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Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population

Abstract

The generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was limited to only a subset of chromosomes, thereby eliminating the ability to accurately impute genome-wide denser marker panels. Data used consisted of 10,933 candidate SNPs on 9,390 purebred sheep. These data consisted of 1,876 validated genotyped sire–offspring pairs and 2,784 validated genotyped dam–offspring pairs. The SNP panels developed consisted of 87 SNPs to 500 SNPs. Parentage verification and discovery were undertaken using 1) exclusion, based on the sharing of at least one allele between candidate parent–offspring pairs, and 2) a likelihood-based approach. Based on exclusion, allowing for one discordant offspring–parent genotype, a minimum of 350 SNPs was required when the goal was to unambiguously identify the true sire or dam from all possible candidates. Results suggest that, if selecting SNPs across the entire genome, a minimum of 250 carefully selected SNPs are required to ensure that the most likely selected parent (based on the likelihood approach) was, in fact, the true parent. If restricting the SNPs to just a subset of chromosomes, the recommendation is to use at least a 300-SNP panel from at least six chromosomes, with approximately an equal number of SNPs per chromosome.

Open access
Leptin Promoter Region Genotype Frequencies and Its Variability in the Czech Fleckvieh Cattle

Abstract

To investigate the differences between the lineages of the Czech Fleckvieh cattle in Leptin promoter SNP C963T, 695 Czech Fleckvieh cows (650 from production herds and 45 from the Genetic Resources Program (GR)) were examined using PCR-RFLP. The C and T alleles of Leptin promoter were observed with a predominance of C allele in both groups. The most frequent genotypes were CC (63%) in production herds and CT (48%) in the GR population. The present study describes, for the first time, the genetic differences in production herds and GR population in Leptin promoter C963T SNP. Variation within the Czech Fleckvieh population was observed and resulted in an advantage to the GR population. Results presented herein emphasized the importance of the GR program as a reservoir of genetic diversity for indigenous breeds.

Open access
Genomic descriptors of biodiversity – A review

Summary

The characterization of livestock genetic diversity has experienced extensive changes with the availability of dense nucleotide markers. Among the various forms of markers, the single nucleotide polymorphisms (SNP) have arguably the largest influence. A wide range of indicators for the assessment of genetic diversity was developed, or the existing methods were improved, enabling us to make informed decisions on the management of livestock populations. This review discusses the selected aspects of diversity assessment, with special attention to the SNP based methods.

One of the core concepts in genomics of diversity is the linkage disequilibrium (LD), as it was shaped by demographic events during the development of breeds and species. These events, either natural or artificial, left detectable signals within the livestock genomes. Further changes were induced by human activity when mating related animals, leading to fixing or improving the desired traits in the breed, but reducing their genetic variability. The assessment of relatedness is also pivotal to construct meaningful mating plans and to avoid the negative consequences of inbreeding depression that might be detrimental especially in small, endangered populations. Both LD and relatedness are of interest on their own, as well as in their follow-up applications deriving overall measures of effective population size.

Open access
Insulin-like growth factor-I gene polymorphism and its association with growth and slaughter characteristics in broiler chickens

Insulin-like growth factor-I gene polymorphism and its association with growth and slaughter characteristics in broiler chickens

Chicken insulin-like factor 1 gene (IGF1) is a biological candidate gene for the investigation of growth, body composition, and metabolic and skeletal traits, and is also a positional candidate gene for growth and fat deposition in chickens. Two broiler populations Ross 308 and Cobb 500 were used to study the relationship between IGF1 gene polymorphism and phenotypic traits. A single nucleotide polymorphism (SNP) was identified in 132 individuals using the PCR-RFLP technique. Genotypical frequencies were, for genotype AA: 0.83-0.86, and for AC: 0.14-0.17. Associations between IGF1 promotor polymorphism and liver weight (P≤0.05) and liver weight as a percentage of the weight of the poultry carcass with the giblets (P≤0.05), were found in the AC genotype in a comparison of broiler homozygous chickens AA in the Cobb 500 line. In these broilers, the breast muscle and leg muscle weight in the AC genotype were higher, and abdominal fat weight lower compared with AA genotype chickens, but these differences were not significant.

