Utilizing DNA markers today ... and tomorrow
Recently, it seems that seedstock and commercial producers are being bombarded with advertising that promotes a variety of DNA marker technologies for application in selection and management programs.
Moreover, the volume of advertisements reporting a particular AI sire’s, donor dam’s or yearling bull’s genotype results for a variety of production traits has increased dramatically over the last year. In fact, it is hard to pick up a seedstock or trade publication without finding a number of animals being merchandised on the basis of their DNA marker profiles, sometimes without reference to the animal’s expected progeny differences (EPDs). Producers frequently pose questions regarding which technologies they might want to be using in their operation and the utility of these new tools. Hopefully, a little basic information and advice will enhance the ability to appropriately use and understand the results of a variety of DNA marker tests.
What is a DNA marker?
A DNA marker is simply a sequence of nucleotides, the tiny building blocks of DNA, that uniquely identifies a location in the genome.
This location can be in a gene or near a gene and is used to identify a specific allele or form of a gene. Each animal carries 30 pairs of chromosomes and each chromosome carries one copy of each gene. As a result, animals have two copies of every gene. Mutations, or changes in the coding sequence of a gene, can be used as DNA markers.
These mutations may or may not cause a change in the protein product. Variation near a gene can also be used as a DNA marker. One can simply think of a DNA marker as a “tag” that allows us to identify a piece of DNA and track its inheritance from parent to offspring.
A common type of DNA marker used today is called single nucleotide polymorphism, or SNP (pronounced “snip”). SNPs are the most basic form of DNA markers and describe a single letter or base pair change in the DNA sequence.
These markers are easy to genotype with modern equipment. DNA markers can track the inheritance of simple traits controlled by a single gene or complex traits controlled by many genes. Examples of simple traits include coat color, horn status, and some genetic diseases (including TH and PHA). Complex traits include traits like weaning weight, tenderness and marbling. An SNP DNA marker that is associated with change in performance for a trait like marbling score is called a Quantitative Trait Nucleotide, or QTN. Remember, DNA markers simply identify a sequence of DNA just as ear tags identify individual calves.
What DNA markers are NOT
As mentioned previously, advertisements that include DNA marker results exclusively and no EPD data are now very common.
Alternately, you may observe discordance between an animal’s DNA marker results and its EPD for a particular trait. What’s the problem? The issue boils down to this: EPDs tell us the net effect that all genes and their interactions have on a particular trait; DNA markers explain only the genetic variation associated with that marker, which in many cases is only a small part of the genetic variation in a trait. Even though the DNA marker profiles from various companies explain more genetic variation for a variety of traits than ever before, most of these panels still do not account for large portions of variation within any one trait. For instance, a bull may have all the best DNA markers present in a test utilizing five markers for a specific trait, and he ranks below breed average for the trait given his high accuracy (0.85) EPD. The marker results suggest the bull is desirable for the genes used in the DNA test, but the EPD suggests he’s not very good. What is the problem? Folks who are skeptical of EPDs respond often that the EPD is wrong. Marker skeptics respond the DNA technology doesn’t work. In fact, both of these positions are flawed.
The reality is that EPDs do work and so do DNA markers, they just measure different things. Remember, the EPD describes the effect of all the genes (net effect) an animal has for a trait.
The markers describe the effect of a specific subset of these genes. While the DNA markers may help you make specific mating combinations for marked genes, EPD should be used for overall mating decisions as they are the only measure of “net genetic merit” available. New genotyping platforms that score 50,000 genotypes per animal are being used in marker discovery projects today and should yield dramatic improvements to the existing DNA marker panels, as well as help to generate panels for a variety of new traits.
These new panels will include a much larger number of markers, making interpretation even more difficult than it is today. We will soon see a convergence of DNA marker results with EPD computation. This process will produce a single genetic prediction for each trait for every animal using both performance records and genotypic information.
This convergence of genetic prediction tools will improve the utility of both DNA marker tests and EPD.
Tools available today for cattle breeders
Marker tests are available for a variety of anatomic and metabolic genetic defects in cattle. Most recently, tests were released for identification of animals that were either free or carriers of Arthrogryposis Mul tiplex or TH and PHA. Many of the genetic disease e traits are single gene muta-tions and are recessive con-ditions, meaning that af-fected animals must inherit a disease allele from each parent to be affected. These e tests are very effective e (~100%) identifying carriers of disease genes.
A number of laboratories offer DNA parent validation and identification services s for breed association pedi-gree validation and breed-er use to identify paternity in multi-sire breeding groups.
Several companies offer effective tests for coat color (homozygous or heterozy-gous black) and tests are available for several breeds for absence or presence of horn genes to classify animals as homozygous or heterozygous polled. — Bob Weaber, Ph.D., State Extension Specialist-Beef Cattle Genetics, University of Missouri