236. Investigating Genetic Redundancy As a Source of Genetic Diversity and Adaptability in the U.S. Holstein Breed

The continuous increase in inbreeding in the U.S. Holstein is a threat to genetic diversity. Loss of genetic diversity can hinder adaptation to changing environments and consumer demands. K-means clustering on the genomic relationship matrix was used to stratify 20,099 selected candidates into five clusters. These clusters were shown to be different through expected inbreeding within- and across cluster, the fixation index (Fst), and genetic correlations for stature between clusters. Expected inbreeding within cluster was mostly higher than across-cluster. The average Fst across cluster was 0.03. Genetic correlations ranged from <0.50 to >0.90. Families were formed by tracing pedigrees of each cluster back for 10 generations. Allele frequency changes over generations were evaluated. Polygenic shifts, selective sweeps, hitch-hiking, and epistasis were observed. The Replicate Frequency Spectrum was used to measure genetic redundancy. Results show that sub-populations within the breed have developed differently over time.