Search Results (6,451)

Linkage disequilibrium (LD) maps are fundamental tools for exploring the genetic basis of traits of interest in any species. Quantifying LD patterns in cattle breeds has been made possible due to the availability of huge quantities of SNPs through modern sequencing technology. The present research aims to determine and compare linkage disequilibrium levels at different distances on the genome of Sistani domestic cattle and subspecies of Bos taurus and Bos indicus based on genome SNP data. A total of 60 Bos indicus Sahiwal (dairy) and Nellore (beef), Bos taurus Hereford (beef) and Holstein (dairy), and Sistani cattle were sampled and genotyped using Illumina Bovine HD 770 k chip. To ensure the caliber of the sequencing, 10 samples (genetically sequenced cattle) were randomly chosen among all breeds represented. LD was evaluated at distances of 1–50 Kb, 50–100 Kb, 100–500 Kb, and 0.5–1 Mb, and average r² values for all autosomes were calculated within distance classes. For all breeds, the average r² was over 0.2 at distances less than 100 Kb, while for Sistani, Nellore, and Sahiwal, the average r² was above 0.2 between 100 and 500 Kb. Furthermore, for all breeds, the average r² exceeding 0.3 was noted at distances smaller than 50 Kb, while this amount for Holstein and Hereford was observed at distances between 50 and 100 Kb. In various breeds, greater changes in LD levels were observed (at <10 Kb distance). In this study, the Sistani breed showed LD decay patterns similar to indicine cattle (Nellore and Sahiwal), which may be due to the geographic proximity of the Sistan and Baluchestan province to Pakistan, the origin of indicine breeds (they may have had genetic or kinship relationships over a long historical period), or due to ascertainment bias in the SNP chips used. Full article

Indoleamine 2,3-dioxygenase 1 (IDO1) and IDO2 originated from gene duplication before vertebrate divergence. While IDO1 has a well-defined role in immune regulation, the biological role of IDO2 remains unclear. Discovered in 2007, IDO2 is located near the IDO1 gene. Because of their high sequence similarity, IDO2 was initially thought to be a tryptophan (Trp)-degrading enzyme like IDO1. Differently from what expected, IDO2 displays extremely low catalytic activity toward Trp. Nevertheless, many studies, often contradictory, have tried to demonstrate that IDO2 modulates immune responses by catabolizing Trp into kynurenine, an unconvincing hypothesis linked to an incomplete understanding of IDO2’s activity. In this study, we review IDO2’s functional role beyond Trp metabolism. IDO2’s evolutionary persistence across species, despite being almost inactive as an enzyme, suggests it has some relevant biological importance. IDO2 expression in human normal cells is poor, but significant in various cancers, with two prevalent SNPs. Overall, the comparison of IDO2 to IDO1 as a Trp-degrading enzyme may have led to misunderstandings about IDO2’s true physiological and pathological roles. New insights suggest that IDO2 might function more as a signaling molecule, particularly in cancer contexts, and further studies could reveal its potential as a target for cancer therapy. Full article

Benzene, toluene, and xylene (BTX) co-exist in human environments, yet their individual and combined effects on genetic damage at low exposure levels are not fully understood. Additionally, single nucleotide polymorphisms in microRNAs (mirSNPs) might be involved in cancer etiology by affecting the related early health damage. To investigate the influence of BTX exposure, mirSNPs, and their interactions on genetic damage, we conducted a cross-sectional study in 1083 Chinese petrochemical workers, quantifying the BTX cumulative exposure levels and multiple genetic damage biomarkers. Additionally, we genotyped multiple common mirSNPs. Benzene and a BTX mixture were positive associated with the olive tail moment (OTM) and tail DNA% (p < 0.05). Higher levels of toluene and xylene enhanced the association of benzene with genetic damage levels. Genotypes and/or mutant allele counts of miR-4482-related rs11191980, miR-4433-related rs136547, miR-27a-related rs2594716, miR-3130-related rs725980, and miR-3928-related rs878718 might significantly influence genetic damage levels. Stronger effect estimates of benzene/BTX exposure were found in carriers of miR-196a-2-related rs11614913 heterozygotes and of wild homozygotes of miR-1269b-related rs12451747, miR-612-related rs12803915, and miR-4804-related rs266437. Our findings provide further support of the involvement of BTX co-exposure, mirSNPs, and their gene–environment interactions in determining the severity of DNA strand break in a complex manner. Full article

