SNP Genotyping Research Articles

Association of genetic variations of interleukin-6 polymorphism (rs1800795) with susceptibility to Hashimoto’s thyroiditis in West Algerian population

Aim: Hashimoto’s thyroiditis is a polygenic auto-immune disease with a complex etiopathogenesis. It is more common in females. An imbalance between pro-inflammatory and anti-inflammatory cytokines may play an important role in the disease pathogenesis. Numerous studies have been conducted to find an association between genetic polymorphisms and the development of Hashimoto’s thyroiditis. In this context, we proposed to study the impact of the interleukin-6 (IL-6) gene polymorphism (rs1800795) on the genetic susceptibility to Hashimoto’s thyroiditis. Methods: Polymorphism in IL-6 gene (rs1800795) was assessed in a case-control study involving a population of Western Algeria with 81 Hashimoto’s thyroiditis patients and 211 unrelated healthy subjects, matched in age and sex. The DNA was extracted by a magnetic bead-based technique. The genetic study was performed by molecular biology: real-time PCR using TaqMan single nucleotide polymorphism (SNP) genotyping assay with Applied Biosystems 7500 device. Results: Results showed that the GG and GC genotypic distribution is similar between patient and control groups with a higher frequency of the GG genotype (80.25% in patients and 78.67% in controls vs. 19.75% of patients and 20.38% of controls with the GC genotype). The CC genotype is absent in patients and present in only 02/211 healthy subjects. The frequency of the polymorphic G allele was similar in the two groups, with 90.1% and 88.8% in patients and controls respectively (P > 0.05). Conclusions: This study reports no significant difference in IL-6 (-174 G/C) gene polymorphism at the allelic or the genotypic level between Hashimoto’s patients and the control group (P > 0.05). No association between the SNP IL-6 rs1800795 and susceptibility to Hashimoto’s thyroiditis in Western Algerian population.

Investigation of polymorphism and expression of the tyrosinase (TYR) gene as a gene controlling coat color in Bali cattle

Cattle coat color is governed by numerous genes, notably the tyrosinase gene (TYR). This study analyzed coat color anomalies like albinism and white spotting in Bali cattle. It aims to discern the TYR gene's diversity, expression patterns, and correlation with coat color abnormalities. The research encompassed 189 cattle, including those with standard coat color (n=53), white-spotted (n=11), and albino (n=17) Bali cattle, as well as Simmental (n=37), Limousin (n=14), Madura (n=21), and Peran-akan Ongole (PO) cattle (n=36). Total DNA was extracted and the TYR gene in exon 1 was amplified using forward and reverse primers with a target amplicon length of 994 bp. Direct sequencing unveiled TYR gene diversity, analyzed using BioEdit and MEGA6 software to identify SNPs. PCR-RFLP was used for SNP genotyping, while qPCR analyzed TYR gene expression. Two mutations (SNP g. 939A>G and SNP g. 887C>T) were discovered in Bali cattle TYR exon 1. SNP g. 939A>G exhibited polymorphism, with the highest GG genotype frequency in standard Bali cattle, indicating a high G allele frequency. Conversely, Madura, Simmental, Limousin, and PO cattle had the lowest allele fre-quency. Chi-square (χ² test) results showed non-significance across all cattle types. TYR gene expres-sion differed significantly between standard Bali cattle and albinos (p<0.05).

Higher relapse and worse overall survival in recipients with CTLA-4 AA genotype of rs231775 following single-unit cord blood transplantation in adults

We retrospectively investigated the impact of CTLA-4 polymorphism on outcomes for adult patients who received single-unit cord blood transplantation (CBT) at our institution. CTLA-4 genotyping was performed using real-time polymerase chain reaction with the TaqMan® SNP genotyping assay for rs231775. This study included 143 recipient–donor pairs. The multivariate analysis showed that recipient rs231775 AA was associated with worse overall survival (OS) (hazard ratio [HR], 2.92; p = 0.008) and a higher relapse rate (HR, 4.79; p = 0.002), but donor rs231775 was not. The rs231775 polymorphism in recipients and donors did not affect non-relapse mortality, hematopoietic recovery, or acute and chronic graft-versus-host disease. The beneficial effects of rs231775 GG+GA recipients on OS and relapse were notable in subgroups of patients with high-risk disease status and those with myeloid diseases. The polymorphism of CTLA-4 rs231775in recipients might be associated with the clinical outcomes of single-unit CBT.

