Genomic Heritability and Genome-Wide Association Studies of Plasma Metabolites in Crossbred Beef Cattle

Frontiers in Genetics
Jiyuan LiGraham S Plastow

Abstract

Metabolites, substrates or products of metabolic processes, are involved in many biological functions, such as energy metabolism, signaling, stimulatory and inhibitory effects on enzymes and immunological defense. Metabolomic phenotypes are influenced by combination of genetic and environmental effects allowing for metabolome-genome-wide association studies (mGWAS) as a powerful tool to investigate the relationship between these phenotypes and genetic variants. The objectives of this study were to estimate genomic heritability and perform mGWAS and in silico functional enrichment analyses for a set of plasma metabolites in Canadian crossbred beef cattle. Thirty-three plasma metabolites and 45,266 single nucleotide polymorphisms (SNPs) were available for 475 animals. Genomic heritability for all metabolites was estimated using genomic best linear unbiased prediction (GBLUP) including genomic breed composition as covariates in the model. A single-step GBLUP implemented in BLUPF90 programs was used to determine SNP P values and the proportion of genetic variance explained by SNP windows containing 10 consecutive SNPs. The top 10 SNP windows that explained the largest genetic variation for each metabolite were identified and mapped...Continue Reading

References

Jun 15, 1979·The Biochemical Journal·A R NeillR M Dawson
Mar 9, 2004·Progress in Lipid Research·Chieko AoyamaKozo Ishidate
Sep 2, 2005·Nature·Steve E CalvanoUNKNOWN Inflamm and Host Response to Injury Large Scale Collab. Res. Program
Jun 3, 2008·The Plant Cell·Heather C RoweDaniel J Kliebenstein
Oct 25, 2008·Nature·Jeremy K Nicholson, John C Lindon
Aug 4, 2009·Genome Research·David H AlexanderKenneth Lange
Oct 14, 2009·Genetics·A P W de RoosM E Goddard
Dec 29, 2009·Nature Genetics·Thomas IlligKarsten Suhre
Nov 17, 2010·PLoS Genetics·Eva K F ChanDaniel J Kliebenstein
Sep 1, 2011·Molecular Systems Biology·George NicholsonChris C Holmes
Sep 3, 2011·Nature·Karsten SuhreChristian Gieger
Jun 13, 2012·Bioinformatics·Valentin WimmerChris-Carolin Schön
Aug 23, 2012·Frontiers in Genetics·Duc LuStephen P Miller
Sep 2, 2014·Metabolomics : Official Journal of the Metabolomic Society·Noha A YousriKarsten Suhre
Apr 16, 2017·Biochimica Et Biophysica Acta. Biomembranes·Jelske N van der VeenRené L Jacobs
Nov 21, 2017·Nucleic Acids Research·Daniel R ZerbinoPaul Flicek
May 1, 2018·Journal of Dairy Science·Andrew MareteDidier Boichard
May 29, 2018·Expert Review of Molecular Diagnostics·Ángeles López-LópezCoral Barbas
Aug 25, 2018·Animal : an International Journal of Animal Bioscience·G Cantalapiedra-HijarI Ortigues-Marty
Nov 8, 2018·Journal of Cellular and Molecular Medicine·Wenguang ChangMan Wang
Dec 6, 2018·Frontiers in Immunology·Yaoyao XiaWenkai Ren
Sep 19, 2019·Cell Reports·Noga Ron-HarelMarcia C Haigis

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Methods Mentioned

BETA
Nuclear Magnetic
NMR
Profiler

Software Mentioned

Ensembl
ASReml
IPA
Synbreed
Ingenuity Pathway Analysis software
BLUPF90
R package qqman
ADMIXTURE
Library Manager
WssGBLUP

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