Authors as Published

Eleonor Cayford, M.S. Graduate Student with Dr. Rebecca Cockrum,

Selecting only the top percentage of animals in traits useful to humans has allowed dairy farmers to mold the dairy cow into the highly efficient, excellent producer that it is today. However, this intensity and speed of selection causes close genetic relatives to produce offspring, which is  known as inbreeding. Inbreeding can lead to a reduced production, known as inbreeding  depression. Dairy breeders have been combating inbreeding for decades, but it has continued to rise. Now, as genomic selection becomes more popular, it is important to consider the implications for inbreeding of this new component to dairy selection. Genomics could help to reduce inbreeding using changes in genomic breeding programs, alternative measures of inbreeding, and selection against inbreeding depression.

Since the first official genomic evaluation in 2009, genomic selection in the dairy industry has increased exponentially. The main advantage to this type of selection is that bull calves can be tested for their genetic merit before they even reach sexual maturity, which drastically decreases the generation interval as compared to traditional breeding programs. Although this has led to a much faster rate of genetic gain overall, shorter generation intervals has also meant a steep rise in inbreeding. However, Boichard et al. (2015) propose that that a change in how genomics are currently being used inbreeding programs could start to reduce - and even reverse - this increase. Currently, genomic breeding systems are designed to be faster versions of traditional breeding programs, by testing a bull's DNA instead of his daughter's performance. There are two main areas where the researchers believe improvement can be made. First, testing more bull calves. Genotyping bulls is 5-10 times cheaper than progeny testing them, so increasing the genetic range of AI semen could be done without additional cost to suppliers. Second, reducing the number of offspring produced by each bull. Genotyping causes faster genetic gain, which should lead to newer bulls with fresher genetics being chosen more rapidly anyway, so dairy breeds could easily promote this quicker bull turnover while still maintaining a profit. Overall, both changes would reduce the current increase in inbreeding that genomic selection is causing and would not be difficult or costly for dairy breeders to implement.

Traditional measures of inbreeding use pedigrees to calculate the probability of animals having the same alleles. Until recently, this estimation was the only way to consider how inbred offspring will be. However, Pryce et al. (2012) compared traditional measures of inbreeding to genomic inbreeding estimates from looking directly at animals' DNA. These researchers ran 50 simulations apiece for 3 measures of inbreeding: traditional, highdensity genomic, and low-density genomic. The genomic measures compared the DNA of the animals themselves to determine the amount of inbreeding. Within these simulations, a selection of 2,117 bulls were “bred” using an equation that rewarded performance and penalized inbreeding. The simulated offspring were then compared to find which of the 3 methods allowed for the greatest reduction in inbreeding, without negatively impacting genetic gain. They concluded that both high- and low -density genomic selection were effective measures for reducing inbreeding with minimal effect on genetic gain.

There are two mechanisms by which inbreeding creates inbreeding depression, the recessive deleterious alleles and overdominance. Both of these stem from having a pair of identical alleles, otherwise known as homozygosity. But, homozygosity is not detrimental for every allele. In fact, most of a cow’s DNA is made up of alleles in common with every other cow. To identify the specific genomic regions associated with inbreeding depression, Pryce et al. (2014) ran genome wide association studies to find specific genomic regions associated with inbreeding depression. Using this knowledge, inbreeding depression could be avoided by selecting against homozygosity in these specific regions. This would theoretically allow for dairy breeders to benefit from inbreeding without the detrimental effects of inbreeding depression.

In conclusion, genomics is a growing area of dairy breeding. Currently, the sharp reduction it produces in generation interval has led to an increase in inbreeding. However, through increased bull testing, decreased offspring per bull, genomic measures of inbreeding, and selection against inbreeding depression, genomics has the potential to combat inbreeding’s detrimental effects.

• Boichard, D., et al (2015). “Sustainable dairy cattle selection in the genomic era.” Journal of Animal Breeding and Genetics 132 (2): 135-143.
• Pryce, J.E., et al. (2012). “Novel strategies to minimize progeny inbreeding while maximizing genetic grain using genomic information.” Journal of
Dairy Science 95(1): 377-388.
• Pryce, J.E., et al. (2014). “Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy
cattle.” Genetics Selection Evolution 46(1): 71-71.

Virginia Cooperative Extension materials are available for public use, reprint, or citation without further permission, provided the use includes credit to the author and to Virginia Cooperative Extension, Virginia Tech, and Virginia State University.

Issued in furtherance of Cooperative Extension work, Virginia Polytechnic Institute and State University, Virginia State University, and the U.S. Department of Agriculture cooperating. Edwin J. Jones, Director, Virginia Cooperative Extension, Virginia Tech, Blacksburg; M. Ray McKinnie, Administrator, 1890 Extension Program, Virginia State University, Petersburg.

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