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

dc.contributor.authorLi, Jiyuan
dc.contributor.authorAkanno, Everestus C.
dc.contributor.authorValente, Tiago S. [UNESP]
dc.contributor.authorAbo-Ismail, Mohammed
dc.contributor.authorKarisa, Brian K.
dc.contributor.authorWang, Zhiquan
dc.contributor.authorPlastow, Graham S.
dc.contributor.institutionUniv Alberta
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionCalif Polytech State Univ San Luis Obispo
dc.contributor.institutionMinist Agr & Forestry
dc.description.abstractMetabolites, 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 andin silicofunctional 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 SNPPvalues 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 to detect corresponding candidate genes. Functional enrichment analyses were performed on metabolites and their candidate genes using the Ingenuity Pathway Analysis software. Eleven metabolites showed low to moderate heritability that ranged from 0.09 +/- 0.15 to 0.36 +/- 0.15, while heritability estimates for 22 metabolites were zero or negligible. This result indicates that while variations in 11 metabolites were due to genetic variants, the majority are largely influenced by environment. Three significant SNP associations were detected for betaine (rs109862186),L-alanine (rs81117935), andL-lactic acid (rs42009425) based on Bonferroni correction for multiple testing (family wise error rate <0.05). The SNP rs81117935 was found to be located within theCatenin Alpha 2gene (CTNNA2) showing a possible association with the regulation ofL-alanine concentration. Other candidate genes were identified based on additive genetic variance explained by SNP windows of 10 consecutive SNPs. The observed heritability estimates and the candidate genes and networks identified in this study will serve as baseline information for research into the utilization of plasma metabolites for genetic improvement of crossbred beef cattle.en
dc.description.affiliationUniv Alberta, Fac Agr Life & Environm Sci, Dept Agr Food & Nutr Sci, Livestock Gentec, Edmonton, AB, Canada
dc.description.affiliationSao Paulo State Univ, Dept Anim Sci, Ethol & Anim Ecol Res Grp, Jaboticabal, Brazil
dc.description.affiliationCalif Polytech State Univ San Luis Obispo, Coll Agr Food & Environm Sci, Dept Anim Sci, San Luis Obispo, CA 93407 USA
dc.description.affiliationMinist Agr & Forestry, Edmonton, AB, Canada
dc.description.affiliationUnespSao Paulo State Univ, Dept Anim Sci, Ethol & Anim Ecol Res Grp, Jaboticabal, Brazil
dc.description.sponsorshipAlberta Livestock and Meat Agency (ALMA)
dc.description.sponsorshipAlberta Innovates - Bio Solutions (AIBio)
dc.description.sponsorshipAlberta Innovates
dc.description.sponsorshipIdAlberta Livestock and Meat Agency (ALMA): 2014F068R
dc.description.sponsorshipIdAlberta Innovates - Bio Solutions (AIBio): 2014F068R
dc.description.sponsorshipIdAlberta Innovates: 200800538
dc.identifier.citationFrontiers In Genetics. Lausanne: Frontiers Media Sa, v. 11, 12 p., 2020.
dc.publisherFrontiers Media Sa
dc.relation.ispartofFrontiers In Genetics
dc.sourceWeb of Science
dc.subjectcandidate genes
dc.subjectcrossbred beef cattle
dc.subjectfunctional enrichment analyses
dc.subjectsingle-step GBLUP
dc.titleGenomic Heritability and Genome-Wide Association Studies of Plasma Metabolites in Crossbred Beef Cattleen
dcterms.rightsHolderFrontiers Media Sa