Objective The strategy of crossbreeding Simmental with Holstein cattle (Simmental×Holstein) has been identified as an effective approach for enhancing dairy herd efficiency. In some parts of China, a certain scale of hybrid population has been obtained by using the crossbreeding model in various regions of China. The aim of this study is to establish a precise methodology for assessing the ancestry composition of Simmental-Holstein crossbreeding cattle.

Methods Leveraging Holstein, Simmental, and Norwegian Red cattle as purebred reference populations, this study employed genomic SNP markers and admixture analysis to estimate the ancestry proportions of 161 Simmental-Holstein crossbreeding cattle.

Results The results showed that the first-generation hybrids (Simmental×Holstein) comprised approximately 41.80% ± 9.00% Holstein and 52.59% ± 10.38% Simmental ancestries. For the second-generation hybrids, including backcrosses to both Holstein and Simmental, the estimated ancestries were 80.01% ± 6.68% and 17.20% ± 4.43% for Holstein, and 17.01% ± 7.83% and 81.80% ± 4.62% for Simmental, respectively. Notably, a fraction of the hybrid individuals exhibited a certain proportion of Norwegian red cattle ancestry.

Conclusion The estimated ancestry proportions are close to the theoretical values (1꞉1 for the first generation, 3꞉1 for the second generation) which is align with the hybridization history of the population, indicating that this method can accurately assess the genetic background of crossbreeding cattle. This findings lay a solid technical foundation for effectively monitoring the ancestry composition of crossbreeding cattle herds and implementing precise selection and breeding strategies in the future.