Open access
Melatonin Receptor 1B Gene Polymorphisms, Haplotypes and Susceptibility to Schizophrenia

Abstract

Melatonin has an important role in the regulation of human sleep circadian rhythms. Sleep disturbances commonly exist in schizophrenia (SCZ) patients. To begin its performance, melatonin must interact to its receptor. In the present study, Single Nucleotide Polymorphisms (SNPs) of melatonin receptor gene 1 B (MTN1B) with SCZ development in Iranian population were investigated. The current case-control study was performed on 92 SCZ patients and 92 healthy control (HC) subjects. NESTED-PCR and ARMS-PCR modified methods (combination) and ARMSPCR method were used on the genotype. The impact of MTN1B rs3781637 (T/C) and rs10830963(C/G) polymorphism variants on the risk SCZ in the sample of Iranian population was investigated. The findings showed significant association between MTN1B rs10830963(C/G) variant and SCZ (OR=2.78, 95%CI=1.25-6.25, P=0.012, GG vs. CC, OR=1.66, 95%CI=1.09-2.51, P=0.021 G vs. C, OR=3.85 95%CI=.89-8.33, P<0.0001, GG vs. CC+CG). There was no association between MTN1B rs3781637 (T/C) and SCZ risk. In addition, haplotype analysis revealed that TG and CC haplotype of rs3781637 (T/C) and rs10830963 (C/G) polymorphisms were associated with SCZ risk (P=0.039) and protective (P<0.0001) effects, respectively. The findings revealed that MTN1B rs10830963 (C/G) polymorphism was associated with the risk of SCZ; while another SNP rs3781637 (T/C) MTN1B gene did not show any risk/protection association with SCZ. Further studies with larger sample sizes and different ethnicities are required to approve the results.

Open access
TLR4 polymorphisms seem not to be associated with prediabetes and type 2 diabetes but predispose to diabetic retinopathy; TLR4 polymorphisms in glucose continuum

Abstract

Objectives. Compared to type 1 diabetes, the role of the immune and autoimmune pathogenetic mechanisms is much less studied in the type 2 diabetes. Toll-like receptors 4 (TLR4) have a leading role in inflammation, insulin resistance, and vascular damage. This study aimed to analyze the relationship between the polymorphisms in TLR4 gene and different stages in the glucose continuum from prediabetes to the type 2 diabetes and chronic microvascular complications.

Materials and Methods. The study included 113 patients with the type 2 diabetes, 29 participants with prediabetes, and 28 controls. Polymerase chain reaction (PCR) was used for genotyping Asp299Gly and Thr399Ile polymorphism, followed by restriction analysis.

Results. The difference in the genotype frequency for both polymorphisms in patients with the type 2 diabetes or prediabetes compared to that in controls was not significant. Patients with heterozygous genotype of Asp299Gly polymorphism had a higher prevalence of diabetic retinopathy (42.9%) than participants with homozygous genotype (9.0%) (OR [95%CI]=7.61 [1.41–41.08]; p=0.018). No association was established for diabetic polyneuropathy and nephropathy. Prevalence of chronic diabetes complications was not related to Thr399Ile polymorphism.

Conclusion. Our study demonstrates that Asp299Gly and Thr399Ile polymorphisms seem not to be associated with the type 2 diabetes and prediabetes but Asp299Gly may contribute to diabetic retinopathy predisposition.

Open access
Polymorphisms of AZIN1 rs2679757 and TRPM5 rs886277 are Associated with Cirrhosis Risk in Chinese Patients with Chronic Hepatitis B

Abstract

Objective Genome-wide association studies (GWAS) have linked many single nucleotide polymorphisms (SNPs) to the outcomes of a variety of liver diseases. The aim of the present study was to evaluate the association of several candidate SNPs with the risk and severity of cirrhosis due to chronic hepatitis B in a Chinese population.

Methods A total of 714 Chinese participants with persistent HBV infection were studied. Patients were divided into cirrhotic (n = 429) and non-cirrhotic (n = 285) groups based on clinical and pathological evidence. The progression rate and severity of liver cirrhosis were evaluated with an arbitrary t-score system. Genotypes of six SNPs in five candidate genes were detected with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The genotypic distributions of the SNPs were compared between the age-matched cirrhotic and non-cirrhotic subjects. The association between the risk of SNPs and the severity and progression rate of cirrhosis was further analyzed.

Results Rs2679757 polymorphism of the antizyme inhibitor 1 (AZIN1) gene and Rs886277 in the transient receptor potential cation channel subfamily M, member 5 gene (TRPM5) were found to be associated with cirrhosis risk in CHB. They were also correlated with the overall severity and progression rate of cirrhosis. Genotype frequencies of other SNPs were not different between the cirrhosis and non-cirrhosis groups.

Conclusions AZIN1 rs2679757 and TRPM5 rs886277 are associated with the risk and the progression rate of HBV-related liver fibrosis in Chinese patients. The emerging SNPs associated with cirrhosis prognosis warrant further clinical validation in other CHB cohorts or ethnic groups, and merit mechanistic studies to reveal their roles in fibrosis progression.

