Molecular Cloning of the B4GALNT2 Gene and Its Single Nucleotide Polymorphisms Association with Litter Size in Small Tail Han Sheep

A new fecundity gene named the FecL (mutation), which regulates the ovulation rate, was discovered in French Lacaune sheep. The B4GALNT2 (beta-1, 4-N-acetyl-galactosaminyl transferase 2) gene was considered as the potential FecL mutation gene. This study explores whether the effect of the FecL mutation exists in other sheep breeds, and the features of the B4GALNT2 gene in terms of the molecular structure and its expression profile. Using Sanger sequencing, we found that high and low fecundity breeds from among 11 measured sheep breeds all had no variation in the three specific mutation sites, which were linked with the FecL mutation. However, two mutations of g.36946470C > T and g.36933082C > T in the exon of B4GALNT2 had a significant effect on litter size in the first parity for Small Tail Han (STH) Sheep (p < 0.05). Two transcription start sites (TSS) of B4GALNT2 in its 5′-flanking region were discovered in ovine granule cells in vitro, through the RACE (Rapid amplification of cDNA ends) method. Except for in the kidney and oviduct, no significant difference in expression levels had been found between STH sheep and Tan sheep breeds. The B4GALNT2 gene, as a candidate for FecL, may have a relationship with the differences in litter size in STH sheep. B4GALNT2 is mainly expressed in the ovine ovary, which also suggests that B4GALNT2 plays an important role in sheep reproduction.

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Associations between single nucleotide polymorphisms of GDF9 and BMP15 genes and litter size in two dairy sheep breeds of Greece

Small Ruminant Research ◽

10.1016/j.smallrumres.2012.04.004 ◽

2012 ◽

Vol 107 (1) ◽

pp. 16-21 ◽

Cited By ~ 3

Author(s):

E. Liandris ◽

A. Kominakis ◽

M. Andreadou ◽

K. Kapeoldassi ◽

S. Chadio ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Litter Size ◽

Nucleotide Polymorphisms ◽

Dairy Sheep ◽

Single Nucleotide ◽

Sheep Breeds ◽

Of Greece

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Anti-Müllerian Hormone Gene Polymorphism is Associated with Clinical Pregnancy of Fresh IVF Cycles

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph16050841 ◽

2019 ◽

Vol 16 (5) ◽

pp. 841

Author(s):

Cheng-Hsuan Wu ◽

Shun-Fa Yang ◽

Hui-Mei Tsao ◽

Yu-Jun Chang ◽

Tsung-Hsien Lee ◽

...

Keyword(s):

Pregnancy Outcomes ◽

Clinical Pregnancy ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Vitro Fertilization ◽

Ethnic Populations ◽

Significant Difference ◽

Significant Independent Factor ◽

Polymerase Chain

The aim of this study was to examine the effects of single-nucleotide polymorphisms (SNPs) in the anti-Müllerian hormone (AMH) and AMH type II receptor (AMHRII) genes on in vitro fertilization (IVF) outcomes. In this prospective cohort study, we genotyped the AMH 146 T > G, AMHRII −482 A > G and AMHRII IVS1 +149 T > A variants in 635 women undergoing their first cycle of controlled ovarian stimulation for IVF. DNA was extracted from the peripheral blood of all participants, and the SNPs were genotyped by real-time polymerase chain reaction. The distributions, frequencies of genes, and correlation with clinical pregnancy of IVF were analyzed. The AMH 146 T > G G/G genotype in women was associated with a lower clinical pregnancy rate (T/T: 55.0%, T/G: 51.8%, G/G: 40.0%; p < 0.05). Women with the AMH 146 T > G GG genotype were half as likely to have a clinical pregnancy compared with women with TT genotypes (OR = 0.55, 95% CI: 0.34–0.88, p = 0.014). With multivariate analysis, the AMH 146 T > G GG genotype remains as a significant independent factor to predict clinical pregnancy (p = 0.014). No significant difference was found between AMHRII polymorphisms and clinical pregnancy outcomes of IVF. In conclusion, our results show that AMH 146 T > G seems to be a susceptibility biomarker capable of predicting IVF pregnancy outcomes. Further studies should focus on the mechanism of these associations and the inclusion of other ethnic populations to confirm the findings of this study.

