title: Reliability of molecular breeding values for Warner-Bratzler shear force and carcass traits of beef cattle - an independent validation study.
abstract: Interest in genetic improvement of carcass and tenderness traits of beef cattle using genome-based selection (GS) and marker-assisted management programs is increasing. The success of such a program depends on the presence of linkage disequilibrium between the observed markers and the underlying QTL as well as on the relationship between the discovery, validation, and target populations. For molecular breeding values (MBV) predicted for a target population using SNP markers, reliabilities of these MBV can be obtained from validation analyses conducted in an independent population distinct from the discovery set. The objective of this study was to test MBV predicted for carcass and tenderness traits of beef cattle in a Canadian-based validation population that is largely independent of a United States-based discovery set. The discovery data set comprised of genotypes and phenotypes from >2,900 multibreed beef cattle while the validation population consisted of 802 crossbred feeder heifers and steers. A bivariate animal model that fitted actual phenotype and MBV was used for validation analyses. The reliability of MBV was defined as square of the genetic correlation (R(2) g) that represents the proportion of the additive genetic variance explained by the SNP markers. Several scenarios involving different starting marker panels (384, 3K, 7K, and 50K) and different sets of SNP selected to compute MBV (50, 100, 200, 375, 400, 600, and 800) were investigated. Validation results showed that the most reliable MBV (R(2) g) were 0.34 for HCW, 0.36 for back fat thickness, 0.28 for rib eye area, 0.30 for marbling score, 0.25 for yield grade, and 0.38 for Warner-Bratzler shear force across the different scenarios explored. The results indicate that smaller SNP panels can be developed for use in genetic improvement of beef carcass and tenderness traits to exploit GS benefits.
authors.affiliation: Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
authors.forename: E C
authors.initials: EC
authors.lastname: Akanno
authors.affiliation: Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
authors.forename: G
authors.initials: G
authors.lastname: Plastow
authors.affiliation: NextGen, Lawrenceville, GA.
authors.forename: B W
authors.initials: BW
authors.lastname: Woodward
authors.affiliation: GeneSeek, 4665 Innovation Drive, Suite 120, Lincoln, NE.
authors.forename: S
authors.initials: S
authors.lastname: Bauck
authors.affiliation: Department of Animal Science, Biometry and Genetic Branch, University of Yuzuncu Yil, Van, Turkey.
authors.forename: H
authors.initials: H
authors.lastname: Okut
authors.affiliation: Department of Dairy Science, Department of Animal Sciences, University of Wisconsin, Madison.
authors.forename: X-L
authors.initials: XL
authors.lastname: Wu
authors.affiliation: National Association of Animal Breeders, Columbia, MO.
authors.forename: C
authors.initials: C
authors.lastname: Sun
authors.affiliation: Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, Canada.
authors.forename: J L
authors.initials: JL
authors.lastname: Aalhus
authors.affiliation: Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Australia.
authors.forename: S S
authors.initials: SS
authors.lastname: Moore
authors.affiliation: Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, ON, Canada.
authors.forename: S P
authors.initials: SP
authors.lastname: Miller
authors.affiliation: Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
authors.forename: Z
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada Lacombe Research Centre, Alberta Agriculture and Rural Development, 6000 C & E Trail, Lacombe, AB, Canada John.Basarab@gov.ab.ca.
authors.forename: J A
authors.initials: JA
authors.lastname: Basarab
mesh_terms: D000818:Animals; D001947:Breeding / Q000379:methods / Q000592:standards*; D002417:Cattle / Q000033:anatomy & histology / Q000235:genetics*; D005260:Female; D005819:Genetic Markers / Q000235:genetics; D008297:Male; D008460:Meat / Q000592:standards*; D008967:Molecular Biology / Q000379:methods / Q000592:standards; D018482:Muscle, Skeletal / Q000033:anatomy & histology; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results
chemical_list: D005819:Genetic Markers
keywords: genetic improvement; genome-based selection; single nucleotide polymorphism; tenderness; validation