title: The effect of using genealogy-based haplotypes for genomic prediction.
abstract: BACKGROUND
  Genomic prediction uses two sources of information: linkage disequilibrium between markers and quantitative trait loci, and additive genetic relationships between individuals. One way to increase the accuracy of genomic prediction is to capture more linkage disequilibrium by regression on haplotypes instead of regression on individual markers. The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information.
  
  
  METHODS
  A total of 4429 Danish Holstein bulls were genotyped with the 50K SNP chip. Haplotypes were constructed using local genealogical trees. Effects of haplotype covariates were estimated with two types of prediction models: (1) assuming that effects had the same distribution for all haplotype covariates, i.e. the GBLUP method and (2) assuming that a large proportion (π) of the haplotype covariates had zero effect, i.e. a Bayesian mixture method.
  
  
  RESULTS
  About 7.5 times more covariate effects were estimated when fitting haplotypes based on local genealogical trees compared to fitting individuals markers. Genealogy-based haplotype clustering slightly increased the accuracy of genomic prediction and, in some cases, decreased the bias of prediction. With the Bayesian method, accuracy of prediction was less sensitive to parameter π when fitting haplotypes compared to fitting markers.
  
  
  CONCLUSIONS
  Use of haplotypes based on genealogy can slightly increase the accuracy of genomic prediction. Improved methods to cluster the haplotypes constructed from local genealogy could lead to additional gains in accuracy.
authors.affiliation: Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele DK-8830, Denmark. Vahid.Edriss@agrsci.dk
authors.forename: Vahid
authors.initials: V
authors.lastname: Edriss
authors.forename: Rohan L
authors.initials: RL
authors.lastname: Fernando
authors.forename: Guosheng
authors.initials: G
authors.lastname: Su
authors.forename: Mogens S
authors.initials: MS
authors.lastname: Lund
authors.forename: Bernt
authors.initials: B
authors.lastname: Guldbrandtsen
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002417:Cattle; D019295:Computational Biology / Q000379:methods; D005789:Genealogy and Heraldry; D023281:Genomics; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable