Harnessing the Benefits of Genomics in an Angus Seedstock Enterprise

October 22, 2018 2:29 pm

Genomics, a term used to describe a range of technologies that analyse an animal’s DNA and provide information about its genetics, is increasingly being adopted by Angus seedstock breeders in Australia, with considerable numbers of Angus animals being genomically tested each year.  

Genomics has been used for some time for purposes such as pedigree verification and the management of genetic conditions, but increasingly, is being used to improve the description of an animal’s genetics for traits associated with the productivity and profitability of Angus genetics within the beef supply chain.

When combined with pedigree and performance information, genomic information adds an additional source of information to the calculation of Angus BREEDPLAN Estimated Breeding Values (EBVs), enabling the generation of EBVs with additional accuracy, and ultimately enabling animals with superior genetics to be identified more reliably.

Genomic testing is however a considerable expense and so any investment in testing seedstock animals needs to be carefully reviewed to evaluate the cost-benefit of the investment. 

One of the common questions asked of staff at Angus Australia by seedstock breeders is “how should I be using genomics within my operation?” The following article attempts to summarise some of the key considerations when addressing this question.

Genomics is Part of the Future 

Genomics is undoubtedly a technology that will play an important role in future Angus breeding programs, and alongside other technologies that are available, such as reproductive technologies like artificial insemination (AI) and embryo transfer (ET), or mating allocation technologies like TGRM or MateSel, all Angus breeders should be considering how genomics can be best applied within their enterprise.

This does not mean that all Angus seedstock breeders should immediately begin routinely genotyping all animals in their herd with a high density genomic product, far from it, but rather all breeders should carefully review the genomic technology that is available and develop a strategy as to how they will most appropriately utilise the technology within their enterprise.   

Performance Information Remains King 

While genomic information provides a useful additional source of information for the calculation of Angus BREEDPLAN EBVs, it is important to stress that it does not replace the need for performance information, and the collection of performance information remains as important as ever. 

The development of genomic technologies has emphasised the need for accurate performance information, and the ability of Angus breeders to harness the benefits of genomics, both individually and collectively, is dependent on the collection of comprehensive performance information for as many animals and traits of importance as possible. 

Prior to considering genomic technology, all Angus seedstock breeders should develop a performance recording strategy for their herd that clearly articulates what performance traits will be measured, on what animals, and when. 

If aiming to maximise the accuracy of the EBVs that are available on animals, all Angus breeders should endeavour to collect performance information for as many traits of importance within their breeding objective, and for as many animals within their herd as possible. The only exception to this may be very small herds where the collection of effective performance is challenging.

Collect & Store DNA Samples 

Irrespective of whether genomic testing is to be conducted, a good practice for all Angus seedstock enterprises to adopt is the collection and storage of DNA samples as a resource that can be called upon, if and when needed.

At a minimum, this should include the collection and storage of DNA samples for all sires at the time of joining, all donor dams at the time of embryo collection, and all animals being sold as breeding animals at the time of sale.

A better practice is to routinely collect and store DNA samples for all animals in the breeding herd at a young age. 

DNA samples can be collected and stored in a number of forms, with the use of hair samples or tissue sampling units (TSUs), being the most common. 

TSUs have the advantage of enabling collection at or shortly after birth, but there are some questions as to the stability of samples if stored at room temperature for long periods, and there is a cost associated with the TSU equipment.   

Hair samples have the disadvantage of requiring clearly visible follicles before being suitable for testing, which usually prevents collection before 3 – 4 months of age, but can be stored easily for long periods by placing the sample in an envelope and storing in a dry, dark environment.  

Further assistance regarding the collection of DNA samples is available from the Angus Australia website. 

Genotype Key Animals 

Angus Australia’s new Regulations regarding DNA and parentage verification (see page xx) require any sires or donor dams born after 1/1/2018 to have a genomic profile of 5,000 SNPs or greater before their progeny can be registered. 

Essentially this means that any sires or donor dams born after 1/1/2018 should be genotyped with either the HD50K for Angus or Angus GS products.  

While there is still a lag time before this Regulation has an effect and all sires and donor dams require a genomic profile, genotyping all influential animals within the breeding program as a routine practice, such as sires and donor dams, is worthy of consideration.  

