Evaluating genetic evaluation systems

Ian McLean, Bush Agribusiness, 01/09/2023

Following on from genetics presentations at last week’s Northern Australian Beef Research Conference in Darwin, agribusiness consultant Ian McLean from Bush Agribusiness offers some observations about genetic evaluation systems…..   



BEING able to understand the genetic information available on individual bulls and seedstock sources is an essential skill for the modern cattle producer – however it can take some refreshing to get back up to speed on the language, terminology and numbers when bull-buying time comes around each year.

This is made harder by the increasing number of traits evaluated, EBVs and selection indexes published and, more recently, genetic evaluation systems being promoted to breeders in our industry.

Since we released the Top Studs publication, we’ve had a number of queries on why we used BreedPlan as the method for identifying the top studs within each breed. This, along with some client work around bull selection, and discussions at the recent Northern Beef Research Update Conference has prompted me to think that there is a need for an industry discussion on the genetic evaluation systems available.

The three main ones I’ll discuss (from a northern perspective) are BreedPlan (EBVs), Genomic Breeding Values (GBVs) and International Genetics Solutions (EPDs).


BreedPlan is an industry-owned genetics evaluation system and, of the three systems listed, is the one I am most familiar with.

All of our seedstock clients use BreedPlan., we’ve taken groups of commercial producers down to Armidale to meet with the team there to build their understanding of the system, the science underpinning it and how to apply it. Within BreedPlan there are some very talented scientists, geneticists and researchers working to improve industry.

I’m aware therefore that I may be biased towards BreedPlan, as I view it as a world leading genetic evaluation system, developed for and by the Australian livestock industry which is underpinned by significant published research and development to ensure ongoing improvement.

It is not, however, perfect and this is something we address in the Top Studs report.

One limitation is that it is presently breed-specific, and genetic comparisons can presently only be made within individual breeds. This makes it difficult for commercial breeders assessing multiple breeds, as they cannot compare bulls or seedstock sources across breeds.

However, if they select from the top half of the bell curve of breeds under consideration (which Top Studs lists), then they will likely be on the right track.

The need for a multi-breed EBV was a topic that was raised in a very informative genetics session at last week’s NBRUC conference. The delegates were told that it requires extensive data from animals of multiple breeds being run under the same conditions and that this was currently being done in research projects in both the north and the south, with the southern one close to finalisation as recently reported by Beef Central.

A strength of BreedPlan is its rigour and robustness; the consequence of this is that a new development, such as a multi-breed EBV, is not going to be introduced until they are confident that it is sound and has been rigorously tested.

Another limitation is that not all studs using BreedPlan provide sufficient phenotypic measurements to get the most out of the system, which reduces the accuracy of their genetic data. Assessing this is part of the due diligence that commercial buyers must undertake when evaluating potential seedstock sources.

Genomic Breeding Values

Genomic Breeding Values are available for northern producers from the Northern Genomics project undertaken by another team of talented scientists, geneticists and researchers at Queensland Alliance for Agriculture and Food Innovation for Meat & Livestock Australia.

The project measured traits from 30,000 heifers of various breeds and breed mixes running on commercial properties in northern Australia. The heifers were all genotyped and the results used to derive GBVs for a number of traits including age of puberty, P4M (ability to re-conceive whilst lactating), weight, and body condition score. The accuracy of the GBVs is 0.5 for heifer puberty and 0.45 for others. This is similar to the BreedPlan EBV accuracies derived purely from genotypes.

The significant advantages of GBVs are that they are multi-breed (northern only) and do not require pedigrees. GBVs offer great potential in commercial applications and I see three main uses for them:

  • Provide a summary of your current genetic profile.

This is done by selecting a sample of your herd (e.g., 50 of your youngest age group of heifers) and conducting genomic tests of them (through tissue or hair sample). This is an excellent way of getting an understanding of your current profile and can help in deciding what genetics to introduce into the herd and is recommended for northern producers.

