DNA based calf registration – Not only possible but also feasible

‘Mark Waters, ICBF goes through the next step for animal traceability’. In 1996, Ireland became world leaders in the traceability of cattle from birth to factory when the Cattle Movement Monitoring System (CMMS) was introduced. This system required all farmers to apply identification tags to each calf at birth and register this unique number in the Animal Identification and Movements (AIM) database. The farmer is then issued a passport for each animal (famously known as the “blue card”) and must notify AIM each time the animal changes hands.

This system revolutionized the traceability of cattle across the country allowing an accurate picture of the national herd to be taken and monitored on a continuous basis. It has served Ireland very well, accurately tracking over 2 million new calves each year and similar systems have since become the standard all around the world.

Move on 20+ years and we see the advent of a new technology (genomics) which now has the potential to enhance these initial groundbreaking traceability systems, by giving additional assurances around areas such as ancestry and gender.

ICBF and DAFM have been collecting genotype (DNA) samples on cattle since 2009. Over 350,000 new animals are sampled each year with ICBF now storing almost 2 million genotypes in the central cattle breeding database.

The genomic data stored by ICBF is used to verify the parentage and sex recorded by breeders at registration and identify errors. Parentage errors (mainly sires) are identified in up to 15% of cases, with 0.5% errors in the recorded sex. The parentage errors are invariably due to simple mix-ups in AI sires versus stock bulls, or perhaps the running of multiple stock sires. The genomic data is also used to predict (where possible) the correct parentage where an error is identified. Where a sire error is identified, the correct sire can be identified in up to 70% of cases, based on genotypes now stored in the ICBF database. In time, this will grow to 100%.

Correcting these errors leads to more accurate genetic indexes (Beef Euro-Star, EBI etc.), helps avoid accidental inbreeding, corrects mistakes in pedigree certs and overall makes the entire system more accurate. That said, it can also lead to additional work and headaches for the farmer in question such as updating blue cards, updating pedigree certs, genetic indexes changing after selection for breeding or sale etc.

The older the animal is when genotyped, the greater the potential knock-on of discovering these errors. The animal may already have progeny, who would then also be affected by the change. To minimize the impact of these corrections therefore, it makes sense to genotype animals as early in their life as possible.

The best solution by far is if these genomic samples could be taken at birth and incorporated into the registration process. Mis-recorded parentage and sex could then be corrected before any blue card or pedigree cert is printed making each animal 100% DNA parentage verified from birth. Sires could also potentially be added to thousands of animals who are currently being registered without a recorded sire.

To this end, ICBF and DAFM have been conducting DNA registration pilots since 2018, beginning with just 18 herds in year 1, increasing to 35 in year 2 and now 270 herds for spring 2020. These herds have followed the following simple procedure:

  1. The calf is tagged at birth leaving 2 separate tissue samples (1 for DNA and 1 for BVD)
  2. The 2 samples are posted away separately to the relevant labs
  3. The farmer records the calving details as normal, but the registration details are temporarily held pending the results of the DNA test.
  4. When the DNA results are returned (about 1 week later) the farmer reviews, corrects any errors found, and completes the registration with the DAFM AIM system.

Over the course of the pilots to date over 4,000 calves have been registered in this manner with up to 20,000 expected to be registered in Spring 2020.

Improvements have also been made during these pilots. Work had been undertaken to integrate DNA registration into Farm Software packages and the testing of double tissue national tags, removing the need for additional button tags or hair-cards for DNA samples.

Though not without its challenges, these pilots have been highly successful and have proven that DNA based calf registration is not only possible but also feasible.

If these DNA Registrations were to become the standard nationally, there are lots of additional benefits to the industry as whole. Ireland would once again rise to world leaders in the area of traceability from farm to fork; traceability that could be proven beyond doubt at any link in the chain with a simple DNA sample from the product. The benefits of this can be evidenced from the roll-out of the technology within the Irish pig industry. This level of traceability opens up possibilities with new technologies such as blockchain.

The accuracy of the EBI and Euro-star indexes would also increase. More animals with genotypes mean that genomic predictions for traits would be more accurate. In addition, it would help us more quickly identify superior outlier animals for key traits of importance for the future, such as methane output and health/disease traits.  Having 100% accurate parentage for all animals would mean all animals would be credited with the correct performance data, all of which would lead to increased rates of genetic gain, resulting in increased economic and environmental benefits for the industry.

Fraud and cattle theft would become extremely difficult. Cross compliance questions on issues such as twin calves would already be answered. Processors could introduce incentives or bonuses for the use of better-quality sires confident that they would be getting what they are paying for. Similarly, the days of calf rearers buying a black calf expecting it to be Angus or Limousin from a dairy cow, to subsequently find that it was Jersey bred would disappear, resulting in increased trust in our currently challenged dairy calf to beef supply chain.

All in all, the potential of DNA based calf registration for the overall Irish AgFood industry are significant. One of the key challenges for Ireland is the cost associated with genotyping the national herd to allow a DNA based calf registration on a widespread level. This will require all stakeholders in the industry to come together to see how that can be achieved and over what period of time. Thankfully our government and industry acknowledge the benefits of DNA based registration, which bodes well for Ireland continuing to be world leaders in production of safe, high quality and environmentally sustainable food for an expanding global population.