DNA is in much of the popular press these days, even in agriculture. In the cattle business DNA testing is being marketed under various banners. One of the key features of this technology is its’ incredibly rapid pace of change.
Of cattle producers using DNA in the past, the majority would be seedstock breeders using microsatellite technology to determine parentage on calves. The latest technology called SNP (Single Nucleotide Polymorphism pronounced ‘snip’) is revolutionizing DNA and making it accessible to the masses.
Let’s start at the beginning. We know each beef animal contains 30 pairs of chromosomes (60 total) of which one-half of one of each pair is passed on to their offspring. SNP markers are unique pieces of DNA that are spread across the chromosomes. If the chromosome is the highway, SNP are like mile markers on that highway. By themselves they do not tell you very much and some of them are in the middle of nowhere.
SNP are run on what is called a panel. I always think of the Super Dave Osborne show when I think of SNP panels. If you remember how the light bulbs behind Super Dave used to light up to spell the name of the performer, then you basically understand what a SNP chip does. DNA from a sample such as hair, blood or tissue is extracted and placed in a machine. If the DNA contains SNPs that are detected by the chip the panel will “light up” a specific bulb for that SNP.
Researchers are constantly looking at various SNP markers and how they relate to animals that exhibit specific traits such as more yield, or more marbling, or higher growth. When an animal exhibits various traits, specific SNP markers tend to light up. These pieces of DNA are not the specific gene that controls the trait but are said to be “associated” with the trait of interest, or they are “informative”. When a SNP panel is designed, it is built to include markers that are associated with various traits. Currently most commercial panels in beef cattle range from 100 to several hundred SNPs. Recently prices on the technology have come down dramatically (think personal computers) and movement is being made into panels with 50,000 SNP markers on them. In human research, work is already being conducted with 1,000,000 SNP chips.
This pace of rapid change often creates confusion amongst users when DNA results change if a test is rerun. The company offering the testing may now have several more SNP markers in their panel (even in the space of a couple of weeks) and so the end results can differ. For example if a company tests for feed efficiency and uses five markers and a calf has all five they may score a perfect 10. Over the next week they incorporate five additional markers into the panel and a new owner retests the calf. The calf still has the original five markers, but none of the new ones. Now the calf scores a five out of 10, even though they contain the same DNA as before. The resolving power of the test has improved.
So when does DNA replace weighing, measuring, ultrasound, EPD and other things?
To make a long story short, it doesn’t. DNA SNP markers are very good at explaining some of the variation in a trait. A single SNP may explain quite a bit of the difference between animals for an individual trait, but many things we are concerned about in beef production involve several or potentially several hundred genes. A good example of this is fertility and longevity of a cow. This represents a very complex scenario and involves a huge variety of genes. The value of the DNA is that it lets us jump start and get a good indication of where things are going very early on. Again fertility provides a good example. By the time a female has proven herself or a sire has proven his daughters they may be 10 years old or older. DNA technology has the potential to help us predict a difficult trait that otherwise would take a long time to measure.
Most experts believe that the DNA technology will be incorporated into genetic evaluation in much the same way weights are incorporated today. The result will be EPD for traits with vastly enhanced accuracy values. For example, if a yearling bull had ultrasound data and a SNP panel for carcass genetics included in the evaluation, their EPD for carcass traits may be as accurate as a sire with several hundred carcass progeny reported. This development is important as we try to deal with data overload.
So do you believe the DNA or the EPD or the actual performance measurement? We should believe all three to varying degrees. Generally DNA tests offered to industry are fairly well proven across the broad spectrum of the beef cattle population. There are however specific breed differences that may make a test less informative in some breeds than others. In the dairy industry, where production is dominated by a single breed, DNA technology is proving extremely useful and is being adopted in a huge way. The beef business consists of several different breeds and part of what makes a breed a breed are the differences in DNA contained in that breed. In other words, the genes that create growth in a Simmental may not be 100 per cent identical to the genes that create growth in an Angus or a Charolais. Thus a specific SNP marker may be more or less useful or informative in one breed over another.
In fact the only good way to find informative SNP markers is to collect as many DNA samples and as much data on traits of interest as possible for the group of cattle we are interested in working with.
In Part II of this feature, I will touch on some practical applications of the new DNA technology.
Sean McGrath is a rancher and consultant from
Vermilion, AB. He can be reached at [email protected]or (780)853-9673. For additional
information visit www.ranchingsystems.com