| Genomic inbreeding measures were studied in several groups of domestic cattle. First, effects of increases in three measures of genomic inbreeding on economically important traits in US Holstein cattle were studied. Genomic inbreeding measures of percent homozygosity, inbreeding derived from runs of homozygosity, and inbreeding derived from a genomic relationship matrix were calculated. Increases in all three measures of genomic inbreeding resulted in decreases in total milk yield, conception rate, and days open. Next, genomic inbreeding measures were compared between genetically elite Holsteins, commercial Holsteins, Jerseys, Angus, and Brazilian Nelore cattle. Genomic inbreeding measures of percent homozygosity, as well as inbreeding derived from runs of homozygosity with minimum lengths of runs of 4,000 and 8,000 kilobases were calculated for three densities of SNP panels. The first SNP panel contained the 54,001 SNP available in the most common commercial genotyping panel, the second SNP panel contained 6,909 selected SNP, while the third SNP panel contained about 6,400 equally spaced SNP derived from the 54,001 SNP panel. Differences were observed between breeds, with the Jersey cattle having the highest average inbreeding coefficients, and the Nelore having the lowest. The genetically elite Holsteins, on average, had higher genomic inbreeding coefficients than commercial Holsteins, indicating the greater selection intensity in the genetically elite animals results in higher inbreeding. Selection bias was evident when analyzing the two lower density SNP panels, whereas Holsteins had much lower percent homozygosity in the selected 6,909 SNP panel than either of the other two panels. As Nelore animals were not utilized in the SNP selection for the 6,909 panel, all three measures of percent homozygosity for Nelore were similar. Lastly, the effects of increases in expected genomic inbreeding from mating pairs was analyzed. Genotypic information from 374 sire-dam-progeny trios was available. Measures of expected genomic inbreeding were calculated from the sire-dam pairs and compared to the actual progeny to determine if the most inbred animals died embryonically. No differences were seen between expected and actual levels of genomic inbreeding. When analyzing only the high expected inbreeding pairs, more variation was evident, suggesting a possible effect at this level. |
