ABRI_Services_03

ABRI Implements Single Step Genomic TBLUP (GTBLUP) to Support Large Number of Genotypes for Genetic Evaluation

by PostUncategorized

No strangers to innovation, Agricultural Business Research Institute (ABRI) have become one of the world’s first users of the Single Step Genomic TBLUP (Best Linear Unbiased Prediction) (GTBLUP) method, which allows for an almost unconstrained use of genomic data in calculating Estimated Breeding Values (EBVs).  The implementation within BREEDPLAN addresses the challenges faced by increasing rates of genotyping for ABRI clients and 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 explains “the issue that has evolved from increasing rates of genotyping is 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. Others seek to keep the full genotypes, but reduce the genotypes used to priority animals in the evaluation.

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 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.” 

In a test case scenario of around 400,000 genotypes and 50K 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 2020 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 organization regardless of the number of genotypes and number of animals.  ABRI have embraced GTBLUP to maintain their 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. To find out more about GTBLUP and BREEDPLAN please contact the ABRI team.

 

Charolais

Outstanding Progress by Hungarian Charolais

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The National Association of Hungarian Charolais Cattle Breeders is the ABRI’s first central European BREEDPLAN client to make use of the BREEDPLAN genetic evaluation system for their national population. In addition, they are the first central European client to make use of ABRI’s genomic data storage system with a goal of incorporating this genomic information into a Single-Step BREEDPLAN evaluation.

The investment made by Hungarian Charolais breeders in the genotyping of seedstock animals has resulted in them having the fifth largest genomic database hosted by ABRI among ABRI’s BREEDPLAN clients, globally. To add to their investment in successful breeding, the National Association of Hungarian Charolais Cattle Breeders released three economic indexes using BreedObject v6.2 earlier this year.

ABRI are thrilled to pursue this collaboration with the National Association of Hungarian Charolais Cattle Breeders and continue to pursue ongoing research and development throughout the European beef breeding industry.  

Lip

ABRI & CSIRO Develop Next Gen LIP

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The Livestock Information Platform (LIP) is a secure cloud-based tool that enables the rapid development of information systems to store and analyse animal production, breeding, health, and welfare data.

LIP was created to address an industry-wide issue, for many primary producers who gather phenotype and productivity information on-farm. Producers collate this data with on farm software systems, to produce reports and make decisions about farm management accordingly. However, productivity performance is also affected by other factors that are not readily captured in a form that is able to provide additional value for the producer, such as weather information, and carcase feedback.

The solution? ABRI, together with the Commonwealth Scientific Industrial Research Organisation (CSIRO), have designed and built an internet “cloud” based system that supports a data storage and analysis system optimised for the needs of the livestock industry.

Data can be uploaded, downloaded, and analysed using the applications that we provide, or third-party developers can develop their own applications, accessing the system via the LIP Gateway. Raw data can be efficiently processed within the platform itself.

The positive economic impact of LIP includes a significant shift in the way systems can be developed to address data collection, storage, and analysis of farm, corporate or industry data. As new applications are developed, LIP’s capabilities will also continue to grow.

If you’re interested, please get in touch to learn more about the tool and how it could sit behind your next data management project.