Association of MicroRNA-146a-5p Polymorphism with Cognitive Impairment in Adolescents with Depressive Disorder

Introduction: The incidence of depression in adolescents is increasing and is associated with severe cognitive impairment. This paper aimed to investigate the relationship between polymorphisms in microRNA-146a-5p (miR-146a-5p) and cognitive impairment in adolescent depression patients. Methods: Quantitative real-time polymerase chain reaction was used to quantify miR-146a-5p in serum. Detection of miR-146a-5p gene polymorphism was performed by TaqMan SNP Genotyping Assay. Odds ratios and 95% confidence intervals (CIs) were calculated by chi-square test (χ2) and logistic regression analysis. Results: Genotyping of miR-146a rs2910164 showed that CC (OR = 0.443, 95% CI, 0.264–0.741, p = 0.002) and GC (OR = 0.445, 95% CI, 0.279–0.712, p = 0.001) genotype reduced the risk of cognitive impairment in adolescent depression. The C allele (OR = 0.794, 95% CI, 0.694–0.741, p = 0.001) was a protective factor for cognitive impairment in adolescent depression compared to the rs2910164 G allele. Rs2910164 (OR = 0.425, 95% CI = 0.273–0.662, p = 0.000) showed a negative correlation with adolescents with cognitive impairment in depression by logistic regression analysis. The level of miR-146a-5p was decreased in carriers of the CC and CG genotypes. Conclusion: Rs2910164 C allele carriers have a low risk of cognitive impairment in adolescent depression and could reduce miR-146a-5p level.

Molecular Analysis of Genes CEBPA, NPM1, IDH1, and RUNX1 Polymorphisms as Biomarker Potential in Leukemia Patients.

Leukemia is found in approximately 2.3 million people worldwide and causes many deaths all over the world. This research study was conducted to figure out the link of single nucleotide polymorphisms of genes CEBPA (rs34529039), NPM1 (rs753788683), IDH1 (of rs11554137) and RUNX1 (rs13051066) polymorphisms as biomarker potential in leukemia patients. A total of 600 subjects were included in the study which included 300 patients and 300 healthy controls with age and gender matched. After DNA extraction, PCR was carried out to analyze polymorphisms of selected genes. A significant association with increased risk of leukemia by almost twofolds is observed in homozygous mutant (AA) of rs34529039 SNP of gene CEBPA (odds ratio [OR] = 1.71; 95% confidence interval [CI] = 1.04-2.82; p = 0.03) while highly significant association but with decrease risk of leukemia is observed in heterozygote genotype (CA) of same SNP (OR = 0.36; 95% CI = 0.22-0.59; p = 0.0001). A highly significant association with increased risk of leukemia up to twofolds is observed in heterozygote genotype (AG) of rs753788683 of gene NPM1 (OR 2.10: 95% CI 1.32-3.36 p = 0.0017) while increasing risk by two-fold and show significant association in homozygous mutant (AA) (OR = 1.75; 95% Cl = 1.09-2.79; p = 0.01). Leukemia risk increases by twofold and shows significant association in the homozygous mutant (AA) of rs11554137 (OR = 1.75; 95%Cl = 1.09-2.79; p = 0.01). Leukemia risk increases by twofold and shows significant association in the homozygous mutant (AA) of rs13051066 of gene RUNX1 (OR = 0.63; 95%Cl = 0.39-1.63; p = 0.06).

History and genetic diversity of African sheep: Contrasting phenotypic and genomic diversity.

Domesticated sheep have adapted to contrasting and extreme environments and continue to play important roles in local community-based economies throughout Africa. Here we review the Neolithic migrations of thin-tailed sheep and the later introductions of fat-tailed sheep into eastern Africa. According to contemporary pictorial evidence, the latter occurred in Egypt not before the Ptolemaic period (305-25 BCE). We further describe the more recent history of sheep in Egypt, the Maghreb, west and central Africa, central-east Africa, and southern Africa. We also present a comprehensive molecular survey based on the analysis of 50 K SNP genotypes for 59 African breeds contributed by several laboratories. We propose that gene flow and import of fat-tailed sheep have partially overwritten the diversity profile created by the initial migration. We found a genetic contrast between sheep north and south of the Sahara and a west-east contrast of thin- and fat-tailed sheep. There is no close relationship between African and central and east Asian fat-tailed breeds, whereas we observe within Africa only a modest effect of tail types on breed relationships.