Open access
Association Analysis for Neuronal Nitric Oxide Synthase Gene Polymorphism with Plasma Nitrite/Nitrate Concentration in Schizophrenia

Summary

Background: Single nucleotide polymorphisms (SNP) of many genes, including the gene for neuronal nitric oxide syn-thase (NOS1), were found significantly associated with schizo-phrenia. According to our previously published results of increased plasma nitric oxide concentration in patients with schizophrenia, we hypothesized that the NOS1 gene polymorphism might be a cause of increased nitric oxide production in patients with schizophrenia and tested the interdependence between plasma nitrite/nitrate concentrations and SNP (a CT transition located in exon 29) of the human NOS1 gene.

Methods: Nitrite/nitrate concentration was measured in blood plasma of 38 patients with schizophrenia and of 39 age and gender matched healthy persons by the colorimet-ric test. The NOS1 gene polymorphism was determined by polymerase chain reaction analysis.

Results: A significantly higher plasma nitrite/nitrate concentration was found in patients with schizophrenia (97.5±33.3 μmol/L, p<0.001) in comparison with controls (61.4±18.9 μmol/L). No T/T genotype was found in healthy individuals and there was a significant difference in the genotype distribution between patients and controls (χ2=24.54, p=0.0000047). Furthermore, a significant difference in the allele frequencies between patients and controls (χ2=19.00, p<0.000013, OR=4.45, 95% CI=2.12–9.39) was noted. Also, a significant difference in plasma nitrite/nitrate concentration was observed between patients having the C/T genotype (99.97±33.83 μmol/L) and the corresponding control (C/T) subgroup (63.88±10.26 μmol/L, p<0.01). However, there were no significant differences in nitrite/nitrate concentration between the patient subgroups with different genotypes (C/C, C/T, T/T).

Conclusions: CT transition located in exon 29 of the human NOS1 gene may be responsible for the increased plasma nitrite/nitrate levels.

Open access
Rs1799817 in INSR associates with susceptibility to polycystic ovary syndrome

Summary

Background

Insulin and its receptor (INSR) have been implicated in the etiology of the polycystic ovarian syndrome (PCOS). Here, we investigate the association between INSR rs1799817 polymorphism and PCOS in Saudi Arabian women.

Methods

study group included 126 PCOS women and 118 normo-ovulatory matched controls. The demographic data was recorded, and the plasma levels of glucose, lipids, leptin, E2, LH, FSH, T, SHBG, and insulin were determined. The genotypic and allele frequencies of rs1799817 were evaluated in both PCOS and control group. Polymerase chain reaction (PCR) was used to amplify Exon 17 of the INSR gene, and the amplified products were analyzed by direct sequencing. A single-nucleotide polymorphism (C to T) was found at locus 10923 (His1058) of rs1799817.

Results

In the PCOS group, the mutant allele T occurs at a significantly higher frequency (0.306) compared to the control group (0.174) (p<0.001). It shows a dominant effect and elevates the relative risk of PCOS even in the heterozygotes (RR=2.82). After stratification of the participants by body mass index, the frequency of T allele was significantly higher in the lean patients with PCOS compared to the lean control. The obese PCOS also had a higher frequency than the obese control, but the difference was not statistically significant. Several parameter values were affected by the INSR genotype, particularly W/H ratio, lipid, insulin and glucose levels and insulin resistance in PCOS patients.

Conclusion

The INSR gene polymorphism rs1799817 is a susceptibility locus associated with PCOS in Saudis and associated metabolic and hormonal changes, particularly, in the lean PCOS females.

Open access
Association of serum paraoxonase 1 activities, polymorphisms and oxidative stress in breast cancer patients with type 2 diabetes mellitus

Summary

Background

The aim of the study was to investigate the association of paraoxonase 1 (PON1) polymorphism, PON1/arylesterase (ARE) activity and oxidative stress index (OSI) in breast cancer (BC) patients with type 2 diabetes (DM).

Methods

Our study group consisted of 30 healthy women (HV group) and 66 female BC patients. The BC patients were divided into two groups: those with (n=37) and without DM (n=29) (BDM and NBDM group). Genotyping of PON1 Q192R and L55M polymorphisms were done by polymerase chain reaction (PCR) – restriction fragment length polymorphism (RFLP) method. Serum PON1/ARE enzyme activities, total oxidant status (TOS) and total antioxidant status (TAS) were analysed by spectrophotometric method. The ratio of TOS to TAS was accepted as the oxidative stress index (OSI).

Results

PON1 Q192R genotype frequency distribution was significantly different in the BDM group compared to the NBDM group (p=0.021). When alleles distribution was examined, R and L alleles were significantly lower, Q and M alleles were significantly higher in the BDM group than in the NBDM group (p<0.001). TOS and OSI were statistically higher in BC patients than HV group (p<0.001).

Conclusions

Our results suggest that PON1 gene Q and M alleles may be the risk factors predisposing formation of BC due to increased oxidant damage seen in DM. However, these statements require further confirmation with screening PON1 polymorphism in a greater number of patients with DM, and also wide range follow-up studies are necessary for the same purpose.

Open access