Bolting time is a critical trait that affects crop yield, adaptability, and overall productivity, making its regulation vital for agricultural success. In this study, we explored the genetic mechanisms controlling flowering time in radish (Raphanus sativus) via a combination of quantitative trait locus (QTL) analysis and genome-wide association study (GWAS). By developing an F₂ population from a cross between the relatively late-bolting variety ‘L432’ and the early-bolting variety ‘L285’, we identified 12 QTLs associated with bolting time. Furthermore, a GWAS performed on 60 East Asian radish accessions revealed 14 candidate genes potentially involved in flowering and bolting regulation. FLOWERING LOCUS C (FLC2) was the major candidate gene explaining the early and late bolting types. One locus was commonly detected from QTL and GWAS on chromosome 4, where CONSTANS-like (COL4) is located. To validate these findings, SNP markers were designed and applied to F₂ populations, revealing a correlation between marker presence and bolting phenotypes. These results offer valuable insights into the molecular control of bolting time in radish and identify candidate genes for use in marker-assisted breeding. These findings could enhance breeding efforts for optimizing bolting time in various radish markets. Full article

Background/Objectives: Nutrigenetics investigates the role of genetic variants that contribute to the inter-individual variation in response to food intake. Risk factors for cardiovascular disease (CVD) are influenced by the complex interplay of genetic and environmental factors, including the diet. The aim of this scoping review is to analyze the literature on the effect of genotypes on the response to dietary interventions for the treatment of CVD risk factors. Methods: A literature search was conducted in MEDLINE to identify published articles fulfilling the inclusion criteria. Studies published in English between 2014 and 2024 were selected. Data were extracted according to the population, intervention, comparison, and outcome (PICO) format. Results: Forty-eight studies met the inclusion criteria. The studies differed in design, intervention characteristics, tested genotypes, and ancestry. The most frequently analyzed variants were single-nucleotide polymorphisms (SNPs) in genes associated with lipid metabolism, inflammation, and energy balance, among others. The interventions tested the effects of different dietary patterns, diets modified in macronutrient content and types of fat, natural and processed foods, nutraceuticals, and nutrient supplements. Common APOE variants were the most analyzed genotypes showing significant interactions with different dietary interventions affecting blood lipids. Other genotypes found in pathways involving folic acid, lipid metabolism and transport have shown interactions with diverse dietary components across studies. Conclusions: Gene–diet interactions are observed in multiple dietary interventions. Replication of findings of nutrigenetic studies is required across different populations. The response to dietary treatments modifies CVD-related risk factors and shows variation associated with genotypes. Full article

Background/Objectives: Understanding the genetic architecture of autochthonous European cattle breeds is important for developing effective conservation strategies and sustainable breeding programs. Spanish beef cattle, which trace their origins to ancient migrations from the Near East with later admixture from African populations, exhibit a rich genetic diversity shaped by environmental adaptation and selective breeding. Runs of Homozygosity (ROH) are extended stretches of identical genetic material inherited from both parents. They serve as indicators of inbreeding and selection signatures within populations. ROH islands, or regions of the genome where ROH segments are highly concentrated across individuals within a breed, indicate genomic regions under selective pressure. Methods: This study explores the distribution of ROH islands across seven Spanish beef cattle breeds (Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Retinta, Pirenaica, and Rubia Gallega). By analyzing high-density SNP data, we characterized ROH patterns and identified genomic regions with high levels of homozygosity, which may indicate selection pressures or common ancestry. Results: Our findings revealed breed-specific ROH patterns as well as shared ROH islands, underscoring genetic relationships and differentiation among the breeds. Notably, Morucha displayed the highest number of ROH, while Asturiana de los Valles had the fewest. F_ROH values, which indicate genomic inbreeding, varied among the breeds, with Morucha and Retinta being associated with higher values. We identified 57 ROH islands, with shared regions among populations that suggest common ancestral selection pressures. Key genes within these regions, like MSTN, are associated with muscle growth, body weight, and fertility. Conclusions: This study offers valuable insights for breeding strategies and conservation efforts, highlighting the genetic diversity and historical background of Spanish cattle breeds. Full article

