Everything You Need To Know About Sheep DNA Testing

There is a lot of confusion surrounding sheep DNA testing in the industry, and that is why we have decided to talk about DNA testing in this blog. Below are some tips to make the most of this tech in your flock, and also how to avoid some of the pitfalls and mistakes that many people new to the process make.

What is DNA Testing?

DNA testing involves taking a tissue sample from an individual test that is sent to a registered testing lab for DNA extraction and analysis. It can be used to understand parentage, predict poll/ horn status, enhance the accuracy of ASBV’s, as well as provide ASBV’s that are not easily measured or tested early in a sheep’s life.

There are two kinds of DNA testing commonly available at the moment.

Parentage Test

• Uses a lower number of DNA segments and provides a parentage result only (a poll/ horn prediction is normally included)
• A slightly cheaper test but provides significantly less information
• Can be used even if you aren’t a client of Sheep Genetics

Genomics Test (recommended as best value for money)

• Uses 50,000 segments of DNA and provides a parentage test, poll/horn prediction and ASBV’s
• A slightly more expensive test but significantly more information provided
• Need to be a member of Sheep Genetics
• Caveat: Not all breeds are available for Genomic testing (more on this down the page)

How does the process work?

This process can take around 9 weeks (if you need to resample then you add another 9 weeks). This includes the full process of shipping, lab testing, reviewing returned results, importing to BreedELITE and sending them to Sheep Genetics and then waiting for the results to appear in Sheep Genetics.

BEWARE: The lab will often quote you a 2-3 week turnaround time – this only covers a part of the process and too often we see people get themselves caught with insufficient time to get their results in (more on this later).

The basic process works as follows:

1. Purchase the number of Tissue Sampling Units (TSU’s) you need (1 per sheep) and an applicator – BreedELITE provide these at member discounted prices. Let us know if you want a quote.

2. Use the BreedELITE Sheep Software, barcode scanner, and Smart Reader to assign the TSU ID to the sheep and take the DNA sample

3. Once all samples have been collected send them to your lab of choice. 
   • Include a copy of your sample submission form (refer to the instructions process in the BreedELITE members area)
   • Provide a potential sire and potential dam list. For purchased rams/semen sires that have been DNA tested in the past just need to provide the 16 digit sheep genetics code
   • Make sure the lab is registered with Sheep Genetics, that way you will always have access to your data in the future even if there is an issue with the company
   • BreedELITE buyers group members receive great member discounts with XytoVet for genomics

4. Wait for DNA Lab to extract the DNA from the samples

5. If the DNA Lab has all the parentage data they can complete the parentage in the lab – otherwise this will need to be done by Sheep Genetics

6. The lab will send you back a results file which needs to be checked to make sure it looks fine (BreedELITE can assist with this if you need)

7. Import the results file into the BreedELITE Sheep Software. Submit it to Sheep Genetics if you are with them

8. Retake any DNA samples that need to be retested – this will be identified by getting an error

Some important notes:

• Keep the samples out of direct sunlight after they have been taken

• Make sure the Sire and Dam list is as complete as possible particularly for parentage tests – this is all that is used to make the match

• If you are just taking parentage tests then you don’t need to be a member of sheep genetics

• The likely errors you will see in the data include:
  • No Usable Genotype – normally indicates there was an issue with the DNA sample and the lab couldn’t extract the DNA
  • Not Present Parentage – they were unable to match to the list of sires and dams provided
  • Too Close – the potential parents were too close to make a decision (the parents may be highly related), contact the lab about this

• If this happens then you will either need to:
  • Extend the sire and dam list, and/or;
  • Resample and resubmit new DNA samples – it is best to discuss this with the lab beforehand and BreedELITE can assist with this.

What should you expect in terms of accuracy?

This is the most misunderstood part of DNA testing and we find that people’s expectations around what will be achieved are not aligned with what is realistic. So let’s look at the numbers:

If you submit 100 samples

• A good result is that more than 90% of these will have a successful DNA extraction (90 sheep get parents assigned to them)

• Of the sheep that have a parent assigned, you can be 98% certain that the parentage results are accurate

• If you want to improve on this then the 10% of samples that didn’t work properly can be resampled and resubmitted with similar expectations

• Resubmit 10 new samples

• 9 will be successful 1 will have an error (assuming parentage data is available and assuming the errors for those 10 are fixable – not always the case!)