  • Selecting (or culling) home-bred bulls

Profiles of individual animals can be used to determine which animals to keep or sell. This will help inform the process, however, whilst the accuracy is good it will not be as good as EBV’s from seedstock sources who are using BreedPlan to its full potential. If this is done, I would prefer to see testing of bull calves from females who produced weaners in at least their first two years of reproducing.

  • Selecting (or culling) replacement heifers.

The GBVs are a potentially useful tool if a decision on selling younger heifers has to be made. Research has shown that female reproductive performance on their first two joinings is an excellent predictor of lifetime performance. This means the bulls do an exceptional job of identifying the fertile ones, so let them if you can. Those that do end up being culled have gained kilograms and value in the meantime.

International Genetics Solutions

International Genetics Solutions (IGS) is an international multi-breed genetic evaluation system used by breed societies across America and Canada. Recently a couple of Australian breed societies have moved over to it also.

It provides a single set of measures for all breeds, allowing direct comparison of animals and seedstock sources across breeds using the system.

The main question I have regarding IGS and EPDs is whether they are applicable and suited to Australian production systems. We looked at some IGS data recently for a client looking to buy bulls from a stud that had both BreedPlan and IGS data on their bulls. We compared the IGS Australian All Purpose Index against the relevant BreedPlan maternal index and found no correlation at all, which concerned me greatly.

It isn’t a question of which is wrong or right; the indices take all genetic information on an animal to produce a single figure that reflects its relative profitability within that production system. Therefore, I would expect there to be some correlation between the two.

This means bull buyers are going to get very different results depending on which index they use. We know that the BreedPlan index is underpinned by BreedObject and we can see what weightings are applied to the various traits within the index; which gives me confidence in it.

I have not been able to find equivalent information for the IGS index, such as how it is derived and what the weightings are. This is necessary information for a commercial producer to use in making an informed decision.

The lack of a direct fertility EPD also concerns me, given that fertility is a major profit driver, and opportunity, for many Australian beef producers.

There is an EPD for ‘stayability’, which is a measure of percent of daughters remaining in the herd at six years of age. There was an interesting paper presented on this topic at the NBRUC conference relating to a study of this measure within the NT Primary Industries’ Brahman herd. That herd, which is one of our Top Studs, has been selecting for fertility since 1994 and now has the fourth lowest (lower is better) Days to Calving (DTC) EBV of the top Brahman studs.

The study looked at the proportion of daughters in the herd over six years of age (stayability) over the 30 year journey of improved fertility, and found no increase in the measure, despite a reducing DTC by more than 10 days over the period.

This indicates that the Stayability EPD is not currently a measure that can be used with confidence to select for fertility in northern Australia.

Another limitation of EPDs is that there appears to be no Bos indicus genetics in their reference population.

My conclusion is that EBVs and GBVs are complementary genetic evaluation systems in the north.

GBVs lend themselves to on-property application by commercial producers. EBVs provide a useful and sound way for seedstock producers to describe and improve their genetics and for commercial producers to select genetics to introduce to their herd.


In a previous Beef Central article I suggested that seedstock producers are nominating themselves as industry leaders, putting themselves out there as people who are producing genetics that will improve clients herds.

With this comes the responsibility to be transparent about how their genetics will improve the bottom line of potential buyers.

I also proposed the following definition for transparency in seedstock production:

‘Objective genetic data relevant to Australian production systems, underpinned by quality phenotypic measurements presented in a way that allows valid comparison with peers.’

Based on my present understanding of EPDs, I do not think they allow this definition to be met, despite the appeal of a single set of measures that apply irrespective of breed.

I am all in favour of competition, it leads to better long term outcomes for consumers, however, it could be argued that a world-class, industry-owned genetic evaluation system for seedstock producers is a natural monopoly. I am loathe to be critical of any genetic data, as any may be better than none, however, producers must have confidence that the data they are using will help them achieve their breeding objectives.

From all of this, I have two questions for breed societies and individual seedstock producers who do not currently use BreedPlan:

  • How does your definition of transparency in seedstock production differ from the one suggested above?
  • How does the genetic evaluation system you use facilitate that transparency?

