day) and placebo (1.5 g of sunflower oil/day). The dietary intervention consisted of a four-month follow-up. Anthropometric, biochemical, and dietary variables were evaluated monthly. The total fatty acid profile in RBC was determined using gas chromatography. The rs174547 variant was analyzed through allelic discrimination. Results: The n-3 index (O3I) increased at the end of the intervention in both groups. Subjects carrying the CC genotype showed significant differences (minor increase) in n-6, n-3, total PUFA, EPA, DHA, and the O3I in RBCs compared to TT genotype carriers in the n-3 group. Conclusions: The diet supplemented with EPA and DHA is ideal for providing the direct products that bypass the synthesis step affected by the FADS1 rs174547 variant in subjects carrying the CC genotype. The O3I confirmed an increase in n-3 fatty acids in RBCs at the end of the intervention. Full article

Brachiaria forages are known to be drought-tolerant as mature plants, but no information about drought tolerance at the seed germination stage is currently available. This study aimed to determine the impacts of different temperature and moisture conditions on the seed germination characteristics of five Brachiaria genotypes. Brachiaria seeds were germinated under constant temperatures of 5 °C–45 °C at increments of 5 °C. Within each temperature treatment, five osmotic treatments (0 MPa, −0.1 MPa, −0.3 MPa, −0.5 MPa, and −0.7 MPa) were applied, and germination was recorded daily for 20 days. The results showed that seed germination in all Brachiaria species was significantly negatively impacted (p < 0.05) by osmotic stress as well as by high and low temperatures. For all species, germination only occurred between 15 and 40 °C. Under optimum moisture conditions (0 MPa), the optimum germination temperatures for B. humidicola were 15 to 35 °C, for B. brizantha and B. nigropedata, they were 15 to 20 °C, for B. decumbens, they were 15 to 25 °C, and for the hybrid Brachiaria species, the optimum germination temperature was only 20 °C. In all species, seed germination decreased as moisture conditions became more limiting. Only B. humidicola germinated optimally at a high temperature (35 °C). At these temperatures, the species had more than 82% germination when moisture was not a limiting factor (0 MPa), but at low osmotic stress conditions (−0.1 MPa) at 30 °C, the germination of this species decreased to 67%. In conclusion, the results from this study indicate that the seed germination and early seedling establishment stages of Brachiaria grasses are only moderately tolerant to drought stress. Further work on early seedling responses to temperature and moisture stresses is needed to quantify early seedling responses to these stresses and to develop more detailed planting time guidelines for farmers. Full article

The genotype-by-environment interaction (G × E) might have crucial impacts on the performance and fitness of agricultural species, such as Pacific whiteleg shrimp (Litopenaeus vannamei). This study explores how enhancements in management practices can counteract G × E effects on growth traits. We analyzed a selectively bred population of whiteleg shrimp spanning the latest two generations, encompassing 259 full-sib and half-sib families with 40,862 individual shrimp, measured for body weight and total length. Our analysis revealed moderate genetic correlations (0.60–0.65) between trait expressions in pond and tank environments, a significant improvement compared to earlier generations. Employing the average information-restricted maximum likelihood (REML) approach in mixed model analysis showed significant differences in heritability (h²) estimates between the two environments; however, the extent of these differences varied by trait (h² = 0.68 in pond vs. 0.37 in tank for weight, and 0.41 vs. 0.67 for length). Our results indicate that G × E effects on growth traits in this population of L. vannamei were moderate but biologically significant. Consistent with our previous estimates in this population, genetic correlations between body weight and total length remained high (close to one) in pond and tank environments. The present findings collectively demonstrate that management improvements targeting stocking density, aeration, water quality, feeds, and feeding regimes mitigated the G × E effects on two economically significant traits in this population of whiteleg shrimp. Full article