We studied the associations between 3′UTR genetic variants in ADME genes, clinical factors, and the risk of breast cancer chemotherapy toxicity. Those variants and factors were tested in relation to seven symptoms belonging to myelotoxicity (anemia, leukopenia, neutropenia), gastrointestinal side effects (vomiting, nausea), nephrotoxicity, and hepatotoxicity, occurring in overall, early, or recurrent settings. The cumulative risk of overall symptoms of anemia was connected with AKR1C3 rs3209896 AG, ERCC1 rs3212986 GT, and >6 cycles of chemotherapy; leukopenia was determined by ABCC1 rs129081 allele G and DPYD rs291593 allele T; neutropenia risk was correlated with accumulation of genetic variants of DPYD rs291583 allele G, ABCB1 rs17064 AT, and positive HER2 status. Risk of nephrotoxicity was determined by homozygote DPYD rs291593, homozygote AKR1C3 rs3209896, postmenopausal age, and negative ER status. Increased risk of hepatotoxicity was connected with NR1/2 rs3732359 allele G, postmenopausal age, and with present metastases. The risk of nausea and vomiting was linked to several genetic factors and premenopausal age. We concluded that chemotherapy tolerance emerges from the simultaneous interaction of many genetic and clinical factors. Full article

The Murciano-Granadina goat (MUG) is a renowned dairy breed, known for its adaptability and resilience, as well as for its exceptional milk traits characterized by high protein and fat content, along with low somatic cell counts. These traits are governed by complex biological processes, crucial in shaping phenotypic diversity. Thus, it is imperative to explore the factors regulating milk production and lactation for this breed. In this study, we investigated the genetic architecture of seven milk traits in MUGs, employing a two-step computational analysis to examine genotype–phenotype associations. Initially, a random forest algorithm identified the relative importance of each single-nucleotide polymorphism (SNP) in determining the traits of interest. The second step applied an information theory-based approach to exploring the complex genetic architecture of quantitative milk traits, focusing on epistatic interactions that may have been overlooked in the first step. These approaches allowed us to identify an almost distinct set of candidate genes for each trait. In contrast, by analyzing the promoter regions of these genes, we revealed common regulatory networks among the milk traits under study. These findings are crucial for understanding the molecular mechanisms underlying gene regulation, and they highlight the pivotal role of transcription factors (TFs) and their preferential interactions in the development of these traits. Notably, TFs such as DBP, HAND1E47, HOXA4, PPARA, and THAP1 were consistently identified for all traits, highlighting their important roles in immunity within the mammary gland and milk production during lactation. Full article

Background: Chronic gastritis caused by Helicobacter pylori (H. pylori) infection can progress to gastric cancer through atrophic gastritis (AG). The risk of gastric cancer increases with the progression of AG. Therefore, investigating the risk factors for the progression of AG is important. Methods: Using the GTEx and GEO databases, we extracted thirty-four candidate genes involved in the progression of AG. Then, with in silico analysis using HaploReg v4.1 and JASPAR (Matrix ID: MA0113.3), we extracted rs1231760 of RGS2 as a key single-nucleotide polymorphism (SNP) that could be involved in the functional change in the candidate gene. A correlation analysis between the selected SNP and AG in 200 H. pylori-positive and 302 H. pylori-negative participants was conducted. For functional analysis of the SNP, a dual-luciferase assay using reporter plasmids with a major or minor allele sequence was carried out. Results: The frequency of the C/C genotype of rs1231760 was higher in the AG group than in the non-AG group (p = 0.0471). Functional analysis showed that the transcriptional activities were higher at the dexamethasone-stimulating C allele than at the others (p < 0.05). Conclusions: The C/C genotype of rs1231760 in RGS2 could be a biomarker of high-risk H. pylori-positive AG because of an increase in RGS2 expression. Full article

