Genetic variations of HSBP1 gene and its effect on thermal performance traits in Chinese Holstein cattle

Molecular chaperones have been understood to be preferentially transcribed to prevent perturbations in response to various stresses. In this study, three single nucleotide polymorphisms (SNPs), g.324G>C, g.589C>T and g.651C>G in Heat shock factor binding protein 1 (HSBP1) gene were found and genotyped in 930 Chinese Holstein cattle. The results indicated that only g.589C>T polymorphism locus met Hardy–Weinberg equilibrium (P > 0.05). Pair linkage disequilibrium analysis and haplotype construction of HSBP1 gene were performed using SHEsis software. Seven haplotypes were constructed and fourteen haplotype combinations were found. Association analysis showed that H2H2 haplotype combination was advantageous for thermo tolerance breeding in Chinese Holstein. The cows with H2H2 haplotype combination have lower decrease rate of milk yield than those with H2H3 haplotype combination (P < 0.05) and lower potassium content in erythrocytes (PCE) than those with H2H5 (P < 0.05), H4H4 (P < 0.05) and H4H5 (P < 0.01) haplotype combination. The association between SNP and thermo tolerance traits showed that PCE of cows with GG genotype was lower than those with CG genotype at g.651C>G locus (P < 0.01). Pair linkage disequilibrium analysis revealed that the three loci were at a strong disequilibrium state. So we presumed that the effect of H2H2 haplotype combination on thermo tolerance traits major due to the SNP of g.651C>G.     

Three Novel SNPs in the Coding Region of the Bovine MC3R Gene and Their Associations with Growth Traits

The involvement of melanocortin-3 receptor (MC3R) is well recognized in the regulation of feeding efficiency, body weight, and energy homeostasis. The objective of this study was to investigate the associations between MC3R gene polymorphisms and growth traits. Three novel SNPs (c.24C→T, c.220T→A, c.734G→C) and five haplotypes were identified in 234 Xiangxi cattle. The associations between MC3R gene polymorphisms and growth traits indicated that the individuals with TT and AT genotypes maintained higher body weight than those with the AA genotype at the c.220T→A locus (P < 0.05). The animals with GG and CG genotypes had higher heart girth and body weight than those with the CC genotype at c.734G→C (P < 0.05). The animals with H3H3 and H2H3 haplotype combinations had higher body weight than those with other haplotype combinations (P < 0.05). The results suggest that these SNPs in the MC3R gene might be useful genetic markers for marker-assisted selection and cattle breeding.     

Plaque Image Characteristics, Hyperhomocysteinemia, and Gene Polymorphism of Homocysteine Metabolism-Related Enzyme (MTHFR C677T) in Acute Coronary Syndrome

This study aims to investigate the correlation between the different characteristics of plaques, plasma level of homocysteine (Hcy), and gene polymorphism of Hcy metabolism-related enzyme. In this consecutive case–control study, we measured the plasma Hcy level using fluorescence biochemistry method and examined the gene polymorphism of Hcy metabolism-related enzyme methylenetetrahydrofolate reductase (MTHFR) C677T using TaqMan probe technology. We also examined these using intravascular ultrasound. We studied the characteristics of the plaque, measured the cross-sectional areas of the external elastic membrane and the lumen, calculated the plaque area, plaque burden, and eccentricity index, and examined the remodeling index. Hard plaques were more dominant in the (SPA) group, whereas soft plaques were more dominant in the acute coronary syndrome (ACS) group (P < 0.001). The risk of plaque rupture and thrombus is higher in the ACS group (P < 0.05). Compared with SPA group, plaque burden was heavier in the ACS group (P < 0.05), but the eccentricity index is significantly higher in SPA group than in the ACS group (P < 0.001). Positive remodeling was more frequent in ACS group, whereas negative remodeling was more frequent in the SPA group (P < 0.001). Plasma Hcy levels were higher in the unstable than in the stable plaque group (P < 0.001). The constituent ratio of MTHFR C677T genotype were different in stable plaque group and vulnerable plaque group (P < 0.05). The T genotype can increase the incidence rate of vulnerable plaque. Hcy and MTHFR C677T gene polymorphism were found to be risk factors for vulnerable plaque. Therefore, these can be used as indices to predict the instability of atherosclerotic plaque.     

