TNF-α polymorphisms may influence dyslipidaemia, but their role remains unclear. This case–control study investigated associations between TNF-α gene polymorphisms (–1031T/C, −863C/A, −857C/T, −308G/A and −238G/A) and dyslipidaemia in 595 participants (162 cases, 433 controls) from the Chaoshan region of China. Anthropometric, biochemical and genetic data were analysed using χ2 tests and logistic regression, with the false discovery rate (FDR) method applied to correct for multiple comparisons. Results revealed that only the −1031T/C and −863C/A polymorphisms were significantly associated with dyslipidaemia. Carriers of the TC + CC genotype for −1031T/C (OR = 0·48; 95 % CI: 0·30, 0·78; PFDR = 0·006) and the CA + AA genotype for −863C/A (OR = 0·41; 95 % CI: 0·24, 0·70; PFDR = 0·004) had lower odds of dyslipidaemia. Protective effects were observed for the C allele at −1031T/C (OR = 0·58, PFDR = 0·012) and the A allele at −863C/A (OR = 0·47, PFDR = 0·004). Stratified analyses showed that these associations were significant in males but not females. Functional annotation linked these TNF-α gene polymorphisms to transcription factors (e.g. HNF-1A, STAT1β) in the adipogenesis pathway. This study reveals genetic associations between TNF-α polymorphisms and dyslipidaemia, particularly in males, and provides mechanistic insights into their role in transcriptional regulation.

Despite previous observational studies suggesting that malnutrition could be involved in venous thromboembolism (VTE), definitive causality still lacks high-quality research evidence. This study aims to explore the genetic causal association between malnutrition and VTE. The study was performed using summary statistics from genome-wide association studies for VTE (cases = 23 367; controls = 430 366). SNP associated with exposure was selected based on quality control steps. The primary analysis employed the inverse variance weighted (IVW) method, with additional support from Mendelian randomisation (MR)-Egger, weighted median and weighted mode approaches. MR-Egger, leave-one-SNP-out analysis and MR pleiotropy residual sum and outlier (MR-PRESSO) were used for sensitivity analysis. Cochran’s Q test was used to assess heterogeneity between instrumental variables (IV). IVW suggested that overweight has a positive genetic causal effect on VTE (OR = 1·1344, 95 % CI = 1·056, 1·2186, P < 0·001). No genetic causal effect of malnutrition (IVW: OR = 0·9983, 95 % CI = 0·9593, 1·0388, P = 0·9333) was found on VTE. Cochran’s Q test suggests no possible heterogeneity in both related exposures. The results of the MR-Egger regression suggest that the analysis is not affected by horizontal pleiotropy. The results of the MR-PRESSO suggest that there are no outliers. The results revealed a statistical genetic association where overweight correlates with an increased risk of VTE. Meanwhile, no genetic causal link was observed between malnutrition and VTE. Further research is warranted to deepen our understanding of these associations.

Maize (Zea mays L.) is one of the main staples in the Peruvian Andes. Phenotypic diversity is extremely high in terms of plant morphology, grain colour, grain size and uses. However, little is known about the genetic component of the Peruvian maize. Genotyping-by-sequencing was used, for the first time, to infer the genetic diversity and population structure of 25 accessions of maize collected from two ecoregions of the departments of the Peruvian highlands, Cajamarca and Huancavelica, to provide a basis for the conservation and breeding of this crop genetic resource. A total of 29,332 single-nucleotide polymorphisms were identified along all 10 chromosomes of maize. STRUCTURE analysis revealed two clusters (open-pollinated cultivars and landraces). Principal coordinate analysis and our dendrogram showed that these accessions of Peruvian maize do not group based on their geographic origin but on their improvement status, however, this is weakly supported. Average genetic diversity was very high (0.35). Analysis of molecular variance showed a reduced variation between populations (2.85%) and indicated that variability within populations is 97.15%. The lowest population divergence was zero for populations of Colcabamba versus Pichos and Daniel Hernandez versus Colcabamba and the highest population divergence (0.041) was observed for population Cajamarca versus Santiago de Tucuma. As expected, FIS values were positive. Additional samples from other Andean and west coast Peruvian localities are needed to provide a better understanding of the genetic components of this important crop aiming to develop a modern breeding programme of maize in Peru.

