scholarly journals Single Nucleotide Polymorphism in the Coding Region of Bovine Chemerin Gene and Their Associations with Carcass Traits in Japanese Black Cattle

2015 ◽  
Vol 28 (8) ◽  
pp. 1084-1089 ◽  
Author(s):  
Eri Yamauchi ◽  
Yutaka Suzuki ◽  
Kyoung-Ha So ◽  
Kei-ichi Suzuki ◽  
Kazuo Katoh ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Carcass Traits ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Japanese Black Cattle ◽  
Single Nucleotide

Genomic prediction for carcass traits in Japanese Black cattle using single nucleotide polymorphism markers of different densities

2017 ◽  
Vol 57 (8) ◽  
pp. 1631 ◽  
Author(s):  
Shinichiro Ogawa ◽  
Hirokazu Matsuda ◽  
Yukio Taniguchi ◽  
Toshio Watanabe ◽  
Yuki Kitamura ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genomic Prediction ◽  
Carcass Traits ◽  
Snp Markers ◽  
Carcass Weight ◽  
Nucleotide Polymorphism ◽  
Japanese Black Cattle ◽  
Marbling Score ◽  
Single Nucleotide ◽  
Breeding Values

Genomic prediction (GP) of breeding values using single nucleotide polymorphism (SNP) markers can be conducted even when pedigree information is unavailable, providing phenotypes are known and marker data are provided. While use of high-density SNP markers is desirable for accurate GP, lower-density SNPs can perform well in some situations. In the present study, GP was performed for carcass weight and marbling score in Japanese Black cattle using SNP markers of varying densities. The 1791 fattened steers with phenotypic data and 189 having predicted breeding values provided by the official genetic evaluation using pedigree data were treated as the training and validation populations respectively. Genotype data on 565837 autosomal SNPs were available and SNPs were selected to provide different equally spaced SNP subsets of lower densities. Genomic estimated breeding values (GEBVs) were obtained using genomic best linear unbiased prediction incorporating one of two types of genomic relationship matrices (G matrices). The GP accuracy assessed as the correlation between the GEBVs and the corrected records divided by the square root of estimated heritability was around 0.85 for carcass weight and 0.60 for marbling score when using 565837 SNPs. The type of G matrix used gave no substantial difference in the results at a given SNP density for traits examined. Around 80% of the GP accuracy was retained when the SNP density was decreased to 1/1000 of that of all available SNPs. These results indicate that even when a SNP panel of a lower density is used, GP may be beneficial to the pre-selection for the carcass traits in Japanese Black young breeding animals.

Analysis of porcine OSBPL5 gene allelic expression in skeletal muscle and association of a single-nucleotide polymorphism in the coding region with production traits

2019 ◽  
Vol 99 (4) ◽  
pp. 914-920
Author(s):  
Meng Wang ◽  
Deli Wei ◽  
Guiling Cao ◽  
Guiyu Zhu ◽  
Yunliang Jiang
Keyword(s):  
Skeletal Muscle ◽  
Single Nucleotide Polymorphism ◽  
Growth Regulation ◽  
Average Daily Gain ◽  
Allelic Expression ◽  
Production Traits ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Specific Expression ◽  
Single Nucleotide

Genes that exhibit allelic expression imbalance and imprinted genes play important roles in the survival of the embryo and postnatal growth regulation. In this study, the porcine oxysterol-binding protein-related 5 (OSBPL5) gene was examined, and the 2140G>A mutation (rs318687202) was found in its coding region by a comparison of Laiwu and Landrace pigs. By allele-specific expression analysis based on a specific single-nucleotide polymorphism (SNP), the imprinting status of OSBPL5 gene in skeletal muscle from both neonate and adult pigs was determined. The results showed that the OSBPL5 was paternally imprinted in skeletal muscle from adults but biallelically expressed with predominantly maternal imprinting in neonates. The distribution of the 2140G>A SNP in four pig populations was analyzed, which showed that GG genotype was dominant in Duroc and Dapulian populations, whereas the AG genotype was dominant in Junmu-1 and Laiwu populations. Pigs with the GG genotype had significantly larger litters and greater cannon bone circumferences but a lower average daily gain than pigs with the AA genotype. In conclusion, we determined the difference in the allelic expression of OSBPL5 between adult and neonate pigs and identified an SNP in its coding region that is associated with production traits.

