Nonparallel genome changes within subpopulations over time contributed to genetic diversity within the US Holstein population.

Maintaining genetic variation in a population is important for long-term genetic gain. The existence of subpopulations within a breed helps maintain genetic variation and diversity. The 20,990 genotyped animals, representing the breeding animals in the year 2014, were identified as the sires of animals born after 2010 with at least 25 progenies, and females measured for type traits within the last 2 yr of data. K-means clustering with 5 clusters (C1, C2, C3, C4, and C5) was applied to the genomic relationship matrix based on 58,990 SNP markers to stratify the selected candidates into subpopulations. The general higher inbreeding resulting from within-cluster mating than across-cluster mating suggests the successful stratification into genetically different groups. The largest cluster (C4) contained animals that were less related to each animal within and across clusters. The average fixation index was 0.03, indicating that the populations were differentiated, and allele differences across the subpopulations were not due to drift alone. Starting with the selected candidates within each cluster, a family unit was identified by tracing back through the pedigree, identifying the genotyped ancestors, and assigning them to a pseudogeneration. Each of the 5 families (F1, F2, F3, F4, and F5) was traced back for 10 generations, allowing for changes in frequency of individual SNPs over time to be observed, which we call allele frequencies change. Alternative procedures were used to identify SNPs changing in a parallel or nonparallel way across families. For example, markers that have changed the most in the whole population, markers that have changed differently across families, and genes previously identified as those that have changed in allele frequency. The genomic trajectory taken by each family involves selective sweeps, polygenic changes, hitchhiking, and epistasis. The replicate frequency spectrum was used to measure the similarity of change across families and showed that populations have changed differently. The proportion of markers that reversed direction in allele frequency change varied from 0.00 to 0.02 if the rate of change was greater than 0.02 per generation, or from 0.14 to 0.24 if the rate of change was greater than 0.005 per generation within each family. Cluster-specific SNP effects for stature were estimated using only females and applied to obtain indirect genomic predictions for males. Reranking occurs depending on SNP effects used. Additive genetic correlations between clusters show possible differences in populations. Further research is required to determine how this knowledge can be applied to maintain diversity and optimize selection decisions in the future.