PSXIV-25 Search for the association of SNP in GRM8 gene with sperm quality in stallions

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 257-257
Author(s):  
Elena Nikitkina ◽  
Anna Krutikova ◽  
Artem Musidray
Keyword(s):  
Volume Concentration ◽  
Sperm Quality ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Progressive Motility ◽  
Wide Range ◽  
Sperm Volume ◽  
Polymorphic Variants ◽  
Genetic Analyzer

Abstract The formation and functioning of the animal reproductive system occurs as a result of the coordinated interaction of a wide range of genes. To search for causal mutations, work was carried out to search for polymorphic variants in the marker regions detected using GWAS. The four single-nucleotide substitutions in the exon of the GRM8 gene identified during the studies and the association of these SNPs with sperm quality was carried out. Semen from 22 stallions was collected. Sperm volume, concentration and progressive motility were assessed. Sequencing of the sections of the candidate GRM8 gene was carried out using an Applied Biosystems 3500 genetic analyzer. For the rs1138419111 genotype, no significant differences were found in the studied parameters. According to the identified single nucleotide substitution rs1147388106, the highest ejaculate volume was in stallions with the GG genotype (55.9±26.5 ml) compared to stallions with the GA genotypes (32.5±13.9 ml) and AA (18.0±33,6) (p < 0.05). When analyzing data on SNP rs395286150, stallions with a heterozygous CT genotype had the best sperm quality. Thus, the cell concentration was 317.0±66.5 million/ml in stallions with the CT genotype, 209.6±58.2 and 189.5±74.9 % with the CC and TT genotypes, respectively (P < 0.05). The progressive sperm motility of stallions with the CT genotype was 65.5±20.5% versus 48.7±22.0% in stallions with the TT genotype and 48.4±18.6% with CC. Analysis of data on SNP rs394524550 revealed a significant effect of the genotype on progressive motility. Stallions with the AG genotype had a progressive motility of 64.6±16.3%, and those with GG and AA 32.7±15.7 and 49.6±18.1%, respectively (P < 0.05). Thus, as a result four single nucleotide polymorphisms were identified in the exon of the GRM gene. Three of them were significantly associated with such indicators of sperm quality as ejaculate volume, concentration and progressive motility. Project No. 0445-2021-0011.

scholarly journals 34 Search for the association of polymorphisms in inhibin alpha and prolactin genes with sperm quality in Russian Holstein bulls

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 12-13
Author(s):  
Elena Nikitkina ◽  
Anna Krutikova ◽  
Artem Musidray ◽  
Polina Anipchenko
Keyword(s):  
Reproductive System ◽  
Volume Concentration ◽  
Cell Function ◽  
Sperm Quality ◽  
Molecular Genetic ◽  
Wide Range ◽  
Pcr Rflp ◽  
Holstein Bulls ◽  
Sperm Traits ◽  
Genetic Analyzer

Abstract The formation and functioning of the animal reproductive system occurs as a result of the coordinated interaction of a wide range of genes. The hormone inhibin (INHA) is a marker of Sertoli cell function and exocrine testicular function (spermatogenesis state). The hormone prolactin (PRL) is a regulatory factor in the male reproductive system and affects gametogenesis. The aim of the work was to search for associations of inhibin alpha (INHA) and prolactin (PRL) gens polymorphism in the population of Russian Holstein bulls. Sperm traits (doublet ejaculate volume, concentration, progressive motility) were evaluated over three years of bull use and the highest rates for each trait were selected. 32 bulls had contrasting traits. DNA was isolated from semen samples. Samples were sequenced using the Applied Biosystems 3500 Genetic Analyzer using the BigDye® Terminator v3.1 Sequencing Standard Kit according to the protocol. Genotyping was then performed by PCR-RFLP. Data was analyzed using ANOVA. All pairwise multiple comparison between means were conducted by t-test. No polymorphism was detected in two regions of the PRL gene. The frequency of genotype AA in INHA gene was 0.813, the genotype AG -0.187. The GG genotype has not been identified. Bulls with the genotype AG had a higher concentration of cells (1.64 ± 0.093 billion/ml) than bulls with the genotype AA (1.35 ± 0.058) (P˂0.05). No significant differences were found in the volume of ejaculate and motility. But bulls with the AG genotype had greater ejaculate volume and motility than bulls with the AA genotype. The study of polymorphism in the genes that determine the formation and functioning of the reproductive system will help to understand the basics of these processes, as well as use them as molecular genetic markers for culling young bulls according to sperm quality. Project № АААА-А18-118021990006-9.

