Detection of single nucleotide polymorphisms at major prolificacy genes in the Mehraban sheep and association with litter size

Abstract The present study aimed to investigate the presence of polymorphisms at four known genes controlling ovine prolificacy i.e. BMP15, GDF9, BMPR1B and B4GALNT2 in a sample of 115 Iranian Mehraban ewes and their association with litter size (LS) and lambs’ birth weight (BW) traits. Using Sanger sequencing of exons and polymorphism specific genotyping, ten SNPs (Single Nucleotide Polymorphisms) were observed in only two genes, GDF9 and BMPR1B. Seven SNPs were found in the GDF9 gene on the chromosome 5. Among them, six were already described in the coding sequence, and a new one (g.41840985C>T) was found in the 3’UTR. In the BMPR1B gene on the chromosome 6, three novel SNPs were detected in the exon 7 (g.29382184G>A; g.29382337G>A and g.29382340G>A). Allelic frequencies were established for six SNPs among the ten identified and they were in Hardy-Weinberg equilibrium. A significant association was found between the novel SNPs found in the exon 7 of BMPR1B and LS. Present results indicate the potential role of the BMPR1B locus in controlling prolificacy of Mehraban sheep and provide genetic markers for further exploitation in selection to improve reproductive efficiency.

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Identification of single nucleotide polymorphisms in GDF9 gene associated with litter size in Garut sheep

Indonesian Journal of Biotechnology ◽

10.22146/ijbiotech.42095 ◽

2019 ◽

Vol 24 (1) ◽

pp. 51 ◽

Cited By ~ 1

Author(s):

Resti Yuliana Rahmawati ◽

Sumadi Sumadi ◽

Tety Hartatik

Keyword(s):

Single Nucleotide Polymorphisms ◽

Litter Size ◽

Direct Sequencing ◽

Pcr Amplification ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Growth Differentiation Factor 9 ◽

Hardy Weinberg Equilibrium ◽

Reference Sequences ◽

Gdf9 Gene

The growth differentiation factor 9 (GDF9) gene has been regarded as having major impacts on ovulation rate and litter size in sheep. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) of the GDF9 gene and their association with litter size in Garut sheep. For this purpose, a total of 60 ewes of Garut sheep were included in this study. Based on the sheep GDF9 reference sequences (Genbank Acc. No. AF078545.2), one pair of primers (5’-CTGCTGTTTAACCTGGATCGTG-3 5’-GGAGAGCCATACCGATGTCC-3 as forward and reverse, respectively) was used for PCR amplification. The results revealed that four SNPs (g.54C>T, g.60G>A, g.304G>A, and g.333G>A) were found in Garut sheep by direct sequencing. For SNP g.54C>T, the sheep exhibited the highest frequency of allele C and genotype CC. On the other hand, SNPs g.60G>A, g.304G>A, and g.333G>A showed a higher frequency of allele G than allele A, and the GG genotype was predominant in the population. SNP g.333G>A had a significant effect on litter size (p < 0.05), and ewes with the GG genotype had a higher litter size than those with the GA genotype. Genotype distributions for all identified SNPs were in agreement with Hardy-Weinberg equilibrium. We highlight that SNP g.333G>A may be useful as a genetic marker for litter size in Garut sheep.

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Potential Role of Single Nucleotide Polymorphisms of XRCC1, XRCC3, and RAD51 in Predicting Acute Toxicity in Rectal Cancer Patients Treated With Preoperative Radiochemotherapy

American Journal of Clinical Oncology ◽

10.1097/coc.0000000000000182 ◽

2017 ◽

Vol 40 (6) ◽

pp. 535-542 ◽

Cited By ~ 10

Author(s):

Mattia F. Osti ◽

Luca Nicosia ◽

Linda Agolli ◽

Giovanna Gentile ◽

Teresa Falco ◽

...