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Identification of Polymorphisms in GDF9 and BMP15 Genes in Jamunapari and Crossbred Goats in Bangladesh

10.21203/rs.3.rs-1102219/v1 ◽

2021 ◽

Author(s):

Mishuk shaha ◽

Gous Miah ◽

Arjuman Lima ◽

Omar Faruk Miazi ◽

Ashutosh Das

Keyword(s):

Litter Size ◽

Future Research ◽

Nucleotide Polymorphisms ◽

Cycle Sequencing ◽

Single Nucleotide ◽

Exon 2 ◽

Morphogenetic Protein ◽

Significant Difference ◽

Growth Differentiation Factor 9 ◽

Pcr Products

Abstract Growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) are two crucial fecundity genes 15 associated with litter size traits in the goat. Our previous study on GDF9 and BMP15 genes detected single nucleotide polymorphisms (SNPs) associated with litter size in Bangladeshi Black Bengal goats. In this study, Jamunapari and crossbred goats of Bangladesh were screened to identify polymorphisms in the GDF9 and BMP15 genes and to assess the association between identified SNPs and litter size. The genomic DNA from 100 goats (50 Jamunapari and 50 crossbred) was used in Polymerase Chain Reaction (PCR) to amplify the exon 2 of the GDF9 and exon 2 of the BMP15 gene. PCR products were sequenced employing the BigDye Terminator cycle sequencing protocol, to identify SNPs. A generalized linear model was utilized to perform the association analysis for identified SNPs and litter size. Seven SNPs were identified, of which four: C818CT, G1073A, G1189A and G1330T were in the GDF9 gene, three: G616T, G735A and G811A were in the BMP15 gene. G735A was a synonymous SNP, whereas the remaining were non-synonymous SNPs. Identified SNP loci in GDF9 were low polymorphic (PIC<0.25) while loci in BMP15 were moderately polymorphic (PIC≥0.25). The genotypes at the G1330T locus had a significant (p<0.05) difference in litter size in Jamunapari goat, but no significant difference was observed for all genotypes at other loci. This study provides additional molecular markers that would be useful for future research on the litter size trait in goats of Bangladesh.

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Mutations in NLRP5 and NLRP9 Are Associated with Litter Size in Small Tail Han Sheep

Animals ◽

10.3390/ani10040689 ◽

2020 ◽

Vol 10 (4) ◽

pp. 689 ◽

Cited By ~ 2

Author(s):

Zhuangbiao Zhang ◽

Jishun Tang ◽

Xiaoyun He ◽

Ran Di ◽

Mingxing Chu

Keyword(s):

Genetic Analysis ◽

Litter Size ◽

Population Genetic ◽

Nucleotide Polymorphisms ◽

Population Genetic Analysis ◽

Single Nucleotide ◽

Sheep Breeds ◽

Reproductive Genes ◽

Pyrin Domain ◽

Hardy Weinberg Equilibrium

Previous studies showed that the NLR family pyrin domain-containing 5 (NLRP5) and NLRP9 genes are two important reproductive genes; however, their effects on sheep litter size are unknown. Therefore, in this study, we first genotyped seven sheep breeds via the MassARRAY® SNP system at the loci g.60495375A > G, g.60495363G > A, and g.60499690C > A in NLRP5, and g.59030623T > C and g.59043397A > C in NLRP9. Our results revealed that each locus in most sheep breeds contained three genotypes. Then, we conducted population genetic analysis of single nucleotide polymorphisms in NLRP5 and NLRP9, and we found that the polymorphism information content value in all sheep breeds ranged from 0 to 0.36, and most sheep breeds were under Hardy–Weinberg equilibrium (p > 0.05). Furthermore, association analysis in Small Tail Han sheep indicated that two loci, g.60495363G > A in NLRP5 and g.59030623T > C in NLRP9, were highly associated with litter size. The mutation in g.60495363G > A may decrease interactions of NLRP5 with proteins, such as GDF9, whereas the mutation in g.59030623T > C may enhance the combining capacity of NLRP9 with these proteins; consequently, these mutations may influence the ovulation rate and even litter size. The findings of our study provide valuable genetic markers that can be used to improve the breeding of sheep and even other mammals.

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Somatic variants for seed and fruit set in grapevine

BMC Plant Biology ◽

10.1186/s12870-021-02865-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Laura Costantini ◽

Paula Moreno-Sanz ◽

Chinedu Charles Nwafor ◽

Silvia Lorenzi ◽

Annarita Marrano ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Fruit Set ◽

