Genetics

Weekly genetics review: Keep measuring your performance and phenotype

Genetics editor Alastair Rayner, 22/06/2021

Brahmans are among the growing list of breeds where genomic information is used to increase the accuracy of EBVs

THE rapid uptake of genomic testing across the Australian cattle industry is quite remarkable.

From a position where DNA samples were once collected and analyzed for only very specific traits and conditions, genomic information has rapidly become an integral part of the information used to inform seedstock breeders on the genetic merit of the next generation of livestock.

As reported in last week’s column, genomic information is used to increase the accuracy of EBVs and is incorporated in Breedplan EBVs produced for breeds including Hereford, Angus, Brahman, Droughtmaster and Santa Gertrudis.

Other programs using genomic information have been adopted by the Shorthorn Breed and others in their move to increase producer knowledge of genetic suitability for use in herds.

While genomics offers the opportunity to increase the accuracy of an Estimated Breeding Value, genomics must be assessed in reference to the population of a breed.

In simple terms, a single genomic sample, or even a herd sample will help shape a profile of that herd. However, without reference to the broader population, it becomes extremely difficult to know if the profile is within the top, middle or lowest ranges of performance for the breed.

The ability to use actual performance measures collected on the phenotype of animals within the breed opens the power of genomic information.

A key factor is the ability to access a much broader range of phenotypes from a range of environments that share common genetic links. This population also allows the opportunity to obtain data on some of the harder-to-measure traits such as fertility or carcase data.

In the case of a reference population, size is a key factor. The larger the population the greater the opportunity to measure and record the variation of animals across the entire group.

These performance measures underpin and help place the genomic information in a context of the population, and as a result drive the accuracy of individual animals EBVs. As well as being large, well-recorded and relevant to a breed, information collected should come from comparable production systems.

To develop such a reference population is no small undertaking. This is potentially one of the limitations for breeds with smaller numbers.

As part of Angus Australia’s recent Technology Update for Northern Australia, the organisation’s northern development officer, Jen Peart, demonstrated the importance of using both genomic data and the information collected from phenotype to achieve high levels of accuracy.

In the example below, she highlighted how many animals would be required to be gnomically tested for reproduction traits. These traits have a heritability of about 30pc.

Without any phenotypic information, to achieve a 50pc accuracy in the breeding predictions, at least 10,000 animals would need to be included in the reference population.

This poses a challenge for breeds without the ability to build and test so many animals.

Without access to these numbers, the ability to construct a population of sufficient size, genomic testing alone will not enable a breed to develop EBVs with high accuracies.

It is also important to note the value of linkages to the population. One of the key opportunities genomic testing provides is to develop EBVs with reasonable accuracy for young animals.

Often these animals have had no progeny and limited opportunity to have phenotype information recorded and analysed in the development of an EBV. As a result, the EBVs on these young bulls are often published with low accuracy or no accuracy.

However, the existence of genetic linkages to the broader population allows the opportunity for breeders to obtain EBVs on younger animals with reasonably high levels of accuracy across a number of traits.

To demonstrate the importance of these linkages, Ms Peart showed an example of two young Brahman bulls that had only genomic information recorded. The bull at the top of the image is well linked to the broader reference population, and as result has good levels of accuracy across growth traits as well as accuracies on the other EBVs for the breed. It has also allowed the calculation of Index values for that bull.

 

In the case of the second bull, without linkages to the population, the opportunity to use the genomic information is limited.

While EBVs can be calculated for growth traits, flight time and shear force, at these levels of accuracy, the EBVs will change dramatically as more data is analysed for that animal.  It also prevents the calculation of Index values.

So while genomic information is immensely valuable, producers wanting to make the most of the technology need to continue to collect and submit phenotype data to keep the population information large and relevant to their breed.

Many breeds are also fortunate in the ongoing research projects that are collecting immense amounts of data on production traits.

Northern BIN steer project

As an example, the Northern BIN steer project collects data across growth and carcase traits, which adds immeasurably to reference population for the breeds in this program.

The Northern Repronomics project similarly contributes a large amount of data, which aids in ensuring the northern breeds have both a well-sized population, but one that is relevant and well recorded.

While many breeds, such as Angus and Hereford have benefited from the capacity to draw on high numbers of member records as well as data from sire and BIN programs, it is important to note that the larger industry programs can offer space for smaller breeds to participate and start developing a data-set that will lead to meaningful developments.

Making full use of genomic information without these links and the population to compare to will make “going it alone” a much more problematic option.

More broadly, without the initial commitment to record, measure and submit phenotype data for herds and for breeds, the true opportunities for breeders will fail to be realised.

 

Alastair Rayner is the Principal of RaynerAg, an agricultural advisory service based in NSW.  RaynerAg is affiliated with BJA Stock & Station Agents. He regularly lists and sell cattle for clients as well attending bull sales to support client purchases.  Alastair provides pre-sale selections and classifications for seedstock producers in NSW, Qld and Victoria.  He can be contacted here or through his website www.raynerag.com.au

 

 

 

 

 

 

 

 

 

 

 

 

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