Keyword(s):

Rectal Cancer ◽

Single Nucleotide Polymorphisms ◽

Acute Toxicity ◽

Cancer Patients ◽

Potential Role ◽

Nucleotide Polymorphisms ◽

Preoperative Radiochemotherapy ◽

Single Nucleotide

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Two strongly linked single nucleotide polymorphisms (Q320P and V397I) in GDF9 gene are associated with litter size in cashmere goats

Theriogenology ◽

10.1016/j.theriogenology.2018.10.013 ◽

2019 ◽

Vol 125 ◽

pp. 115-121 ◽

Cited By ~ 46

Author(s):

Xinyu Wang ◽

Qing Yang ◽

Ke Wang ◽

Hailong Yan ◽

Chuanying Pan ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Litter Size ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cashmere Goats ◽

Gdf9 Gene

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Genetic Effects of Single Nucleotide Polymorphisms in the Goat GDF9 Gene on Prolificacy: True or False Positive?

Animals ◽

10.3390/ani9110886 ◽

2019 ◽

Vol 9 (11) ◽

pp. 886 ◽

Cited By ~ 11

Author(s):

Xinyu Wang ◽

Qing Yang ◽

Sihuan Zhang ◽

Xiaoyu Zhang ◽

Chuanying Pan ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Litter Size ◽

Information Search ◽

Reproductive Traits ◽

High Fertility ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Growth Differentiation Factor 9 ◽

Linkage Effects ◽

Gdf9 Gene

Goat reproductive traits are complex quantitative traits controlled by polygenes and multipoint. To date, some high-fertility candidate genes in livestock have been unearthed and the growth differentiation factor 9 (GDF9) gene is one of them, which plays a crucial role in early folliculogenesis. According to the relevant previous studies and the National Center for Biotechnology Information Search database (NCBI), a total of 45 single nucleotide polymorphisms (SNPs) have been detected in the goat GDF9 gene, but which one or which ones have important effects on goat fecundity is still uncertain. Hence, in order to find effective molecular markers for goat genetic breeding and accelerate the goat improvement, this study summarized and classified the above 45 SNPs into four kinds, as well as compared and analyzed the same SNP effects and the different SNPs linkage effects on the reproductive traits in different goat breeds. Since there were many SNPs in the goat GDF9 gene, only 15 SNPs have been identified in more than 30 goat breeds worldwide and they showed different effects on the litter size. Therefore, this study mainly chose these 15 SNPs and discussed their relationship with goat productivity. Results showed that three non-synonymous SNPs A240V, Q320P, and V397I and three synonymous ones L61L, N121N, and L141L played a “true” role in the litter size trait in many goat breeds around the world. However, the regulatory mechanisms still need further research. These results provide an effective tool for follow-up research developing the goat molecular breeding strategies and improving the goat reproductive traits.

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The role of IFIH1 gene rs1990760 and rs2111485 single-nucleotide polymorphisms in generalized vitiligo predisposition

TURKISH JOURNAL OF MEDICAL SCIENCES ◽

10.3906/sag-1808-63 ◽

2019 ◽

Author(s):

DURU ONAN ◽

AHU YORULMAZ ◽

FATİH SÜHEYL EZGÜ ◽

KADİR MUTLU HAYRAN ◽

SERAY KÜLCÜ ÇAKMAK ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Gene Locus ◽

Statistical Significance ◽

Additive Models ◽

Nucleotide Polymorphisms ◽

Age And Gender ◽

Single Nucleotide ◽

Hardy Weinberg Equilibrium ◽

And Gender

Background and Aim: Interferon-induced helicase (IFIH1) is a gene locus that has been recently defined as a candidate for susceptibility to generalized vitiligo (GV). The objectives of this study were to assess the association of IFIH1 gene, rs2111485 and rs1990760 single-nucleotide polymorphisms (SNP) with susceptibility to GV and the autoimmune diseases accompanying to GV. Materials and Methods: We prospectively studied GV patients and frequency-matched healthy controls by age and gender. The genotypes of the participants were determined for rs1990760 and rs2111485 SNPs of IFIH1. Dominant, recessive and additive models were evaluated for each SNP adjusted for age and gender. Results: The patients and their controls were demonstrated to be in the Hardy-Weinberg equilibrium for SNP1 (2q24.2, rs1990760, IFIH1, T/C) and SNP2 (2q24.2, rs2111485, IFIH1, G/A) respectively (all p> 0.7). For SNP1 every T allel addition was significantly associated with 1.53 times protectiveness in terms of vitiligo risk (P= 0.033). As for SNP2 every G allel addition was associated with 1.42 times protectiveness, close to statistical significance (P= 0.100). Conclusions: We detected that for SNP1 each T allel and for SNP2 each G allel are protective in terms of vitiligo development. Hereby, we confirmed that IFIH1 gene locus has a role in GV susceptibility. Keywords: Vitiligo, single nucleotide polymorphism, genes

