title: Pedigree and genomic evaluation of pigs using a terminal-cross model.
abstract: BACKGROUND
  In crossbreeding schemes, within-line selection of purebreds is performed mainly to improve the performance of crossbred descendants under field conditions. The genetic correlation between purebred and crossbred performance is an important parameter to be assessed because purebred performance can be a poor predictor of the performance of crossbred offspring. With the availability of high-density markers, the feasibility of using crossbred information to evaluate purebred candidates can be reassessed. This study implements and applies a single-step terminal-cross model (GEN) to real data to estimate the genetic parameters of several production and quality traits in pigs.
  
  
  METHODS
  Piétrain sires were mated with Piétrain and Large White dams to produce purebred and crossbred male half-sib piglets; growth rate, feed conversion ratio, lean meat, pH of longissimus dorsi muscle, drip loss and intramuscular fat content were recorded on all half-sibs. Animals were genotyped using the Illumina Porcine SNP60 BeadChip. The genetic correlation between purebred and crossbred performance was estimated separately for each trait. Purebred animals were evaluated using an animal model, whereas the additive genetic effect of a crossbred individual was decomposed into the additive effects of the sire and dam and a Mendelian sampling effect that was confounded with the residual effect. Genotypes of the Piétrain animals were integrated in the genetic evaluation by using a single-step procedure. As benchmarks, we used a model that was identical to GEN but only accounted for pedigree information (PED) and also two univariate single-step models (GEN_UNI) that took either purebred or crossbred performance into account.
  
  
  RESULTS
  Genetic correlations between purebred and crossbred performance were high and positive for all traits (>0.69). Accuracies of estimated breeding values of genotyped sires and purebred offspring that were obtained with the GEN model outperformed both those obtained with the PED and the GEN_UNI models. The use of genomic information increased the predictive ability of the GEN model, but it did not substantially outperform the GEN_UNI models.
  
  
  CONCLUSIONS
  We present a single-step terminal-cross model that integrates genomic information of purebred and crossbred performance by using available software. It improves the theoretical accuracy of genetic evaluations in breeding programs that are based on crossbreeding.
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France. llibertat.tusell-palomero@toulouse.inra.fr.
authors.forename: Llibertat
authors.initials: L
authors.lastname: Tusell
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Gilbert
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France.
authors.forename: Juliette
authors.initials: J
authors.lastname: Riquet
authors.affiliation: IFIP - Institut du porc, La Motte au Vicomte, BP 35104, 35651, Le Rheu Cedex, France.
authors.forename: Marie-José
authors.initials: MJ
authors.lastname: Mercat
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France.
authors.forename: Andres
authors.initials: A
authors.lastname: Legarra
authors.affiliation: GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Larzul
mesh_terms: D000818:Animals; D005260:Female; D016678:Genome; D005838:Genotype; D006824:Hybridization, Genetic / Q000235:genetics*; D008297:Male; D008957:Models, Genetic; D015233:Models, Statistical; D010375:Pedigree; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012984:Software; D034421:Sus scrofa / Q000235:genetics*