The influence of the SNP rs174575 (C/G) within the fatty acid desaturase 2 gene on the levels of long-chain PUFA was determined through statistical meta-analysis. Six databases were searched to retrieve the relevant literature. Original data were analysed using Stata 17·0, encompassing summary statistics, tests for heterogeneity, assessment of publication bias, subgroup analysis and sensitivity analysis. A total of ten studies were identified and grouped into twelve trials. Our results showed that individuals who carried the minor G allele of rs174575 had significantly higher dihomo-γ-linolenic acid levels (P = 0·005) and lower arachidonic acid levels (P = 0·033) than individuals who were homozygous for the major allele. The subgroup analysis revealed that the G-allele carriers of rs174575 were significantly positively correlated with linoleic acid (P = 0·002) and dihomo-γ-linolenic acid (P < 0·001) and negatively correlated with arachidonic acid (P = 0·004) in the European populations group. This particular SNP showed a potential association with higher concentrations of dihomo-γ-linolenic acid (P = 0·050) and lower concentrations of arachidonic acid (P = 0·030) within the breast milk group. This meta-analysis has been registered in the PROSPERO database (ID: CRD42023470562).

This study aimed to understand the potassium voltage-gated channel KQT-like subfamily, member 1 gene polymorphism in a rural elderly population in a county in Guangxi and to explore the possible relationship between its gene polymorphism and blood sugar. The 6 SNP loci of blood DNA samples from 4355 individuals were typed using the imLDRTM Multiple SNP Typing Kit from Shanghai Tianhao Biotechnology Co. The data combining epidemiological information (baseline questionnaire and physical examination results) and genotyping results were statistically analyzed using GMDR0.9 software and SPSS22.0 software. A total of 4355 elderly people aged 60 years and above were surveyed in this survey, and the total abnormal rate of glucose metabolism was 16·11 % (699/4355). Among them, male:female ratio was 1:1·48; the age group of 60–69 years old accounted for the highest proportion, with 2337 people, accounting for 53·66 % (2337/4355). The results of multivariate analysis showed that usually not doing farm work (OR 1·26; 95 % CI 1·06, 1·50), TAG ≥ 1·70 mmol/l (OR 1·19; 95 % CI 1·11, 1·27), hyperuricaemia (OR 1·034; 95 % CI 1·01, 1·66) and BMI ≥ 24 kg/m2 (OR 1·06; 95 % CI 1·03, 1·09) may be risk factors for abnormal glucose metabolism. Among all participants, rs151290 locus AA genotype, A allele carriers (AA+AC) were 0.70 times more likely (0.54 to 0.91) and 0.82 times more likely (0.70 to 0.97) to develop abnormal glucose metabolism than CC genotype carriers, respectively. Carriers of the T allele at the rs2237892 locus (CT+TT) were 0.85 times more likely to have abnormal glucose metabolism than carriers of the CC genotype (0.72 to 0.99); rs2237897 locus CT gene. The possibility of abnormal glucose metabolism in the carriers of CC genotype, TT genotype and T allele (CT + TT) is 0·79 times (0·67–0·94), 0·74 times (0·55–0·99) and 0·78 times (0·66, 0·92). The results of multifactor dimensionality reduction showed that the optimal interaction model was a three-factor model consisting of farm work, TAG and rs2237897. The best model dendrogram found that the interaction between TAG and rs2237897 had the strongest effect on fasting blood glucose in the elderly in rural areas, and they were mutually antagonistic. Environment–gene interaction is an important factor affecting abnormal glucose metabolism in the elderly of a county in Hechi City, Guangxi.

