title: Comparison of alternative approaches to single-trait genomic prediction using genotyped and non-genotyped Hanwoo beef cattle.
abstract: Genomic predictions from BayesA and BayesB use training data that include animals with both phenotypes and genotypes. Single-step methodologies allow additional information from non-genotyped relatives to be included in the analysis. The single-step genomic best linear unbiased prediction (SSGBLUP) method uses a relationship matrix computed from marker and pedigree information, in which missing genotypes are imputed implicitly. Single-step Bayesian regression (SSBR) extends SSGBLUP to BayesB-like models using explicitly imputed genotypes for non-genotyped individuals.
  
  
  
  Carcass records included 988 genotyped Hanwoo steers with 35,882 SNPs and 1438 non-genotyped steers that were measured for back-fat thickness (BFT), carcass weight (CWT), eye-muscle area, and marbling score (MAR). Single-trait pedigree-based BLUP, Bayesian methods using only genotyped individuals, SSGBLUP and SSBR methods were compared using cross-validation.
  
  
  
  Methods using genomic information always outperformed pedigree-based BLUP when the same phenotypic data were modeled from either genotyped individuals only or both genotyped and non-genotyped individuals. For BFT and MAR, accuracies were higher with single-step methods than with BayesB, BayesC and BayesCπ. Gains in accuracy with the single-step methods ranged from +0.06 to +0.09 for BFT and from +0.05 to +0.07 for MAR. For CWT, SSBR always outperformed the corresponding Bayesian methods that used only genotyped individuals. However, although SSGBLUP incorporated information from non-genotyped individuals, prediction accuracies were lower with SSGBLUP than with BayesC (π = 0.9999) and BayesB (π = 0.98) for CWT because, for this particular trait, there was a benefit from the mixture priors of the effects of the single nucleotide polymorphisms.
  
  
  
  Single-step methods are the preferred approaches for prediction combining genotyped and non-genotyped animals. Alternative priors allow SSBR to outperform SSGBLUP in some cases.
authors.affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
authors.forename: Joonho
authors.identifier: 0000-0002-0099-6907
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.|Department of Statistics, Iowa State University, Ames, IA, 50011, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Cheng
authors.affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.|Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.|ThetaSolutions, LLC, Atascadero, CA, USA.
authors.forename: Dorian
authors.initials: D
authors.lastname: Garrick
authors.affiliation: ThetaSolutions, LLC, Atascadero, CA, USA.
authors.forename: Bruce
authors.initials: B
authors.lastname: Golden
authors.affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
authors.forename: Jack
authors.initials: J
authors.lastname: Dekkers
authors.affiliation: Department of Animal Biotechnology, Chonbuk National University, Chonju, Jeollabuk-do, South Korea.
authors.forename: Kyungdo
authors.initials: K
authors.lastname: Park
authors.affiliation: Department of Animal Science, Hankyong National University, Anseong, Gyeonggi-do, South Korea.
authors.forename: Deukhwan
authors.initials: D
authors.lastname: Lee
authors.affiliation: Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. rohan@iastate.edu.
authors.forename: Rohan
authors.identifier: 0000-0001-5821-099X
authors.initials: R
authors.lastname: Fernando
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002417:Cattle; D056726:Genetic Association Studies; D016678:Genome; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D005838:Genotype; D008957:Models, Genetic; D015233:Models, Statistical; D010641:Phenotype; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results