scholarly journals Survey of SNPs Associated with Total Number Born and Total Number Born Alive in Pig

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 491 ◽  
Author(s):  
Siroj Bakoev ◽  
Lyubov Getmantseva ◽  
Faridun Bakoev ◽  
Maria Kolosova ◽  
Valeria Gabova ◽  
...  
Keyword(s):  
Production Efficiency ◽  
Association Studies ◽  
Reproductive Traits ◽  
International Studies ◽  
Genome Wide Association Studies ◽  
Large White ◽  
Genome Wide ◽  
Genome Map ◽  
Trait Locus ◽  
The Given

Reproductive productivity depend on a complex set of characteristics. The number of piglets at birth (Total number born, Litter size, TNB) and the number of alive piglets at birth (Total number born alive, NBA) are the main indicators of the reproductive productivity of sows in pig breeding. Great hopes are pinned on GWAS (Genome-Wide Association Studies) to solve the problems associated with studying the genetic architecture of reproductive traits of pigs. This paper provides an overview of international studies on SNP (Single nucleotide polymorphism) associated with TNB and NBA in pigs presented in PigQTLdb as “Genome map association”. Currently on the base of Genome map association results 306 SNPs associated with TNB (218 SNPs) and NBA (88 SNPs) have been identified and presented in the Pig QTLdb database. The results are based on research of pigs such as Large White, Yorkshire, Landrace, Berkshire, Duroc and Erhualian. The presented review shows that most SNPs found in chromosome areas where candidate genes or QTLs (Quantitative trait locus) have been identified. Further research in the given direction will allow to obtain new data that will become an impulse for creating breakthrough breeding technologies and increase the production efficiency in pig farming.

scholarly journals Genome-Wide Association Studies Identify the Loci for 5 Exterior Traits in a Large White × Minzhu Pig Population

PLoS ONE ◽  
2014 ◽  
Vol 9 (8) ◽  
pp. e103766 ◽  
Author(s):  
Ligang Wang ◽  
Longchao Zhang ◽  
Hua Yan ◽  
Xin Liu ◽  
Na Li ◽  
...  
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Large White ◽  
Genome Wide

scholarly journals Evidence for GRN as part of a neuroinflammatory mechanism connecting common neurodegenerative diseases

2020 ◽  
Author(s):  
Mike A. Nalls ◽  
Cornelis Blauwendraat ◽  
Lana Sargent ◽  
Dan Vitale ◽  
Hampton Leonard ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Neurodegenerative Diseases ◽  
Genetic Risk ◽  
Association Studies ◽  
Molecular Data ◽  
Genome Wide Association Studies ◽  
Data Types ◽  
Genome Wide ◽  
Trait Locus ◽  
Lateral Sclerosis

SUMMARYBackgroundPrevious research using genome wide association studies (GWAS) has identified variants that may contribute to lifetime risk of multiple neurodegenerative diseases. However, whether there are common mechanisms that link neurodegenerative diseases is uncertain. Here, we focus on one gene, GRN, encoding progranulin, and the potential mechanistic interplay between genetic risk, gene expression in the brain and inflammation across multiple common neurodegenerative diseases.MethodsWe utilized GWAS, expression quantitative trait locus (eQTL) mapping and Bayesian colocalization analyses to evaluate potential causal and mechanistic inferences. We integrate various molecular data types from public resources to infer disease connectivity and shared mechanisms using a data driven process.FindingseQTL analyses combined with GWAS identified significant functional associations between increasing genetic risk in the GRN region and decreased expression of the gene in Parkinson’s, Alzheimer’s and amyotrophic lateral sclerosis. Additionally, colocalization analyses show a connection between blood based inflammatory biomarkers relating to platelets and GRN expression in the frontal cortex.InterpretationGRN expression mediates neuroinflammation function related to general neurodegeneration. This analysis suggests shared mechanisms for Parkinson’s, Alzheimer’s and amyotrophic lateral sclerosis.FundingNational Institute on Aging, National Institute of Neurological Disorders and Stroke, and the Michael J. Fox Foundation.

A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies

2019 ◽  
Vol 35 (21) ◽  
pp. 4327-4335
Author(s):  
Meiyue Wang ◽  
Shizhong Xu
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait Locus Mapping ◽  
Bayesian Learning ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Sparse Bayesian Learning ◽  
Genome Wide ◽  
Trait Locus ◽  
Locus Mapping

