Genetics

ABRI implements advanced prediction model to support large numbers of genotypes for genetic evaluation

Beef Central, February 23, 2021

THE Agricultural Business Research Institute has become one of the world’s first users of the Single Step Genomic Best Linear Unbiased Prediction (GTBLUP) prediction method, which allows for an almost unconstrained use of genomic data in calculating Estimated Breeding Values.

GTBLUP is being implemented through ABRI’s advanced system of genetic evaluations, BreedPlan, to address the challenges faced by increasing rates of genotyping* for its clients.

The move was made possible through developments at the Animal Genetics and Breeding Unit (AGBU) led by principal scientist Dr Vinzent Boerner.

ABRI’s genetics research and development manager Dr Brad Crook said the issue that had arisen from increasing rates of genotyping was that when the number of genotyped individuals exceeds the number of Single Nucleotide Polymorphisms** (SNPs) in the genotype used, the process of evaluation does not always function properly.

This issue is not exclusive to BreedPlan, rather an industry-wide problem, regardless of service provider. Yet each provider approaches this constraint in different ways.

“Some do this by using a small number of SNPs and changing the model to a quite simple one,” Dr Crook said. “Others seek to keep the full genotypes, but reduce the genotypes used to priority animals in the evaluation,” he said.

The GTBLUP method has been implemented by BreedPlan to keep all the SNPs and all the genotyped animals in a way that seems to be unlimited in its capability.

Dr Stephen Miller, AGBU deputy director explains the significance of this milestone.

“The implementation of genomics has been the biggest development in livestock breeding around the world in recent decades. The increase in the rate of genotyping in beef cattle, including Angus cattle in this case, is truly remarkable. Equipping the industry with the latest technology to best harness the power of these new genotyping technologies is something AGBU is quite proud of, with the launch of GTBLUP within BreedPlan,” Dr Miller said.

In a test case scenario of around 400,000 genotypes and 50,000 SNPs per genotype, AGBU was able to demonstrate that the GTBLUP method was not only computationally feasible, but was able to outperform other single-step approaches in terms of processing times and computational costs.

AGBU made GTBLUP available within BreedPlan in October, and ABRI has implemented the technology for the Trans-Tasman Angus Cattle Evaluation. With GTBLUP available within BreedPlan, ABRI is capable of servicing any breeding organisation regardless of the number of genotypes and number of animals.

Hugh Nivison

ABRI’s managing director, Hugh Nivison, said ABRI’s decision to embrace GTBLUP, was a conscious effort to maintain position at the forefront of providers for genetic evaluations.

“This is an exciting opportunity for the inclusion of substantial amounts of genomic data in BreedPlan multi-trait evaluations,” he said. “This unlimited capacity provides BreedPlan users with an enormous amount of flexibility to submit as much genomic data as they want, without limitation,” Mr Nivison said.

So what does the development mean for beef producers?

Genetics Research and Development Manager, Dr Brad Crook said as far as he was aware, there were no other beef evaluation services using this approach in large scale multi-trait and multi-country evaluations.

“With some genotyping companies now offering 100K products, our implementation of GTBLUP means we can continue using in our Single-Step BreedPlan evaluations the full SNP result available per animal and all genotyped animals available,” he said.

“Using the genotypes in this way makes best use of the density of genomic tests being purchased by seedstock breeders – if they pay for 50K, we will use their 50K, and if they pay for 100K, we will use their 100K, and so on.”

Some evaluation services only use around 2K of SNPs, regardless of what density of test the breeder has opted to pay for, while other services might use all genotypes, though not use them all equally.

“In contrast, BreedPlan is striving to utilise all SNPs and all genotyped animals to their full extent in the evaluation,” Dr Crook said.

 

* The process of determining differences in an animal at a DNA level

** The building blocks used to analyse DNA

To find out more about GTBLUP and BreedPlan, readers can contact ABRI through its website – click here to access.

 

 

 

 

 

 

 

 

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  1. Mike Introvigne, February 23, 2021

    Good to see ABRI finally catching up to the tail of the beef genomic peleton.

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