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A sheep pangenome for the benefit of primary production 

In Aotearoa you don’t have to be a farmer to know that not all sheep breeds are the same. The sheep pangenome project (officially the Ovine Pangenome project) aims to deliver high-quality genomes for 16 sheep breeds, chosen for their divergent and important traits.

It is part of the Genomics Aotearoa goal to develop gold standard high quality assemblies, to better predict traits of economic importance.

What we are doing

This pangenome project aims to deliver a more detailed understanding of the genes that influence productivity in sheep, in turn helping the sheep industry in Aotearoa stay ahead of future needs for meat and wool. 


The sheep pangenome is an international collaboration headed by Dr Brenda Murdoch from Idaho University and funded by the USDA-NIFA. Aotearoa is represented by Shannon Clarke and Rudiger Brauning from AgResearch. 

The project has direct local industry input and alignment. The mating, raising and subsequent tissue collection (parents and offspring) were provided as in-kind contributions by local industry partners. 

So far, the project has identified genomic regions associated with a range of phenotypically distinct and important traits in different breeds. The assembly of multiple genomes overlaid with information from phenotype datasets (such as transcription and methylation profiling), enables the researchers to compare genomic regions associated with traits of importance. 

“This capability will allow us to fill in the gaps in genomic knowledge, to analyse genetic variants to understand traits and take full advantage of the diversity within local sheep breeds,” Shannon said. 

The impact

Pangenome assemblies provide fundamental resources needed for industry to use functional genomics as a tool. 

For sheep, it will support more accurate prediction of traits and improved breeding strategies. 

“It’s about understanding the genomic architecture behind phenotype, so we can take the breed in whatever direction we want to go. This enables more accurate selection now, but also helps answer questions for the future, such as how breeds will adapt to a changing environment – how to improve breed resilience, and how to maintain production under the predictions of climate change,” Shannon said. 

The sheep pangenome will also contribute to comparative studies among species, while complementing and leveraging the pangenomes being constructed for cattle, and other ruminants.

Read more about High Quality Genomes and Population Genomics here