Relationships between growth characteristics and GDF9 gene polymorphisms in Awassi sheep

ABSTRACT The Awassi sheep, a breed with a distinctive fat tail, is bred specifically in the south-eastern region in Turkey. It has proven its adaptability to the hot environment of this region, especially in the provinces of Şanlıurfa, Hatay and Gaziantep, which are close to the Syrian border. The aim of this study was to investigate the SNP polymorphisms in the GDF9 gene/exon2 using DNA sequencing. In addition, the study investigated the relationships between SNP genotypes and growth traits, in particular birth weight (BW), weaning weight (WW) and weight at the end of the grazing season (GSW), in Awassi sheep. Four different flocks with a total of 131 Awassi lambs were used. PCR was used to amplify exon2 of the GDF9 gene region, which has a length of 815 base pairs (bp), from the genomic DNA of the Awassi sheep. Thus, four new single nucleotide polymorphisms (SNPs) were identified. The results showed that although the effects of SNP2 and SNP4 on body weight (BW) were statistically significant, only SNP4 had a significant effect on weaning weight (WW) (P < 0.05). In addition, SNP1 and SNP3 were found to have no significant effect on any developmental trait in the dataset.

The development of two fast genotyping assays for the differentiation of hemp from marijuana

AbstractThe legalization of hemp cultivation in the United States has raised the need for reliable methods to distinguish between legal hemp and illegal marijuana. Genetic analysis has emerged as a powerful tool, surpassing traditional chemical methods in specific aspects, such as analyzing trace amounts, aged samples, and different parts of the sample. Genetic differences in cannabinoid synthase genes offer promise for precise crop type determination, particularly focusing on genes like tetrahydrocannabinolic acid synthase (THCAS), cannabidiolic acid synthase (CBDAS), and cannabichromenic acid synthase (CBCAS). However, previous research faced several challenges in developing discriminatory genetic markers, including limited sample sizes, high similarity between the synthase genes, and the presence of pseudo synthase genes. A comprehensive study using Next‐Generation Sequencing (NGS) introduced a differentiation flowchart based on THCAS, CBDAS, and THCAS pseudogenes. To bridge the gap between NGS and the practical requirements of crime laboratories, two rapid genotyping assays were developed: a CE‐based SNaPshot™ assay and a TaqMan™ real‐time PCR assay. While the SNaPshot™ assay effectively differentiated various hemp and marijuana types, differentiation was limited with marijuana samples containing THC% close to the 0.3% legal threshold (0.3%–1%). The TaqMan™ qPCR SNP genotyping assay provided quicker results, making it an efficient choice for crime laboratories. However, this method had the same limitations as the SNaPshot™ assay with addtional challenges in differentiating edible hemp seed samples, and it did not provide additional CBD information. The study also highlighted the influence of two variants of one THCAS pseudogene on chemotype determination, emphasizing the necessity for precise genetic analysis for accurate categorization of cannabis varieties.

Association between the rs1800624 and rs80096349 SNPs and diabetic retinopathy: a pilot study

ABSTRACT Background One of the conditions that might harm your eyesight is diabetic retinopathy (DR), DR may set in slowly but surely for those with long-term diabetes and poor glucose control. ‎ Objective To establish a connection between the various genotypes of the rs1800624 SNP and the rs80096349 SNP located in the AGER gene and DR patients. ‎ Methods The current case-control research examined one hundred thirty-four individuals diagnosed with type 2 diabetes and thirty-six healthy individuals who did not have DM. These samples were obtained from Amir Al-Muminin, a private hospital in Najaf, Iraq. The tetra primers ARMS-PCR method was utilized to determine the genotype of rs1800624 SNP of the AGER gene. Results A significant association was found between genotypes (AA, AG, and GG) and DR subgroups (NPDR & PDR) in patients (p = 0.001). The AG genotype of rs1800624 SNP is associated with a lowering the risk of developing NPDR (OR = 0.30; 95% CI = 0.12-0.74; p = 0.009 between controls and NPDR, OR = 0.36; 95% CI = 0.14-0.90; p = 0.029 between NDR and NPDR). HRM analysis verified the presence of only two genotypes in the samples: wild type (GG) and a heterozygous mutant (GA). However, a significant association between genotypes was observed when comparing DR status with controls and NDR (p = 0.031). Conclusion The rs1800624 SNP of the AGER gene is associated with the risk of NPDR and PDR in T2DM, and the polymorphism of the rs80096349 may be associated with retinopathy in the Iraqi population.

