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

Kathryn E. Kemper*, David L. Emery, Stephen C. Bishop, Hutton Oddy, Benjamin J. Hayes, Sonja Dominik, John M. Henshall, Michael E. Goddard

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Genetic 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.

Original languageEnglish
Pages (from-to)203-219
Number of pages17
JournalGenetics Research
Volume93
Issue number3
DOIs
Publication statusPublished - Jun 2011

Keywords / Materials (for Non-textual outputs)

  • quantitative trait loci linkage disequilibrium gastrointestinal nematodes parasite resistance genomic predictions complex traits population cattle disease heritability

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