title: The distribution of SNP marker effects for faecal worm egg count in sheep, and the feasibility of using these markers to predict genetic merit for resistance to worm infections.
abstract: SummaryGenetic resistance to gastrointestinal worms is a complex trait of great importance in both livestock and humans. In order to gain insights into the genetic architecture of this trait, a mixed breed population of sheep was artificially infected with Trichostrongylus colubriformis (n=3326) and then Haemonchus contortus (n=2669) to measure faecal worm egg count (WEC). The population was genotyped with the Illumina OvineSNP50 BeadChip and 48 640 single nucleotide polymorphism (SNP) markers passed the quality controls. An independent population of 316 sires of mixed breeds with accurate estimated breeding values for WEC were genotyped for the same SNP to assess the results obtained from the first population. We used principal components from the genomic relationship matrix among genotyped individuals to account for population stratification, and a novel approach to directly account for the sampling error associated with each SNP marker regression. The largest marker effects were estimated to explain an average of 0·48% (T. colubriformis) or 0·08% (H. contortus) of the phenotypic variance in WEC. These effects are small but consistent with results from other complex traits. We also demonstrated that methods which use all markers simultaneously can successfully predict genetic merit for resistance to worms, despite the small effects of individual markers. Correlations of genomic predictions with breeding values of the industry sires reached a maximum of 0·32. We estimate that effective across-breed predictions of genetic merit with multi-breed populations will require an average marker spacing of approximately 10 kbp.
authors.affiliation: Faculty of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Kemper
authors.affiliation: Faculty of Veterinary Science, University of Sydney, Camden, NSW 2006, Australia.
authors.forename: David L
authors.initials: DL
authors.lastname: Emery
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian EH25 9RG, UK.
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Bishop
authors.affiliation: School of Environmental and Rural Sciences, University of New England, Armidale, NSW 2351, Australia.
authors.forename: Hutton
authors.initials: H
authors.lastname: Oddy
authors.affiliation: Victorian Department of Primary Industries, AgriBiosciences Centre, LaTrobe Research and Development Park, Bundoora, Victoria 3083, Australia.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Hayes
authors.affiliation: CSIRO Livestock Industries, Armidale, NSW 2350, Australia.
authors.forename: Sonja
authors.initials: S
authors.lastname: Dominik
authors.affiliation: CSIRO Livestock Industries, Armidale, NSW 2350, Australia.
authors.forename: John M
authors.initials: JM
authors.lastname: Henshall
authors.affiliation: Faculty of Land and Environment, University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Goddard
mesh_terms: D000818:Animals; D060467:Disease Resistance / Q000235:genetics*; D005243:Feces / Q000469:parasitology*; D005819:Genetic Markers; D007113:Immunity, Innate / Q000235:genetics; D009349:Nematode Infections / Q000235:genetics / Q000469:parasitology / Q000662:veterinary*; D010270:Parasite Egg Count / Q000662:veterinary*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012756:Sheep / Q000235:genetics* / Q000469:parasitology; D012757:Sheep Diseases / Q000469:parasitology*
chemical_list: D005819:Genetic Markers