Inbreeding trends and pedigree analysis of Irish dairy and beef cattle populations

The objective of this study was to determine the inbreeding levels and to analyze the pedigree of Irish purebred populations of Charolais, Limousin, Hereford, Angus, and Simmental beef cattle, as well as the Holstein-Friesian dairy breed. Pedigree analyses included quantifying the depth of known pedigree, average generation intervals, effective population size, the effective number of founders, ancestors, and founder genomes, as well as identifying the most influential animals within the current population of each breed. The annual rate of increase in inbreeding over the past decade was 0.13% (P < 0.001) in the Hereford, 0.06% (P < 0.001) in the Simmental, and 0.10% (P < 0.001) in the Holstein-Friesian breeds. Inbreeding in the other breeds remained relatively constant over the past decade. Herefords had the greatest mean inbreeding in 2004, at 2.19%, whereas Charolais had the lowest, at 0.54%. Over half of each purebred population in 2004 was inbred to some degree; the population with the greatest proportion of animals inbred was the Hereford breed (85%). All 6 breeds displayed a generation interval of approximately 6 yr in recent years. In the pure-bred females born in 2004, the 3 most influential animals contributed between 11% (Limousin) and 24% (Hereford) of the genes. Effective population size was estimated for the Hereford, Simmental, and Holstein-Friesian only, and was 64, 127, and 75, respectively. The effective number of founders varied from 55 (Simmental) to 357 (Charolais), whereas the effective number of ancestors varied from 35 (Simmental and Hereford) to 82 (Limousin). Thus, despite the majority of animals being inbred, the inbreeding level across breeds is low but rising at a slow rate in the Hereford, Simmental, and Holstein-Friesian.