Background/Objectives: This study aims to investigate whether Signal Transducer and Activator of Transcription 4 (STAT4) influences the anti-tumor immune response and is possibly involved in the initiation or relapse of pituitary adenomas (PAs) by examining STAT4 polymorphisms and serum levels. This research seeks to uncover potential connections that could inform future therapeutic strategies and improve our understanding of PA pathogenesis. Materials and Methods: This study was conducted at the Laboratory of Ophthalmology, Lithuanian University of Health Sciences. DNA was extracted from peripheral venous blood samples, and the genotyping of four STAT4 SNPs (rs7574865, rs10181656, rs7601754, and rs10168266) was performed using real-time PCR with TaqMan^® Genotyping assays. The serum STAT4 levels were measured via ELISA, and the optical density was read at 450 nm. Genotype frequencies, allele distributions, and serum STAT4 levels were statistically analyzed to assess associations with pituitary adenoma occurrence. Results: A binary logistic regression revealed that the STAT4 rs7574865 GT + GG genotypes vs. TT were associated with 1.7-fold increased odds of PA occurrence under the dominant genetic model (p = 0.012). The stratification by gender showed no significant associations in females; however, in males, the STAT4 rs10168266 CC + CT genotypes compared to TT were linked to 2.5-fold increased odds of PA under the dominant genetic model (p = 0.005). STAT4 rs10181656, rs7574865, rs7601754, and rs10168266 were analyzed to evaluate the associations with the pituitary adenoma size. We found that the STAT4 rs7574865 GG genotype was statistically significantly less frequent in the macro PA group compared to in the reference group (p = 0.012). For PA relapse, the rs7574865 G allele was less frequent in the PA group without relapse (p = 0.012), and the GT + GG genotypes were associated with a 1.8-fold increase in the PA group without relapse occurrence (p = 0.008). The serum STAT4 levels were higher in the PA patients compared to those of the reference group (p < 0.001). Elevated STAT4 serum levels were observed in PA patients with the STAT4 rs10181656 CC or CG genotypes (CC: p = 0.004; CG: p = 0.023), and with the rs7574865 GG or GT genotypes (GG: p = 0.003; GT: p = 0.021). The PA patients with the STAT4 rs7601754 AA genotype exhibited higher serum levels compared to those of the reference group (p < 0.001). Similarly, higher serum levels were found in the PA patients with the STAT4 rs10168266 CC or CT genotypes (CC: p = 0.004; CT: p = 0.027). A haplotype frequency analysis revealed no statistically significant results. Conclusions: The STAT4 genotypes were significantly associated with the PA occurrence, size, and relapse. Elevated serum STAT4 levels were observed in the PA patients, highlighting its potential role in PA pathogenesis. Full article

In this study, a new species of Alanomyces was isolated as an endophyte from the bark of Azadirachta indica from Mulshi, Maharashtra. The identity of this isolate was confirmed based on the asexual morphological characteristics as well as multi-gene phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) nuclear ribosomal RNA (rRNA) regions. As this was the second species to be reported in this genus, we sequenced the genome of this species to increase our knowledge about the possible applicability of this genus to various industries. Its genome length was found to be 35.01 Mb, harboring 7870 protein-coding genes as per Augustus and 8101 genes using GeMoMa. Many genes were annotated using the Clusters of Orthologous Groups (COGs) database, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Swiss-Prot, NCBI non-redundant nucleotide sequences (NTs), and NCBI non-redundant protein sequences (NRs). The number of repeating sequences was predicted using Proteinmask and RepeatMasker; tRNA were detected using tRNAscan and snRNA were predicted using rfam_scan. The genome was also annotated using the Pathogen–Host Interactions Database (PHI-base) and AntiSMASH. To confirm the evolutionary history, average nucleotide identity (ANIb), phylogeny based on orthologous proteins, and single nucleotide polymorphisms (SNPs) were carried out. Metabolic profiling of the methanolic extract of dried biomass and ethyl acetate extract of the filtrate revealed a variety of compounds of great importance in the pharmaceutical and cosmetic industry. The characterization and genomic analysis of the newly discovered species Alanomyces manoharacharyi highlights its potential applicability across multiple industries, particularly in pharmaceuticals and cosmetics due to its diverse secondary metabolites and unique genetic features it possesses. Full article

Milk fat is an important indicator for evaluating milk quality and a symbol of the core competitiveness of the dairy industry. It can be improved through genetic and feed management factors. Interferon alpha-inducible protein 27 (IFI27) was found to be differentially expressed when comparing the transcriptome in high- and low-fat bovine mammary epithelial cells (bMECs) in our previous research. Therefore, this study aimed to investigate whether the IFI27 gene had a regulatory effect on lipid metabolism.We detected six SNPs in the IFI27 gene (UTR-(-127) C>A, UTR-(-105) T>A, UTR-(-87) G>A, I1-763 G>T, E2-77 G>A, E2-127 G>T) in a Chinese Holstein cow population. Association analysis of the polymorphism of IFI27 and milk quality traits showed that the AG and GG genotype of E2-77 G>A, and the GG and TT genotypes of E2-127 G>T were connected to milk fat (p < 0.05). Haplotype frequency analysis showed that H5H5 was associated with lower milk fat content (p < 0.05), while milk from H5H6 animals had a higher fat content (p < 0.05). Subsequently, IFI27 overexpression vectors (PBI-CMV3-IFI27) and interference vectors (Pb7sk-GFP-shRNA) were constructed. Overexpression of the IFI27 gene in bMECs caused a significant increase in triglycerides (TGs) content (p < 0.05) and decreases in cholesterol (CHOL) and nonestesterified fatty acid (NEFA) content (p < 0.05), while interference with IFI27 expression produced opposing changes (p < 0.05). In summary, IFI27 E2-77 G>A and IFI27 E2-127 G>T may be useful as molecular markers in dairy cattle to measure milk fat, and the IFI27 gene may play an important role in milk lipid metabolism. Full article