Toxocara vitulorum is one of the deadliest parasite of buffalo calves in Bangladesh. This study was conducted to explore genetic variability within and among the T. vitulorum populations in buffalo calves of Bangladesh. Genomic DNA was extracted, ITS2, COX1 and NAD1 gene were amplified and sequenced. Distinct 29 ITS2, 21 unique NAD1 and 24 COX1 genotypes were detected among the T. vitulorum of different geographic regions. These three gene genotypes similarities ranged from 97 to 99%, when these were compared to best hit scoring T. vitulorum sequences retrieved from GenBank. A total of 12 and 6 unique haplotypes were detected for COX1 and NAD1 gene sequences. The average nucleotide and haplotype diversity for COX1 and NAD1 were 0.0931 & 0.89493 and 0.00658 & 0.77895 respectively and the recorded values were more dispersed than previously published values. The pairwise Nst values ranged from −0.050 to 0.602 and Fst from −0.050 to 0.600 between all the T. vitulorum genotypes indicated huge genetic differentiation which were reportedly higher than other published reports Fst values. This is the first report of T. vitulorum on the basis of COX1 gene in Bangladesh. The study findings will be helpful for further extensive epidemiological studies regarding anthelmintic resistance, control and prevention of T. vitulorum infection in buffalo calves.

A breeding programme of aromatic vanilla, dating back to 1944, was conducted in Ambohitsara, Antalaha, SAVA (Sambava, Antalaha, Vohemara, Andapa) – Madagascar. Imported, local, wild and cultivated vanillas were used as progenitors and thousands of hybrids were generated. However, this germplasm has not undergone any genetic evaluation, and it appears that these valuable genetic resources have been dispersed or lost after the end of the programme (2000). This study aims to investigate the genetic diversity and structure of rescued genotypes currently held in a local collection in Antalaha. Double digest restriction associated-site (RAD)-seq (ddRAD)-seq protocol was applied, providing 865 million read sequences from 56 accessions. The ddRAD sequences have been deposited to the SRA archive of NCBI. From the data, 23,701 filtered concordant common Single Nucleotide Polymorphisms (SNPs) were identified using the three widely used tools (Stacks, BCFtools, Genome Analysis ToolKit - GATK) for short-read library sequencing. These SNPs were used for germplasm evaluation. Clustering analysis segregated samples into five genetic groups: Vanilla planifolia, Vanilla pompona, hybrid Tsitaitra, Vanille Banane and the phenotype Tsivaky. Our analysis revealed distinct subgroups within V. pompona and Tsitaitra, emphasizing the importance of further characterization to accurately reflect the genetic diversity and facilitate better utilization of these accessions in future research and germplasm management. The presence of private alleles in all groups (from 487 to 2866) indicated that populations were diverging and represented a large gene pool that could be useful for future breeding efforts. The genetic data obtained from this study offers valuable insights into the genetic diversity and structure of the vanilla population, with potential applications in breeding and conservation efforts.

Fine mapping and discovery of watermelon rind trait candidate genes are of great significance for modern watermelon breeding and development. In this study, we used the high-resolution genetic mapping and genome-wide genetic variation detection technology, combined with genome survey and sequencing technology, to locate and discover the candidate genes for rind traits of star watermelon varieties ‘Su XuanBai’ and ‘SHLX21’. Firstly, we identified a total of eight quantitative trait loci (QTLs) related to watermelon rind traits on chromosome 6. Secondly, a total of 208,240 single nucleotide polymorphisms and 75,345 small Indels (insertions/deletions) were detected in the two parents by high-coverage re-sequencing, respectively. Based on the genetic variation of the two parents and combined with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis using the planta database, the QTL region was reduced to 0.02 Mb. Finally, we identified the six potential regulatory factors for watermelon rind traits using real-time quantitative PCR. In conclusion, our results revealed the fine localization of candidate genes for watermelon rind traits and the successful discovery of candidate genes for regulating watermelon rind traits, which is of importance for watermelon rind traits and breeding-improved watermelon varieties.

