Best Practice for Genomic Testing

With the opportunity for genomics to provide a greater level of prediction – particularly in non-parent animals, many breeders are considering how to best use genomics in their herds.

Best Practices for Genomic Testing

Using Genomics

Genomic selection offers an opportunity to increase the rate of genetic change and breaks the antagonistic relationship between generation interval (the average age of the parents when the next generation is born) and the accuracy of selection (e.g., accuracy of EPD) — two components that determine the rate of genetic change. However, as with any tool, genomic information must be used correctly and to its fullest extent. Here is a list of ‘best practices’ for producers relative to genomic testing.

1.All animals within a contemporary group should be genotyped.

If genomic data are meant to truly enable selection decisions, then genotyping before selection decisions are made makes the most sense for producers.  The return on investment of this technology is substantially reduced if it is used after the decision is made.

It is always important to measure all animals in the contemporary group where possible. Only measuring the “best” from each contemporary will bias the results. Essentially, measuring the worst cattle makes the best cattle better.

Importantly, genotyping non-parent animals will give you increased accuracy of EPD’s for the lifetime of the animal, which maximises your return on investment.

2.Females should be genotyped too, not just males.

The promise of genomic selection has always suggested the largest impact is for lowly heritable and/or sex-limited (e.g., fertility) traits or those that are not routinely collected (e.g., disease). This is indeed true, but it necessitates that genotyped animals also have recorded phenotypes.  For sex-limited traits, this becomes a critical choke point given that most genotyped cattle are males.

Genotyping females increases the accuracy on lowly heritable maternal traits, which improves accuracy of selection of females for breeders. This has desirable knock on effects for the herd, including the next crop of sale bulls.

3. Genotypes need Phenotypes

Whilst some believe that genotyping will replace the need for collecting traits (phenotypes), nothing could be further from truth. Even in the genomic world, phenotypes are still king.
Some members may look to genotyping as a way of reducing the amount of phenotypes that need to be recorded, however to get the most out of genomics in non-parent animals it becomes more important that phenotypes are also submitted on the same animals. We recommend for breeders that when you consider genotyping animals that you also ensure that you accurately collect the phenotypes too.

It is also worth collecting traits that are not currently used such as structural assessments, morphology etc….. These can be used later to further develop the value of genotyping if enough phenotypes for each trait have been recorded on genotyped animals.

4. Genotypes can provide useful information in addition to predictions of additive genetic merit.

Do not forget the value in correcting parentage errors, tracking inbreeding levels, identifying unfavorable haplotypes, estimating breed composition, and estimating retained heterozygosity.  All of these can be garnered from populations that have a well-defined set of genotyping protocols. The beef industry should be congratulated for the rapid adoption of genomic technology, but there is a lot of work to do.  Of critical importance is the fact that genomic technology will continue to change and does not replace the need for phenotypes nor the fundamental understanding of traditional selection principles including EPD and accuracy.

Genomics certainly has the ability to greatly improve the accuracy of prediction for breeders, particularly on non-parent animals, however like any tool it needs to be used wisely. Ensuring that genomic tools deliver the best outcomes for the future means ensuring that they are used correctly today.

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About Shorthorn

The Shorthorn breed is truly unique, from their distinctive roan colour, to their rich breed history and most importantly, the wonderful community of breeders, there is nothing else quite like a Shorthorn.

The key to the Shorthorn breeds advantage lies in their balanced genetic profile, driven by market participation that has been developed and refined, after more than 200 years of genetic selection under Australian conditions.

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