DNA Oct 2020

DNA Glossary

SNP is the type of testing technology. It is the most up to date type of testing. SNP stands for single nucleotide polymorphisms.

Microsatellite is also testing technology - except it’s older and being phased out.

TSU is a sample type - in this case it refers to a tissue sampling unit. A tissue sample is generally collected from the middle of the ear. Hair and in some cases, semen can also be used for SNP DNA testing.

Single-step evaluation refers to a genetic evaluation method that combines pedigree, performance and genomic (DNA) information.

100K, 50K etc refer to the number of DNA markers used to gain the DNA test result, or the level of SNP testing).

The world of DNA is fast paced with technology improving and changing all the time.

Most breeders will now be aware that some breeds are conducting single-step group runs - this is the combination of SNP testing and data, such as pedigree and performance recording to provide more accurate EBVs.

Currently Hereford and Angus are doing single-step group runs.

The single-step evaluation is a new era in genetic evaluation available to the beef sector. This new genetic analysis combines pedigree, performance and genomic (DNA) information together in a complete multi-trait Breedplan analysis of birth, growth, fertility, carcase and feed intake traits. In a single-step evaluation, genomic information now contributes to the Estimated Breeding Values (EBVs) and accuracy calculations of genotyped animals and their relatives meaning the EBVs calculated in a single-step evaluation are a step ahead of those generated in a “standard” group run.

PBBs bovine DNA expert Megan Ellett says while there is a lot of technology and terminology to keep track of, DNA is not as daunting as it seems at first glance.

“Breeders just need to take the first step - get in touch with us and we can help with as much or as little as breeders might like or need.”

She said the world of cattle DNA is moving away from micro satellite technology to SNP testing - single nucleotide polymorphisms.

This combined with some breeds employing the single-step genetic evaluation is proving to be a powerful tool.

“The single-step group runs combine the SNP data with performance data. It is still important for breeders to submit as much performance recording as they can.”

The benefits of single-step Breedplan evaluations are:-

  • Genomic information will contribute to all traits that have EBVs calculated within the main multi-trait Breedplan analysis.
  • Unknown parents may be identified (providing animals have genomic information available).
  • Genomic information contributes not only to EBVs of genotyped animals but also contributes to EBVs of their relatives (eg parents, progeny).
  • With a traditional pedigree based approach, the relationships between animals are determined by pedigree alone. For example, pedigree would predict that the genetic relationship between full siblings (ie animals with the same sire and dam) is 0.5. This means that full siblings are predicted to have 50% of genes in common. In Single Step Breedplan, SNP genotypes are used to determine the actual degree of relationship between individuals. In the case of full siblings, this may now vary from 0.35 to 0.65 – rather than 0.5 as would be assumed in a traditional approach to genetic evaluation. This will allow for improved accuracy in the EBVs calculated.

Megan says a SNP test is carried out on a tissue sample by Neogen, PBBs partner in DNA. She says the TSUs reduce the possibility of sample contamination and are more efficient for testing.

“TSUs are the preferred sample.”

She goes on to explain they are generally wet samples and the tubes have a solution in them to help preserve the sample and they can be tested up to 12 months after being collected.

“Ideally they should be kept chilled - but not frozen. Definitely not frozen,” she says. Room temperature is acceptable too.

Megan says SNP testing will help improve EBV accuracy as it will provide more markers than the older microsatellite DNA testing technology.

Another bonus is that with PBB handling DNA, it can all be loaded directly into Breedplan, regardless of whether the breed is concluding single step group runs or not.

PBB is a beef breeders one stop shop. We can register animals, breeders can buy their ear tags and TSUs for DNA testing with the results being automatically fed into Breedplan,” says Megan.

All breeders need to do is get in touch or download, complete and return the order form. She did stress that the order form, which is available here needs to be completed electronically. That means the order details can be merged with the ordering system seamlessly removing the risk of error.

“It makes the system more efficient and we can offer some technical support if needed with the form.” There may be a small fee.

PBB and Neogen offer breed test bundles to meet the needs of each breed but pricing is standard with the exceptions being for breed-specific tests.

“Neogen and PBB have customised the bundles to suit each breed. Some breeds have a horn/poll test or a dilutor test for example.”

She said that BVD can now also be included during the genetic SNP testing process and can be added onto the breed bundles.

Megan also noted Neogen have upgraded PBB breeders from the 50K test to the 100K test for the same price.

“They are always improving testing and more markers means more data.”

Following a DNA test, the results are returned to PBB and checked by staff and confirmed with the breeder before being loaded into ILR2/Breedplan.

PBB will run, check and provide reports on parent verification as well as any genetic conditions. The genomic profile data will be loaded into Breedplan and will then be used to calculate EBVs if the breed is running single step group runs.

“That means breeders can relax with confidence knowing their data is in safe and capable hands and won’t fall through the cracks, resulting in gaps in your performance recording data.”

To get started, email dna@pbbnz.com or call Megan on 06 323 0747.

To learn more visit http://www.pbbnz.com/dna_testing.php

TSUs At A Glance

The advantages of TSUs are:-

  1. Processed 6 times faster than hair*
  2. 99% success rate*
  3. Half the failure rate of hair*
  4. More efficient on farm
  5. Reduces the chance of a sample mix up
  6. Limits potential for sample contamination
  7. Consistent sample size and quality
  8. Less double handling of samples
  9. All in one solution
  10. Can be used for BVD testing

*on average, may vary depending on test requests & times of year etc

The process of collecting a TSU is fairly straight forward, however it does need some specialized TSU collection equipment.

TSU collection is different to ear notching as each TSU tube contains a liquid buffer solution that preserves the sample.

To get started you’ll need an applicator (this holds the TSU tube). The TSU sits in the small grooved cup and is held in place by a pair of spring-loaded clips. By squeezing the handles of the applicator together, the applicator will pick up the TSU cutter, remove the red connector and you’re ready to sample.

You will need an individual TSU for every animal you wish to sample. TSU’s can be purchased in boxes of 10 or 100 from PBB.

They are designed as a complete unit. Every animal gets its own cutter to reduce chances of contamination & the TSU self-seals as you take the sample. Every TSU unit has its own unique ID code on the side that can be cross-referenced to the animals ear tag/NAIT number. No two TSU’s carry the same ID code. It is important to record the TSU ID code AND the animals ID as you collect samples - these get provided to PBB.

Quick tips from Neogen for successful TSU collection;-

  • Read the instructions included with your applicator
  • Ensure that the TSU is lined up straight when loading into the applicator
  • Keep the TSU all together as one piece
  • DO NOT remove the red stopped until the cutter has been picked up by the applicator
  • Collect the sample from the centre of the ear
  • Gently tap the base of each TSU tube on a solid surface to ensure the sample is sitting in the buffer
  • Store samples out of directly sunlight
  • Refrigerate if you live in a hot area
  • DO NOT FREEZE your TSU samples prior to testing
  • Test samples within 12 months of collection