So the crux of this is that if you want a high chance of doing better than 90% you need to budget enough time and additional money for 10% retesting.

Our saying is: 90% and 9 weeks

Parentage Testing or Genomics?

The advantage of genomics is that it provides you with significantly more information than just the parentage test. For clients of ours, a Genomic test is the same price as parentage only, and you get the following advantages:

• The accuracy of your ASBV’s will increase

• You can get highly accurate ASBV’s at an early age stage to inform decision making, including ASBV’s for traits that cannot be easily measured or observed (eg. eating quality)

• Parentage verification is undertaken as part of Genomics tests as well
  • Sheep Genetics will check against every sheep they have in their database (not just your sire and dam list) and can result in a higher number of parentage matches (these need to be verified by you, BreedELITE can assist)

• ASBV’s will improve irrespective of whether there was a pedigree match for them due to the relative analysis for measured data

Note that for animals that already have a number of performance recorded progeny the benefit of genomics testing reduces dramatically (ie. genomic testing dams/sires that have many performance recorded progeny) 

Is my breed available for Genomics? This is an important fact to find out before undertaking genomic testing. Genomic predictions rely on a pool of genetic sequences backed up by real-world performance data. The test you take then compares the similarity of that sheep to the pool and thus can predict the real-world performance with good accuracy. To see if your breed is available head to the Sheep Genetics website here and scroll down the page

My breed isn’t available, do I still pay for Genomics? It depends, let me explain more: If you are not planning to submit your performance data to Sheep Genetics and you’re only interested in parentage, then paying for a genomic test will not benefit you much. If you are planning on submitting these animals’ performance going forward, and/or the performance of their progeny, then see the extra cost of genomics as a contribution to your breed of choice. Remember, genomic prediction relies on a pool of genetic sequences backed up by real-world performance, therefore paying for genomics even when you aren’t getting the benefits now, you are increasing the size of that pool and backing it up with data. If enough people have this view, then as soon as the genetic pool gets big enough, genomic analysis will become available! This is really important in meat breeds where early-stage traits, as well as carcase quality traits, are important to your marketing and breeding decisions.

Predictive vs Causative Genes

Not all gene markers are equal. Some gene markers guarantee that the trait exists (Causative). Other gene markers predict that a trait will exist but do not guarantee it (Predictive). 

A good example of this is the Poll/Horn test which predicts with a level of certainty that the animal has the horn gene (but does not guarantee it). There are two approved gene markers for the horn gene and different labs may use different markers in their genomics test. Both are approved by Sheep Genetics and have similar predictability, however using the different gene marker may see the same sheep get a different result! We have observed this recently and is something to be aware of. This is no fault of any one lab, it is just a limitation that needs to be understood. You cannot guarantee a PP ram is PP based on a genomic result, you can only be close to certain.

We guess that the only certainties in life are death and taxes! 

How do you make the most of Sheep DNA testing?

• Take your DNA tests at lamb marking time. This means that you have:
  • ASBV data earlier to make classing and selection decisions
  • Plenty of time to work through the process and any retesting that might be required

• If you are with sheep genetics, get a Genomics Test rather than just the Parentage Tests – the extra information is definitely worth it. If your breed doesn’t have genomics available, then you are submitting data for the future availability of the test

• Budget for 10% resampling costs and the additional time required for this

• Be careful of Ram Syndicates that are highly related (e.g. same sire and mother from an ET program). This can make it difficult to get good results with the parentage

• Genomic testing is not a silver bullet, it is another tool to accelerate and enhance genetic progress
  • Data should still be measured (the more measured data that is submitted, the more accurate future genomic results are)
  • it is not a substitute for mothering up if you want birth site data (DOB, BT, DABs, MBS etc)

Want to learn more about how Sheep DNA Testing can benefit your business? Contact us with any questions you might have. Our team will be happy to answer them for you.