LIC launch SSAM – a step towards better animal predictions

LIC has invested more than $70 million over the last three decades to increase the accuracy of its animal evaluation system with improved data providing better predictions for breeding worth for our farmers.

February 2020 saw LIC release its new Single Step Animal Model (SSAM) which uses animal genomic information in a more efficient way – combining ancestry, phenotypic and genomic information all in one single step. This improves the efficiency of LIC’s breeding scheme, as we work to identify the bulls whose daughters will be the most profitable and efficient cows on farm.

LIC dairy cows grazing

Differences currently exist between NZAEL BW, which does not include genomic information, and LIC’s genetic merit outputs (gBW), which do. LIC gBW uses the new LIC SSAM and contain a component of genomic information included for breeding values and breeding worth, which remains throughout the lifetime of an animal, including that of daughter proven bulls.

Herd Improvement Technical Manager for LIC, Rachel Bloxham, explains “The more cows that are genotyped, the more information we have, and the more accurate our predictions will become to ensure we continue to support breeding profitable and efficient cows that will convert feed into profit for dairy farmers now and for the future. The new model is perhaps the greatest step forward in animal evaluations since Breeding Worth was introduced in 1996 – it’s an exciting development.”

FAQs about the Single-Step Animal Model:

Here are some commonly asked questions. If you have others, please contact your local LIC representative.

What’s different between the new model to the old model?

A key aspect is the way data is analysed in the new model. The Single-Step Animal Model analyses the complete New Zealand dairy population simultaneously, (approx. 30 million deceased and current, genotyped and non-genotyped animals), allowing the benefit of genomic data to flow through a larger proportion of the population.

Why do bulls have a different BW on LIC’s website compared to NZAEL’s?

While both evaluation systems (NZAEL 2.0 and SSAM) utilise the same ancestry and phenotypic information, the LIC Breeding Worth, (gBW) and Breeding Values contain genomic information as well, whereas NZAEL’s results currently don’t.

Why can an animal’s values be affected by genomics when the animal hasn’t been genotyped?

Ancestry and known relationships to an animal play a critical part in any animal evaluation system. This is no different with the inclusion of genomic data. The new Single-Step Animal Model uses all information (production, TOP, genomics, pedigree) for all animals (all breeds, historical, current, genotyped, non-genotyped) in one single step, resulting in the flow of genomic information across multiple generations, up and down the pedigree.

Is the new model better than the previous model

Yes. Validation by LIC scientists of the 11-code, 12-code, 13-code and 14-code cohorts of LIC’s Sire Proving Scheme , (these animals now have daughters with milk recording data),  shows use of the new Single Step Animal Model has resulted in an 8% increase in genetic merit prediction accuracy (i.e. comparing genomic predictions to actual daughter proofs).

Does the gBW of bulls increase or decrease with the inclusion of genomic information?

Genomic data is just another piece of information used in the estimation of an animal’s genetic merit. The inclusion of genomics can result in an animal’s gBW moving up or down.  The outcome is more reliable estimates for all genomic bulls.

Why does LIC still include genomic information in daughter proven bulls?

The inclusion of genomic information with bulls that are already daughter proven gives LIC additional information on the slower maturing traits like fertility and longevity.

As a bull’s daughters complete additional lactations and we gain more phenotypic data, the amount of genomic influence decreases.

For traits where the daughter phenotype is measured later in life, it takes longer for the information provided by genomics to become dominated by phenotypic data.

What measure is LIC marketing their bulls on?

LIC is marketing bulls on gBW. We will continue to select bulls on a wide range of traits with the intention of providing dairy farmers with the best bulls to meet their individual breeding objectives.

Was the earlier genomic information inaccurate?

No – the earlier models produced positive results, as reflected in the number of LIC bulls currently featuring on the RAS List.

These bulls were bred and purchased on the previous genomic models. As the science advances and our dataset of genotyped animals keeps growing, we will continue to make iterations to the model to improve the accuracy of genomic selection.

How does genomic data improve accuracy of prediction of the genetic merit for an animal?

A reference population of well recorded animals that have been genotyped, including both females and proven males, which allows us to predict the impact of various SNP effects.

Genotyping provides us with information on the alleles/genes an animal has actually received from its parents and the known SNP effects can be used in its evaluation. LIC’s reference population comprises over one hundred thousand animals.

Genomics provides an estimate of what ‘good’ or ‘poor’ genes the animal inherited well before the animal’s own performance, or that of her progeny, can be measured. Where we don’t have lots of progeny (which is generally the case for cows), genomics helps us better understand what proportion of an animal’s performance superiority will be inherited by their offspring.

If you have other questions please contact your local LIC Farm Solutions Manager

by Katrina Younger
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