Marker-Assisted Selection in Beef Cattle

Visible or measurable characteristics or traits like hornlessness, coat color, increased marbling, increased tenderness, large weaning weight or presence of a white belt make up an animal’s phenotype. The characterization of phenotypes and use of this information in the selection of animals for breeding is the foundation of successful seedstock and cow-calf operations. 

Traditionally, observational methods such as the breeder’s “eye,” linear measurements, ultrasound and carcass analysis have been used to make the decisions regarding selection of breeding stock. These observational data have been augmented by analysis of the characteristics of the sire or dam’s calves over time. This latter process is termed Expected Progeny Differences (EPD).

However, there are limitations to the traditional observational method for breeding stock selection. This is due to the fact that multiple factors govern the complex traits of cattle. As an example, there are two types of polled cattle. One type is homozygous, meaning that it has two copies of the dominant form of the polled gene. The other is heterozygous, meaning it has one dominant form of the polled gene and one recessive form. Heterozygous polled cattle may sire horned offspring. The homozygous dominant polled gene animals produce only polled calves. The homozygous recessive polled gene animals produce cattle with horns. When multiple genes along with environmental factors control the trait, it becomes more difficult to select breeding stock. 

The distinguishing traits of an animal are encoded in its genetic material. This genetic material is composed of DNA and occurs in paired strands with each strand coming from one of the animal’s parents. The genes code for amino acids that combine to form proteins and the proteins combine to make the animal’s characteristics or combination of traits or phenotype. All of the animal’s genes combined make up its genome.

Using modern biotechnology, scientists can tell the difference between homozygous and heterozygous animals for certain traits. This knowledge can then be used by breeders to assist their selection of breeding stock. This process, called marker-assisted selection, allows for the accurate selection of specific DNA variations that have been associated with a measurable difference, or effect, on complex traits. The markers represent specific sites on the DNA molecule. The markers are usually near, or actually a part of, the gene regulating the formation of the trait of interest. Since the marker is close to the gene regulating the trait of interest, they tend to stay together with each generation of cattle. This is called genetic linkage. It is important to recognize that currently available markers for many complex traits are associated with only one of the many genes that contribute to the trait. As a consequence, marker-assisted selection should be seen as an adjunct to, and not a replacement for, observational data and EPD.

The use of marker-assisted selection can reduce the number of years it takes to introduce phenotypic improvement in cattle by selecting for cattle that carry two copies of the marker of interest (homozygous marker for the trait) and against those animals that carry no copies of the marker. Since all of the offspring from a homozygous parent will inherit a single copy of the marker of interest, continuous use of homozygous sires for 4 generations should result in approximately 90% of the resultant herd carrying two copies of the marker.

One of the best known uses of marker-assisted selection is parentage and species verification. The most common markers used for this purpose are termed microsatellites or short tandem repeat polymorphisms. These are variations in the DNA molecule in which one or more of the bases (A=adenine, C=cytosine, G-guanine, T=thymine) that make up the molecule are repeated in a tandem fashion. 

The number of tandem repeats found at any microsatellite marker will vary between individual animals. An animal will inherit one size of each specific microsatellite from each parent. Therefore the two sizes at any specific microsatellite position in the DNA molecule may or may not be identical, since the size of each microsatellite possessed by the calf must correspond to the sizes at each site in the presumed parents. There are thousands of these sites containing tandem repeats in mammalian DNA. 

As more microsatellite markers are used, the accuracy of prediction is increased. However, while this technique is 100% accurate at parentage exclusion, and 99% at parentage qualification when both parents are included in the analysis, the accuracy drops to ~ 95% when only one parent is included in the analysis. The accuracy will drop even further when the potential parents are being selected from a group of closely related cattle. In those cases the panel used for analysis must be enlarged to improve accuracy. Parentage analysis has proven useful, not only for establishing accurate pedigrees, and to improve accuracy of progeny testing, but also to uncover individual bull performance in multi-sire pastures. In addition the same method can be used for tracing beef from birth to table.

One of the important attributes of Belted Galloway cattle is the double coat which is thought to be important in reducing energy expenditure in cold climates and in reducing the formation of back fat, thus increasing carcass yield. Inherited interference with development of this coat or defects leading to hair loss is therefore functionally as well as cosmetically important. One of the more common genetically inherited hair diseases of cattle is congenital hypotrichosis, which is the complete or partial absence of hair from birth. This is a recessive trait. At least 13 types of hypotrichosis have been described in cattle. Associated defects include failure of horn development, hypophyseal hypoplasia, macroglossia, dental anomalies, abnormal coat coloration, and death (lethal hypotrichosis). Six genetic loci have been identified. As these markers are further developed and related to the Belted Galloway breed, marker-assisted selection could be used to eliminate this defect in our animals.

Traditional carcass quality traits including marbling, tenderness and yield have been measured at slaughter, thus obviating the use of the involved animal in the breeding program. Predicting these traits in live animals has been one of the major goals of beef cattle breeders. Although ultrasound assessment has added greatly to the assessment of an individual live animal, it does not necessarily predict the ability of the animal to pass those traits on to the next generation. Several markers for carcass quality traits are now commercially available.

In the beef cattle industry, where everyone is looking for a magical solution, it’s imperative to resist overestimating this technology. Performance in economically important quantitative traits is due to many genes. While it is likely true that some genes play a bigger role, there still are many in the picture.

Tremendous progress has been made in the past decade toward understanding the bovine genome. We are beginning to see the possibility of providing breeders with DNA information to improve the accuracy of marker-assisted selection decisions. This application of DNA technology will likely prove most beneficial for traits that are difficult to measure.
 
It’s important to understand, however, that the Marker-Assisted Selection approach will only improve our current genetic evaluation procedures by incrementally adding to breeding value accuracy in some traits. In a concerted effort, powerful genetic prediction programs coupled with marker-assisted selection will ultimately move cattle breeding forward by allowing genetic decisions on traits that are difficult or costly to measure.