The impact of using genotype information for flystrike breeding values in Australian Merino sheep

Background: Flystrike presents substantial financial and animal welfare challenges for the Australian sheep industry. As flystrike resistance has proven to be heritable, breeding for genetic resistance offers a sustainable, long-term solution

Research objective: This study evaluated the impact of incorporating genomic information into breeding values compared to traditional methods relying on phenotypic and pedigree data.

Methods: Data were sourced from 22 research and industry breeder flocks, comprising animals born between 2006 and 2023, with documented cases of breech strike at the early stage (yearling). Prediction accuracy was assessed through forward validation, excluding animals born after 2018 from the initial analysis. Genomic breeding values (partial GEBVs) for these animals (7,993 born from 2018 onwards) were compared with GEBVs derived from the full dataset. Accuracy (rank correlation), dispersion (regression slope, a value closer to one is preferred), and bias (mean difference between partial and full GEBVs) were evaluated for progeny and sires.

Results: Incorporating genomic data improved prediction accuracy in progeny (from 0.64 to 0.81) and sires (from 0.59 to 0.77). Dispersion also improved in progeny (from 1.40 to 1.22) and sires (from 1.07 to 1.06). Bias was reduced in progeny (from 0.03 to 0.02) and sires (from 0.03 to 0.01). Despite a large dataset (24,571 records) and comprehensive pedigree (99,261 animals from 7,679 sires and 43,240 dams), incorporating genomic information still further enhanced accuracy and reduced bias.

Conclusions: These findings highlight the value of genomics in breeding programs, supporting improved genetic selection for flystrike resistance and advancing animal welfare.