Association of genetic polymorphism of cytokines and antioxidant enzymes with the development of asbestosis

2020 ◽  
Vol 60 (12) ◽  
pp. 898-903
Author(s):  
Lyudmila P. Kuzmina ◽  
Anastasiya G. Khotuleva ◽  
Evgeniy V. Kovalevsky ◽  
Nikolay N. Anokhin ◽  
Iraklij M. Tskhomariya
Keyword(s):  
Antioxidant Enzymes ◽  
Genetic Polymorphism ◽  
Genetic Predisposition ◽  
Risk Groups ◽  
Dust Exposure ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Gstp1 Gene ◽  
Polymorphic Variants

Introduction. Various industries widely use chrysotile asbestos, which determines the relevance of research aimed at the prevention of asbestos-related diseases. It is promising to assess the role of specific genes, which products are potentially involved in the development and regulation of certain links in the pathogenesis of asbestosis, forming a genetic predisposition to the disease. The study aims to analyze the presence of associations of genetic polymorphism of cytokines and antioxidant enzymes with asbestosis development. Materials and methods. Groups were formed for examination among employees of OJSC "Uralasbest" with an established diagnosis of asbestosis and without lung diseases. For each person included in the study, dust exposure doses were calculated considering the percentage of time spent at the workplace during the shift for the entire work time. Genotyping of single nucleotide polymorphisms of cytokines IL1b (rs16944), IL4 (rs2243250), IL6 (rs1800795), TNFα (rs1800629) and antioxidant enzymes SOD2 (rs4880), GSTP1 (rs1610011), CAT (rs1001179) was carried out. Results. The authors revealed the associations of polymorphic variants A511G IL1b gene (OR=2.457, 95% CI=1.232-4.899) and C47T SOD2 gene (OR=1.705, 95% CI=1.055-2.756) with the development of asbestosis. There was an increase in the T allele IL4 gene (C589T) frequency in persons with asbestosis at lower values of dust exposure doses (OR=2.185, 95% CI=1.057-4.514). The study showed the associations of polymorphism C589T IL4 gene and C174G IL6 gene with more severe asbestosis, polymorphism A313G GSTP1 gene with pleural lesions in asbestosis. Conclusion. Polymorphic variants of the genes of cytokines and antioxidant enzymes, the protein products directly involved in the pathogenetic mechanisms of the formation of asbestosis, contribute to forming a genetic predisposition to the development and severe course of asbestosis. Using the identified genetic markers to identify risk groups for the development and intense period of asbestos-related pathology will optimize treatment and preventive measures, considering the organism's characteristics.

scholarly journals A Novel Test System for Genotyping rs43703016 Single-nucleotide Substitutions in the Bovine CSN3 Gene

2019 ◽  
pp. 1-5
Author(s):  
Svetlana Kovalchuk ◽  
Arina Tagmazyan ◽  
Eugene Klimov
Keyword(s):  
Nucleotide Substitution ◽  
Milk Proteins ◽  
Test System ◽  
Nucleotide Polymorphisms ◽  
Dna Testing ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Selection Of

