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Genome-Wide Selection – The Answer to All Our Prayers?

Article by Alison Glasgow, Signet. April 2011

Animal performance is a combination of genetic merit and the effects of the environment, such as season, management regime etc. By adjusting performance records for the known environmental effects, BLUP technology (Best Linear Unbiased Predictor) provides an estimate of the genetic component of performance in the form of an Estimated Breeding Value (EBV). Selection of breeding stock using this method is therefore based on the effects of genes, rather than on the genes directly.

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Great strides are being made in the study of molecular genetics and in a relatively short space of time, information about an animal’s genetic make up will be used to enhance these more traditional estimates of breeding value.

Often heralded as a golden key to selection for breeding, this article explains some of the background, benefits and implications of this new technology.

What is Genome-Wide Selection?

Genomic selection refers to the use of genetic information as well as the traditional pedigree and performance records to predict an animal’s breeding value. Breeding values produced in this way are referred to as GEBVs (Genomic Estimated Breeding Values) rather than the EBVs we currently have.

How is it done?

An animal’s DNA (from blood, hair or tissue samples) is compared to a DNA ‘key’:

  • This key is developed from a reference population within a breed, usually involving several thousand animals. Using a whole genome scan, areas that may relate to differences in performance in the traits of interest are identified.
  • Each area where genetic variation is assessed is called a SNP (pronounced ‘snip’); the key is therefore commonly referred to as a SNP Key (or SNP chip) and these are available at different levels of density according to the number of SNPs under assessment. Keys with 54000 SNPs are commonly used in livestock evaluations.

The results from the comparison between the individual and the breed’s SNP key are then used to produce the GEBV.

GEBVs More Accurate than Current EBVs?

The accuracy of breeding value estimates for unproven youngstock can be enhanced by as much as 30% using GEBVs, but this does depend on the following:

  • The trait in question (less to gain in traits that are well recorded, have high heritabilities etc than those that are difficult to record with low heritabilities)
  • The population in which the trait is being evaluated.
  • The quantity and quality of the pedigree and performance records.
  • The quality of the SNP key

GEBVs will have significantly less impact in assessing easily measured traits (such as growth) in bloodlines that have been widely used and progeny tested – but they may be useful in assessing less well measured, low heritability traits in these animals (such as cow fertility and longevity).

So Will We Need to Keep Collecting On-Farm Performance Records?

Yes. For two reasons…

  • As explained above, science to date has revealed that, depending on the trait, enhancements to accuracy only come about when pedigree and performance records (i.e. current EBV information) are added to the evaluation. This may change as technology develops in the years to come and higher density SNP keys are developed. These will identify many more common types of genetic variation and be able to pin point genetic potential with a higher degree of accuracy.
  • An important aspect of SNP key technology is regular validation of the SNP key against the actual performance of the population/breed. This means that the key has to be regularly examined in relation to possible genetic change going on within the population/breed so we are confident it is correctly identifying variation. For this purpose, each population/breed will ideally have a constant ’reference population’ of several thousand genotyped animals that are or have been fully recorded on-farm. These records will form the basis of the validation process to ensure the key remains relevant in the face of genetic change.

In fact in the short term the level of data collection required to validate SNP technology may increase, as breeders and researchers work together to identify genetic variation in a range of important new traits – such as disease resistance and meat eating quality.

So What Are The Benefits?

Genome-wide selection has three main benefits…

  • Speed: Genotypes can be obtained shortly after a calf is born, thereby enhancing the accuracies of genetic merit predictions much quicker than performance recording alone. This allows for faster rates of genetic improvement resulting from shorter generation intervals and is particularly valuable for traits that can only be measured later in life such as 200 Day Milk Weight and Longevity.
  • Improved accuracy of low heritability traits/traits that are difficult to record: Breeders should experience greater response to their breeding decisions on traits with low heritability if the accuracy of the predictions is higher using genome-wide selection. It also offers opportunities to predict the breeding values of traits that are difficult to measure. Health, fitness, fertility, meat quality, methane emissions and feed efficiency would all be current examples of these.
  • Lower Cost: Because accuracies are enhanced much more quickly using genome-wide selection compared to collecting records on-farm (depending on the trait) there can be less cost involved in getting breeding value estimates to similar levels of accuracy. (Compare the cost of genotyping a young bull (in the region of $300 in USA) to the costs in having to wait until it has become a sire and amassed performance recorded progeny in a number of herds to reach the same levels of accuracy).

Is Genome-Wide Selection the same as the Gene Tests currently available?

They are similar but different! Genome-Wide Selection – referred to throughout this article, is a technique that uses a key with many thousands of SNPs (small bits of DNA) on it to compare individual DNA samples against and predict genetic merit. The density of SNP keys range from 30,000 SNPs per key to 700,000 SNPs, each SNP identifying an area of genetic variation.

Gene Tests – These are DNA tests currently available to the industry to identify either a) a specific gene or genes whose location within the DNA is known (such as polledness) or b) areas within DNA that are closely associated with areas of DNA known to be important for specific traits (known as a Gene Marker test)

The potential for genetic change that can be gained through Genome-Wide Selection is typically by far greater than the use of stand alone Gene Marker tests since most beef production traits we are interested in are affected by many genes having a small effect, rather than a single gene having a big effect. These many genes are more likely to be found by a SNP key that identifies many thousand areas of variation than a Gene Test that identifies considerably fewer. In instances where single genes are known to have significant effects, however, the opposite will be true.

Investing in Genome-Wide Selection

Genome-Wide Selection provides significant opportunities to make genetic improvement in existing and important new traits, but some important questions must first be addressed:

  • Has the SNP key been adequately tested in your population/breed? Without accurate validation, the key will be ineffective at correctly identifying genetic variation for all animals in the breed.
  • Will sufficient on-farm recording be continued to re-validate the SNP key in the future? Continued breeder support is crucial to the long-life success of this technology, since the genetic make-up of breeds changes in response to selection and factors such as gene mutations.
  • Will investment in sampling be returned to the enterprise? The cost to the breeder of this technology in the UK is not yet known. In the USA, typical costs are in the region of $250-$300/sample although, as with all technologies, this is falling as systems develop and uptake increases. (For this reason, the animals sampled are chosen carefully and typically involve young sires selected for breeding and dams deemed to be of high breeding importance and/or to be used for ET purposes).

Herds will need to address their use of the information to recoup their costs. This will either be directly (marketing the availability of the information to lift breeding stock sales) and/or indirectly (due to the benefits of better animal selection and increasing rates of genetic improvement within the herd).

How Soon Will GEBVs be available?

Development of this technology in the UK is in its early stages. Different agencies and breed societies are approaching it in different ways. Common to all are the difficulties surrounding the need of a reference population of several thousand well-recorded animals. It is anticipated that the introduction of GEBVs in to some breed evaluations will be within the next 3 to 4 years.

Conclusion

The myth surrounding this new technology is that it will mean an end to on-farm recording and that all our questions about an animal’s genetic merit will be answered by a blood test, a hair sample or a tissue sample.

Not so. It should be remembered that the enhancement of EBV accuracy will vary according to the trait in question and the type of animal being evaluated (young bull, proven bull etc). Once in place, it will only be breeders that can collectively make Genome-Wide Selection work, by supporting it with high-quality on-farm records and actively using the results to improve the animals they are producing and provide return on their investment.

All said, the opportunities it offers to breeds and breeders are exciting and significant, not least in providing genetic information on traits we can not currently measure that are likely to have an impact on all beef herds in the future.

Alison Glasgow, Signet Breed Specialist
Telephone 0131 535 3237
Email [email protected]