Genomic selection for improved crossbred performance

Lopes, M.S. (2016). Genomic selection for improved crossbred performance. PhD thesis, Wageningen University, the Netherlands With the implementation of genomic selection in pig breeding, the genetic progress in purebred populations is expected to increase up to 55% compared to traditional selection based on pedigree information. However, as most of the animals in the pork production system are crossbreds, the increase in genetic progress in purebreds will only be observed on production farms if this progress is expressed in the performance of crossbreds. The main aim of this thesis was to evaluate different models based on genomic information which can be applied to improve performance of crossbred animals. Another aim was to gain insight into genetic architecture of (complex) traits and to investigate how selection history has influenced haplotype patterns of current commercial pigs.  This thesis shows that by going beyond traditional genomic selection models, phenotypes can be predicted more accurately. Therefore, these improved models should be considered to improve crossbred performance. Further, this thesis provides important insights into the genetic architecture of the evaluated (complex) traits and also shows evidence that human-driven introgression and selection have shaped the genome of current commercial pig breeds. The research presented in this thesis was performed using data from pigs and the discussion on the practical application of results was focused on pig breeding. The results are relevant for all livestock species where crossbreeding is applied