Gender-modulated influence of BDNF concentration and Val66Met polymorphism on cognitive outcomes in chronic limb ischemia patients.

While numerous studies have established associations between brain-derived neurotrophic factor (BDNF) and cognitive functioning, limited research has delved into the role of BDNF concerning cognitive outcomes in atherosclerosis-related conditions. This study aimed to investigate the correlations between cognitive performance, serum BDNF levels, and the BDNF Val66Met polymorphism in individuals diagnosed with chronic limb ischemia (CLI). The study encompassed 159 CLI patients (52 females, 107 males) aged 59-73 years. Genetic analysis involved assessing the BDNF Val66Met single-nucleotide polymorphism using a TaqMan SNP Genotyping Assay and the ViiA™ 7 Real-Time PCR System. Serum BDNF levels were quantified. Cognitive functioning was evaluated through a computerized battery of tests, including the simple reaction test (SRT) for speed and accuracy assessment, verbal memory test (VMT) for short and long-term memory evaluation, and the GoNoGo test for cognitive control and inhibition. Gender differences in cognitive performance were observed, with women excelling in VMT, while men demonstrated superior performance in SRT and the GoNoGo test. No statistically significant differences were noted between the Met/Met or Met/Val and Val/Val subgroups. However, notable differences emerged in female Met carriers, exhibiting superior VMT scores but more incorrect Go responses in the GoNoGo test. Conversely, female Val homozygotes showed significantly more incorrect NoGo responses compared to male Val homozygotes. In men carrying the Met allele, higher BDNF concentrations correlated with improved GoNoGo test results (r = 0.248, p = 0.01). Conversely, in women with the Val/Val variant, lower BDNF concentrations were associated with better VMT scores. This study underscores the sex-specific impact of BDNF serum levels and the BDNF polymorphism on cognitive processes among CLI patients. The findings highlight the nuanced influence of BDNF in shaping cognitive functioning, emphasizing the need for further research into these sex-dependent associations.

Rare copy number variant analysis in case–control studies using snp array data: a scalable and automated data analysis pipeline

BackgroundRare copy number variants (CNVs) significantly influence the human genome and may contribute to disease susceptibility. High-throughput SNP genotyping platforms provide data that can be used for CNV detection, but it requires the complex pipelining of bioinformatic tools. Here, we propose a flexible bioinformatic pipeline for rare CNV analysis from human SNP array data.ResultsThe pipeline consists of two major sub-pipelines: (1) Calling and quality control (QC) analysis, and (2) Rare CNV analysis. It is implemented in Snakemake following a rule-based structure that enables automation and scalability while maintaining flexibility.ConclusionsOur pipeline automates the detection and analysis of rare CNVs. It implements a rigorous CNV quality control, assesses the frequencies of these rare CNVs in patients versus controls, and evaluates the impact of CNVs on specific genes or pathways. We hence aim to provide an efficient yet flexible bioinformatic framework to investigate rare CNVs in biomedical research.