In recent years, obesity is a growing pandemic in the world and has likely contributed to increasing the incidence of obesity-related diseases. Fat mass and obesity-associated gene (FTO) is the first gene discovered which has a close connection with fat. Recent studies suggested that FTO gene has played an important role in the molecular mechanisms of many diseases. Obesity is considered to be a hereditary disease and can evoke many kinds of diseases, including polycystic ovary syndrome (PCOS), type 2 diabetes mellitus (T2DM), cancer, etc., whose exact possible molecular mechanisms responsible for the effect of FTO on obesity and obesity-related diseases remain largely unknown. In this review, we comprehensively discuss the correlation between FTO gene and obesity, cancer, PCOS, T2DM, as well as the molecular mechanism involved in these diseases.

Several studies have examined the association between CD36 rs1761667 polymorphism with cardiometabolic risk factors and metabolic syndrome (MetS). This study aimed to investigate the interactions between rs1761667 polymorphism and dietary patterns on the cardiometabolic risk factors and the risk of MetS in apparently healthy individuals aged 20–70 years. Food consumption data were acquired using a validated semi-quantitative FFQ. Dietary patterns were identified by factor analysis. CD36 rs1761667 was genotyped by PCR-restriction fragment length polymorphism. The gene–diet interaction was detected by the general linear model or logistic regression. Significant or marginally significant interactions were observed between healthy dietary pattern (HDP) and CD36 rs1761667 on weight (P = 0·006), BMI (P = 0·009), waist circumference (P = 0·005), hip circumference (P = 0·06), body muscle percentage (P = 0·02), body fat percentage (P = 0·09), TAG-glucose index (P = 0·057), atherogenic index of plasma (P = 0·07), the risk of MetS (P = 0·02), risk of abdominal obesity (P = 0·02) and elevated blood pressure (P = 0·07). Besides, a gene–diet interaction was detected between the traditional dietary pattern and rs1761667 variants on odds of hypertriglyceridaemia (P = 0·02). The adherence to HDP was associated with a lower weight, BMI and higher odds of HDL-cholesterol only in A-allele carriers. In conclusion, adherence to HDP (a diet with high fibre, fish and dairy products) can be more effective on some cardiometabolic risk factors and risk of MetS components in the A-allele carrier than the GG genotype of rs1761667 polymorphism. However, future studies are required to shed light on this issue.

The aim was to study the effect of the threshold number on the accuracy of genomic evaluation of the threshold traits using support vector machine (SVM), genomic best linear unbiased prediction (GBLUP) and Bayesian method B (BayesB). For this purpose, a genome consisting of three chromosomes was simulated for 1000 individuals on which 3000 bi-allelic single nucleotide polymorphism markers were evenly distributed. Genomic breeding values were predicted in different scenarios of threshold number (1–6 thresholds), QTL number (30 and 300 QTLs) and heritability level (0.1, 0.3 and 0.5). By increasing the number of thresholds from 1 to 6 thresholds, especially at higher levels of heritability, the accuracy of genomic evaluation increased; however, the increase in accuracy was not linear so that it was much more noticeable when the number of thresholds increased from 1 to 2 thresholds. In the most studied scenarios, SVM showed a very poor performance compared to other methods. BayesB ranked first regarding prediction accuracy, though in some cases the observed differences with GBLUP was not significant. While increase in heritability increased the accuracy of genomic evaluation, change in the QTL number had a slight effect on the prediction accuracy. According to the results, the SVM is not recommended for genomic evaluation of threshold traits, especially those which have only one threshold and instead, use of GBLUP and BayesB is recommended. For traits with more than one threshold, fortunately we can achieve accuracy similar to continuous traits by applying traditional genomic evaluation methods.

