Effect of single-nucleotide polymorphisms on the breeding value of fertility and breeding value of beef in Hungarian Simmental cattle

The aim of this study was to reveal the effect of single-nucleotide polymorphisms (SNPs) on the total number of piglets born (TNB), the litter weight born alive (LWA), the number of piglets born dead (NBD), the average litter weight on the 21st day (M21D) and the interval between litters (IBL). Genotypes were determined on a high-density Illumina Porcine SNP 60K BeadChip. Data screening and data identification were performed by a multi-locus mixed-model. Statistical analyses were carried out to find associations between individual genotypes of 290 Hungarian Large White sows and the investigated reproduction parameters. According to the analysis outcome, three SNPs were identified to be associated with TNB. These loci are located on chromosomes 1, 6 and 13 (−log10P = 6.0, 7.86 and 6.22, the frequencies of their minor alleles, MAF, were 0.298, 0.299 and 0.364, respectively). Two loci showed considerable association (−log10P = 10.35 and 10.46) with LWA on chromosomes 5 and X, the MAF were 0.425 and 0.446, respectively. Seven loci were found to be associated with NBD. These loci are located on chromosomes 5, 6, 13, 14, 15, 16 and 18 (−log10P = 10.95, 5.43, 8.29, 6.72, 6.81, 5.90, and 5.15, respectively). One locus showed association (−log10P = 5.62) with M21D on chromosome 1 (the MAF was 0.461). Another locus was found to be associated with IBL on chromosome 8 (−log10P = 7.56; the MAF was 0.438). The above-mentioned loci provide a straightforward possibility to assist selection by molecular tools and, consequently, to improve the competitiveness of the Hungarian Large White (HLW) breed.

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The Glucocorticoid Receptor Polymorphism Landscape in Patients With Diamond Blackfan Anemia Reveals an Association Between Two Clinically Relevant Single Nucleotide Polymorphisms and Time to Diagnosis

Frontiers in Physiology ◽

10.3389/fphys.2021.745032 ◽

2021 ◽

Vol 12 ◽

Author(s):

Annalisa Lonetti ◽

Valentina Indio ◽

Irma Dianzani ◽

Ugo Ramenghi ◽

Lydie Da Costa ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Glucocorticoid Receptor ◽

Compensatory Mechanism ◽

Nucleotide Polymorphisms ◽

Disease Manifestation ◽

Single Nucleotide ◽

Diamond Blackfan Anemia ◽

Glucocorticoid Response ◽

Minor Alleles ◽

Population Demographic

NR3C1, the gene encoding the glucocorticoid receptor, is polymorphic presenting numerous single nucleotide polymorphisms (SNPs) some of which are emerging as leading cause in the variability of manifestation and/or response to glucocorticoids in human diseases. Since 60–80% of patients with Diamond Blackfan anemia (DBA), an inherited pure red cell aplasia induced by mutations in ribosomal protein genes became transfusion independent upon treatment with glucocorticoids, we investigated whether clinically relevant NR3C1 SNPs are associated with disease manifestation in DBA. The eight SNPs rs10482605, rs10482616, rs7701443, rs6189/rs6190, rs860457, rs6198, rs6196, and rs33388/rs33389 were investigated in a cohort of 91 European DBA patients. Results were compared with those observed in healthy volunteers (n=37) or present in public genome databases of Italian and European populations. Although, cases vs. control analyses suggest that the frequency of some of the minor alleles is significantly altered in DBA patients with respect to healthy controls or to the Italian or other European registries, lack of consistency among the associations across different sets suggests that overall the frequency of these SNPs in DBA is not different from that of the general population. Demographic data (47 females and 31 males) and driver mutations (44 S and 29 L genes and eight no-known mutation) are known for 81 patients while glucocorticoid response is known, respectively, for 81 (36 responsive and 45 non-responsive) and age of disease onsets for 79 (55 before and 24 after 4months of age) patients. Neither gender nor leading mutations were associated with the minor alleles or with disease manifestation. In addition, none of the SNPs met the threshold in the response vs. non-responsive groups. However, two SNPs (rs6196 and rs860457) were enriched in patients manifesting the disease before 4months of age. Although the exact biomechanistical consequences of these SNPs are unknown, the fact that their configuration is consistent with that of regulatory regions suggests that they regulate changes in glucocorticoid response during ontogeny. This hypothesis was supported by phosphoproteomic profiling of erythroid cells expanded ex vivo indicating that glucocorticoids activate a ribosomal signature in cells from cord blood but not in those from adult blood, possibly providing a compensatory mechanism to the driving mutations observed in DBA before birth.