AbstractMotivationGenomic scanning approaches that detect one locus at a time are subject to many problems in genome-wide association studies and quantitative trait locus mapping. The problems include large matrix inversion, over-conservativeness for tests after Bonferroni correction and difficulty in evaluation of the total genetic contribution to a trait’s variance. Targeting these problems, we take a further step and investigate a multiple locus model that detects all markers simultaneously in a single model.ResultsWe developed a sparse Bayesian learning (SBL) method for quantitative trait locus mapping and genome-wide association studies. This new method adopts a coordinate descent algorithm to estimate parameters (marker effects) by updating one parameter at a time conditional on current values of all other parameters. It uses an L2 type of penalty that allows the method to handle extremely large sample sizes (>100 000). Simulation studies show that SBL often has higher statistical powers and the simulated true loci are often detected with extremely small P-values, indicating that SBL is insensitive to stringent thresholds in significance testing.Availability and implementationAn R package (sbl) is available on the comprehensive R archive network (CRAN) and https://github.com/MeiyueComputBio/sbl/tree/master/R%20packge.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals Genome‐wide association studies for iris pigmentation and heterochromia patterns in Large White pigs

2020 ◽  
Vol 51 (3) ◽  
pp. 409-419
Author(s):  
G. Moscatelli ◽  
S. Bovo ◽  
G. Schiavo ◽  
G. Mazzoni ◽  
F. Bertolini ◽  
...  
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Large White ◽  
Genome Wide ◽  
Iris Pigmentation

scholarly journals Association of CNVs with methylation variation

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Xinghua Shi ◽  
Saranya Radhakrishnan ◽  
Jia Wen ◽  
Jin Yun Chen ◽  
Junjie Chen ◽  
...  
Keyword(s):  
Association Studies ◽  
Copy Number Variants ◽  
Cpg Methylation ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Cellular Phenotype ◽  
Genome Wide ◽  
A Genome ◽  
Physical Interactions ◽  
Trait Locus

Abstract Germline copy number variants (CNVs) and single-nucleotide polymorphisms (SNPs) form the basis of inter-individual genetic variation. Although the phenotypic effects of SNPs have been extensively investigated, the effects of CNVs is relatively less understood. To better characterize mechanisms by which CNVs affect cellular phenotype, we tested their association with variable CpG methylation in a genome-wide manner. Using paired CNV and methylation data from the 1000 genomes and HapMap projects, we identified genome-wide associations by methylation quantitative trait locus (mQTL) analysis. We found individual CNVs being associated with methylation of multiple CpGs and vice versa. CNV-associated methylation changes were correlated with gene expression. CNV-mQTLs were enriched for regulatory regions, transcription factor-binding sites (TFBSs), and were involved in long-range physical interactions with associated CpGs. Some CNV-mQTLs were associated with methylation of imprinted genes. Several CNV-mQTLs and/or associated genes were among those previously reported by genome-wide association studies (GWASs). We demonstrate that germline CNVs in the genome are associated with CpG methylation. Our findings suggest that structural variation together with methylation may affect cellular phenotype.

Genetic factors of polygenic urolithiasis

2020 ◽  
Vol 87 (2) ◽  
pp. 57-64
Author(s):  
Filippova Tamara Vladimirovna ◽  
Khafizov Кamil Faridovich ◽  
Rudenko Vadim Igorevich ◽  
Rapoport Leonid Mikhailovich ◽  
Tsarichenko Dmitry Georgievich ◽  
...  
Keyword(s):  
Genetic Factors ◽  
Preventive Measures ◽  
Association Studies ◽  
Case Control ◽  
International Studies ◽  
Genome Wide Association Studies ◽  
Case Control Studies ◽  
Genome Wide ◽  
Genetic Technologies ◽  
High Throughput Dna Sequencing

The article summarizes the findings of Russian and international studies of the genetic aspects of polygenic urolithiasis associated with impairment of calcium metabolism. The article analyzes the genetic risk factors of polygenic nephrolithiasis that show significant association with the disease in case-control studies and Genome-Wide Association Studies (16 genes). We described the gene functions involved in concrement formation in polygenic nephrolithiasis. The modern molecular and genetic technologies (DNA microarray, high-throughput DNA sequencing, etc.) enable identification of the genetic predisposition to a specific disease, realization of the individualized treatment of the patient, and carrying out timely preventive measures among the proband’s relatives.

Genome‐wide association studies for the number of teats and teat asymmetry patterns in Large White pigs

2020 ◽  
Vol 51 (4) ◽  
pp. 595-600
Author(s):  
G. Moscatelli ◽  
S. Dall’Olio ◽  
S. Bovo ◽  
G. Schiavo ◽  
H. Kazemi ◽  
...  
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Large White ◽  
Genome Wide

P5018 Genome-wide association studies for dry-cured ham quality traits in Italian Large White and Italian Duroc pigs

2016 ◽  
Vol 94 (suppl_4) ◽  
pp. 124-124
Author(s):  
L. Fontanesi ◽  
G. Schiavo ◽  
G. Galimberti ◽  
S. Bovo ◽  
F. Bertolini ◽  
...  
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Quality Traits ◽  
Large White ◽  
Genome Wide ◽  
Dry Cured Ham
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