Genetics

Weekly genetics review: What are the key differences in genetic information available in 2020?

Genetics editor Alastair Rayner, October 13, 2020

In 2020, Shorthorn catalogues offered breeding values generated by IGS at sales across Australia. Understanding the difference between Breedplan EBVs and IGS generated EPDs (Expected Progeny Differences) has been a challenge for many producers to address.

AS THE 2020 bull selling season starts to draw to a close, many people will look back over a year that has become notable for its extreme variability.

No doubt many will reflect on the records prices seen across breeds throughout the country as well as the challenges of adapting to a sales environment restricted by a global pandemic.

These and other reflections on sale numbers, the rebuilding of the national breeding herd and other areas may well occupy much of the post-2020 selling season reflections.

However, there are other changes and lessons that breeds, and breeders are considering, which may have longer and more significant impacts on the face of the seedstock sector in years to come.

Options emerge in performance recording

The way genomic information and performance records are gathered and presented in Australia now includes two sources of reporting.

For many years BreedPlan was the only source of performance recording used in Australia, with EBVs published for most breeds. In recent years the establishment of International Genetic Solutions (IGS) has offered an alternative way for breeds to collect and analyse genetic and performance data to develop breeding values.

As highlighted last year, the Shorthorn breed made the decision to move to the IGS system.

While the move by Shorthorn Beef has attracted much of the attention, there are other producers who have also taken up the opportunity to submit data and receive breeding values generated by IGS.

In response to last year’s overview of the Shorthorn move, Mike Introvigne of Bonnydale Black Simmentals in WA pointed out that in 2018 Bonnydale had genomically profiled its entire stud herd with the American Simmental Association (ASA), utilising IGS, and has continued to genomically profile every calf since.

In its February 2018 sale, Bonnydale provided potential buyers with Genomically Enhanced EPDs (Estimated Progeny Differences) via ASA, the first seedstock operation in Australia to do so.

In 2020, Shorthorn catalogues offered breeding values generated by IGS at sales across the country. Understanding the difference between Breedplan EBVs (Estimated Breeding Values) and IGS generated EPDs (Expected Progeny Differences) has been a challenge for many producers to address.

Given the uncertainty felt by many in the industry regarding the two systems now in use, it’s worth spending some time considering the key differences, and what that may mean moving into the 2021 breeding season.

BreedPlan remains the most widely used system in the Australian seedstock industry. Developed to provide the Australian beef seedstock and commercial industry with a scientifically based approach to genetic evaluation, BreedPlan reflects traits that are relevant to the Australian domestic beef industry and the various parameters sets used are derived from Australian performance data.

Dr Brad Crook from Agricultural Business Research Institute in Armidale highlights that these traits can be varied to ensure the breed-specific relevance of the EBVs.

He said there had been several MLA-funded initiatives over the years to demonstrate “proof of profit”, an evaluation of how well the BreedPlan EBVs predict actual differences in progeny performance in different Australian environments. These initiatives provided direction for the ongoing development of BreedPlan.

One of the most significant developments in BreedPlan has been the inclusion of genomic information. For Herefords, Angus, Brahman and Wagyu breeds, genomic information is included within the BreedPlan analysis, along with traditional data sources collected on-farm, through linkages to progeny, siblings and pedigree. The method used to undertake this incorporates all available information includes determining how animals are related gnomically and to then use this Genomics Relationship Matrix (GRM) in the evaluation.

This is known as Single-Step Genomic Best Linear Unbiased Prediction (GBLUP), and is the approach used in BreedPlan as well as the evaluation of other Australian livestock species and other international companies, such as Angus Genetics Inc.

At a user level, sorting bulls in a catalogue prior to sale, the only noticeable change to EBVs has been the increase in accuracy for many traits where genomic information has been included in the evaluation.  This tends to see some EBVs change value with greater accuracy, however increased accuracy does increase confidence of users in ranking bulls on their suitability to individual environments and market objectives.

Dr Crook also highlights the importance of the BreedPlan structure for the broader industry.