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Association between single-nucleotide polymorphisms within candidate genes and fertility in Landrace and Duroc pigs

Acta Veterinaria Scandinavica ◽

10.1186/s13028-019-0493-x ◽

2019 ◽

Vol 61 (1) ◽

Author(s):

Nina Hårdnes Tremoen ◽

Maren Van Son ◽

Ina Andersen-Ranberg ◽

Eli Grindflek ◽

Frøydis Deinboll Myromslien ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Candidate Genes ◽

Genetic Variants ◽

Genetic Variance ◽

Female Fertility ◽

Breeding Value ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cox 2 ◽

Snp Panels

AbstractFinding effective predictors of traits related to boar fertility is essential for increasing the efficiency of artificial insemination systems in pig breeding. The objective of this study was to find associations between single-nucleotide polymorphisms (SNPs) within candidate genes and fertility in the breeds Landrace and Duroc. Animals with breeding values for total number of piglets born, were re-sequenced for exonic regions of 14 candidate genes related to male and female fertility using samples from 16 Landrace boars and 16 Duroc boars (four with high and four with low breeding value of total number of piglets born for each breed for male fertility, and the same for female fertility) to detect genetic variants. Genotyping for the detected SNPs was done in 619 Landrace boars and 513 Duroc boars. Two SNPs in BMPR1 and one SNP in COX-2 were found significantly associated with the total number of piglets born in Landrace. In Duroc, two SNPs in PLCz, one SNP in VWF and one SNP in ZP3 were found significantly associated with total number of piglets born. These SNPs explained between 0.27% and 1.18% of the genetic variance. These effects are too low for being used directly for selection purposes but can be of interest in SNP-panels used for genomic selection.

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Single Nucleotide Polymorphisms in Carnosinase Genes (CNDP1 and CNDP2) are Associated With Power Athletic Status

International Journal of Sport Nutrition and Exercise Metabolism ◽

10.1123/ijsnem.2017-0098 ◽

2017 ◽

Vol 27 (6) ◽

pp. 533-542 ◽

Cited By ~ 4

Author(s):

João Paulo Limongi França Guilherme ◽

Antonio Herbert Lancha

Keyword(s):

Single Nucleotide Polymorphisms ◽

Endurance Athletes ◽

Genotype Distribution ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Athletic Status ◽

Genotype Frequencies ◽

Significant Difference ◽

Minor Alleles ◽

Representative Cohort

Carnosine (β-alanyl-L-histidine), abundantly found in skeletal muscle, plays an important role during exercise, especially for high-intensity contractions. Variability in muscle carnosine content between individuals exists and may also be explained by different genetic bases, although no study has addressed the association of polymorphisms in genes related to carnosine metabolism in athletes. This study aimed to investigate the frequency of single nucleotide polymorphisms (SNPs) in the carnosinase genes (CNDP1 and CNDP2) in a large Brazilian cohort of athletes and nonathletes. Eight SNPs were compared between a representative cohort of elite athletes from Brazil (n = 908) and a paired group of nonathletes (n = 967). The athletes were stratified into three groups: endurance (n = 328), power (n = 415), and combat (n = 165). The CNDP2 rs6566810 (A/A genotype) is overrepresented in endurance athletes, but only in international-level endurance athletes. Three SNPs (CNDP2 rs3764509, CNDP2-CNDP1 rs2346061, and CNDP1 rs2887) were overrepresented in power athletes compared with nonathletes. Carriers of the minor allele had an increased odds ratio of being a power athlete. For the rs2346061, no significant difference was observed in genotype frequencies between power and combat sports athletes, but for rs2887 the power and combat groups showed an inverse genotype distribution. In conclusion, we found that minor alleles carriers for CNDP2 rs3764509 (G-allele), CNDP2-CNDP1 rs2346061 (C-allele), and CNDP1 rs2887 (A-allele) are more likely to be a power athlete. These polymorphisms may be novel genetic markers for power athletes. Furthermore, these results are suggestive of a distinct CNDP genotype for sporting development.