Genetic and epigenetic factors affecting carotid intima-media thickness in monozygotic twins

Background and aimsThe intima-media thickness (IMT) of the carotid artery, an indicator of subclinical atherosclerosis, varies in close association with various factors such as diabetes and immune response. The extent of changes in IMT varies among individuals owing to both genetic and epigenetic factors. In this study, we aimed to identify single nucleotide polymorphisms (SNPs) and DNA methylation patterns that affect carotid IMT in monozygotic (MZ) twins. MethodsWe measured the maximum IMT (IMT-Cmax) and the mean IMT in the common carotid artery wall using ultrasonography in 107 pairs of MZ twins recruited from the Osaka University Twin Registry. The genotyping of SNPs and the measurement of methylation levels were performed using a beads array, and the expression of each gene was determined by RNA sequencing. Linear regression analysis was performed on each of the two groups: one group consisted of twins randomly selected from each pair, and the other group consisted of co-twins. ResultsWe identified a CpG site (cg02432467) on HS3ST6 as a significant epigenetic factor in both IMT-Cmax and mean IMT analyses. The methylation level at another site (cg07927379) was negatively correlated with LINC01006 expression and IMT-Cmax. Furthermore, there were significant differences in AP2A2 expression and mean IMT among individuals with each genotype of the rs10902263 polymorphism. ConclusionsWe identified genetic and epigenetic factors associated with carotid IMT that may be useful for individualized assessments.

Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping in Litopenaeus vannamei.

The application of whole-genome resequencing in genetic research is rapidly expanding, yet the impact of sequencing depth on data quality and variant detection remains unclear, particularly in aquaculture species. This study re-sequenced 31 Litopenaeus vannamei (L. vannamei) samples at over 28× sequencing depth using the Illumina NovaSeq system and down-sampled the data to simulate depths from 0.5× to 20×. Results showed that when the sequencing depth was below 10×, the number of SNP identifications increased sharply with the rise in depth, with single nucleotide polymorphisms (SNPs) detected at 10× accounting for approximately 69.16% of those detected at 20×. The genotyping accuracy followed a similar trend to SNP detection results, being approximately 0.90 at 6×. Further analyses showed that the main cause of genotyping errors was the misidentification of heterozygous variants as homozygous variants. Therefore, considering both the quantity and quality of SNPs, a sequencing depth of 10× is recommended for whole-genome studies and genetic mapping, while a depth of 6× is more cost-effective for population structure analysis. This study underscores the importance of selecting optimal sequencing depth to ensure reliable variant detection and high data quality, providing valuable guidance for whole-genome resequencing in shrimp and other aquatic species.

Parental Reconstruction from a Half-Sib Population of Stoneless Jujube Ziziphus jujuba Mill. Based on Individual Specific SNP Markers Using Multiplex PCR.

The selection of unique and individual-specific SNPs is important as compared with universal SNPs for individual identification. Therefore, the main significance of this research is the selection of specific SNPs in male parent and the identification of offspring with these specific SNPs in their genome by multiplex PCR, which is utilized for genotyping of 332 half-sib plants of Ziziphus jujuba.This cost-effective method makes as much as possible to utilize the same amount of each pair of various targeted loci primers. After PCR amplification of targeted genome parts, the mixed products can be directly used in a next-generation sequencing platform. We concomitantly amplified 10 unique SNP loci at 10 different chromosomes of male JingZao 39 plants in 332 half-sib plants and sequenced them on the Illumina Novaseq 6000 platform. Analysis of SNP genotyping accuracy of 332 half-sib plants showed that all 10 unique SNPs in all 332 plants were correctly amplified in this multiplex PCR method. Furthermore, based on Mendelian inheritance, we identified 124 full-sib plants that have 10 unique SNPs in their genomes. These results were further confirmed by whole genome resequencing of 82 randomly selected half-sib plants, and the identity-by-descent values of all full-sib plants were between 0.4399 to 0.5652. This study displayed a cost-effective multiplex PCR method and proper identification of pollen parent through specific SNPs in half-sib progenies and firstly obtained a full-sib population between 'Wuhezao' and 'JingZao 39', segregating for stone and stoneless fruit.

Extended sperm storage recorded in red-tailed phascogale (Phascogale calura) during a trial translocation to Vulkathunha-Gammon Ranges National Park, South Australia

We present a case of extended sperm storage in a female red-tailed phascogale (Phascogale calura) during a trial reintroduction in 2022. Parentage reported by single nucleotide polymorphism genotyping revealed the father of one litter had died approximately 50 days before the litter was born. The recorded gestation period for red-tailed phascogales is 28–32 days. Our record indicates sperm storage and/or diapause of up to 15–27 days, at least double the previously recorded sperm storage duration in this species.

Fluorescent primers amplification refractory mutation system qPCR (FP ARMS-qPCR) for MTHFR C677T SNP genotyping.

