by: Matthew D. Garcia
M.S., MBA, PhD, Louisiana State University Assistant Professor of Beef Cattle Genomics

What are genotyping technologies?

The genotyping technologies that are currently being marketed to beef producers are based off of genetic markers that have been identified to be associated with economically important traits.

Specifically, these markers are said to be inherited by animals that are either high producers for a trait or low producers for a trait. Typically, these markers are located on a single gene or in a specific place in the bovine genome. The goal of these technologies that are currently being marketed to producers is to increase the accuracy of selection from traits ranging from growth, efficiency, carcass quality, fertility and disease resistance.

The genotyping technologies essentially are trying to identify the underlying genetic predisposition for important traits so that producers can select for their superior animals early in the production process or prior having to maintain an animal to a specific production point to visualize if that animal is indeed superior.

These technologies if developed further could provide a method for producers to more rapidly improve lowly heritable traits such as fertility or disease resistance. In this article I will discuss the usefulness of this technology as it currently developed as well as its limitations.

With so many methods of selection, why do producers need another?

For centuries the methods which cattlemen have utilized to select superior breeding animals has continually evolved. Initially, there was phenotypic selection in which a producer would select the best looking or highest performing animals as breeding individuals. However, this method was only optimal for highly heritable traits (cow and bull were superior for the trait so the offspring would be superior) and did not always yield progeny that were desirable for lowly heritable traits thus, the outcome for these traits could be highly variable.

The next tools that became available were centralized performance testing and expected progeny differences (EPDs). Although these methods are still widely utilized as selection techniques they do have limitations. Performance testing documents growth and efficiency characteristics in breeding age animals, but these individuals are not typically tested in the environment in which they are expected to perform. Thus, the animals that are purchased after these tests will experience a dramatic drop off in performance and weight loss when they are placed in a forage driven beef production setting.

Expected progeny differences were then introduced as another method to increase the accuracy of selection of breeding animals. The use of EPDs gives producers a scientific prediction of how certain individual offspring are "expected" to perform. Virtually every breed association generates EPDs for multiple traits from birth weight, growth and efficiency traits and even fertility traits. However, in order for an EPD to be accurate, an individual bull must have many offspring with recorded performance data. This means that young bulls with highly desirable EPDs may sire offspring that are extremely variable when compared to their initial EPDs, and these EPDs will also change as more progeny data is collected for that individual.

What genotyping technologies are currently available for producers?

A new tool that is being proposed to further increase the accuracy in identifying superior animals is marker assisted selection (MAS). This technique evaluates an animal at the DNA level and aims to identify mutations that are contributing to the variation that is observed in economically important traits. This technique became a reality due to the many collaborating research institutions that continue to participate in the bovine genome sequencing and annotation projects. The bovine sequencing project gave researchers the tools to evaluate genes and mutations on those genes that may in fact may be making animals superior or inferior for economically important traits.

Currently, there are multiple molecular tests that are commercially available for producers to select for specific traits cattle, including tests for coat color, varying diseases and even meat quality. If further developed in the future, MAS would allow producers to identify animals that were going to be superior for their trait of interest early in the production process rather than having to wait for the animal to mature or until the animal was harvested to see if the end product (carcass) was optimal.

Producers could manage their "genetically superior" animals in one scheme, choose breeding individuals to propagate those genetics and make the appropriate investment with their inferior animals as to not lose income. However, even though this technology is available to producers, individuals looking to use this technology should be cautious as even MAS has limitations.

How can genotyping technologies have limitations if we are looking at the genetic make-up of an animal?

The idea that producers could make selection decisions much earlier in the production process led to the commercialization of some genotyping tests. Producers can send tissue, blood or even hair samples to specific companies to have their animal's genetic make-up analyzed for a few mutations affecting certain traits. Initially, this type of testing seemed like a good method to try and improve traits that were highly desirable or might be hard to measure in a live animal. However, producers must really understand that the concept of selecting animals based on their genetic make-up is still in the early development stages for a couple of reasons.

First, there are an estimated 30,000 genes and three billion individual nucleotides in the bovine genome. Researchers are still attempting to understand where exactly these genes are and in what tissues of the body that those genes influence.

Secondly, many of the traits that producers are interested in such as disease resistance and fertility are lowly heritable and most likely influenced by multiple genes. As such, relationships among genes and mutations on these genes need to be evaluated prior to MAS becoming an accurate method of selection.

Selecting for single markers affecting a single trait may not be the most accurate method of selection as that particular marker may not account for a large amount of variation for that trait. Thus, if producers begin selecting for single markers for single traits it may in fact result in little if any significant improvement for that trait.

How does genotyping technology need to be developed in order to be useful?

The concept of MAS has given way to a new concept called whole genome selection (WGS). Whole genome selection is another form of MAS but would be applicable in the future when all markers associated with a trait were identified.

As researchers have been provided with more information through the continued improvement of the bovine sequencing project, it became very apparent that relationship of significant markers be evaluated with multiple traits, and that as many markers as possible be evaluated for single traits. The reason for this is two genetic factors call pleitropy and epistasis.

In the case of pleitropy a single gene or mutation may actually influence multiple traits. In this instance selecting a marker that has been deemed to be significantly associated with marbling for example may also be influencing traits like fertility. Thus, over selection for this marker to improve one trait may actually be very detrimental to other economically important traits.

Epistatic effects are exactly the opposite of pleiotropic effects. In this instance, multiple genes or mutations on those genes are actually influencing the final performance of an animal for a specific trait. In this case, selecting animals based on only a few markers may lead to little or no improvement as the limited number of markers may in fact not have an overriding effect on the final outcome of that trait's performance. Many of the traits that producers would like to make improvements in are very complex (fertility), very hard to measure (carcass traits) and most likely controlled by many genes. For this reason, for MAS to make a real impact in the beef production industry, researchers must identify as many significant markers as possible and evaluate their relationships with multiple traits for MAS to truly be a valuable tool to the beef producer. In the future it will be necessary to make WAGS tests available to producers that evaluate marker's multiple trait relationships while still making markers available that account for a large amount of variability for the trait of interest.

Should a producer currently use genotypic technologies?

There are four questions producers should ask themselves prior to implementing this technology into their selection:

1) What traits am I trying to improve?

2) Are these traits highly or lowly heritable?

3) How much improvement can I expect to see by implementing this tool as part of my selection strategy?

4) Will I be able to cover the cost of testing with the increased performance of my animals?

As previously stated, this technology has been around for many years but is still in the early development stages. While this technology may prove to be beneficial for some producers it may not be feasible for others. It is always important to know as much as you can about these technologies prior to implementation so that a decision can be made as to whether it is going to bring an added benefit to your operation. While genotyping technologies are still relatively new they are getting more accurate and will only continue to improve. As such, this technology, if developed correctly, will provide producers a new selection tool in the future to make them more profitable and sustainable.

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