Genetic parameters and genomic regions associated with horn fly resistance in organic Holstein cattle

Horn flies (Haematobia irritans [L.]) contribute to major economic losses of pastured cattle operations, particularly in organic herds because of limitations on control methods that can be used. The objectives of this research were to determine if resistance to horn flies is a heritable trait in organic Holstein cattle, determine associations with yield traits, and to detect genomic regions associated with fly infestation. Observations of fly load were recorded from 1,667 pastured Holstein cows, of which 640 were genotyped, on 13 organic dairies across the United States. Fly load score was determined using a 0 to 4 scale based on fly coverage from chine to loin on one side of the body, with 0 indicating few to no flies and 4 indicating high infestation. The scoring system was validated by counting flies from photographs taken at the time of scoring from 252 cows. To mitigate the effect of our data structure on potential selection bias effects on genetic parameter estimates, survival to subsequent lactations of scored animals and herd-mates that had been culled before the trial was accounted for as the trait stayability. Genetic parameters were estimated using single-step genomic analysis with 3-trait mixed models that included fly score, stayability, and a third phenotype. Model effects differed by variable, but fixed effects generally included a contemporary group, scorer, parity, and stage of lactation; random effects included animal, permanent environment, and residual error. A genome-wide association study was performed by decomposing estimated breeding values into marker effects to detect significant genomic regions associated with fly score. The rank correlation between the subjective fly score and the objective count was 0.79. The average heritability of fly score (± standard error) estimated across multiple models was 0.25 ± 0.04 when a known Holstein maternal grandsire was required and 0.19 ± 0.03 when only a known Holstein sire was required. Genetic correlation estimates with yield traits were moderately positive, but a greater fly load was associated with reduced yield after accounting for genetic merit. Lower fly loads were associated with white coat coloration; a significant genomic region on Bos taurus autosome 6 was identified that contains the gene KIT, which was the most plausible candidate gene for fly resistance because of its role in coat pattern and coloration. The magnitude of heritable variation in fly infestation is similar to other traits included in selection programs, suggesting that producers can select for resistance to horn flies.