Genetic architecture of a composite beef cattle population

Composite breeds are widely used in the beef industry. Composites allow producers to combine desirable traits from the progenitor breeds and simplify herd management, without repeated crossbreeding and maintenance of purebreds. In this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed beef cattle composite. This composite population referred to as Composite Gene Combination (CGC) consisted of 50% Red Angus, 25% Charolais, and 25% Tarentaise. A total of 248 animals were used in this study: CGC (n = 79), Red Angus (n = 61), Charolais (n = 79), and Tarentaise (n = 29). All animals were genotyped with 777k HD panel. Principal component and ADMIXTURE analyses were carried out to evaluate the genetic structure of CGC animals. The ADMIXTURE revealed the proportion of Tarentaise increased to approximately 57%, whereas Charolais decreased to approximately 5% and Red Angus decreased to 38% across generations. To evaluate these changes in the genomic composition across different breeds and in CGC across generations, runs of homozygosity (ROH) were conducted. This analysis showed Red Angus to have the highest total length of ROH segments per animal with a mean of 349.92 Mb and lowest in CGC with a mean of 141.10 Mb. Furthermore, it showed the formation of new haplotypes in CGC around the sixth generation. Selection signatures were evaluated through Fst and HapFlk analyses. Several selection sweeps in CGC were identified especially in chromosomes 5 and 14 which have previously been reported to be associated with coat color and growth traits. The study supports our previous findings that progenitor combinations are not stable over generations and that either direct or natural selection plays a role in modifying the progenitor proportions. Furthermore, the results showed that Tarentaise contributed useful attributes to the composite in a cool semi-arid environment and suggests a re-exploration of this breed's role may be warranted.Composite breeds are commonly used in the U.S. beef industry since they provide producers with benefits such as breed complementarity and retained heterosis. However, cattle composite genomes are not well characterized. Therefore, in this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed composite (50% Red Angus, 25% Charolais, and 25% Tarentaise). The analysis showed an increase in the proportion of Tarentaise to approximately 57%, whereas Charolais decreased to approximately 5% and Red Angus decreased to 38%. Furthermore, new genome segments formed around the sixth generation. These changes show that progenitor breed proportions are not stable over generations and that either direct or natural selection plays a role in modifying the proportions. The increase in Tarentaise proportion suggests useful attributes to the composite in a cool semi-arid environment.