The dairy community has done a tremendous job collecting phenotypic animal performance data for decades. More recently, we supplemented that knowledge by being on the forefront of genomic analysis. Dairy farmers today have more information at their fingertips when making mating decisions than producers generations ago could have ever dreamed of. It is easy to identify top-performing males and females based on whichever metric you desire.
Of course, everyone wants to use those best genetics in their herd. Thus, in more recent years, the industry has found itself in a realm of growing inbreeding as the highest bulls and cows are used repeatedly.
The year 1960 is often referred to as the point of “zero” inbreeding, explained Roger Shanks during the Holstein Horizons program held during the National Holstein Convention. This is partially due to the amount of pedigree information available on computers through the years. Nonetheless, Shanks, a professor emeritus from the University of Illinois, said that prior to 1960, the Journal of Dairy Science published an average of just three papers a year that discussed inbreeding.
By contrast, since 2011, the preeminent body of dairy industry research has added nearly 31 papers on inbreeding, on average, every year.
Shanks now serves as a dairy genetic consultant for Holstein Association USA, and he painted the picture of how inbreeding has affected the country’s most popular dairy breed. From 1960 to 2024, the maximum inbreeding level among registered Holstein females ranged from 31% to 44%, with an average of 38%, he said. The average pedigree inbreeding — which counts common ancestors and is calculated as half the relationship of the parents — has risen for females every year since 1981.
On the bull side, maximum inbreeding has averaged 31% during the same time period and has climbed higher every year except for 1986 and 2020, Shanks explained.
Another measure of inbreeding is genomic inbreeding, which looks to predict homozygosity in an animal’s DNA. This has also been rising since 2010.
Five generations
Inbreeding is a concern because it shrinks the gene pool while leading to potentially damaging results. Shanks noted that 50% more mortality is observed when daughters are mated back to their sires. Research has even shown that cows that are 10% inbred may produce up to 440 pounds less milk, 20 pounds less fat, and 14 pounds less protein per lactation.
Despite the clear negative effects, it has also been difficult to get a handle on. Shanks recognized that average milk production per cow in the U.S. took 60 years to double; inbreeding levels did so in 20 years.
Most Holsteins are already related to one another due to the influence of Round Oak Rag Apple Elevation and Pawnee Farm Arlinda Chief, sires that are each related to about 15% of the breed population. Currently, the Holstein breed seems to have between four and eight distinct lineages, Shanks said. It has been suggested that a breed needs 16 lines to limit inbreeding. To achieve that, an animal’s pedigree would need to have no common ancestors for five generations.
Shanks is confident that this is possible — in fact, it is already happening. While we can’t avoid inbreeding entirely, he said we must work to control it. That means taking steps like using a mating program, monitoring pedigrees, and being more inclusive in your mating selections. This will slow down genetic progress to some degree, he recognized. However, it will also help contribute to the longevity and viability of the breed and its positive characteristics.