The currently used methods for the detection of methylene tetrahydrofolic acid reductase (MTHFR) C677T single nucleotide polymorphism (SNP) are either time-consuming or expensive. In this study, we devised an accurate, rapid and easy-to-use SNP detection system based on fluorescent primers amplification refractory mutation system qPCR, known as FP ARMS-qPCR. Fluorescent primers (FPs) modified by fluorescent dye or quencher near the 3' terminal thymine were designed. The reaction conditions were optimized and the performance was evaluated. Using commercial kits as controls, 242 samples were tested in parallel to verify the feasibility of the FP ARMS-qPCR assay. We demonstrated the good sensitivity and specificity of the FP ARMS-qPCR with optimized conditions. The assay was able to accurately distinguish between different SNP sites of MTHFR C677T in less than 2h using as low as 50 pg of template genomic DNA. Completely consistent genotyping results reveal that FP ARMS-qPCR is concordant with commercial kits. We established a specific, sensitive, and rapid FP ARMS-qPCR method for the detection of MTHFR C677T genotype. This could also serve as a potential diagnostic tool for a variety of diseases.

Tenascin-C-Matrix Metalloproteinase-3 Phenotype and the Risk of Tendinopathy in High-Performance Athletes: A Case-Control Study.

Background/Objectives: Tendon structure is predominantly composed of the extracellular matrix (ECM), and genetic variants in non-collagenous ECM components may influence susceptibility to tendinopathy. We investigated the potential influence of single nucleotide polymorphisms (SNPs) in fibrillin-2 (FBN2), tenascin-C (TNC), and matrix metalloproteinase-3 (MMP3) on the tendon regeneration failure phenotype and impact on the susceptibility to tendinopathy in Brazilian high-performance athletes. Methods: This case-control study was conducted with 397 high-performance athletes from different sports modalities (197 tendinopathy cases and 200 controls), and they were analyzed by validated TaqManTM SNP genotyping assays of the SNPs FBN2 (rs331079), TNC (rs2104772), and MMP3 (rs591058). Results: Out of the 197 tendinopathy cases, 63% suffered from chronic tendon pain and 22% experienced more than three episodes of disease manifestation. The TNC-rs2104772-A allele was significantly associated with tendinopathy (OR: 1.4; 95% CI: 1.1-1.8), while athletes carrying the MMP3-rs591058-T allele were linked to an increased risk of more episodes of disease manifestation (OR: 1.7; 95% CI: 1.1-2.8). The TNC-MMP3 tendon regeneration failure phenotype (TNC-A/MMP3-T) was associated with an increased risk of tendinopathy (OR: 1.4; 95% CI: 1.1-2.0) and episodes of disease manifestation (OR: 2.0; 95% CI: 1.2-3.5). Athletes with tendinopathy who had the TNC-A/MMP3-T interaction were more prone to experiencing more than three disease exacerbations (OR: 4.3; 95% CI: 1.8-10.5) compared to TNC-A/TNC-C. Conclusions: This study suggests that rs2104772 and rs591058 SNPs could be involved in the tendon regeneration failure phenotype and may influence the molecular mechanism related to the regulation of the tendon ECM during training workload.

Genetic association of the kynurenine pathway to suicidal behavior

Suicidal behavior has been associated with dysfunctions in the kynurenine pathway, including alterations in the levels of neuroprotective and neurotoxic metabolites. Changes in the catalytic activity of enzymes within the pathway may contribute significantly. Variations in the genes encoding enzymes within the pathway can significantly affect their catalytic activity, playing a crucial role in the process. To explore this possibility, we hypothesized that these genetic variations would occur more frequently in patients with a history of suicidal behavior compared to non-suicidal individuals. Thus, we investigated the relationship between a history of suicide attempts and five single nucleotide polymorphisms (SNPs) within genes involved in the kynurenine pathway: IDO1 (rs7820268), IDO2 (rs10109853), KMO (rs1053230), KAT1 (rs10988134), and ACSMD (rs2121337). Our sample comprised 849 subjects: 325 individuals who had attempted suicide in their lifetime (SAs), 99 individuals with a history of major depression disorder but no previous suicide attempts (non-SAs), and 425 non-psychiatric controls (CTRL). We performed SNP association analyses using codominant, dominant, and recessive models. Adjustment for sex and multiple comparisons was applied. After adjustment, the analysis revealed that SAs showed a significantly higher frequency of T alleles and TT genotypes of the rs1053230 SNP compared to CTRL across nearly all models. Furthermore, in the recessive model, non-SAs displayed a higher prevalence of the TT genotype of the rs10109853 SNP compared to CTRL.The rs1053230 and rs10109853 SNPs could play a role in the previously observed metabolic dysregulation among SAs and non-SAs, respectively. To validate our findings, it is crucial to conduct functional analyses to investigate the impact of rs10109853 and rs1053230 SNPs on the expression and/or catalytic activity of the corresponding enzymes.

