Beef cattle

Genomic insights into horn fly resistance in beef cattle

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Abstract

Horn flies are a major pest in cattle operations, resulting in more than $1 billion in annual losses due to reduced productivity and compromised animal welfare. While chemical control remains widely implemented, the emergence of insecticide resistance and growing environmental concerns underscore the need to develop sustainable alternatives for mitigating horn fly burden in cattle. Hence, host genetic resistance to horn flies represents a promising long-term strategy. However, the mechanisms and genomic regions underlying natural variation in horn fly susceptibility remain poorly characterized. This study aimed to dissect the genetic architecture of horn fly resistance in beef cattle. Calves from the UF purebred Brahman (478 BRA) and Multibreed Angus-Brahman (748 MAB) herds were video-recorded at weaning using a GoPro camera mounted on the top of the chute. Fly infestation was quantified as the average fly count across 3-5 longitudinal images per animal, manually recorded using ImageJ software. Genotyping was performed with the Illumina Bovine GGPF250 array, retaining autosomal SNP markers after quality control. Analyses of variance were conducted within herds to evaluate the impact of non-genetic factors on horn fly counts. For MAB calves, breed groups (BG) were defined based on Brahman breed percentage: BG1 (0-19%), BG2 (20-39%), BG3 (40-59%), BG4 (60-79%), and BG5 (80-100%), with similar number of individuals per group. Fly count values were natural-log transformed (log[count+1])to ensure normally distributed residuals. As expected, substantial phenotypic variability in horn fly load was observed within and across breed groups. Animals with darker pigmentation and smoother coats tended to attract more flies, whereas cattle with higher Bos indicus influence exhibited lower infestations. Genetic parameters were estimated using mixed linear model under the genomic best linear unbiased prediction (GBLUP) approach, and GWAS was conducted using the weighted GBLUP method, both implemented in the BLUPF90 suite. Gene set enrichment analysis was performed using the overrepresentation test in PANTHER. Genomic analyses revealed that resistance to horn flies is moderately heritable (h²=0.20), indicating potential for genetic improvement through selection. Multiple genomic regions explaining at least 1% of the additive genetic variance for horn fly load were identified, including regions harboring genes involved in skin structure, immune modulation, sensory signaling, and pigmentation. These findings indicate that horn fly resistance is a polygenic trait shaped by a complex combination of physiological, immunological, and morphological pathways rather than single major-effect loci. Overall, this work advances our understanding of the biological and genetic determinants of horn fly resistance in beef cattle and provides foundational information for developing marker-assisted and genomic selection strategies aimed at reducing horn fly burden. Incorporating resistance to horn flies into breeding objectives has strong potential to enhance productivity and animal welfare while decreasing reliance on insecticides and contributing to more sustainable beef production systems.

Keywords: 2026

How to Cite:

Alvarado-Vargas, A., Alvares, L., Boscollo, P., C. Ladeira, G., Cavender, C., Rezende, F. & Tayama, P., (2026) “Genomic insights into horn fly resistance in beef cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287001. doi: https://doi.org/10.31274/wcgalp.24193

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