title: Persistence of accuracy of genomic estimated breeding values over generations in layer chickens.
abstract: BACKGROUND
  The predictive ability of genomic estimated breeding values (GEBV) originates both from associations between high-density markers and QTL (Quantitative Trait Loci) and from pedigree information. Thus, GEBV are expected to provide more persistent accuracy over successive generations than breeding values estimated using pedigree-based methods. The objective of this study was to evaluate the accuracy of GEBV in a closed population of layer chickens and to quantify their persistence over five successive generations using marker or pedigree information.
  
  
  METHODS
  The training data consisted of 16 traits and 777 genotyped animals from two generations of a brown-egg layer breeding line, 295 of which had individual phenotype records, while others had phenotypes on 2,738 non-genotyped relatives, or similar data accumulated over up to five generations. Validation data included phenotyped and genotyped birds from five subsequent generations (on average 306 birds/generation). Birds were genotyped for 23,356 segregating SNP. Animal models using genomic or pedigree relationship matrices and Bayesian model averaging methods were used for training analyses. Accuracy was evaluated as the correlation between EBV and phenotype in validation divided by the square root of trait heritability.
  
  
  RESULTS
  Pedigree relationships in outbred populations are reduced by 50% at each meiosis, therefore accuracy is expected to decrease by the square root of 0.5 every generation, as observed for pedigree-based EBV (Estimated Breeding Values). In contrast the GEBV accuracy was more persistent, although the drop in accuracy was substantial in the first generation. Traits that were considered to be influenced by fewer QTL and to have a higher heritability maintained a higher GEBV accuracy over generations. In conclusion, GEBV capture information beyond pedigree relationships, but retraining every generation is recommended for genomic selection in closed breeding populations.
authors.affiliation: Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska st, 33, 60-637 Poznan, Poland. awolc@jay.up.poznan.pl
authors.forename: Anna
authors.initials: A
authors.lastname: Wolc
authors.forename: Jesus
authors.initials: J
authors.lastname: Arango
authors.forename: Petek
authors.initials: P
authors.lastname: Settar
authors.forename: Janet E
authors.initials: JE
authors.lastname: Fulton
authors.forename: Neil P
authors.initials: NP
authors.lastname: O'Sullivan
authors.forename: Rudolf
authors.initials: R
authors.lastname: Preisinger
authors.forename: David
authors.initials: D
authors.lastname: Habier
authors.forename: Rohan
authors.initials: R
authors.lastname: Fernando
authors.forename: Dorian J
authors.initials: DJ
authors.lastname: Garrick
authors.forename: Jack C M
authors.initials: JC
authors.lastname: Dekkers
mesh_terms: D000818:Animals; D001947:Breeding; D002645:Chickens / Q000235:genetics*; D005260:Female; D005819:Genetic Markers; D016678:Genome; D023281:Genomics / Q000379:methods*; D005838:Genotype; D008297:Male; D010375:Pedigree; D040641:Quantitative Trait Loci; D012641:Selection, Genetic
chemical_list: D005819:Genetic Markers