title: Bivariate genome-wide association analysis of the growth and intake components of feed efficiency.
abstract: Single nucleotide polymorphisms (SNPs) associated with average daily gain (ADG) and dry matter intake (DMI), two major components of feed efficiency in cattle, were identified in a genome-wide association study (GWAS). Uni- and multi-SNP models were used to describe feed efficiency in a training data set and the results were confirmed in a validation data set. Results from the univariate and bivariate analyses of ADG and DMI, adjusted by the feedlot beef steer maintenance requirements, were compared. The bivariate uni-SNP analysis identified (P-value <0.0001) 11 SNPs, meanwhile the univariate analyses of ADG and DMI identified 8 and 9 SNPs, respectively. Among the six SNPs confirmed in the validation data set, five SNPs were mapped to KDELC2, PHOX2A, and TMEM40. Findings from the uni-SNP models were used to develop highly accurate predictive multi-SNP models in the training data set. Despite the substantially smaller size of the validation data set, the training multi-SNP models had slightly lower predictive ability when applied to the validation data set. Six Gene Ontology molecular functions related to ion transport activity were enriched (P-value <0.001) among the genes associated with the detected SNPs. The findings from this study demonstrate the complementary value of the uni- and multi-SNP models, and univariate and bivariate GWAS analyses. The identified SNPs can be used for genome-enabled improvement of feed efficiency in feedlot beef cattle, and can aid in the design of empirical studies to further confirm the associations.
authors.affiliation: Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: Nick V L
authors.initials: NV
authors.lastname: Serão
authors.forename: Dianelys
authors.initials: D
authors.lastname: González-Peña
authors.forename: Jonathan E
authors.initials: JE
authors.lastname: Beever
authors.forename: Germán A
authors.initials: GA
authors.lastname: Bollero
authors.forename: Bruce R
authors.initials: BR
authors.lastname: Southey
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Faulkner
authors.forename: Sandra L
authors.initials: SL
authors.lastname: Rodriguez-Zas
mesh_terms: D000821:Animal Feed; D000818:Animals; D002417:Cattle / Q000235:genetics* / Q000254:growth & development*; D004435:Eating; D053263:Gene Regulatory Networks; D055106:Genome-Wide Association Study; D008460:Meat; D015999:Multivariate Analysis; D020641:Polymorphism, Single Nucleotide; D015430:Weight Gain / Q000235:genetics*