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An Analysis of the Association between Epilepsy-Related Genes and Vertigo in the Polish Population

Audiology and Neurotology ◽

10.1159/000491992 ◽

2018 ◽

Vol 23 (3) ◽

pp. 135-144

Author(s):

Katarzyna Pawlak-Osińska ◽

Katarzyna Linkowska ◽

Karolina Hołub ◽

Katarzyna Winiarska ◽

Bartosz Stankiewicz ◽

...

Keyword(s):

Gene Regulation ◽

Single Nucleotide Polymorphisms ◽

Genetic Background ◽

Potential Role ◽

Control Group ◽

Polish Population ◽

Nucleotide Polymorphisms ◽

Chromosome 11 ◽

Single Nucleotide

Considering the possibility of a common genetic background of vertigo and epilepsy, we genotyped an affected group of individuals with vertigo and an unaffected group, by studying 26 single-nucleotide polymorphisms (SNPs) in 14 genes which were previously reported to be of particular importance for epilepsy. Significant differences were found between the patients and the control group (χ2 = 38.3, df = 3, p = 1.6 × 10–7) for the frequencies of haplotypes consist ing of 2 SNPs located in chromosome 11 (rs1939012 and rs1783901 within genes MMP8 and SCN3B, respectively). The haplotype rs1939012:C-rs1783901:A, consisting of the minor-frequency alleles was found to be associated with a higher risk of vertigo (OR = 5.0143, 95% CI = 1.6991–14.7980, p = 0.0035). In contrast, the haplotype rs1939012:T-rs1783901:A showed a significant association with a decreased risk of the disease (OR = 0.0597, 95% CI = 0.0136–0.2620, p = 0.0002). Our results suggest that the SNPs rs1939012 and rs1783901 may play a potential role of gene regulation and/or epistasis in a complex etiology of vertigo.

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The potential role of germline single nucleotide polymorphisms for selecting the ideal candidates for sunitinib therapy in patients with locally-advanced renal cell carcinoma

Annals of Translational Medicine ◽

10.21037/atm.2019.02.24 ◽

2019 ◽

Vol 7 (S1) ◽

pp. S37-S37

Author(s):

Alberto Martini ◽

Reza Mehrazin

Keyword(s):

Renal Cell Carcinoma ◽

Single Nucleotide Polymorphisms ◽

Cell Carcinoma ◽

Renal Cell ◽

Potential Role ◽

Locally Advanced ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

The Ideal

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The role of 25-hydroxyvitamin-D3 and vitamin D receptor gene in human periodontal ligament fibroblasts as response to orthodontic compressive strain: an in vitro study

BMC Oral Health ◽

10.1186/s12903-021-01740-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Erika Calvano Küchler ◽

Agnes Schröder ◽

Vinicius Broska Teodoro ◽

Ute Nazet ◽

Rafaela Scariot ◽

...

Keyword(s):