The virulence analysis of Puccinia stiiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is essential for predicting and managing the disease epidemic in Southwest China, where the wheat cultivation has significantly reduced in the past few decades due to the impact of this disease. From 2020 to 2021, 196 Pst isolates were collected from Guizhou, Yunnan, and Sichuan. The virulence and race assessments were conducted using Chinese differential genotypes. Additionally, the resistance expression of 102 wheat lines was evaluated in 2021 in two disease nurseries located in Ningnan and Jiangyou. All the 45 Pst isolates from Guizhou and Yunnan belonged to pathogroup Hybrid 46, with 36 identified as race CYR32. Among the 69 isolates from the Liangshan Prefecture, 67 belonged to the Hybrid 46 group, while the remaining two were identified as race CYR34 in the G-22 group. Furthermore, all 79 isolates from the western Sichuan Basin belonged to the G-22 group, with 54 identified as race CYR34. The diversity indices of the Pst populations from Guizhou, Sichuan, and Yunnan exhibited a sequential decline. Virulence variation among the Pst populations from Yunnan, Guizhou, and the Ganzi-Liangshan region was minimal; however, significant virulence differences were observed when these populations were compared to those from the western Sichuan Basin. Results from disease nurseries indicated that Pst virulence was notably stronger in Ningnan compared to that in Jiangyou. The Sichuan Basin exhibits a notable diversity in Pst virulence, coupled with a more frequent genetic exchange occurring between the Liangshan Prefecture and the Yunnan-Guizhou Plateau. This information is essential for developing effective management strategies to mitigate the impact of wheat stripe rust in this region. Full article

A lower mortality rate from coronary artery disease (CAD) and a more favourable lipid profile have been reported in Afro-Caribbeans compared with people of European ancestry. The aim of this study was to determine whether common lipid variants identified in other populations are associated with lipid levels and CAD in Afro-Caribbeans. We studied 705 Afro-Caribbeans (192 with CAD) who were genotyped for 13 lipid-associated variants. We calculated three polygenic risk scores (PRSs) for elevated LDL (LDL-PRS), decreased HDL (HDL-PRS), and elevated triglycerides (TG-PRS). LDL-PRS, HDL-PRS, and TG-PRS were associated with LDL, HDL, and TG levels, respectively. The LDL-PRS was positively associated with LDL > 2.6 mmol/L and with LDL > 3.0 mmol/L with ORs (odds ratios) of 1.33 (95% confidence interval (CI) = 1.14–1.56) and 1.40 (CI = 1.21–1.62), respectively. The HDL-PRS was associated with a low HDL category (HDL < 1.03 mmol/L) with an OR of 1.3 (CI = 1.04–1.63) and inversely associated with a high HDL category (HDL > 1.55 mmol/L) with an OR of 0.79 (CI = 0.65–0.96). The LDL-PRS was positively associated with CAD after adjustment for age, gender, hypertension, diabetes, and smoking with an OR of 1.27 (CI = 1.06–1.51) but not the HDL-PRS nor the TG-PRS. Results of the present study indicate that common lipid variants are associated with lipid levels and prevalent CAD in Afro-Caribbeans. Full article

Spotted sea bass (Lateolabrax maculatus) is an important marine economic fish in China, ranking third in annual production among marine fish. However, a declined growth rate caused by germplasm degradation has severely increased production costs and reduced economic benefits. There is an urgent need to develop the fast-growing varieties of L. maculatus and elucidate the genetic mechanisms underlying growth traits. Here, whole-genome resequencing technology combined with extreme phenotype genome-wide association analysis (XP-GWAS) was used to identify candidate markers and genes associated with growth traits in L. maculatus. Two groups of L. maculatus, consisting of 100 fast-growing and 100 slow-growing individuals with significant differences in body weight, body length, and carcass weight, underwent whole-genome resequencing. A total of 4,528,936 high-quality single nucleotide polymorphisms (SNPs) were used for XP-GWAS. These SNPs were evenly distributed across all chromosomes without large gaps, and the average distance between SNPs was only 175.8 bp. XP-GWAS based on the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (Blink) and Fixed and random model Circulating Probability Unification (FarmCPU) identified 50 growth-related markers, of which 17 were related to body length, 19 to body weight, and 23 to carcass weight. The highest phenotypic variance explained (PVE) reached 15.82%. Furthermore, significant differences were observed in body weight, body length, and carcass weight among individuals with different genotypes. For example, there were highly significant differences in body weight among individuals with different genotypes for four SNPs located on chromosome 16: chr16:13133726, chr16:13209537, chr16:14468078, and chr16:18537358. Additionally, 47 growth-associated genes were annotated. These genes are mainly related to the metabolism of energy, glucose, and lipids and the development of musculoskeletal and nervous systems, which may regulate the growth of L. maculatus. Our study identified growth-related markers and candidate genes, which will help to develop the fast-growing varieties of L. maculatus through marker-assisted breeding and elucidate the genetic mechanisms underlying the growth traits. Full article