Aims: Caseins are among the main milk proteins that determine many of its properties. Bovine kappa-casein (CSN3) is associated with the qualitative composition of milk, as well as with the quality of cheese obtained from this milk. The rs43703016 single-nucleotide substitution (g.88532332A>C; Asp148Ala) in exon 4 of the bovine CSN3 gene plays an important role in the production of quality hard cheeses. Various methods for the DNA testing of this substitution have been developed in the last three decades. Emergent DNA technologies provide an opportunity to modernize methods of genotyping single-nucleotide polymorphisms. Results: We have developed and verified a method to differentiate A/C alleles of the rs43703016 substitution in the bovine CSN3 gene by real-time PCR using allele-specific fluorescent probes. Conclusion: Our new method allows fast genotyping of animals, and may be used for selection of cows carrying the CC genotype, which determines good cheese-making properties of milk.

scholarly journals simuG: a general-purpose genome simulator

2019 ◽  
Vol 35 (21) ◽  
pp. 4442-4444 ◽  
Author(s):  
Jia-Xing Yue ◽  
Gianni Liti
Keyword(s):  
Copy Number Variants ◽  
General Purpose ◽  
Supplementary Information ◽  
Nucleotide Polymorphisms ◽  
Bioinformatics Analyses ◽  
Full Spectrum ◽  
Single Nucleotide ◽  
Genomic Variants ◽  
Wide Range ◽  
Simulation Based

Abstract Summary Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single nucleotide polymorphisms, Insertions/Deletions, copy number variants, inversions and translocations) for any organisms (including human). The simplicity and versatility of simuG make it a unique general-purpose genome simulator for a wide-range of simulation-based applications. Availability and implementation Code in Perl along with user manual and testing data is available at https://github.com/yjx1217/simuG. This software is free for use under the MIT license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals POLYMORPHISMS IN THE GENES OF REPARATIONS AMONG EMPLOYEES OF THE ATOMIC INDUSTRY OF KAZAKHSTAN

2020 ◽  
Vol 1 (337) ◽  
pp. 5-10
Author(s):  
D. M. Botbаeyev ◽  
А. M. Belkozhаev ◽  
A. K. Khanseitova ◽  
A. Zh. Borbayeva ◽  
N. А. Аitkhozhinа
Keyword(s):  
Nuclear Industry ◽  
Repair System ◽  
Nucleotide Polymorphisms ◽  
Low Dose Radiation ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Variable Regions ◽  
And Control ◽  
Dose Radiation

Single nucleotide polymorphisms (SNPs) are the most convenient marker and the widespread subject of polymorphism testing. To identify the presence or absence of the effects of chronic low-dose radiation on nuclear industry personnel, the occurrence of single-nucleotide substitutions at the polymorphic sites of the genes of the repair system 3 and 6 of the introns of the APC gene P53.11 gene, in positions -2549 of the VEGF gene, XPD gene rs313181 ( Lys751Gln) and rs25487 of the XRCC gene (Аrg399Gln) were compared. Analysis of allele frequencies and distribution of genotypes in the variable regions of the tested genes was performed by the method of polymerase chain reaction (PCR), followed by determination of restriction fragment length polymorphism (RFLP). When com-paring the frequencies of alleles and the distribution of genotypes between the second group of miners (11–20 years’ experience) and control, differences in the distribution of genotypes in the rs25487 XRCC plot (χ2 = 7.11, p = 0.028) were revealed. These differences satisfy the criterion p <0.05 and, accordingly, are statistically significant. Key words: polymorphism, genes, a nuclear industry.