“Within our systems, development of new traits and enhancements to analytical models are underpinned by considerable investment of research funding, primarily from Meat & Livestock Australia,” he said.

“This means that the science behind BreedPlan remains open to scrutiny by MLA, the wider scientific community, and the users of the BreedPlan system – the Australian beef industry.  So, while we know that BreedPlan will deliver tangible outcomes for the industry, it does mean that changes in services such as BreedPlan are generally introduced over a longer timeframe compared to alternative international providers.”

There can be little doubt the ease in which genomic information can be collected and analysed has been a “game changer” for the beef industry. The opportunity to compare Australian genetics across international boundaries is seen by many in industry as a key outcome.

The IGS collaboration of 17 North American breeds does allow Australian genetics to be compared directly with cattle in other countries.

A number of breeders were approached for their thoughts on the ability to compare cattle in this way. While none wanted to be quoted directly for this article, there was cautious approval of the benefits of looking at how their cattle may fit within an international population. As one central western NSW breeder said, “Comparison across countries should keep the breed progressing.”

However, Dr Crook highlighted the importance of recognising that international providers are defined for their specific location’s beef industry, with models, traits and parameters based on an overseas locality.

“It remains unclear as to how these models would assist Australian producers in breeding more productive and efficient genetics for an Australian market,” he said.

Understanding the IGS system

For many producers, the question remains how does IGS work? The system uses BOLT (Biometry Open Language Tools) to undertake its genetic evaluation.

Unlike the single-step method used within BreedPlan, the analysis does not use all available information collected and provided by breeders. Instead analysis is done through a Marker Effects Model and assumes only around 2000 markers are required to provide the information needed regardless of breed and trait.

One of the key difficulties in explaining the underlying differences between the two methods of modeling (Single-Step and Marker-Effects) is an ability to compare the two systems on an equal basis. Single-Step model has been widely reviewed and validated by the wider research community. The same cannot be said for the Marker-Effects model as used by IGS, because the small sub-set of markers actually used is not reported publicly.

As an international system, this means producers who are working through catalogues to rank bulls will see EPDs published in imperial units rather than the metric system used in Australia.

While many EPDs report similar traits to those recorded in BreedPlan, producers do need to note these operational differences as well as considering the accuracy and ranking of animals against these traits. It also should be remembered that as an international system models, traits and parameters for analysis are based on an overseas locality.

A key part of the 2020 season reflection will be how well these models are assisting Australian producers in breeding more productive and efficient genetics for an Australian market.

 

Alastair Rayner is the Principal of RaynerAg, an agricultural advisory service based in NSW.  He regularly attends bull sales to support client purchases and undertakes pre-sale selections and classifications.  He can be contacted here or through his website www.raynerag.com.au

 

 

 

 

 

 

 

 

 

 

 

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Comments

  1. Steve Taylor, October 14, 2020

    Without a full understanding of the higher human purpose that technology is striving to serve, we will become victims of our own technology. ( Professor SEO, A & M University Texas. )
    When will we see some real commercial benefits for our commercial beef industry from this maze of scientific algorithms ?

  2. Garry Gillett, October 14, 2020

    Lancaster Simmentals in South Australia have also been using EPD’s from the ASA/ IGS for many years.
    I believe the IGS system using EPD’s is better than Breedplan, especially for those using imported semen & embryo’s. Using Breedplan we must wait for a couple of seasons calves on the ground before we can get any meaningful data on them.

  3. Martin Gomez, October 14, 2020

    “As an international system, this means producers who are working through catalogues to rank bulls will see EPDs published in imperial units rather than the metric system used in Australia.” I always thought the metric system was the world standard.

  4. Paul D. Butler, October 13, 2020

    “No amount of technology (EPDs, Genomics, Phase C tests) can replace astute observation and common sense.”

    “We don’t need meaningless and confusing “scientific” information (EPD’s, EBV’s) when OBSERVATION can tell us so much more.”

    Johann Zietsman

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