Gene Expression ◽

Vitamin D ◽

Single Nucleotide Polymorphisms ◽

Periodontal Ligament ◽

Compressive Strain ◽

Nucleotide Polymorphisms ◽

Periodontal Ligament Fibroblasts ◽

Single Nucleotide ◽

Cox 2

Abstract Background This study aimed to investigate, if different physiological concentrations of vitamin D (25(OH)D3) and single nucleotide polymorphisms in vitamin D receptor (VDR) gene have an impact on gene expression in human periodontal ligament (hPDL) fibroblasts induced by simulated orthodontic compressive strain. Methods A pool of hPDL fibroblasts was treated in absence or presence of 25(OH)D3 in 3 different concentrations (10, 40 and 60 ng/ml). In order to evaluate the role of single nucleotide polymorphisms in the VDR gene, hPDL fibroblasts from 9 patients were used and treated in absence or presence of 40 ng/ml 25(OH)D3. Each experiment was performed with and without simulated orthodontic compressive strain. Real-time PCR was used for gene expression and allelic discrimination analysis. Relative expression of dehydrocholesterol reductase (DHCR7), Sec23 homolog A, amidohydrolase domain containing 1 (AMDHD1), vitamin D 25-hydroxylase (CYP2R1), Hydroxyvitamin D-1-α hydroxylase, receptor activator of nuclear factor-κB ligand (RANKL), osteoprotegerin (OPG), cyclooxygenase-2 (COX-2) and interleukin-6 (IL6) was assessed. Three single nucleotide polymorphisms in VDR were genotyped. Parametric or non-parametric tests were used with an alpha of 5%. Results RANKL, RANKL:OPG ratio, COX-2, IL-6, DHCR7, CYP2R1 and AMDHD1 were differentially expressed during simulated orthodontic compressive strain (p < 0.05). The RANKL:OPG ratio was downregulated by all concentrations (10 ng/ml, 40 ng/ml and 60 ng/ml) of 25(OH)D3 (mean = 0.96 ± 0.68, mean = 1.61 ± 0.66 and mean = 1.86 ± 0.78, respectively) in comparison to the control (mean 2.58 ± 1.16) (p < 0.05). CYP2R1 gene expression was statistically modulated by the different 25(OH)D3 concentrations applied (p = 0.008). Samples from individuals carrying the GG genotype in rs739837 presented lower VDR mRNA expression and samples from individuals carrying the CC genotype in rs7975232 presented higher VDR mRNA expression (p < 0.05). Conclusions Simulated orthodontic compressive strain and physiological concentrations of 25(OH)D3 seem to regulate the expression of orthodontic tooth movement and vitamin-D-related genes in periodontal ligament fibroblasts in the context of orthodontic compressive strain. Our study also suggests that single nucleotide polymorphisms in the VDR gene regulate VDR expression in periodontal ligament fibroblasts in the context of orthodontic compressive strain.

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NLRP1 influences the systemic sclerosis phenotype: a new clue for the contribution of innate immunity in systemic sclerosis-related fibrosing alveolitis pathogenesis

Annals of the Rheumatic Diseases ◽

10.1136/ard.2010.131243 ◽

2010 ◽

Vol 70 (4) ◽

pp. 668-674 ◽

Cited By ~ 65

Author(s):

P Dieudé ◽

M Guedj ◽

J Wipff ◽

B Ruiz ◽

G Riemekasten ◽

...

Keyword(s):

Innate Immunity ◽

Systemic Sclerosis ◽

Potential Role ◽

Additive Model ◽

Nucleotide Polymorphisms ◽

Fibrosing Alveolitis ◽

Single Nucleotide ◽

Risk Alleles ◽

Caucasian Origin

BackgroundRecent evidence has highlighted a potential role of interleukin 1β (IL-1β) in systemic sclerosis (SSc). NLRP1 provides a scaffold for the assembly of the inflammasome that promotes the processing and maturation of pro-IL-1β. In addition, NLRP1 variants were found to confer susceptibility to autoimmune disorders.ObjectiveTo study a possible association of the NLRP1 rs6502867, rs2670660 and rs8182352, rs12150220 and rs4790797 with SSc in the European Caucasian population.MethodsNLRP1 single nucleotide polymorphisms were genotyped in 3227 individuals comprising a discovery set (870 SSc patients and 962 controls) and a replication set including individuals from Germany (532 SSc patients and 324 controls) and Italy (527 SSc patients and 301 controls), all individuals being of European Caucasian origin.ResultsConditional analyses revealed a significant association for the NLRP1 rs8182352 variant with both anti-topoisomerase-positive and SSc-related fibrosing alveolitis (FA) subsets under an additive model: p=0.0042, OR 1.23 (95% CI 1.07 to 1.41) and p=0.0065 OR 1.19 (95% CI 1.05 to 1.36), respectively. Logistic regression analysis showed an additive effect of IRF5 rs2004640, STAT4 rs7574865 and NLRP1 rs8182352 risk alleles on SSc-related FA.ConclusionsOur results establish NLRP1 as a new genetic susceptibility factor for SSc-related pulmonary fibrosis and anti-topoisomerase-positive SSc phenotypes. This provides new insights into the pathogenesis of SSc, underlining the potential role of innate immunity in particular in the FA-positive SSc subphenotype, which represents a severe subset of the disease.

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