INTERACTION BETWEEN POLYMORPHIC VARIANTS IN ТP53, XRCC1, TNFH, HMMR, MDM2,PALB2 GENES AND THEIR CONTRIBUTIONTO THE FORMATION OF A PREDISPOSITION TO BREAST CANCER IN WOMEN OF THE KYRGYZ POPULATION

2019 ◽  
Vol 65 (3) ◽  
pp. 357-367
Author(s):  
Zhaynagul Isakova ◽  
Vyacheslav Kipen ◽  
Elnura Talaybekova ◽  
Kubanych Aytbaev ◽  
N. Aldasheva ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Rflp Analysis ◽  
Nucleotide Polymorphisms ◽  
Heterozygous Genotype ◽  
Single Nucleotide ◽  
Polymorphic Loci ◽  
Pcr Rflp ◽  
Gene Tp53 ◽  
Polymorphic Variants ◽  
Kyrgyz Population

Aim: We studied the intergenic interactions and the contribution of polymorphic loci p.Arg72Pro (gene TP53), p.Gln399Arg (gene XRCC1), p.Arg194Trp (gene XRCC1), g.4682G>A (gene TNFa), p.Val353Ala (gene HMMR), p.14+309T>G (gene MDM2), g.38444T>G (gene PALB2) in the formation of predisposition to breast cancer (ВС) in women of Kyrgyz nationality. Material and method: The study included 103 women of the Kyrgyz ethnic group with the morphologically verified diagnosis of BC and 102 women without cancer and chronic diseases. Genotyping of single-nucleotide polymorphisms (SNPs) was performed using PCR-RFLP. Analysis of the intergenic interactions conducted with MDR 3.0.2 software. Results: Heterozygous genotype Gln/Arg of gene XRCC1 (ОR=3,15; 95% CI 1,78-5,58), the combination of Arg/Gln // Arg/Pro of genes XRCC1 (p.Gln399Arg) / TP53 (p.Arg72Pro) (OR=3,21; 95% CI 1,21-8,47), Arg/Gln // T/T of genes XRCC1 (p.Gln399Arg) / MDM2 (o.14+309T>G) (OR=3,18; 95% CI 0,99-10,7), Arg/Gln // G/G and Arg/Gln // G/A of genes XRCC1 (p.Gln399Arg) / TNFa (g.4682G>A) (OR=3,84; 95% CI 1,847,90) and (OR=3,91 95% CI 1,29-8,51 respectively), Arg/Gln // T/T of genes XRCC1 (p.Gln399Arg) / PALB2 (p.Thr1100=) (OR=2,92; 95% CI 1,59-5,37), as well as Arg/Gln // Arg/Arg and Arg/Gln // Arg/Trp for polymorphic loci p.Gln399Arg and p.Arg194Trp of gene XRCC1 (OR=2,48; 95% CI 1,12-5,19 and 0R=2,90, 95% CI 1,04-8,12 respectively) were associated with BC in Kyrgyz women. Conclusions: The results of the present study suggest that combinations of variants of ТP53, XRCC1, TNFa, HMMR, MDM2 и PALB2 genes may contribute to the genetic susceptibility of BC in Kyrgyz women.

SRG extractor: a skinny reference genome approach for reduced-representation sequencing

2019 ◽  
Vol 35 (17) ◽  
pp. 3160-3162
Author(s):  
Davoud Torkamaneh ◽  
Jérôme Laroche ◽  
Istvan Rajcan ◽  
François Belzile
Keyword(s):  
Reference Genome ◽  
Computing Time ◽  
Supplementary Information ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Scanning Method ◽  
Reduced Representation ◽  
A Genome ◽  
Wide Range ◽  
Reduced Representation Sequencing

Abstract Motivation Reduced-representation sequencing is a genome-wide scanning method for simultaneous discovery and genotyping of thousands to millions of single nucleotide polymorphisms that is used across a wide range of species. However, in this method a reproducible but very small fraction of the genome is captured for sequencing, while the resulting reads are typically aligned against the entire reference genome. Results Here we present a skinny reference genome approach in which a simplified reference genome is used to decrease computing time for data processing and to increase single nucleotide polymorphism counts and accuracy. A skinny reference genome can be integrated into any reduced-representation sequencing analytical pipeline. Availability and implementation https://bitbucket.org/jerlar73/SRG-Extractor. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals From Single Nucleotide Polymorphisms to Constant Immunosuppression: Mesenchymal Stem Cell Therapy for Autoimmune Diseases

