title: Genomic prediction for tuberculosis resistance in dairy cattle.
abstract: BACKGROUND
  The increasing prevalence of bovine tuberculosis (bTB) in the UK and the limitations of the currently available diagnostic and control methods require the development of complementary approaches to assist in the sustainable control of the disease. One potential approach is the identification of animals that are genetically more resistant to bTB, to enable breeding of animals with enhanced resistance. This paper focuses on prediction of resistance to bTB. We explore estimation of direct genomic estimated breeding values (DGVs) for bTB resistance in UK dairy cattle, using dense SNP chip data, and test these genomic predictions for situations when disease phenotypes are not available on selection candidates.
  
  
  RESULTS
  We estimated DGVs using genomic best linear unbiased prediction methodology, and assessed their predictive accuracies with a cross validation procedure and receiver operator characteristic (ROC) curves. Furthermore, these results were compared with theoretical expectations for prediction accuracy and area-under-the-ROC-curve (AUC). The dataset comprised 1151 Holstein-Friesian cows (bTB cases or controls). All individuals (592 cases and 559 controls) were genotyped for 727,252 loci (Illumina Bead Chip). The estimated observed heritability of bTB resistance was 0.23±0.06 (0.34 on the liability scale) and five-fold cross validation, replicated six times, provided a prediction accuracy of 0.33 (95% C.I.: 0.26, 0.40). ROC curves, and the resulting AUC, gave a probability of 0.58, averaged across six replicates, of correctly classifying cows as diseased or as healthy based on SNP chip genotype alone using these data.
  
  
  CONCLUSIONS
  These results provide a first step in the investigation of the potential feasibility of genomic selection for bTB resistance using SNP data. Specifically, they demonstrate that genomic selection is possible, even in populations with no pedigree data and on animals lacking bTB phenotypes. However, a larger training population will be required to improve prediction accuracies.
authors.affiliation: The Roslin Institute and RDVS, University of Edinburgh, Midlothian, United Kingdom.
authors.forename: Smaragda
authors.initials: S
authors.lastname: Tsairidou
authors.affiliation: The Roslin Institute and RDVS, University of Edinburgh, Midlothian, United Kingdom.
authors.forename: John A
authors.initials: JA
authors.lastname: Woolliams
authors.affiliation: Agri-Food and Biosciences Institute, Belfast, United Kingdom.
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Allen
authors.affiliation: Agri-Food and Biosciences Institute, Belfast, United Kingdom.
authors.forename: Robin A
authors.initials: RA
authors.lastname: Skuce
authors.affiliation: Agri-Food and Biosciences Institute, Belfast, United Kingdom.
authors.forename: Stewart H
authors.initials: SH
authors.lastname: McBride
authors.affiliation: School of Biological Sciences, Queen's University of Belfast, Belfast, United Kingdom.
authors.forename: David M
authors.initials: DM
authors.lastname: Wright
authors.affiliation: The Roslin Institute and RDVS, University of Edinburgh, Midlothian, United Kingdom.
authors.forename: Mairead L
authors.initials: ML
authors.lastname: Bermingham
authors.affiliation: The Roslin Institute and RDVS, University of Edinburgh, Midlothian, United Kingdom.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Pong-Wong
authors.affiliation: The Roslin Institute and RDVS, University of Edinburgh, Midlothian, United Kingdom.
authors.forename: Oswald
authors.initials: O
authors.lastname: Matika
authors.affiliation: Agri-Food and Biosciences Institute, Belfast, United Kingdom.
authors.forename: Stanley W J
authors.initials: SW
authors.lastname: McDowell
authors.affiliation: The Roslin Institute and RDVS, University of Edinburgh, Midlothian, United Kingdom.
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Glass
authors.affiliation: The Roslin Institute and RDVS, University of Edinburgh, Midlothian, United Kingdom.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Bishop
mesh_terms: D000818:Animals; D019540:Area Under Curve; D001947:Breeding; D002417:Cattle / Q000235:genetics* / Q000276:immunology / Q000382:microbiology*; D003612:Dairying; D060467:Disease Resistance / Q000235:genetics*; D023281:Genomics; D020641:Polymorphism, Single Nucleotide; D012372:ROC Curve; D014380:Tuberculosis, Bovine / Q000276:immunology*