Genomic Testing May Be Complex, But Is Finally A Reliable Window Into The Future?
By: Jaime Pullman
Depending on your perspective, the world of cattle breeding has gotten more complicated in the last twenty years just as it has become more transparent. Genetic testing, genetic tools, and the unfurling of the bovine genome have given us the opportunity for more information than you ever dreamed of in years past. But knowing when exactly you need that information, when it will work for you, and when it will make sense for your bottom line and breeding decisions depends on some key considerations.
“DNA testing can be a very valuable resource but it still incurs a significant cost,” says Robert Weaber, Cow-calf Extension Specialist and Associate Professor at Kansas State University. “Producers should understand that they need a comprehensive plan to utilize the information in selection of animals to realize a return on their investment. The realized gain is typically easier for seedstock producers as the genomic information for many breeds is incorporated into the animal’s EPDs.”
Genetic testing can identify carriers of undesirable genetic mutations, enhance EPD accuracy earlier in an animal’s life with genomically enhanced-EPDs, and improve the ability of producers to make informed, thoughtful decisions for breeding and management.
“This is especially helpful for traits like stayability or maternal calving ease where evaluation of an animal using progeny data will take 4 to 8 years,” says Weaber. “With genomic data incorporated into a genomically enhanced genetic evaluation system animals that may be less than a year old can have EPD accuracies similar to those of an animal with 5 to 20 progeny depending on the trait.”
Improved accuracy for young animals doesn’t apply to testing proven sires, however, because most of his genetic potential has already been shown. In either case, it’s clear that genetic testing is not a one-size-fits-all proposition. Perhaps one of the best things producers can do to make the most of genetic tools is simply to refresh their understanding of genetics.
“Unfortunately my experience tells me that there is a disappointingly large fraction of producers, both commercial and seedstock, that do not adequately understand EPD or the accuracy value associated with EPD,” says University of Nebraska Associate Professor and Extension Beef Genetics Specialist Matt Spangler. “It is impossible to understand genomics and the benefit of this information if the fundamentals (EPD and accuracy) are not understood first.”
WHAT DOES IT MEAN?
Most major beef breed associations now incorporate genomic information into EPDs—they aren’t two separate pieces of information.
“The DNA and EPD information represent a part-whole relationship. The DNA test describes a portion of the genetic merit for a trait. The EPD describes the net merit (or sum of the value across all genomic regions and their interactions). Using both pieces separately is confusing as they may point different directions,” cautions Weaber.
“For instance a bull might have a great DNA marker result and rank in the bottom 5% of the breed for Weaning Weight EPD. What does this mean? It means that the net merit is not very good. However, at the regions of the genome included in the DNA test he appears to have very favorable merit. Then by difference, the remaining genetic merit for all other areas in genome, he must be very bad to pull his rank very low.”
Typically breed associations today will handle the genomic testing developed for the particular breed, resulting in the GE-EPD, or genomically enhanced EPD. If you don’t belong to a breed association, genomic testing might be best relegated to parentage and defect testing because one test isn’t accurate across all breed types. High density (HD) testing is now offered by many organizations, which looks at a large number of single nucleotide polymorphisms (SNPs) – the variations in DNA makeup. But that’s not always your only option.
“For seedstock producers they should use the test that their breed organization includes into EPD. Historically this has been the 50K. The density (number of SNP) of these tests has continually grown (e.g. 80K),” informs Spangler.
“While the size of the larger tests has continued to grow there have been some breeds that have offered a lowdensity (ex. 10-30K) test that is less expensive than the larger alternatives. Through a process called imputation (essentially filling in the missing SNP based on information from relatives), the same amount of information can be garnered by a low-density test as can be achieved by a high-density test.”
Commercial producers are typically looking at a narrower scope of testing, usually for parentage, but have to be careful how the testing is used.
“While there are tests marketed for use in commercial cattle for traits like growth, carcass and fertility, commercial producers should use caution and understand the limitations of genomics,” says Spangler. “This technology is not robust across breeds. For example, a test designed for Angus cattle will not work in Red Angus cattle. Consequently the science suggests that using this technology in non-pedigreed crossbred cattle will not yield predictable results. There are some tests that have been developed for straightbred commercial cattle (like Angus) and cost/benefit analysis should be considered before using such a test to ensure that the cost of testing is offset by gains in performance and/or improved management decisions.”
CONSIDER PROFESSIONAL HELP TO MAKE BREEDING DECISIONS
Genetic information allows producers to make more reliable management and breeding decisions. Testing earlier in an animal’s life provides value for both the seedstock producers and the commercial producer that ends up buying those genetics. And as the cost of bulls increases, commercial producers will be looking to seedstock producers to help them find that value in the form of more complete genetic documentation and increased confidence in purchase decisions.
Balancing your knowledge of EPDs and the limitations of DNA tools is key to benefiting your herd. Weaber warns producers to align the traits they select for with the marketing end point. Don’t focus all your selection on carcass traits if you sell calves at weaning in a conventional sale barn. Don’t select replacements based on a terminal or carcass index when you need maternal traits. Remember where your value is coming from. “The genomic tools are useful, but are not a silver bullet,” says Weaber.
“Also, producers don’t always seek out the advice they need to maximize the impact of their testing program. Although producers have historically each made their own genetic selection decisions, many would benefit from seeking professional help in designing and implementing a selection/breeding system. Many don’t do their own tax accounting; selection can be just as complex.”
From identifying genetic mutations to increasing EPD accuracy it’s clear that current DNA technologies provide opportunities for us to better understand cattle genetics. Identifying where your knowledge needs a boost in applying those technologies, or in using the resulting information, and then seeking help from an extension agent, breed association, or veterinarian, will allow your business to benefit the most.