Climatic Factors ◽

Embryo Sac ◽

Wine Industry ◽

Nucleotide Polymorphisms ◽

Wine Quality ◽

Single Nucleotide ◽

Germplasm Collections

Abstract Background Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like seedlessness, berry and bunch size, cluster compactness and berry skin to pulp ratio. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with contrasting seed content in two germplasm collections. Results We identified eight variant pairs that seemingly differ only in seed-related characteristics while showing identical genotype when tested with the GrapeReSeq_Illumina_20K_SNP_chip and several microsatellites. We performed multi-year observations on seed and fruit set deriving from different pollination treatments, with special emphasis on the pair composed by Sangiovese and its seedless variant locally named Corinto Nero. The pollen of Corinto Nero failed to germinate in vitro and gave poor berry set when used to pollinate other varieties. Most berries from both open- and cross-pollinated Corinto Nero inflorescences did not contain seeds. The genetic analysis of seedlings derived from occasional Corinto Nero normal seeds revealed that the few Corinto Nero functional gametes are mostly unreduced. Moreover, three genotypes, including Sangiovese and Corinto Nero, were unexpectedly found to develop fruits without pollen contribution and occasionally showed normal-like seeds. Five missense single nucleotide polymorphisms were identified between Corinto Nero and Sangiovese from transcriptomic data. Conclusions Our observations allowed us to attribute a seedlessness type to some variants for which it was not documented in the literature. Interestingly, the VvAGL11 mutation responsible for Sultanina stenospermocarpy was also discovered in a seedless mutant of Gouais Blanc. We suggest that Corinto Nero parthenocarpy is driven by pollen and/or embryo sac defects, and both events likely arise from meiotic anomalies. The single nucleotide polymorphisms identified between Sangiovese and Corinto Nero are suitable for testing as traceability markers for propagated material and as functional candidates for the seedless phenotype.

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Sex Differences in Circadian Clock Genes and Myocardial Infarction Susceptibility

Journal of Cardiovascular Development and Disease ◽

10.3390/jcdd8050053 ◽

2021 ◽

Vol 8 (5) ◽

pp. 53

Author(s):

Ivana Škrlec ◽

Jasminka Talapko ◽

Martina Juzbašić ◽

Robert Steiner

Keyword(s):

Myocardial Infarction ◽

Cardiovascular Disease ◽

Circadian Rhythm ◽

Single Nucleotide Polymorphisms ◽

Clock Genes ◽

P Value ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Biological Sex ◽

Significant Difference

The growing body of evidence shows a significant difference in the circadian rhythm of cardiovascular disease based on biological sex. The incidence of cardiovascular disease varies between women and men. Additionally, biological sex is vital for the timely application of therapy—chronotherapy, which benefits both sexes. This study aimed to examine the potential difference of single nucleotide polymorphisms (SNPs) of the circadian rhythm genes ARNTL, CLOCK, CRY2 and PER2 in women and men with myocardial infarction. A cross-sectional study was conducted, including 200 patients with myocardial infarction. Altogether, ten single nucleotide polymorphisms in the ARNTL, CLOCK, CRY2 and PER2 genes were analyzed. The Chi-square test yielded statistically significant differences in CLOCK gene rs11932595 polymorphism in a recessive genotype model between women and men with a p-value of 0.03 and an odds ratio 2.66, and a corresponding 95% confidence interval of 1.07 to 6.66. Other analyzed polymorphisms of the circadian rhythm genes ARNTL, CRY2, and PER2 did not significantly differ between the sexes. According to the study’s current results, the CLOCK gene’s genetic variability might affect myocardial infarction concerning biological sex.

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Significant Associations of lncRNA H19 Genotypes with Susceptibility to Childhood Leukemia in Taiwan

Pharmaceuticals ◽

10.3390/ph14030235 ◽

2021 ◽

Vol 14 (3) ◽

pp. 235

Author(s):

Jen-Sheng Pei ◽

Chao-Chun Chen ◽

Wen-Shin Chang ◽

Yun-Chi Wang ◽

Jaw-Chyun Chen ◽

...

Keyword(s):

Confidence Interval ◽

Childhood Leukemia ◽

Healthy Controls ◽

Nucleotide Polymorphisms ◽

Wild Type ◽

Single Nucleotide ◽

Genotypic Distribution ◽

Heterozygous Variant ◽

Significant Difference ◽

The Difference

The purpose of our study was to investigate whether genetic variations in lncRNA H19 were associated with susceptibility to childhood leukemia. Two hundred and sixty-six childhood leukemia patients and 266 healthy controls were enrolled in Taiwan, and two single nucleotide polymorphisms (SNPs), rs2839698 and rs217727, in H19 were genotyped and analyzed. There was a significant difference in the genotypic distribution of rs2839698 between patients and healthy controls (p = 0.0277). Compared to the wild-type CC genotype, the heterozygous variant CT and homozygous variant TT genotypes were associated with significantly increased risks of childhood leukemia with an adjusted odd ratio (OR) of 1.46 (95% confidence interval (CI), 1.08–2.14, p = 0.0429) and 1.94 (95%CI, 1.15–3.31, p = 0.0169), respectively (pfor tread = 0.0277). The difference in allelic frequencies between childhood leukemia patients and controls was also significant (T versus C, adjusted OR = 1.53, 95%CI, 1.13–1.79, p = 0.0077). There were no significant differences in the genotypic and allelic distributions of rs217727 between cases and controls. Interestingly, the average level of H19 rs2839698 was statistically significantly higher for patients with CT and TT genotypes than from those with the CC genotype (p < 0.0001). Our results indicate that H19 SNP rs2839698, but not rs217727, may serve as a novel susceptibility marker for childhood leukemia.