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Single Nucleotide Polymorphisms Associated with Methotrexate-induced Nausea in Juvenile Idiopathic Arthritis

10.21203/rs.3.rs-59432/v2 ◽

2021 ◽

Author(s):

Nini Kyvsgaard ◽

Torben Stamm Mikkelsen ◽

Thomas D. Als ◽

Anne Estmann Christensen ◽

Thomas J. Corydon ◽

...

Keyword(s):

Juvenile Idiopathic Arthritis ◽

Single Nucleotide Polymorphisms ◽

Snp Analysis ◽

Genotype Distribution ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Minor Alleles ◽

Genes Encoding ◽

Metabolizing Enzyme ◽

The Impact

Abstract BackgroundContext: Methotrexate (MTX) is a cornerstone in the treatment of juvenile idiopathic arthritis (JIA). MTX treatment is commonly associated with nausea. Large inter-individual variation exists in the level of MTX-induced nausea, possibly due to genetic factors. Purpose: To investigate whether MTX-induced nausea was associated with single nucleotide polymorphisms (SNPs) in genes encoding MTX-transporter proteins, a MTX metabolizing enzyme and a nausea receptor.FindingsMethods: Children aged ≥9 years treated with MTX for JIA were eligible. MTX-induced nausea was registered by the children’s completion of a nausea diary (min. 7 days) and the parents’ completion of the MTX intolerance severity score (MISS). The selected SNPs were: SLCO1B1 (rs4149056; rs4149081), SLCO1B3 (rs2117032), SLC19A1 (rs1051266), ABCC2 (rs2273697; rs3740066; rs717620), ABCB1 (rs2032582; rs1045642), MTHFR (rs1801131, rs1801133), HTR3A (rs1062613; rs1985242; rs1176713) and HTR3B (rs1176744). Results: Enrolled were 121 JIA patients (82 girls: 39 boys) with a median age of 13.3 years (IQR: 11.3-15.1). The median MTX dose was 9.7 mg/m2/week (IQR: 9.0-10.9). The median MTX treatment duration prior to enrolment was 340 days (IQR: 142-766). The SNP analysis was available for 119 patients. MTX intolerance was associated with the genotype distribution of rs1801133 (MTHFR) (p= 0.02). There was no additive effect of the minor alleles for any of the selected SNPs, nor any significant haplotype associations. Conclusion Summary: MTX-induced nausea may be influenced by genetic polymorphisms in a MTX metabolizing enzyme (rs1801133; MTHFR). Implications: Further analyses involving inclusion of larger cohorts are needed to understand the impact of SNPs on MTX-induced nausea in JIA.

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Single Nucleotide Polymorphisms Associated with Methotrexate-induced Nausea in Juvenile Idiopathic Arthritis

10.21203/rs.3.rs-59432/v1 ◽

2020 ◽

Author(s):

Nini Kyvsgaard ◽

Torben Stamm Mikkelsen ◽

Thomas D. Als ◽

Anne Estmann Christensen ◽

Thomas J. Corydon ◽

...