Association analysis of the SNP (rs345476947) in the <Emphasis Type="Italic">FUT2</Emphasis> gene with the production and reproductive traits in pigs

The FUT2 gene was considered as an important candidate for pathogenic infections, while the potential associations between this gene and the production and reproductive traits of pigs have not been explored. In this study, we detected the genetic variants of porcine FUT2 gene and analyzed the associations of the polymorphisms with FUT2 mRNA expression and production and reproductive traits (age at 100 kg, backfat thickness at 100 kg, eye muscle thickness, the number of newborn piglets, the number of weaned piglets, and birth weight) in 100 Large White sows. One single nucleotide polymorphism (SNP) (rs345476947, C→T) in the intron of FUT2 and three genotypes (TT, CT and CC) were determined. Association analysis revealed significant associations between this SNP with the number of newborn piglets and weaned piglets. Furthermore, individuals with the TT genotype had significantly higher numbers of newborn piglets and weaned piglets than those with the CC genotype (P?<?0.05). Quantitative PCR analysis showed that FUT2 expression in individuals with CC genotype was significantly higher than those with TT and CT genotypes in the liver and lymph gland (P?<?0.05) and higher than that of CT in the spleen, kidney, and duodenum (P?<?0.05). These findings indicated that the TT genotype may be a favorable genotype for the reproductive traits of pigs. Our study revealed the genetic variants of the FUT2 gene and identified a promising candidate SNP (rs345476947) associated with the reproductive traits, which has the potential to be applied in selective breeding of pigs.     

Effect of metabolic syndrome risk factors and MMP-2 genetic variations on circulating MMP-2 levels in childhood obesity

Matrix metalloproteinase-2 is involved in the development of the adipose tissue, and associated with cardiovascular diseases. Metabolic risk factors (MRFs) and functional polymorphisms in the MMP-2 gene may affect its expression and activity. We investigated whether traditional MRFs and two MMP-2 gene polymorphisms (C^?1306T; rs243865, and C^?735T; rs2285053) affect circulating MMP-2 levels in children and adolescents, and whether MMP-2 polymorphisms and/or haplotype are associated with susceptibility to childhood obesity. We studied 114 healthy controls, 43 obese, and 83 obese with ≥3 MRFs children and adolescents. Genotypes were determined by Taqman allele discrimination assay and real-time PCR. Plasma MMP-2 was measured using zymography. We found positive correlations between MMP-2 concentrations and mean blood pressure in all children and adolescents group (r = 0.132; P < 0.05) and in obese children and adolescents (r = 0.247; P < 0.01). We found that the CC genotype for the C^?1306T polymorphism was more common in subjects with higher MMP-2 concentrations in controls (P = 0.003) and in the obese group (P = 0.013). The CT genotype (OR = 0.40; P < 0.01) and the T allele (OR = 0.48; P < 0.01) for the C^?735T polymorphism were less common in obese children and adolescents than in controls. The haplotypes distribution did not show significant differences between control and obese (P > 0.05). Ours findings show that blood pressure is associated with circulating MMP-2 concentrations, and that the CC genotype for the C^?1306T polymorphism was more common subjects (controls and obese) with higher MMP-2 concentrations, whereas the CT genotype and the T allele for the C^?735T polymorphism are less common in obesity.     

Association of the C825T polymorphism in the GNB3 gene with obesity and metabolic phenotypes in a Taiwanese population

The relationship between obesity and a single nucleotide polymorphism (SNP), rs5443 (C825T), in the guanine nucleotide binding protein beta polypeptide 3 (GNB3) gene is currently inconsistent. In this study, we aimed to reassess whether the GNB3 rs5443 SNP could influence obesity and obesity-related metabolic traits in a Taiwanese population. A total of 983 Taiwanese subjects with general health examinations were genotyped. Based on the criteria defined by the Department of Health in Taiwan, the terms “overweight” and “obesity” are defined as 24 ≦ BMI < 27 and BMI ≧ 27, respectively. Compared to the carrier of the combined CT + TT genotypes of the GNB3 rs5443 polymorphism, triglyceride was significantly higher for the carrier of CC genotype in the complete sample population (128.2 ± 93.2 vs. 114.3 ± 79.1 mg/dl; P = 0.041). In addition, the carriers of CC variant had a higher total cholesterol than those with the combined CT + TT variants (194.5 ± 36.8 vs. 187.9 ± 33.0 mg/dl; P = 0.019) in the complete sample population. In the normal controls, both triglyceride (P = 0.018) and total cholesterol (P = 0.011) were also significantly higher in the CC homozygotes than in the combined CT + TT genotypes. However, the GNB3 rs5443 SNP did not exhibit any significant association with obesity or overweight among the subjects. Our study indicates that the CC genotype of the GNB3 rs5443 SNP may predict higher obesity-related metabolic traits such as triglyceride and total cholesterol in non-obese Taiwanese subjects (but not in obese subjects).     

