DNA-Based, Marker-Assisted Selection In Beef Cattle

6/24/2009 2:21:00 PM

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Genetic improvement through selection has been one of the most important contributors to the advancements in animal productivity in the past 50 years. Traditionally, selection in beef cattle has been based on estimating breeding value using expected progeny difference (EPDs). The EPDs are derived from the observable performance (or phenotype) of the animal and its relatives. EPDs statistically predict that animal’s genetic potential for given traits (e.g., weaning weight). The accuracy of the estimate will increase over time as more information from progeny and relatives becomes available.

EPDs are the tools. They are not the plan. In order to effectively use EPDs, it is important to develop a breeding plan with specific goals and objectives (e.g., the most profitable selection criteria) for your herd or production system. Most of the economically relevant traits for cattle production (birth weight, weaning weight, growth, reproduction, milk production, carcass quality, etc.) are complex traits controlled by many genes and influenced by the production environment.

A gene is a segment of deoxyribonucleic acid (DNA) that is made up of pairs of four nucleotides abbreviated as “A”, “C”, “G”, and “T” (see Fig. 1 on the next page). A gene dictates the production of a specific protein. It is possible for the sequence of the DNA that makes up a gene to differ between individuals. These DNA variations in a gene are called alleles, and they often result in differences in the amount or type of protein being produced by that gene among different individual animals.

The protein produced by different alleles may affect the expression of a given trait and influence the observed performance. When an animal has an EPD above the base year average for a certain trait, what that means is that the animal inherited a higher than average proportion of alleles that favorably affect the trait.

It should be noted that traditional selection methods inherently tend to increase the frequency of alleles that have major beneficial effects on selected traits. That is, EPDs as typically used, increase the number of favorable alleles without knowing which specific genes are involved. This contrasts with DNA-based selection where knowledge of which DNA sequences are associated with improvement in a given trait is required, and selection is focused on those known DNA “markers” to make genetic improvement in the trait.

Recently scientists have started to identify regions of DNA that influence production traits. They have used molecular techniques to find differences in the sequence of the nucleotide base pairs in these regions. Tests have been developed to identify these subtle differences in the DNA. This has allowed for the development of genetic markers that scientists can use to identify whether an animal is carrying a segment of DNA that is positively or negatively associated with the trait of interest.

Genetic markers in a given region of DNA may differ from each other by the sequence of only a single nucleotide base pair, such as a single A, C, G, or T (Fig. 1). Such differences are called single nucleotide polymorphisms or SNPs (referred to as “snips”). Genetic tests based on SNPs analyze DNA derived from an individual to determine the DNA sequence that is present at one specific location (nucleotide pair) in among the three billion nucleotide pairs that comprise the genome of the cow!

Genotyping is the term that is used to describe the process of using laboratory methods to determine the equence of nucleotides in the DNA from an individual, usually at one particular gene or specific location in the genome.

Selecting an animal carrying the favorable form of a marker, or one that is associated with a positive impact on the trait of interest, can result in an improvement in the observed phenotype for that trait. Although complex traits are influenced by several genes, the mode of inheritance of each genetic marker is simple. An animal gets one marker allele from both its sire and dam.

Genome Program

Fig. 1. DNA (deoxyribonucleic acid) contains the instructions for making proteins. Differences in the nucleotide sequence of a gene’s DNA can influence the type or amount of protein that is made, and this can have an effect on the observed performance of an animal. Source: Original graphic obtained with permission from the U.S. Department of Energy Human Genome Program (http://www.doegenomes.org).

Marker-Assisted Selection (MAS) is the process of using the results of DNA tests to assist in the selection of individuals to become the parents in the next generation of a genetic improvement program. Genotyping allows for the accurate detection of specific DNA variations that have been associated with measurable effects on complex traits. It is important to remember that markers for complex traits are associated with only one of the many genes that contribute toward that trait.

The presence or absence of the numerous other “unmarked” genes and the production environment will determine whether an animal actually displays the desired phenotype (e.g., large weaning weight, increased marbling). EPDs estimate the breeding value of all the genes (both “marked” and “unmarked”) that contribute toward a given trait and, therefore, should always be considered in selection decisions, even when marker data are available.

Potential benefits from marker-assisted selection are greatest for traits that:

1. Have low heritability (e.g., traits where observed or measured values are poor predictors of breeding value) (Table 1).

2. Are difficult or expensive to measure (e.g., disease resistance).

3. Cannot be measured until after the animal has already contributed to the next generation (e.g., carcass data).

4. Are currently not selected for as they are not routinely measured (e.g., tenderness).

5. Are phenotypically (observed value), but not genetically, correlated with a trait that you do not want to increase (e.g., selection for marbling markers does not genetically increase backfat thickness despite the fact that on the animal these two traits tend to increase in unison).

Table 1

In order of greatest to least degree of benefit, the following categories of traits are likely to benefit the most from marker-assisted selection: (1) disease resistance, (2) carcass quality and palatability attributes, (3) fertility and reproductive efficiency, (4) carcass quantity and yield, and (5) milk production, maternal ability, and growth performance.

This ranking is due to a combination of considerations including: (1) relative difficulty in collecting performance data, (2) relative magnitude of the heritability and phenotypic variation observed in the traits, (3) current amount of performance information available, and (4) when performance data become available in the life cycle.

Recently genetic tests for DNA markers associated with marbling and tenderness have become commercially available. Each of these markers is associated with only one of the genes that contribute toward marbling or tenderness. Other “unmarked” genes, in conjunction with the production setting, will influence whether an animal marbles or has tender meat. Cattle can be genotyped for the desirable form of the marker by analyzing DNA collected from hair, tissue, blood, or semen samples.

It is important to have some idea of how much of the variability for a given trait is accounted for by each DNA marker. Ideally, but not necessarily, the preferred form of a marker would always identify genetically superior animals. Results from studies in commercial herds, comparing the performance of animals with and without the marker, should be an important consideration as they can help to estimate the effect of the marker on the trait under commercial conditions.

In the future it is likely that phenotypic, pedigree, and DNA-marker information will all be included in EPD calculations and that selection on this EPD will be superior to selection based on markers alone. The challenge will be to ensure that the value derived from the genetic progress associated with marker assisted selection for marbling and tenderness, or any other trait, outweighs the expense of collecting the marker information.

Source: Alison Van Eenennaam, University of California, Davis

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