Several single nucleotide polymorphisms (SNPs) could indirectly, as well directly, influence metabolic parameters related to health effects in response to selenium (Se) supplementation. This study aimed to investigate whether the selenoprotein SNPs were associated with the response of Se status biomarkers to the Brazil nut consumption in patients using statins and if the variation in Se homoeostasis could affect antioxidant protection, lipid profile, muscle homoeostasis and selenoproteins mRNA. The study was performed in the Ribeirão Preto Medical School University Hospital. Thirty-two patients using statins received one unit of Brazil nut daily for 3 months. Body composition, blood Se concentrations, erythrocyte glutathione peroxidase (GPX) activity, total cholesterol, low-density lipoprotein (LDL), high-density lipoprotein (HDL), triacylglycerol (TAG), creatine kinase (CK) activity and gene expression of GPX1 and selenoprotein P (SELENOP) were evaluated before and after Brazil nut consumption. The volunteers were genotyped for SNP in GPX1 (rs1050450) and SELENOP (rs3877899 and rs7579). SNPs in selenoproteins were not associated with plasma and erythrocyte Se, but SNPs in SELENOP influenced the response of erythrocyte GPX activity and CK activity, TAG and LDL after Brazil nut consumption. Also, Brazil nut consumption increased GPX1 mRNA expression only in subjects with rs1050450 CC genotype. SELENOP mRNA expression was significantly lower in subjects with rs7579 GG genotype before and after the intervention. Thus, SNP in SELENOP could be associated with interindividual differences in Se homeostasis after Brazil nut consumption, emphasising the involvement of genetic variability in response to Se consumption towards health maintenance and disease prevention.

Soybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

In the present study, we analysed the effects of SNP rs174547 (T/C) in the fatty acid desaturase 1 (FADS1) gene on long-chain PUFA levels. Four databases were searched to retrieve related literature with keywords such as fatty acid (FA), SNP, FADS1 and rs174547. A meta-analysis of the data was performed using Stata12.0 software, including summary statistics, test for heterogeneity, evaluation of publication bias, subgroup analysis and sensitivity analysis. The associations between rs174547 in FADS1 and seven types of FA, and Δ-5 (D5D) and Δ-6 fatty acid desaturase (D6D) activity were assessed based on the pooled results from eleven papers. A total of 3713 individuals (1529 TT and 2184 TC + CC) were included. The results demonstrated that minor C allele carriers of rs174547 had higher linoleic acid (LA; P < 0·001) and α-linolenic acid (P = 0·020) levels, lower γ-linolenic acid (GLA; P = 0·001) and arachidonic acid (P = 0·024) levels, and lower D5D (P = 0·005) and D6D (P = 0·004) activities than the TT genotype group. Stratification analysis showed that minor C allele carriers of rs174547 had higher LA and lower GLA levels and lower D6D activities in plasma (LA, P < 0·001; GLA, P < 0·001; D6D activity, P < 0·001) samples and in Asian populations (LA, P < 0·001; GLA, P = 0·001; D6D activity, P = 0·001) than the TT genotype group. In conclusion, minor C allele carriers of the SNP rs174547 were associated with decreased activity of D5D and D6D.

The FNDC5 gene encodes the fibronectin type III domain-containing protein 5 that is a membrane protein mainly expressed in skeletal muscle, and the FNDC5 rs3480 polymorphism may be associated with liver disease severity in non-alcoholic fatty liver disease (NAFLD). We investigated the influence of the FNDC5 rs3480 polymorphism on the relationship between sarcopenia and the histological severity of NAFLD. A total of 370 adult individuals with biopsy-proven NAFLD were studied. The association between the key exposure sarcopenia and the outcome liver histological severity was investigated by binary logistic regression. Stratified analyses were undertaken to examine the impact of FNDC5 rs3480 polymorphism on the association between sarcopenia and the severity of NAFLD histology. Patients with sarcopenia had more severe histological grades of steatosis and a higher prevalence of significant fibrosis and definite non-alcoholic steatohepatitis than those without sarcopenia. There was a significant association between sarcopenia and significant fibrosis (adjusted OR 2·79, 95 % CI 1·31, 5·95, P = 0·008), independent of established risk factors and potential confounders. Among patients with sarcopenia, significant fibrosis occurred more frequently in the rs3480 AA genotype carriers than in those carrying the FNDC5 rs3480 G genotype (43·8 v. 17·2 %, P = 0·031). In the association between sarcopenia and liver fibrosis, there was a significant interaction between the FNDC5 genotype and sarcopenia status (P value for interaction = 0·006). Sarcopenia is independently associated with significant liver fibrosis, and the FNDC5 rs3480 G variant influences the association between sarcopenia and liver fibrosis in patients with biopsy-proven NAFLD.