title: Efficiency of genomic prediction for boar taint reduction in Danish Landrace pigs.
abstract: Genetic selection against boar taint, which is caused by high skatole and androstenone concentrations in fat, is a more acceptable alternative than is the current practice of castration. Genomic predictors offer an opportunity to overcome the limitations of such selection caused by the phenotype being expressed only in males at slaughter, and this study evaluated different approaches to obtain such predictors. Samples from 1000 pigs were included in a design which was dominated by 421 sib pairs, each pair having one animal with high and one with low skatole concentration (≥0.3 μg/g). All samples were measured for both skatole and androstenone and genotyped using the Illumina SNP60 porcine BeadChip for 62 153 single nucleotide polymorphisms. The accuracy of predicting phenotypes was assessed by cross-validation using six different genomic evaluation methods: genomic best linear unbiased prediction (GBLUP) and five Bayesian regression methods. In addition, this was compared to the accuracy of predictions using only QTL that showed genome-wide significance. The range of accuracies obtained by different prediction methods was narrow for androstenone, between 0.29 (Bayes Lasso) and 0.31 (Bayes B), and wider for skatole, between 0.21 (GBLUP) and 0.26 (Bayes SSVS). Relative accuracies, corrected for h(2) , were 0.54-0.56 and 0.75-0.94 for androstenone and skatole respectively. The whole-genome evaluation methods gave greater accuracy than using only the QTL detected in the data. The results demonstrate that GBLUP for androstenone is the simplest genomic technology to implement and was also close to the most accurate method. More specialised models may be preferable for skatole.
authors.affiliation: Faculty of Agriculture in Osijek, J.J. Strossmayer University of Osijek, Kralja Petra Svačića 1d, 31000, Osijek, Croatia.|The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
authors.forename: B
authors.initials: B
authors.lastname: Lukić
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
authors.forename: R
authors.initials: R
authors.lastname: Pong-Wong
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
authors.forename: S J
authors.initials: SJ
authors.lastname: Rowe
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.|Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
authors.forename: D J
authors.initials: DJ
authors.lastname: de Koning
authors.affiliation: Pig Research Centre, Danish Agriculture & Food Council, Axeltorv 3, København, V 1609, Denmark.
authors.forename: I
authors.initials: I
authors.lastname: Velander
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.|MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
authors.forename: C S
authors.initials: CS
authors.lastname: Haley
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
authors.forename: A L
authors.initials: AL
authors.lastname: Archibald
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
authors.forename: J A
authors.initials: JA
authors.lastname: Woolliams
mesh_terms: D000273:Adipose Tissue / Q000737:chemistry; D000736:Androstenes / Q000032:analysis*; D000818:Animals; D001499:Bayes Theorem; D001947:Breeding; D005838:Genotype; D016014:Linear Models; D008297:Male; D008460:Meat / Q000032:analysis*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012862:Skatole / Q000032:analysis*; D034421:Sus scrofa / Q000235:genetics*
chemical_list: D000736:Androstenes; C000214:androst-16-en-3-one; D012862:Skatole
keywords: Bayes; androstenone; genomic best linear unbiased prediction; genomic selection; skatole