Study on genetic variations of PPARα gene and its effects on thermal tolerance in Chinese Holstein

Peroxisome proliferator-activated receptor alpha (PPARα) regulates responses to chemical or physical stress in part by altering expression of genes involved in proteome maintenance. In this research, polymerase chain reaction (PCR) technique was used to amplify 766 and 589 bp fragments of intron 3 and 7 of PPARα gene in Chinese Holstein (n = 771). Sequencing results showed that three novel single nucleotide polymorphisms (SNPs) were identified at position 44087 (G/A), 65550 (G/A), and 65676(G/A) in the PPARα gene. PCR–restriction fragment length polymorphism technology was used to genotype the three SNPs. Association analysis showed that cows with H1H8 (P < 0.05), H2H8 (P < 0.01), H5H7 (P < 0.05), H5H8 (P < 0.05), and H8H8 (P < 0.05) haplotype combinations had lower potassium content in erythrocytes than those with H2H6 haplotype combination. Cows with H1H8, and H8H8 haplotype combinations had lower decrease rate of milk yield than those with H2H6 and H6H8 haplotype combinations (P < 0.05). Cows with H2H8 and H8H8 haplotype combinations had lower rectal temperature than those with H5H8 and H7H7 haplotype combinations (P < 0.05). In conclusion, H8H8 haplotype combination may be advantageous for heat resistance traits in Chinese Holstein cattle.     

A polymorphism in the visfatin gene promoter is related to decreased plasma levels of inflammatory markers in patients with coronary artery disease

Visfatin, a newly identified proinflammatory adipokine, has been linked to coronary artery disease (CAD). The ?1535C>T polymorphism (rs61330082) located in the visfatin gene promoter is reportedly associated with proinflammatory status. However, it is unclear whether this polymorphism correlates with plasma levels of inflammatory markers including visfatin, hs-CRP, IL-6 and TNF-?? in CAD patients. The present study was to investigate the potential association of the ?1535C>T polymorphism with plasma levels of visfatin, IL-6, C reactive protein (hs-CRP) and TNF-?? in patients with CAD. We conducted a hospital based study with 171 CAD patients to examine the association between the ?1535C>T polymorphism and plasma levels of visfatin, hs-CRP, IL-6 and TNF-??. Plasma visfatin levels were markedly different between patients with stable angina pectoris (SAP, 11.91 ± 0.70 ng/l) and those with unstable angina pectoris (UAP, 17.49 ± 0.20 ng/l) or acute myocardial infarction (AMI, 16.63 ± 0.22 ng/l; SAP versus UAP or AMI, P < 0.05). Compared with the CC genotype, variant genotypes CT and TT correlated with significantly lower levels of visfatin, hs-CRP, IL-6 and TNF-?? in the SAP group (P < 0.05), with lower levels of hs-CRP and IL-6 in the UAP group (P < 0.05), and with lower levels of visfatin in the AMI group (P < 0.05) after adjustment for age, gender, smoking, hypertension, diabetes, dyslipidemia and medication. Our results suggest that the ?1535C>T polymorphism is associated with decreased plasma levels of inflammatory markers in CAD patients, reflecting that this polymorphism might provide a useful marker for predicting the development of CAD events.     

Associations of polymorphism within the GHSR gene with growth traits in Nanyang cattle

GH secretagogue receptor (ghrelin receptor, GHSR) is known to be involved in the control of GH release by mediating the strong stimulatory effect of the endogenous ligand, ghrelin, on GH secretion. Associations between the GHSR gene polymorphism and the growth traits were revealed in Nanyang cattle. The mutations at nt456(G > A) and nt667(C > T) were complete linkage and located in exon 1 of the coding region of the GHSR gene. Least squares analysis revealed a significant statistical effect (P < 0.05) of the GHSR gene different genotypes on body weight and average daily gain at 6 months of age in Nanyang cattle. Individuals with GHSR-MM genotype showed higher body weight and average daily gain than individuals with GHSR-MN genotype.     

Association of heat stress protein 90 and 70 gene polymorphism with adaptability traits in Indian sheep (<Emphasis Type="Italic">Ovis aries</Emphasis>)

Heat stress proteins assist cellular proteins in the acquisition of native structure. The present research was conducted to study how thermo-tolerance is modulated by HSP90 and HSP70 gene polymorphism and its association with hemato-physio-biochemical parameters, supported by their expression profiles in Chokla, Magra, Marwari, and Madras Red sheep breeds. Least square analysis revealed significant effect (P < 0.05) of season and breed on all the physiological parameters, i.e., temperature, respiratory rate, and pulse rate (a.m. and p.m.), as well as hematological parameters like Hb, packed cell volume, total erythrocyte count (TEC), neutrophil/lymphocyte (N/L) ratio, and total leukocyte count (TLC). There was a significant influence (P < 0.05) of breed on biochemical parameters such as glucose, SGOT, phosphorous, triglyceride, and cholesterol. Eight fragments were amplified and sequenced in HSP90, and 70 genes and 13 single-nucleotide polymorphisms (SNPs) were identified. Tetra-primer amplification refractory mutation system PCR, PCR-RFLP, and allele-specific PCR genotyping protocols were developed for large-scale genotyping of five SNPs. A significant difference (P < 0.05) of rectal temperature (a.m.), respiratory rate (p.m.), triglyceride, and total protein was observed at SNP01; albumin at SNP2; pulse rate (p.m.) at SNP3; and rectal temperature (p.m.), pulse rate (p.m.), Hb (g/dL), and N/L ratio at SNP4 and TLC at SNP5. Gene expression analysis revealed lower expression in less adapted animals with Madras Red < Magra < Chokla < Marwari expression pattern. Predominant allele was found to be superior in most of the SNPs (SNP1–4) indicating the selection acting in directional manner (positive selection). Finally, it is concluded that TACCA haplotype combination of SNP1-SNP2-SNP3-SNP4-SNP5 might be of some selection advantage for the identification of animals more adaptable to heat stress.     

Relationships Between Single Nucleotide Polymorphisms of the H-FABP Gene and Slaughter and Meat Quality Traits in Chicken

Using PCR-SSCP with five primer pairs, we detected six single nucleotide polymorphisms of the H-FABP gene: 332G → A, 534G → A, 783C → T, 835C → T, 1198T → C, and 2329C → T. Chi-square results showed significant differences (P < 0.05) in genotype frequency among breeds in Fragment 1 and extremely significant differences (P < 0.01) in Fragments 2–4. We found a significant association between Fragment 2 genotype and muscle fiber number, Arg and Thr (P < 0.05); between Fragment 3 genotype and living weight, carcass weight, breast muscle weight, abdominal fat weight, and abdominal fat percentage (P < 0.05); between Fragment 4 genotype and Thr, Phe, and inosinic acid (P < 0.05). It was concluded that H-FABP was the major gene influencing slaughter performance and meat quality or was linked with the major gene in these strains and that the C783T mutation could be used as a candidate molecular genetic marker for breeding selection. The combination M1C2–B2B2–D1D1 is an ideal model for breeding in these strains because it can improve slaughter and meat quality traits.     

Association of AHSG Gene Polymorphisms with Ischemic Stroke in a Han Chinese Population

Previous studies have shown associations of fetuin-A (alpha₂-Heremans-Schmid glycoprotein, AHSG) with various disorders, including insulin resistance, type 2 diabetes mellitus, metabolic syndrome, and atherosclerosis. In this study, genotype and allele frequencies of the rs4918 SNP in the AHSG gene were examined in 380 patients with ischemic stroke and 350 healthy controls from a Northern Han Chinese population via the PCR-RFLP technique. Frequencies of the GG genotype and the G allele in AHSG (rs4918) were significantly higher in patients with ischemic stroke or atherosclerotic cerebral infarction than those in the control group (P < 0.05). Logistic regression analysis demonstrated the significance of rs4918 in these patients, after adjustment for confounding factors (P < 0.05). These findings suggest that rs4918 SNPs of the AHSG gene are associated with a risk for ischemic stroke in a Northern Han Chinese population.     

