Visualization of the transmission of direct genomic values for paternal and maternal chromosomes for 15 traits in US Brown Swiss, Holstein, and Jersey cattle.

Haplotypes are available for 220,671 Brown Swiss, Holstein, and Jersey bulls and cows that received genomic evaluations in August 2012. Differences in least squares means of direct genomic values (DGV) for paternal and maternal haplotypes of Bos taurus autosomes 1, 6, 14, and 18 for lifetime net merit were significant in all but one case. Those chromosomes were chosen to represent cases with and without known quantitative trait loci, and other chromosomes may differ as well. Paternal haplotypes had higher DGV than maternal haplotypes in most cases, and differences were larger when quantitative trait loci were present. Longer chromosomes generally accounted for more variance than shorter chromosomes, and differences among breeds were consistent with known mutations of large effect. For example, Bos taurus autosome 18 accounted for 2.5, 7, and 2.6% of the variance in lifetime net merit for Brown Swiss (BS), Holsteins, and Jerseys, respectively. Distributions of the number of positive DGV inherited from sires and dams were negatively skewed in all breeds, and modes were slightly higher for paternally than maternally derived haplotypes in Holsteins and BS (22 vs. 20 and 22 vs. 21, respectively) and slightly lower in BS (17 vs. 19). Graphical representations of DGV are available to all users through a query on the Animal Improvement Programs Laboratory (ARS, USDA, Beltsville, MD) web site. Query results were also used to illustrate several quantitative genetic principles using genotype information from real animals. For example, offspring DGV can be compared with parental DGV to demonstrate that a parent transmits the average value of its 2 chromosomes to its progeny. The frequency of DGV with positive and negative values in animals of different ages can be used to show how selection affects allele frequencies. The effect of selection for alleles with large effects versus those with small effects is demonstrated using an animal with undesirable alleles for a marker with a large effect but many desirable alleles for markers with small effects. Strategies for the use of those data in selection programs are being studied, and work is underway to add data on conformation traits to the system.