Keyword(s):

Juvenile Idiopathic Arthritis ◽

Single Nucleotide Polymorphisms ◽

Snp Analysis ◽

Genotype Distribution ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Minor Alleles ◽

Genes Encoding ◽

Metabolizing Enzyme ◽

The Impact

Abstract BackgroundContext: Methotrexate (MTX) is a cornerstone in the treatment of juvenile idiopathic arthritis (JIA). MTX treatment is commonly associated with nausea. Large inter-individual variation exists in the level of MTX-induced nausea, possibly due to genetic factors. Purpose: To investigate whether MTX-induced nausea was associated with single nucleotide polymorphisms (SNPs) in genes encoding MTX-transporter proteins, a MTX metabolizing enzyme and a nausea receptor.FindingsMethods: Children aged ≥9 years treated with MTX for JIA were eligible. MTX-induced nausea was registered by the children’s completion of a nausea diary (min. 7 days) and the parents’ completion of the MTX intolerance severity score (MISS). The selected SNPs were: SLCO1B1 (rs4149056; rs4149081), SLCO1B3 (rs2117032), SLC19A1 (rs1051266), ABCC2 (rs2273697; rs3740066; rs717620), ABCB1 (rs2032582; rs1045642), MTHFR (rs1801131, rs1801133), HTR3A (rs1062613; rs1985242; rs1176713) and HTR3B (rs1176744). Results: Enrolled were 121 JIA patients (82 girls: 39 boys) with a median age of 13.3 years (IQR: 11.3-15.1). The median MTX dose was 9.7 mg/m2/week (IQR: 9.0-10.9). The median MTX treatment duration prior to enrolment was 340 days (IQR: 142-766). The SNP analysis was available for 119 patients. MTX intolerance was associated with the genotype distribution of rs1801133 (MTHFR) (p= 0.02). There was no additive effect of the minor alleles for any of the selected SNPs, nor any significant haplotype associations. Conclusion Summary: MTX-induced nausea may be influenced by genetic polymorphisms in a MTX metabolizing enzyme (rs1801133; MTHFR). Implications: Further analyses involving inclusion of larger cohorts are needed to understand the impact of SNPs on MTX-induced nausea in JIA.

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Effect of single nucleotide polymorphisms on intramuscular fat content in Hungarian Simmental cattle

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.17.0773 ◽

2018 ◽

Vol 31 (9) ◽

pp. 1415-1419 ◽

Cited By ~ 1

Author(s):

István Anton ◽

Balázs Húth ◽

Imre Füller ◽

László Rózsa ◽

Gabriella Holló ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Intramuscular Fat ◽

Fat Content ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Simmental Cattle ◽

Intramuscular Fat Content

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Association of IL-4 Polymorphisms with Allergic Rhinitis in Jordanian Population

Medicina ◽

10.3390/medicina56040179 ◽

2020 ◽

Vol 56 (4) ◽

pp. 179

Author(s):

Baeth Moh’d Al-Rawashdeh ◽

Ahmed Sadaalhanjori ◽

Elnagi Ali ◽

Malek Zihlif

Keyword(s):

Allergic Rhinitis ◽

Single Nucleotide Polymorphisms ◽

Allelic Frequency ◽

Population Variation ◽

Interleukin 4 ◽

Control Group ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Minor Alleles ◽

Polymerase Chain

Background and objectives: Allergic rhinitis has complex patterns of inheritance, and single nucleotide polymorphisms, a common genetic variation in a population, exert a significant role in allergic rhinitis pathology. The current study aimed to investigate the association of Interleukin-4 (IL-4) polymorphisms with allergic rhinitis. Materials and Methods: Our study included 158 patients with allergic rhinitis and 140 healthy controls from Jordan that were genotyped for IL-4 single nucleotide polymorphisms (SNPs) C-589T (rs2243250) and T-2979G (rs2227284) using restriction fragment length polymorphism-polymerase chain reaction. Statistical analysis was conducted using IBM SPSS Statistics version 24 software. Results: The results showed that the allelic frequency of the minor alleles was 0.19 and 0.67 for C-589T (rs2243250) and T-2979G (rs2227284) in the allergic rhinitis patients, respectively, while it was 0.18 for C-589T (rs2243250) and 0.64 T-2979G (rs2227284) in the control group. The homozygous (TT) genotype of C-589T (rs2243250) was significantly associated with allergic rhinitis (p < 0.05), while there was no association of any of T-2979G (rs2227284) genotypes with allergic rhinitis. Conclusions: The results of this study indicate that genetic inter-population variation precipitates the differences in the percentages of many diseases among populations, including allergic rhinitis.

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