Association Study Between Macrophage Migration Inhibitory Factor-173 Polymorphism and Acute Myeloid Leukemia in Taiwan

Acute myeloid leukemia (AML) is the most common acute leukemia diagnosed in adults. Macrophage migration inhibitory factor (MIF) is a pro-inflammatory cytokine that plays a significant role in pathogenesis and autoimmune diseases. The major function of MIF is to promote the cell proliferation, migration, and invasion. The aim of the present study is to identify the association between MIF-173 (rs755662) single nucleotide polymorphism (SNP) and AML in Taiwanese population. DNA samples extracted from 256 AML patients and 256 healthy controls were investigated using polymerase chain reaction followed by restriction fragment length polymorphism analysis. The association between MIF-173 SNP genotype and AML patients were assessed with SPSS software. The results show that the GC genotype of MIF-173 SNP is significantly higher in AML patients than in the healthy controls (OR 1.58, 95 % CI 1.06, P = 0.034). Carrier genotypes GC and CC may be a causative factor for AML cancer (OR 1.39, 95 % CI 0.95, P = 0.085). White blood cell count (10³/µl) were significantly associated with AML MIF-173 polymorphism patients (P = 0.002). Our results in this study provide the first evidence that the MIF-173 polymorphism is associated with AML. MIF is a potential biomarker for development of AML cancer in male adult in Taiwanese population. Further validations in other populations are warranted.     

A novel SNP of liver-type fatty acid-binding protein gene in duck and its associations with the intramuscular fat

Liver-type fatty acid-binding protein (L-FABP) is a member of intracellular lipid-binding proteins involved in the transportation of fatty acids. We detected the polymorphisms of duck L-FABP gene and its association with the intramuscular fat (IMF) and other fat-related traits. The complete sequence of duck L-FABP gene (four exons and three introns, 2,542?bp) was obtained in this study. The polymorphism of L-FABP gene was examined with direct DNA sequencing method in 231 individuals from different breeds, and a novel single nucleotide polymorphism in the exon 3 was detected. The polymorphism was shown to be associated with the contents of C16:0, C18:3 and the total IMF in pectoral muscle. The content of C16:0 in genotype CC was significantly higher than CT (P?<?0.01) and TT (P?<?0.01), and the genotype CT was higher than TT (P?<?0.01). The content of C18:3 in genotype TT was significantly higher than CC and CT (P?<?0.01), whereas the genotype CC and CT had no significant difference (P?>?0.05). The content of IMF in genotype CC was significantly higher than CT (P?<?0.01). However, no significant difference was detected between genotype CC and TT or genotype CT and TT (P?>?0.05).     

A novel 18-bp deletion mutation of the AMPD1 gene affects carcass traits in Qinchuan cattle

The objectives of the present study were focused on detecting deletion mutation in bovine AMPD1 gene, and analyzing its effect on body measurement and carcass traits in Qinchuan cattle by using DNA sequencing and agarose electrophoresis methods. The 198-bp PCR products of AMPD1 gene exhibited three genotypes and two alleles were revealed: A and B. The frequencies of genotype AA/AB/BB in Qinchuan populations was 0.7163, 0.2233 and 0.0605. The χ²-test analysis demonstrated that the breed was not in agreement with Hardy–Weinberg equilibrium (P < 0.05). The association of the 18-bp deletion mutation of AMPD1 gene with body measurement and carcass traits of Qinchuan cattle were analyzed. The cattle with AA genotype had slaughter weight and carcass weight than those with genotype AB (P < 0.01 or P < 0.05). These results suggest that the 18-bp deletion mutation may influence the carcass traits in Qinchuan cattle.     