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Raghavan Chinnadurai ◽  
Edmund K. Waller ◽  
Jacques Galipeau ◽  
Ajay K. Nooka
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Autoimmune Diseases ◽  
Association Studies ◽  
Autoimmune Disorders ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Mesenchymal Stem Cell Therapy ◽  
Immune Mediated ◽  
Wide Range

The regenerative abilities and the immunosuppressive properties of mesenchymal stromal cells (MSCs) make them potentially the ideal cellular product of choice for treatment of autoimmune and other immune mediated disorders. Although the usefulness of MSCs for therapeutic applications is in early phases, their potential clinical use remains of great interest. Current clinical evidence of use of MSCs from both autologous and allogeneic sources to treat autoimmune disorders confers conflicting clinical benefit outcomes. These varied results may possibly be due to MSC use across wide range of autoimmune disorders with clinical heterogeneity or due to variability of the cellular product. In the light of recent genome wide association studies (GWAS), linking predisposition of autoimmune diseases to single nucleotide polymorphisms (SNPs) in the susceptible genetic loci, the clinical relevance of MSCs possessing SNPs in the critical effector molecules of immunosuppression is largely undiscussed. It is of further interest in the allogeneic setting, where SNPs in the target pathway of MSC's intervention may also modulate clinical outcome. In the present review, we have discussed the known critical SNPs predisposing to disease susceptibility in various autoimmune diseases and their significance in the immunomodulatory properties of MSCs.

scholarly journals Diversification of DNA Sequences in the Symbiotic Genome of Rhizobium etli

2005 ◽  
Vol 187 (21) ◽  
pp. 7185-7192 ◽  
Author(s):  
Margarita Flores ◽  
Lucia Morales ◽  
Agustín Avila ◽  
Víctor González ◽  
Patricia Bustos ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nucleotide Polymorphisms ◽  
Rhizobium Etli ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Genetic Elements ◽  
Hypervariable Regions ◽  
The Common ◽  
Different Strains ◽  
Model Strain

ABSTRACT Bacteria of the genus Rhizobium and related genera establish nitrogen-fixing symbioses with the roots of leguminous plants. The genetic elements that participate in the symbiotic process are usually compartmentalized in the genome, either as independent replicons (symbiotic plasmids) or as symbiotic regions or islands in the chromosome. The complete nucleotide sequence of the symbiotic plasmid of Rhizobium etli model strain CFN42, symbiont of the common bean plant, has been reported. To better understand the basis of DNA sequence diversification of this symbiotic compartment, we analyzed the distribution of single-nucleotide polymorphisms in homologous regions from different Rhizobium etli strains. The distribution of polymorphisms is highly asymmetric in each of the different strains, alternating regions containing very few changes with regions harboring an elevated number of substitutions. The regions showing high polymorphism do not correspond with discrete genetic elements and are not the same in the different strains, indicating that they are not hypervariable regions of functional genes. Most interesting, some highly polymorphic regions share exactly the same nucleotide substitutions in more than one strain. Furthermore, in different regions of the symbiotic compartment, different sets of strains share the same substitutions. The data indicate that the majority of nucleotide substitutions are spread in the population by recombination and that the contribution of new mutations to polymorphism is relatively low. We propose that the horizontal transfer of homologous DNA segments among closely related organisms is a major source of genomic diversification.

scholarly journals Genomic descriptors of biodiversity – A review

2018 ◽  
Vol 69 (2) ◽  
pp. 73-83 ◽  
Author(s):  
Gábor Mészáros
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Polymorphisms ◽  
Negative Consequences ◽  
Effective Population ◽  
Single Nucleotide ◽  
Diversity Assessment ◽  
Wide Range ◽  
Core Concepts

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.

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