There is a lot of work going on in the field of genomics these days. While technical terms are somewhat intimidating, genomics is a fancy way to say we are studying DNA — in this case bovine DNA. DNA is the code that determines the genetic potential of an individual. Half of an animal’s DNA comes from the sire and half from the dam. It is possible to have cattle that do not perform to their genetic potential, but it is difficult to have them outperform their innate genetic limitations. DNA is present in every tissue in the animal’s body.
There are basically two broad approaches to genomics, which we will term “after the fact” and “before the fact.” After-the-fact genomics attempts to look at an animal’s DNA after it has been born to define it within a production system. These are the DNA tests many feedlots use to sort cattle into outcome groups. Perhaps one of the most familiar to Canadians is the use of Leptin testing to sort feeder cattle into groups based on projected days on feed.
Before-the-fact genomics involves examining the DNA of animals expected to reproduce in order to assist selection decisions and produce desirable offspring.
Occasionally research turns up a specific gene or chunk of DNA that controls a specific trait, however more often the traits we are interested in are complex and involve many genes working together, such as disease resistance, long-term fertility or even growth. This doesn’t mean we should stop research to find genes, but it does mean we need a faster, broad-scale approach.
Enter the SNP (pronounced snip)
The way we get around the problem of finding genes is through technology called Single Nucleotide Polymorphisms or SNPs for short. These are short pieces of DNA that are relatively evenly spread across the bovine DNA like so many road signs. Researchers then take large amounts of data, and DNA samples that are tied to that data and start digging. In essence they take DNA from influential animals and look at hundreds of thousands of small pieces of DNA. By comparing these pieces of DNA to results in the data, they start to see patterns where specific chunks of DNA appear when certain results are present. In other words, a particular SNP or road marker may show up when calves are heavier than the average of other calves in their group. This specific chunk of DNA may not be “the gene” for weaning weight, but it is “associated with” pre-weaning growth.
Out of these hundreds of thousands of short pieces of DNA, research may find a few thousand that are useful or informative for the things we are interested in about beef cattle. These few thousand SNPs are then put into a commercial panel that can be used for testing cattle at a lower cost than testing hundreds of thousands of pieces of DNA on every calf. These are the type of tests people may be familiar with that are offered by groups such as Igenity (Merial) or Pfizer.
The approach to finding SNPs is then flipped on its head and multiple animals are tested using the smaller panel to see if the DNA chunks we are interested in are present. These results are then compared with their performance to “validate” the research. In other words, to see if the DNA predicts the outcome in the same way the original data found the DNA.
A SNP panel can be used after the fact, as previously mentioned. They are useful for sorting feeder calves, for example. They are also useful before the fact. The leading edge of research right now is not only finding SNPs but incorporating them into EPD results. The knowledge of an individual’s DNA means the predictive ability of an animal’s EPD can be improved, and also traits that are difficult to measure can be estimated early in life.
Set at conception
An animal’s DNA is set at the moment of conception. If a sample is collected on a newborn calf, it will contain the same DNA that calf will pass on to its calves later in life. If we are aware of pieces of DNA associated with improved growth, or health, or longevity of daughters, or meat quality we can measure them directly in that young animal. While these DNA pieces are not the gene for the trait, they provide a good indication of what is going on. By incorporating DNA and phenotypes (measurements on an animal and its offspring) into a single more accurate EPD for a trait of interest we can produce genetic combinations that excel in various production environments. This is working “before the fact.”
The world of genomics is vast and advancing rapidly, but it is very similar to a lot of things in our lives. We don’t need to understand every detail of the technology, as long as we understand how to apply it in our own situation. Cellphones, GPS and satellite television are good examples of this. Commercial DNA panels are becoming more accurate and lower cost all the time and there are a lot of potential applications in the commercial industry we will touch on in the next several weeks. †