scholarly journals THE EFFECT OF SINGLE NUCLEOTIDE POLYMORPHISM (SNP) IN GLIOBLASTOMA MULTIFORME

2021 ◽  
Author(s):  
Asmita Ghosh ◽  
Dattatreya Mukherjee ◽  
Parth Patel ◽  
Debraj Mukhopadhyay
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Glioblastoma Multiforme ◽  
Association Studies ◽  
Disease Onset ◽  
Genetic Alterations ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Single nucleotide polymorphism is a genetic substitution of a base pair at a single position of the genome. SNPs are a common phenomenon and influence mRNA expression. Half of the SNPs occur in the non-coding region with 25% being mis-sense mutation and 25% being silent mutations. SNPs belong to the last generation of molecular markers which is identified through SNP mapping. SNPs are extensively studied to distinguish genetic expression and protein synthesis. These genetic differences are a major source of diseases in humans like cancers. One of the most common types of cancer of the brain is the Glioblastoma Multiforme that accounts for more than 80% of the malignant primary brain tumors (PBT). Researchers have found out a potential role of various SNPs in the genome to have a strong relation with Glioma formation and proliferation. Most SNPs are either not discovered, or their biological mechanisms are unknown, making it difficult to link putative associations with disease onset. The given review aims to identify some of the most common SNPs associated with GBM and classify the genetic basis along with future prospects. These SNPs are pioneer in Genome Wide Association studies to help in cancer research and identification of specific genetic alterations liked to GBM. Single Nucleotide Polymorphisms in a gene can be used as genetic biomarkers to aid better understanding of the mechanism of cancer formation, its aetiology, progression and metastatic behaviour.

Association Between Single-Nucleotide Polymorphisms of NKX2.5 and Congenital Heart Disease in Chinese Population: A Meta-Analysis

2021 ◽  
Author(s):  
Huan Chen ◽  
Tianjiao Li ◽  
Yuqing Wu ◽  
Xi Wang ◽  
Mingyuan Wang ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Single Nucleotide Polymorphism ◽  
Heart Disease ◽  
Chinese Population ◽  
Congenital Heart ◽  
Meta Analysis ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
China National Knowledge Infrastructure ◽  
Single Nucleotide

Abstract Background: NKX2.5 is a transcription factor that plays a key role in cardiovascular growth and development. Many independent studies have been conducted to investigate the association between the single nucleotide polymorphism 606G>C (rs3729753) in the coding region of NKX2.5 and congenital heart disease (CHD), although the results were inconsistent. This study aimed to reveal as much as possible the relationship between NKX2.5 single nucleotide polymorphism 606G>C and the risk of congenital heart disease in the Chinese population through meta-analysis.Methods and Results: After retrieving related articles in PubMed, MEDLINE, EMBASE, Web of science, Coherane, China National Knowledge Infrastructure (CNKI), Wanfang DATA, VIP database until Aug 2021, a total of 8 studies were finally included. Then, we merged the qualified research data into allele model, dominant model, recessive model, heterozygous model, homozygous model, additive model respectively. Overall meta-analysis results showed that 606G>C was not associated with congenital heart disease of the Chinese population in any model. Also, subgroup analysis based on congenital heart disease type gave the same negative result. Sensitivity analysis showed that there was no significant correlation after the deletion of each study. The results were negative and the heterogeneity was not significant.Conclusion: Our results show that NKX2-5 single nucleotide polymorphism 606G> C may not lead to the risk of congenital heart disease in Chinese.

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