Chilling injury during the germination stage (CIGS) of maize significantly hinders production, particularly in middle- and high-latitude regions, leading to slow germination, seed decay, and increased susceptibility to pathogens. This study dissects the genetic architecture of CIGS resistance expressed in terms of the relative germination rate (RGR) in maize through association mapping using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). A natural panel of 287 maize inbred lines was evaluated across multiple environments. The results revealed a broad-sense heritability of 0.68 for chilling tolerance, with 12 significant QTLs identified on chromosomes 1, 3, 5, 6, and 10. A genomic prediction analysis demonstrated that the rr-BLUP model outperformed other models in accuracy, achieving a moderate prediction accuracy of 0.44. This study highlights the potential of genomic selection (GS) to enhance chilling tolerance in maize, emphasizing the importance of training population size, marker density, and significant markers on prediction accuracy. These findings provide valuable insights for breeding programs aimed at improving chilling tolerance in maize. Full article

Background/Objectives: There is a lack of empirical studies of out-of-pocket health expenditures associated with dyslipidemias, which are major cardiovascular risk factors, especially in underrepresented admixed populations. The study investigates associations of health costs with lipid traits, GWAS-derived genetic risk scores (GRSs), and other cardiometabolic risk factors. Methods: Data from the observational cross-sectional 2015 ISA-Nutrition comprised lifestyle, environmental factors, socioeconomic and demographic variables, and biochemical and genetic markers related to the occurrence of cardiometabolic diseases. GWAS-derived genetic risk scores were estimated from SNPs previously associated with lipid traits. There was phenotypic and genetic information available for 490 independent individuals, which was used as inputs for random forests and logistic regression to explain private quantitative and categorical health costs. Results: There were significant correlations between GRSs and their respective lipid phenotypes. The main relevant variables across techniques and outcome variables comprised income per capita, principal components of ancestry, diet quality, global physical activity, inflammatory and lipid markers, and LDL-c GRS and non-HDL-c GRS. The area under the ROC curve (AUC) of quartile-based categorical health expenditure without GRSs was 0.76. GRSs were not significant for this categorical outcome. Conclusions: We present an original contribution to the investigation of determinants of private health expenditures in a highly admixed population, providing insights on associations between genetic and socioeconomic dimensions of health in Brazil. Ancestry information was also among the main factors contributing to health expenses, providing a novel view of the role of genetic ancestry on cardiometabolic risk factors and its potential impact on health costs. Full article

Background: Recently identified Hero proteins, which possess chaperone-like functions, are promising candidates for research into atherosclerosis-related diseases, including ischemic stroke (IS). Methods: 2204 Russian subjects (917 IS patients and 1287 controls) were genotyped for fifteen common SNPs in Hero20 gene C11orf58 using probe-based PCR and the MassArray-4 system. Results: Six C11orf58 SNPs were significantly associated with an increased risk of IS in the overall group (OG) and significantly modified by smoking (SMK) and low fruit/vegetable intake (LFVI): rs10766342 (effect allele (EA) A; P(_OG = 0.02; _SMK = 0.009; _LFVI = 0.04)), rs11024032 (EA T; P(_OG = 0.01; _SMK = 0.01; _LFVI = 0.036)), rs11826990 (EA G; P(_OG = 0.007; _SMK = 0.004; _LFVI = 0.03)), rs3203295 (EA C; P(_OG = 0.016; _SMK = 0.01; _LFVI = 0.04)), rs10832676 (EA G; P(_OG = 0.006; _SMK = 0.002; _LFVI = 0.01)), rs4757429 (EA T; P(_OG = 0.02; _SMK = 0.04; _LFVI = 0.04)). The top ten intergenic interactions of Hero genes (two-, three-, and four-locus models) involved exclusively polymorphic loci of C11orf58 and C19orf53 and were characterized by synergic and additive (independent) effects between SNPs. Conclusions: Thus, C11orf58 gene polymorphism represents a major risk factor for IS. Bioinformatic analysis showed the involvement of C11orf58 SNPs in molecular mechanisms of IS mediated by their role in the regulation of redox homeostasis, inflammation, vascular remodeling, apoptosis, vasculogenesis, neurogenesis, lipid metabolism, proteostasis, hypoxia, cell signaling, and stress response. In terms of intergenic interactions, C11orf58 interacts most closely with C19orf53. Full article