A good strategy is to test any sire or donor dam being genotyped for the first time with either the HD50K for Angus or Angus GS products. While this is a more expensive option ($51.45) than genotyping with a base parentage panel ($25.85 via Zoetis, or $27.50 via Neogen), as currently required for calf registration purposes for sires and donor dams born between 2004 and 2017, genotyping these animals offers considerable benefits, which arguably outweigh the additional cost. 

These benefits include an increase in the accuracy of the EBVs for not only the influential animals in the breeding herd, but also their progeny, particularly for hard to measure traits. Additional benefits also exist such as the ability to add-on genetic condition testing at considerably lower cost, and the availability of greater power when using the genotype for future parentage verification and discovery.

Develop a Genotyping Strategy Specific to Your Herd 

Outside of genotyping key animals, the optimal utilisation of genomics will vary with each individual seedstock enterprise, and there is no single strategy that is considered most suitable. 

In contrast to performance information, there is no requirement to undertake genomic testing for all animals in a contemporary group and so testing can consequently be conducted as many or few animals as desired, depending on the objective. 

Common testing strategies currently undertaken by Angus seedstock breeders include: 

  • genotyping individual animals of interest  
  • genotyping all animals being offered for sale as breeding animals 
  • genotyping a group of animals of specific interest, for example bulls being considered for use in a breeding program 
  • genotyping all heifers selected as replacements 
  • genotyping all calves born in the breeding herd   

Which strategy is most appropriate will ultimately depend on the individual enterprise and what they are aiming to achieve.  

When devising a strategy regarding what animals will be tested, it is important to consider the incorporation of genomic information is of more value when an animal’s existing EBV has low accuracy. This makes genomic testing of most value: 

  • when an animal is very young  
  • for traits that are hard to measure, or for traits that cannot be measured prior to an animal entering the breeding herd 
  • for traits that have a low heritability 
  • in situations where collecting effective performance information is problematic, such as in small herds, or when an animal has been removed from its contemporary group 
  • in situations where little information is recorded with Angus BREEDPLAN for the animal, such as recently imported overseas sires 

It is also important to be mindful that genomic information will only be analysed in Angus BREEDPLAN for animals with sufficient genetic relationship to the reference population, being animals in the genetic evaluation with both genomic and performance information. Breeders should contact staff at either Angus Australia or the DNA companies for advice prior to testing Red Angus animals, or animals recorded on the Multibreed Register.  

Which Genomic Product? 

Once fundamental decision when considering investment in genomic technology is “which genomic product will be used?” 

Angus BREEDPLAN currently incorporates genomic information from two different genomic products, being the HD50K for Angus product offered by Zoetis Animal Genetics, and the Angus GS product offered by Neogen.  

When making a decision as to what genomic product will be used, it is important to consider factors such as: 

  • the cost
  • the cost of any add-on testing that may be required (e.g. for genetic conditions) 
  • the turnaround time for testing 
  • the density of the genotype (i.e. the number of SNPs) 
  • the quality of the genotype 
  • the follow up customer support that is available  

Essentially, while subtle differences exist, genotyping with either the HD50K for Angus or Angus GS products will yield similar results, and so genotyping with either product is suitable. 

Be Organised 

One of the common difficulties faced when utilising genomics is allowing insufficient time between when the testing is requested, and when the results are required. 

Genomic testing takes time, and while it is human nature to wait until the last minute, a turn-around time of 6 – 8 weeks should be allowed. Depending on when genomic results are returned from the DNA laboratory, and how they correspond to Angus BREEDPLAN analysis dates, an additional 2 – 3 weeks can elapse before the genomic results are incorporated into the calculation of EBVs.

A good, albeit conservative, rule of thumb is to ensure DNA testing is requested at least 3 months prior to results being required.    

Ask Questions & Regularly Review Your Strategy 

Genomic technology is evolving rapidly and the options available can be difficult to keep abreast of, even for those who are very informed about the technology.

There are however a number of staff at Angus Australia, along with staff at Zoetis Animal Genetics and Neogen that are available to provide assistance to Angus breeders. All Angus Australia members are encouraged to ask questions, and to regularly review the genomic technology that is available to consider how they will most appropriately utilise genomic technology within their enterprise.

To further discuss this article, or to obtain further advice regarding the utilisation of genomics in an Angus seedstock enterprise, contact Angus Australia’s Breed Development & Extension Manager, Andrew Byrne on (02) 6773 4618 or andrew@angusaustralia.com.au. Information is also available from the Angus Australia website.

 

 

 

 

 

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