title: Genomic prediction of breeding values for carcass traits in Nellore cattle.
abstract: BACKGROUND
  The objective of this study was to evaluate the accuracy of genomic predictions for rib eye area (REA), backfat thickness (BFT), and hot carcass weight (HCW) in Nellore beef cattle from Brazilian commercial herds using different prediction models.
  
  
  METHODS
  Phenotypic data from 1756 Nellore steers from ten commercial herds in Brazil were used. Animals were offspring of 294 sires and 1546 dams, reared on pasture, feedlot finished, and slaughtered at approximately 2 years of age. All animals were genotyped using a 777k Illumina Bovine HD SNP chip. Accuracy of genomic predictions of breeding values was evaluated by using a 5-fold cross-validation scheme and considering three models: Bayesian ridge regression (BRR), Bayes C (BC) and Bayesian Lasso (BL), and two types of response variables: traditional estimated breeding value (EBV), and phenotype adjusted for fixed effects (Y*).
  
  
  RESULTS
  The prediction accuracies achieved with the BRR model were equal to 0.25 (BFT), 0.33 (HCW) and 0.36 (REA) when EBV was used as response variable, and 0.21 (BFT), 0.37 (HCW) and 0.46 (REA) when using Y*. Results obtained with the BC and BL models were similar. Accuracies increased for traits with a higher heritability, and using Y* instead of EBV as response variable resulted in higher accuracy when heritability was higher.
  
  
  CONCLUSIONS
  Our results indicate that the accuracy of genomic prediction of carcass traits in Nellore cattle is moderate to high. Prediction of genomic breeding values from adjusted phenotypes Y* was more accurate than from EBV, especially for highly heritable traits. The three models considered (BRR, BC and BL) led to similar predictive abilities and, thus, either one could be used to implement genomic prediction for carcass traits in Nellore cattle.
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. gerardojjunior@yahoo.com.br.
authors.forename: Gerardo A
authors.initials: GA
authors.lastname: Fernandes Júnior
authors.affiliation: Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA. grosa@wisc.edu.
authors.forename: Guilherme J M
authors.initials: GJ
authors.lastname: Rosa
authors.affiliation: Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA. bvalente@wisc.edu.
authors.forename: Bruno D
authors.initials: BD
authors.lastname: Valente
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. rcar@fcav.unesp.br.
authors.forename: Roberto
authors.initials: R
authors.lastname: Carvalheiro
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. fernandobaldiuy@gmail.com.
authors.forename: Fernando
authors.initials: F
authors.lastname: Baldi
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. diogo.garcia@brf-br.com.
authors.forename: Diogo A
authors.initials: DA
authors.lastname: Garcia
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. danielmansangordo@gmail.com.
authors.forename: Daniel G M
authors.initials: DG
authors.lastname: Gordo
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. espigolan@yahoo.com.br.
authors.forename: Rafael
authors.initials: R
authors.lastname: Espigolan
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. lutakada@gmail.com.
authors.forename: Luciana
authors.initials: L
authors.lastname: Takada
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. rafaeltonussi@yahoo.com.br.
authors.forename: Rafael L
authors.initials: RL
authors.lastname: Tonussi
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. willb.galena@yahoo.com.br.
authors.forename: Willian B F
authors.initials: WB
authors.lastname: de Andrade
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. anafabriciabm@yahoo.com.br.
authors.forename: Ana F B
authors.initials: AF
authors.lastname: Magalhães
authors.affiliation: Faculdade de Medicina Veterinária e Zootecnia, UNESP, Botucatu, SP, 18618-970, Brazil. lachard@ibb.unesp.br.
authors.forename: Luis A L
authors.initials: LA
authors.lastname: Chardulo
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. tonhati@fcav.unesp.br.
authors.forename: Humberto
authors.initials: H
authors.lastname: Tonhati
authors.affiliation: Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, SP, 14884-900, Brazil. lgalb@fcav.unesp.br.
authors.forename: Lucia G
authors.initials: LG
authors.lastname: de Albuquerque
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D001938:Brazil; D002417:Cattle / Q000235:genetics*; D023281:Genomics / Q000379:methods; D005838:Genotype; D008297:Male; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D000069466:Red Meat; D000068618:Selective Breeding
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