First we should tackle the two things that make an application practical: cost and benefit. Cost is affected by the type of DNA test ordered and the number of tests, but it is also affected by available farm labour. A simple parentage or sire verification will be less expensive than a complete suite of tests looking at traits such as carcass merit, feed efficiency, etc. The benefits that can be derived from DNA testing will vary significantly between operations and will range from no benefit to extremely beneficial.
We could split DNA test types into two categories: management testing and genetic testing. Management tests are those that help managers make decisions. A good example of an available management test is the leptin gene test being used to determine the feeding programs and end point for feeder calves. A genetic test is one that is applied to breeding cattle to effect change in the genetic merit of the cattle.
Parentage testing is probably one of the most useful and low cost of the new generation of SNP tests and falls into both the management and genetic test categories. Parentage verification works through a process of exclusion. The parentage markers are matched between calf and potential sires / dams. The calf receives half of its genetic material from the sire and half from the dam. Therefore if the calf has markers that are not present in a potential parent then the parent is excluded. A simple example is shown, however a SNP parentage panel may include over 100 markers and guarantees a high degree of accuracy.
The calf in the example would have Sire 2 excluded since the calf does not contain either an E or F marker in its’ SNP panel results. The calf received the A marker from its sire (#1) and the D marker from its Dam.
–AD Potential Sire 1 –AB Potential Sire 2 –EF Dam -CD
How does this parentage testing fit in? In a seedstock operation, low cost parentage may enable the use of multi-sire pastures improving grass management and potentially lowering costs. As well, accurate pedigree information is required in order to generate genetic improvement. This applies as well in the commercial world and parentage could be useful for marketers of replacement females, management of breed composition of the cowherd, and analysis of fertility. Imagine turning out thee black bulls from two different breeds. With DNA sire verification it is possible to retain only those females with the desired breed composition, sell replacements with specific sires, and identify which sires are breeding the cows. Research has shown that often a few sires are breeding the vast majority of the cows, while others are getting a free ride and doing little or no work. If a herd has DNA on the dams as well, full parentage is possible and determining fertility is easily done. In our own commercial operation we can conduct full parentage (we have samples on the dams) and have determined it costs less to use DNA to determine parentage on our replacement heifers than the labour cost to tag calves at birth. We have also found some sires carrying 80 percent or more of the workload in multi-sire situations.
Breeders of beef cattle have a difficult job. In a business with long generation intervals it takes a lifetime to develop a good working herd. The challenge is further made difficult by the fact that many genes that are desirable are strongly associated with genes that are undesirable. For example the same genes that create growth may also produce growth in utero and create calving difficulty. Compounding this problem is that some of the things we are interested in are expensive or difficult to measure like feed efficiency, disease resistance, tenderness or a long term proposition like sustained fertility. This is where SNP markers have perhaps the greatest potential.
When combined with collected data such as weights and ultrasound SNP markers have the potential to dramatically improve the accuracy of prediction. Our current generation of genetic selection tools decipher the genetic component of an animal’s phenotype from the environmental component. Since only the genetic component can be passed to offspring, this is the part we are truly interested in. As we add data such as birth weights on calves the accuracy or ability to predict the genetic component improves. Most ranchers today are buying yearling bulls with accuracies in the 0.30 range, which means we have an idea of what their relative genetic merit is, but are not completely certain. SNP genetic tests may provide the opportunity to have information on a young bull that is as reliable as that on a sire with several hundred progeny reported. This reduces risk for users and accelerates the ability to match genetics to environment.
Key is the incorporation of these markers into genetic evaluation. I field a lot of calls with people trying to make sense of 15 different EPD, imagine how difficult interpreting 50,000 SNP markers will be. The other area of difficult to measure traits is extremely exciting. This has been brought to the forefront with some of the markers for tenderness testing. SNP tests available today account for several pounds difference in shear force values. This type of testing could be extremely useful in a value chain where meat is being sold at retail. The ability to breed cattle for improved tenderness to reach 100percent customer satisfaction can solve a lot of pain and expense in the overall system.
Another interesting management test that is being worked on is that of traceability. Imagine a DNA sample is taken on every calf that enters a feedlot. If the calves are going through a value chain and a product such as a rib steak is returned for whatever reason, it may be possible to identify that steak back to the individual animal. If the sire and dam have DNA available, it may also be possible to parentage verify that calf. This has food safety implications but with a large database it also has genetic implications for breeding to end user specifications. Most cow folks would agree that eliminating problems is often as profitable as striving for more production.
DNA technology has come a long way over the last few years and continues to accelerate at what seems like light speed. In all likelihood, much of what you are reading today will be out of date by this time next year.
If you are interested in testing there are several key questions to ask:
What is the cost?
What is/are the trait(s)?
Ask for a specific definition of the trait being tested. Is yield percent yield grade 1 or actual carcass yield or cutability?
How many SNPs are used for each trait?
If a trait is extremely complex and only a few SNPs are used, take the results with a grain of salt. It is good to ask how much variation the test explains for a particular trait.
Where will the test be conducted and how much does a retest cost? Can you run new panels as they are developed?
It is extremely helpful if biological samples are tested in your home country. As well, it is also good if samples are stored indefinitely. You never know when you will want to go back into the DNA bank. Most companies will run retests for inconclusive results free of charge, however it is worth finding out about the cost to run potential new marker panels as traits are developed.
Most of us, even in the field of genetics, are on a steep learning curve regarding DNA testing technology, however it is one area that is worth keeping an eye on. As I am sure you are tired of hearing by now, in order to assess the application of the technology you need to be acutely aware of your costs and closely examine the potential benefits; and the potential benefits are growing daily.