If you would like to provide a response, please do so as a comment to this article, or you could discuss a contributed article with the publishers of Beef Central.





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  1. HENRY CARTLEDGE, 21/09/2023

    Breedplan is a great tool or system. Just look at the quality of info you can get on a line of Angus sale bulls and the progress that individual Angus breeders have made over the years in their chosen traits. However, I think your off the mark with your criticism of the IGS.

    The whole point of these tools is to be able to compare traits of different animals by taking the effect of environment out. So, if we are happy to compare an Angus bull from QLD to one in TAS out of potentially hugely different production systems with breedplan, I think the argument against IGS based on whether it is suited to Australian production systems is wrong. There are many different environments and production systems in the US too. (where IGS originated). In fact, I’d go one step further and suggest a real strength of the IGS system is the huge database of numerous breeds across numerous countries.

    The problem I had with the quality of breedplan EBVs was not the tools fault, rather the quantity and sometimes quality of data going in. For smaller breeds the gains in information from the IGS system is immense. Additionally, we can compare different breeds and crossbreeds of varying percentages on the same base and with a similar accuracy of figures that the Angus enjoy.

    Stayability is the # 1 economically relevant trait in commercial cow/calf operations. It obviously includes fertility but it also includes any other reason a cow doesn’t make the 6 year mark. Therefore, improving the stayability of your herd will improve a range of traits including fertility, but not nesessarily in equal amounts.

    You stated in your article that you are biased towards breedplan and that is fair enough, however, some of the issues you raised for IGS are unfounded.

  2. Mike Introvigne, 19/09/2023

    As per my previous response to the article prior to the additional comments provided here on EPD’s by Ian McLean.

    “Objective genetic data relevant to Australian production systems, underpinned by quality phenotypic measurements presented in a way that allows valid comparison with peers.”

    I am not sure how Ian comes to the conclusion that seedstock breeders using IGS (EPD’s) don’t meet the above criteria. I certainly feel very comfortable with our data and how it is presented to our customers. I take offence to Ian’s suggestion otherwise. The best decision we made for our clients was using IGS to assist in providing relevant data for Australian production systems to help them advance their beef businesses. We DNA Parent Verify every calf and collect all possible data which is enhanced with Genomics and the progeny of our sires have never failed to fit market compliance for our customers.
    More informed research required on your part Ian, maybe have a conversation with the IGS team.

  3. Matthew Della Gola, 03/09/2023

    A good article even though it may be decisive. I think mike makes some fair counter arguments. My biggest concern with all of the ebvs and epds is the ability of the breeds societies to continually manipulate the parameters within the systems used. Ive witnessed bulls in the top 10% of the breed for growth as example be relegated to the bottom 10% at the stroke of a button. Only to benefit a certain few studs who flood the breed with high imf, no growth and bottom 90% nfi. Dtc from the studs that i deal with pay little to no attention to as its highly variable and inaccurate. I think we have hit a ceiling for some of our most productive traits and they know it so they are hell bent on manipulation to validate their breed. Im 38 years old and id be pretty sure my calves weaned at 9 months of age in 20 years time arent going to be 20kgs heavier. Cheers Matthew Della Gola

  4. Mike Introvigne, 01/09/2023

    As a Black Simmental seedstock operation we have been using IGS for neartly ten years and Breedplan for a very long time. We were one of the drivers for Simmental Australia to adopt IGS after our experience with both systems. IGS is far superior in our mind and delivers greater correlation to actual performance than Breedplan ever did. IGS also offered us the opportunity to utilise Genomics where Breedplan wasn’t able to provide this in a suitable timeframe.
    IGS is measured in Australian conditions and provides a much larger database for comparison. I agree a problem is that Bos Indicus cattle aren’t included especially since we are producing a northern composite alongside or Black Simmental and Simangus cattle. That data is slowly building and providing improved outcomes.
    It may suit your commentary to focus on Brahmans but I suggest you may want to conduct further research before more speculation.

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