Methotrexate (MTX) is an anti-folate chemotherapeutic agent that is considered to be a gold standard in Acute Lymphoblastic Leukemia (ALL) therapy. Nevertheless, toxicities induced mainly due to high doses of MTX are still a challenge for clinical practice. MTX pharmacogenetics implicate various genes as predictors of MTX toxicity, especially those that participate in MTX intake like solute carrier family 19 member 1 (SLC19A1). The aim of the present study was to evaluate the association between SLC19A1 polymorphisms and its regulatory miRNAs with MTX toxicity in children with ALL. A total of 86 children with ALL were included in this study and were all genotyped for rs2838958, rs1051266 and rs1131596 SLC19A1 polymorphisms as well as the rs56292801 polymorphism of miR-5189. Patients were followed up (48, 72 and 96 h) after treatment with MTX in order to evaluate the presence of MTX-associated adverse events. Our results indicate that there is a statistically significant correlation between the rs1131596 SLC19A1 polymorphism and the development of MTX-induced hepatotoxicity (p = 0.03), but there is no significant association between any of the studied polymorphisms and mucositis or other side effects, such as nausea, emesis, diarrhea, neutropenia, skin rash and infections. In addition, when genotype TT of rs1131596 and genotype AA of rs56292801 are both present in a patient then there is a higher risk of developing severe hepatotoxicity (p = 0.0104). Full article

Salmonellosis is a zoonotic infection that has a major impact on human health; consuming contaminated pork products is the main source of such infection. Vaccination responses to classic vaccines have been unsatisfactory; that is why peptide subunit-based vaccines represent an excellent alternative. Immunopeptidomics was used in this study as a novel approach for identifying antigens coupled to major histocompatibility complex class II molecules. Three homozygous individuals having three different haplotypes (Lr-0.23, Lr-0.12, and Lr-0.21) were thus selected as donors; peripheral blood macrophages were then obtained and stimulated with Salmonella typhimurium (MOI 1:40). Although similarities were observed regarding peptide length distribution, elution patterns varied between individuals; in total, 1990 unique peptides were identified as follows: 372 for Pig 1 (Lr-0.23), 438 for Pig 2 (Lr.0.12) and 1180 for Pig 3 (Lr.0.21). Thirty-one S. typhimurium unique peptides were identified; most of the identified peptides belonged to outer membrane protein A and chaperonin GroEL. Notably, 87% of the identified bacterial peptides were predicted in silico to be elution ligands. These results encourage further in vivo studies to assess the immunogenicity of the identified peptides, as well as their usefulness as possible protective vaccine candidates. Full article

Hypertensive disorders of pregnancy (HDP) are a great danger. A previous GWAS found a relationship between rs259983 of the ZNF831 gene and HDP, such as for chronic hypertension (CHTN) and preeclampsia (PE). We conducted the case-control study to determine the association between rs259983 of the ZNF831 gene and HDP in women with Gestational Diabetes Mellitus (GDM). For target genotyping, we developed primers and TaqMan probes. In analyzing the population, we did not manage to find a relationship between PE and rs259983 of the ZNF831 gene. Additional study of women with PE and PE superimposed on CHTN (SIPE) establishes an association between rs259983 of the ZNF831 gene only with SIPE. Carriers of CC genotypes have been discovered to have a 5.05 times higher risk of SIPE development in women with GDM. Full article

The objective of this study is to assess the influence of genetic polymorphisms in DGAT1, LEP, and SCD1 on the oxidative stress biomarkers and bioactive protein levels in Hereford bulls. A total of sixty-eight bulls were analyzed at 22 months of age to assess growth metrics and carcass quality, with a focus on polymorphisms in these genes. The key markers of oxidative stress, including malondialdehyde (MDA), and the activities of antioxidant enzymes such as glutathione reductase (GluRed), glutathione peroxidase (GPx), and superoxide dismutase (SOD) were measured, alongside bioactive compounds like taurine, carnosine, and anserine. The results show that the TT genotype of DGAT1 is linked to significantly higher MDA levels, reflecting increased lipid peroxidation, but is also associated with higher GluRed and GPx activities and elevated levels of taurine, carnosine, and anserine, suggesting an adaptive response to oxidative stress. The LEP gene analysis revealed that the CC genotype had the highest MDA levels but also exhibited increased GPx and SOD activities, with the CT genotype showing the highest SOD activity and the TT genotype the highest total antioxidant status (TAS). The SCD1 AA genotype displayed the highest activities of GluRed, GPx, and SOD, indicating a more effective antioxidant defence, while the VA genotype had the highest MDA levels and the VV genotype showed lower MDA levels, suggesting protective effects against oxidative damage. These findings highlight genotype specific variations in the oxidative stress markers and bioactive compound levels, providing insights into the genetic regulation of oxidative stress and antioxidant defences, which could inform breeding strategies for improving oxidative stress resistance in livestock and managing related conditions. Full article