Association between the rs12654778 SNP of the β-2 adrenergic receptor and LDL cholesterol levels in the Chilean adult population

IntroductionVarious polymorphisms in the beta-2 adrenergic receptor (ADRB2) gene have been associated with cardiometabolic risk factors, such as hypertension, dyslipidemia, type 2 diabetes mellitus and obesity contributing to the physiopathology of these chronic conditions. However, the association of the single nucleotide polymorphism (SNP) rs12654778 at the ADRB2 gene with metabolic changes has been poorly studied and there is no information on the Chilean adult population. ObjectiveTo investigate the association between the rs12654778 SNP at the ADRB2 gene with cardiometabolic risk markers in a Chilean adult population. MethodsWe conducted a cross-sectional study including 404 participants from the GENADIO study whom were genotyped for rs12654778 and categorized into GG, AG, and AA genotypes. Associations with cardiometabolic risk markers, such as blood pressure, total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, triglycerides, blood glucose and insulin were examined using multivariate regression analysis, while statistical models were adjusted for sociodemographic and lifestyle variables. ResultsOur findings indicate a significant association between the presence of the protective genotype (AA) of the rs12654778 polymorphism and lower low-density lipoprotein cholesterol levels corresponding to 8.75mg/dL per each copy of the protective allele (maximally adjusted model). No significant associations were seen for the remaining variables. ConclusionThe AA genotype of the rs12654778 SNP at the ADRB2 gene had a protective effect specifically against low-density lipoprotein cholesterol levels. This is the first study ever conducted in Chile on this SNP of ADRB2 and one of the few conducted worldwide to establish an association between the rs12654778 SNP at the ADRB2 gene and LDL cholesterol.

Host genetic regulation of specific functional groups in the rumen microbiome of dairy cows: Implications for lactation trait

IntroductionRuminants play a pivotal role in our society by transforming non-consumable substances from industrial by-products and plant fibers into valuable resources such as meat and milk. This remarkable conversion ability is primarily attributed to the rumen microbiota, which is influenced by various factors, including diet, climate, and geographical location. In recent years, increasing research has shown that host factors (breed, genetic variation, etc.) also play vital roles in shaping rumen microbial composition and function in cattle. ObjectiveThis study aims to provide a theoretical basis and an opportunity for further investigating the regulation of lactation traits in dairy cows through host genetics and the interaction with the rumen microbiota. MethodTo investigate the interactions between host genotype, rumen microbiota, and animal phenotype, we curated and analyzed the dairy herd improvement (DHI) data, single nucleotide polymorphisms (SNPs) genotypes, and 16S rumen microbiota data from 1,169 Holstein dairy cows. Heritability and microbiability estimation, along with genome-wide association studies (GWAS) were performed to identify candidate microorganisms and host genetic loci. ResultWe identified thirty-one heritable taxa, whose functions were predominantly enriched in carbohydrate metabolism and energy metabolism. The genome-wide association study revealed that nine heritable bacteria were significantly associated with forty-three SNPs. Functional genes located within or near these SNPs were primarily associated with rumen epithelial development. Additionally, these nine heritable bacteria were primarily annotated as complex polysaccharide degraders and butyrate producers, such as Fibrobacter sp900143055 and Pseudoruminococcus massiliensis, which showed significant associations with milk yield and milk fat percentage. Compared to previous studies, we newly discovered the existence of a high heritability of Olsenella umbonate, Butyrivibrio hungatei, among others.