Establishing a genomic reference population for flystrike resistance in the Australian Merino sheep genetic evaluation

Context Flystrike, caused by blowfly larvae, is a major welfare and economic concern in Australian Merino sheep. Current control strategies rely on management practices such as mulesing, crutching and chemical treatments, which face increasing labour costs, welfare and resistance challenges. Genetic selection offers a sustainable long-term solution, highlighting the need to establish a genomic reference population. Aims This study establishes a genomic reference population to enable more accurate selection for resistance to breech and body strike traits. Methods Data were collected from historic research and development flocks and ram breeder flocks as part of the Flystrike Genomics Reference Flock Project. To optimise the reference population design, key assessments included evaluating expression thresholds, the impact of multi-trait versus single-trait analyses of breech and body strike traits, the value of incorporating genomic information, and the estimation of genetic parameters. Key results The incorporation of genomic data significantly improved prediction accuracy over pedigree-based methods, and multi-trait analyses provided higher accuracy than single-trait models. Results based on current data showed that higher incidence levels increase heritability, with practical thresholds of 2.5% structure balancing genetic variation and breeder participation. Conclusion These results demonstrate that combining genomic information with multi-trait evaluations can support more reliable genetic selection for flystrike resistance in Merino sheep. Current evaluations for breech strike provide reasonably reliable breeding values, but continued phenotyping and genotyping for both breech and body strike are essential to expand the reference population, improve accuracy, and support ongoing genomic selection. Continued collection of flystrike records, particularly for lower-heritability traits, is essential to expand a well-phenotyped and genotyped reference population, providing a robust framework for genomic selection and supporting sustainable, long-term reductions in flystrike incidence. Implications The establishment of a genomic reference population enables the implementation of genomic breeding values for flystrike resistance in the Australian Merino genetic evaluation system. Integrating genomic selection into breeding programs can reduce reliance on chemical and surgical interventions, improve animal welfare, and accelerate genetic gains for flystrike resistance across the Australian Merino flocks.