The impact of using different ancestral reference populations in assessing crossbred population admixture and influence on performance.

Crossbreeding is a process in which animals from different breeds are mated together. The animals produced will exhibit a combination of both additive and non-additive genetic improvement from parental breeds that increase heterozygosity and negate inbreeding depression. However, crossbreeding may also break up the unique and often beneficial gene combinations in parental breeds, possibly reducing performance potential as the benefits of heterosis depends on the type of crossbreeding systems used and heritability of the traits. This effect of crossbreeding, especially on the genome architecture, is still poorly understood with respect to 3-breed crossbreeding systems. Thus, this study examined variation in genomic ancestry estimations relative to pedigree-based estimations and correlated breed composition to key production and health traits. Two rotational crossbred populations, referenced as ProCROSS and Grazecross were assessed and totaled 607 crossbred cattle. ProCROSS is a product of rotational crossbreeding of Viking Red (VKR), Holstein (HOL), and Montbeliarde (MON). In contrast, Grazecross consists of Viking Red (VKR), Normande (NOR), and Jersey (JER). Both breeding programs were aimed at capitalizing on the positive effect of heterosis. The VKR is a marketing term for Swedish Red, Danish Red, and Finnish Ayrshire breed which complicated breed determination. Therefore, genomic breed composition estimates were compared using two different representations of VKR, one of which was based on parents used in the crossing system and a second based on genotypes from the ancestral breeds that comprise VKR. Variation of breed composition estimates were assessed between pedigree and genome-based predictions. Lastly, Genomic estimations were correlated with production and health traits by comparing extreme performance groups to identify the relationship between breed ancestry and performance. With the exception of the JER breed composition in Grazecross, all other estimates of the purebred contribution to the ProCROSS and Grazecross showed a significant difference in their genomic breed estimation when using the VKR ancestral versus the VKR parental reference populations for admixture analysis. These observations were expected given the different relationship of each VKR representation to the crossbred cattle. Further analysis showed that regardless of which VKR reference population was used, the degree of MON and HOL breed composition plays a significant role in milk and fat production in ProCROSS, while the degree of VKR and NOR ancestry were related to improved health performance in Grazecross. In all, identifying the most appropriate and informative animals to use as reference animals in admixture analysis is an important factor when interpreting results of relationship and population structure, but some degree of uncertainty exists when assessing the relationship of breed composition to phenotypic performance.