Cattle Genetics Decoded

The long-awaited day when we can peek inside the "black box" of an animal's genetic make up to help make breeding decisions arrives just a few months from now, writes Blair Murray - Dairy Genetic Improvement/OMAFRA.
calendar icon 15 February 2009
clock icon 6 minute read

A powerful new selection tool can predict a calves genetic potential in our herds shortly after it's born.

 The U.S. Department of Agriculture (USDA) will release genetic evaluations using genome information in January 2009, and the Canadian Dairy Network (CDN) plans to follow later in the year.

The genome of an organism, in this case a dairy animal, is its DNA-encoded hereditary information. Genome selection, coupled with already sophisticated evaluation and selection procedures, will greatly enhance efficiency and accuracy of genetic improvement programs.

Canadian and U.S. genetic improvement labs, facilities and artificial insemination (AI) studs have co-operated to develop Genomic Estimated Breeding Values (GEBVs). They are expected to revolutionize dairy breeding programs by changing the way bulls and cows are selected.

This was the message from the recent meeting of the International Committee on Animal Recording in Niagara Falls, N.Y. Highlighting the meeting were two important reports, one by Dr. George Wiggans on the co-operative effort among American and Canadian industry partners to develop genomic selection, and the other by the University of Guelph's Dr. Larry Schaeffer on how this technology can be used in an AI selection program. Together, their reports answer key questions dairy breeders are asking:

What is genomic: selection?

Genomic selection uses information about an individual animal's genetic make up to estimate its breeding value. Scientists developed whole genome scans using a DNA chip that identifies up to 54,000 tiny bits of genetic information. Each bit of information is called a SNP.

What are SNPs?

SNPs (pronounced snips) are like markers indicating common types of genetic variation. They can be beneficial, harmful or have no known effect.

The cattle genome has millions of SNPs. The more we find, the more we can learn about overall dairy genetics. Although not all 54,000 SNPs identified so far have proven useful in dairy genotyping, a lot of them can now help predict whether we are selecting an animal with the traits we want.

How does selection work?

The first step in the two-step process compares the genetic makeup of a large number of individuals with common characteristics in the general dairy cattle population. This includes milk production, calving ease, type traits and so forth.

The second step uses the information from SNPs found in each animal's genome to predict its breeding value. Computer programs add up all the effects on a given trait identified with the various SNPs. This is combined with the Parent Average used in the traditional genetic evaluation system to calculate an overall GEBV.

As accurate as progeny proofs?

In the USDA project, GEBVs were estimated for 5,825 bulls and cows, and then compared with their actual 2008 breeding values to determine GEBV accuracy. This was done for production traits as well as functional, calving and type traits.

A GEBV will have a reliability factor between the Parent Average and a traditional progeny proof. The relative reliability of Parent Average is 25 to 40 per cent, depending on the trait and amount of information available on the parents. In Canada, a newly proven bull may have a proof with a reliability of 80 to 85 per cent, and proofs for bulls with large numbers of daughters will have a reliability level in the 95 per cent range.

The new GEBVs will combine genotype information from individual animals with Parent Averages, plus any individual proof information if it's available. When the USDA added genotype information plus Parent Averages, the GEBVs for bulls had a reliability ranging between 63 and 75 per cent. These reliabilities may be somewhat overestimated and may prove lower when this program is widely used.

We cannot rely on GEBVs as we would on highly proven progeny proofs, but GEBVs are much more accurate than Parent Average. With females, a GEBV is probably far more reliable than any current genetic evaluation for all but a few exceptional cows, and has the advantage of being available very early in life.

What are the benefits?

Genomic selection has two advantages: speed and lower cost.

Genotypes can be obtained shortly after the birth of a calf that may potentially be used in AI or as a bull mother. When combined with Parent Averages to create GEBVs, the process could speed up genetic trends by 30 to 50 per cent, depending upon the accuracy of GEBVs and the extent to which the industry uses them.

A full genome scan for an individual will cost $250 to $300, compared with $40,000 to progeny-prove a single bull. This test could screen a large number of young sires to select a few to enter into progeny testing. That would potentially improve the rate of genetic gain but at a much lower cost than the current progeny testing program.

Improved reliability from GEBVs may enhance selection to improve low heritability traits such as health, fitness and fertility.

What about Inbreeding?

Since genomic selection can more accurately identify the best superior sires at a young age, it might contribute to higher rates of inbreeding. Breeding programs usually concentrate on achieving the best genetics as quickly as possible.

On the other hand, genomic selection used as a widespread screening method could identify bulls and cows of high genetic merit traditional animal model evaluations would miss.

What about single genes Identified as Important?

Genome-wide selection has rendered useless the approach of identifying single genes as having a positive or negative effect on an economically important trait. Multiple genes control most of these traits and act in an additive nature.

Individual genes identified as important, when included in genome-wide selection, can contribute to overall GEBV accuracy. Identifying more of these genes in years to come would likely improve reliability in the future.

Effect on AI programs?

The advantage of GEBVs would be to pre-screen bulls before entering them into progeny testing, increasing the pace of genetic gain. However, they would still go through the same waiting period to receive a progeny-test EBV before being used in the population.

A more aggressive approach would genotype 2,000 or more young bulls but only enter a reduced number into progeny testing at one year of age. Instead of 400 bulls entering progeny testing per year, there might be only 200, and they would have been drawn from a much wider pool than they are now.

As well, a few of the best genotyped bulls would be used as sires of sons before completing their progeny tests. This method would produce 30 to 50 per cent more genetic gain than a traditional progeny test system at about the same or lower cost.

Will we need records anymore?

We will still need records to identify truly superior AI sires. Progeny tests will continue since they are more reliable than GEBVs but we will probably be progeny testing much fewer bulls.

A large number of records for all economically important traits will be necessary to continue to estimate the SNP effects so we can produce more accurate GEBVs in future.

What about cows?

A GEBV will improve the reliability of estimating the true breeding value of most cows. Typically, except for a few elite cows, we have less information to estimate true genetic merit for cows than for progeny-proven bulls. Genotyping females shortly after birth could provide relatively reliable breeding values.

AI studs interested in bull dams will probably have genotyping done on a large number of prospective females. If you have marketable females that are not the sort AI studs currently want, genotyping at less than $250 per animal could be a good option.

February 2009

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