The Role of NQO1 Polymorphisms in the Susceptibility and Chemotherapy Response of Chinese NSCLC Patients

To investigate whether the NAD(P)H:quinone oxidoreductase 1 (NQO1) gene polymorphisms determine the Platinum-based chemotherapy in advanced non-small cell lung cancer (NSCLC) in a Chinese cohort. A total of 391 patients with inoperable advanced stage of NSCLC, namely, stage III (A + B) and IV NSCLC, and 663 age-and sex-matched healthy were enrolled. The effects of chemotherapy were evaluated. NQO1 C609T polymorphism was determined. The NSCLC patients had a significantly higher prevalence of TT than control subjects (33.76 vs. 21.67 %, P < 0.001). For allele comparison, NSCLC subjects had lower T allele frequency than controls as well (55.63 vs. 44.42 %, P < 0.001). multivariate regression analyses showed the TT carriage had a significantly increased risk for development of NSCLC after adjustments with age, sex, smoke, and cancer family history (OR 1.681, 95 % CI 1.242–2.274, P = 0.001). The TT genotype distribution was significantly higher in non-responders than in responders (31.85 vs. 21.96 %, P = 0.003). Logistic regression analysis showed TT genotype carriers had less chance to gain chemotherapy response compared to CC genotype carriers (OR 0.399, P = 0.003) after adjustment with sex, age, tumor histology, disease stage, and chemotherapy regimens. The NQO1 C609T polymorphism is an important molecular marker for advanced NSCLC, since it is associated with the NSCLC risk as well as the response status of platinum-based chemotherapy.     

Cloning of TPO gene and associations of polymorphisms with chicken growth and carcass traits

Thyroid peroxidase (TPO), which located on the apical membrane surface of thyrocytes, is the key enzyme involved in thyroid hormone synthesis, mainly catalyses the iodination of tyrosine residues and the coupling of iodotyrosines on thyroglobulin to form thyroxine and triiodothyronine. The objectives of this study were to identify genetic polymorphisms of the chicken TPO gene and to analyze potential association between single nucleotide polymorphisms (SNPs) and growth and carcass traits in chicken. Partial sequences of TPO gene were cloned firstly. The nucleotide sequence was found to have 72 % identity with that of humans. The chicken TPO amino acid sequence was 71 %. Through polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing methods, three novel mutations of the chicken TPO gene were detected in the F₂ resource population from Gushi chickens and Anka broilers. The association analysis indicated that all of the three SNPs showed association with chicken growth at different periods. The g.29996C>T polymorphisms was significantly associated with body weight, breast bone length, pectoral angle at 12 weeks, claw weight and leg muscle weight (P < 0.05). In addition, individuals with the TT genotype had higher value for almost all the traits than CC and CT genotype. Meanwhile for CLW, the additive effects were significant (P < 0.05). Hence, we suggest that genotype TT can be regarded as a potential molecular marker for later growth and carcass traits in chicken.     

Ovine insulin induced-gene-2: molecular characterization,polymorphisms and association with milk traits

The aim was to characterize the INSIG-2 gene in Sarda sheep and to highlight associations between polymorphisms and milk traits. Two-hundred ewes, in their third or fourth lactation who lambed a single lamb between 20th and 30th of November, were chosen. Monthly individual milk yield was recorded and from each ewe a sample of milk was taken to analyze fat and protein content. PCR–RFLP and DNA sequencing were carried out to detect polymorphisms. Five exons have been characterized and five mutations have been found G88A, 436TCAGdel, A471G, C1071T and T1737G all in the intronic regions. The ovine sequence and related variations were deposited in GenBank with accession number JX843812.1. The animals carrying AA genotype at position 88 showed a lower milk fat concentration than those with the AG or GG genotype (P < 0.05). A lower milk fat concentration was registered also in the animals with the TCAG deletion in position 436 (P < 0.05) and in the animals carrying AA genotype at position 471 compared to those with the AG or GG genotype (P < 0.05). Moreover, the animals carrying CC genotype at position 1071 had a greater milk yield than those with CT or TT genotype (P < 0.05) while ewes with TT genotype showed a higher milk protein concentration compared to the others (P < 0.05). A total of 11 haplotypes were detected but no significant associations with milk traits were found. In conclusion for the first time the complete coding sequence of INSIG-2 gene and its association with milk trait has been reported in this study.