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In-Silico and In-vitro Analysis of Human SOS1 Protein Causing Noonan Syndrome – A Novel Approach to Explore the Molecular Pathways

Current Genomics ◽

10.2174/1389202922666211130144221 ◽

2021 ◽

Vol 22 ◽

Author(s):

Vinoth Sigamani ◽

Sheeja Rajasingh ◽

Narasimman Gurusamy ◽

Arunima Panda ◽

Johnson Rajasingh

Keyword(s):

Noonan Syndrome ◽

In Silico ◽

Genetic Disorder ◽

In Vitro Study ◽

Human Skin Fibroblast ◽

Nucleotide Polymorphisms ◽

Gene Expressions ◽

Single Nucleotide ◽

Nucleotide Mutation

Aims: Noonan syndrome (NS) is an autosomal dominant genetic disorder caused by single nucleotide mutation in PTPN11, SOS1, RAF1, and KRAS genes. Background: We hypothesize that in-silico analysis of human SOS1 mutations would be a promising predictor in identifying the pathogenic effect of NS. Methods: Here, we computationally analyzed the SOS1 gene to identify the pathogenic non-synonymous single nucleotide polymorphisms (nsSNPs) to cause NS. The variant information of SOS1 was collected from the SNP database (dbSNP). The variants were further analyzed by in-silico tools I-Mutant, iPTREE-STAB, and MutPred to elucidate their structural and functional characteristics. Results: We found that 11 nsSNPs of SOS1 were more pathogenic to cause NS. The 3D modeling of the wild-type and the 11 nsSNPs were performed using I-TASSER and validated via ERRAT and RAMPAGE. SOS1 interacting proteins were analysed through STRING, which showed that SOS1 interacted with cardiac proteins GATA4, TNNT2, and ACTN2. During these interactions, GRB2 and HRAS act as an intermediate molecules between SOS1 and cardiac proteins. These in-silico analyses were validated using induced cardiomyocytes (iCMCs) derived from NS patients carrying SOS1 gene variant c.1654A>G (NS-iCMCs) and compared with control human skin fibroblast-derived iCMCs (C-iCMCs). Our in vitro data further confirmed that the SOS1, GRB2 and HRAS gene expressions as well as the activated ERK protein, were significantly decreased in NS-iCMCs compared to C-iCMCs. Conclusion: This is the first in-silico and in vitro study demonstrating that 11 nsSNPs of SOS1 were playing a deleterious pathogenic role in causing NS.

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Distribution of QPY and RAH haplotypes of granzyme B gene in distinct Brazilian populations

Revista da Sociedade Brasileira de Medicina Tropical ◽

10.1590/s0037-86822012005000001 ◽

2012 ◽

Vol 45 (4) ◽

pp. 496-499

Author(s):

Fernanda Bernadelli Garcia ◽

Simone Kashima ◽

Evandra Strazza Rodrigues ◽

Israel Tojal Silva ◽

Tathiane Maistro Malta ◽

...

Keyword(s):

Granzyme B ◽

Treatment Strategies ◽

Cytotoxic Lymphocytes ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Exon 2 ◽

Significant Difference ◽

Novel Treatment Strategies ◽

Brazilian Populations ◽

Afro Brazilian

INTRODUCTION: The cytolysis mediated by granules is one of the most important effector functions of cytotoxic T lymphocytes and natural killer cells. Recently, three single nucleotide polymorphisms (SNPs) were identified at exons 2, 3, and 5 of the granzyme B gene, resulting in a haplotype in which three amino acids of mature protein Q48P88Y245 are changed to R48A88H245, which leads to loss of cytotoxic activity of the protein. In this study, we evaluated the frequency of these polymorphisms in Brazilian populations. METHODS: We evaluated the frequency of these polymorphisms in Brazilian ethnic groups (white, Afro-Brazilian, and Asian) by sequencing these regions. RESULTS: The allelic and genotypic frequencies of SNP 2364A/G at exon 2 in Afro-Brazilian individuals (42.3% and 17.3%) were significantly higher when compared with those in whites and Asians (p < 0.0001 and p = 0.0007, respectively). The polymorphisms 2933C/G and 4243C/T also were more frequent in Afro-Brazilians but without any significant difference regarding the other groups. The Afro-Brazilian group presented greater diversity of haplotypes, and the RAH haplotype seemed to be more frequent in this group (25%), followed by the whites (20.7%) and by the Asians (11.9%), similar to the frequency presented in the literature. CONCLUSIONS: There is a higher frequency of polymorphisms in Afro-Brazilians, and the RAH haplotype was more frequent in these individuals. We believe that further studies should aim to investigate the correlation of this haplotype with diseases related to immunity mediated by cytotoxic lymphocytes, and if this correlation is confirmed, novel treatment strategies might be elaborated.

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