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Better breeding values

Breeding values represent a prediction of the genetic merit of an individual animal and are commonly generated for economic, environmental or welfare related traits. One way to improve the accuracy of breeding values earlier in the animal’s life than what would otherwise be available is via genomic prediction. Calculating genomic breeding values in this way increases the rate of genetic gain in the target population, and has the potential to help make valuable genetic improvements across New Zealand’s biological industries.

Genomic selection can be employed using a range of genotyping methods, and the volume of data available is increasing dramatically. But genomic prediction can be daunting, particularly for some species other than sheep and cattle in New Zealand, because there is a lack of cohesive and straight-forward statistical and bioinformatics techniques and resources available.

Dairy cattle

Photo: Dairy cattle by Dave Young

There is a need for better approaches to deal with the sheer amount of data and to better use the data we already have. New technologies are also needed to ensure our biological industries benefit from the increased accuracy and are competitive internationally.

Working with industry leaders, this project will develop new statistical approaches, new data sources and produce and apply tools for breeding value prediction. 

The approaches will be made accessible across all primary industries, so that they can cost-effectively adopt genomic selection to suit their own circumstances. They may also be relevant to conservation, where genomic management of endangered species will require similar support. 

The project also includes development of breeding objectives for livestock improvement from Māori world view perspectives, undertaken as a PhD study.

This project brings together researchers from the plant, sheep, beef and dairy industries via two Crown Research Institutes, two universities, Livestock Improvement Corporation (LIC), AbacusBio Limited and industry, as well as crucial skills and capabilities to complement other Genomics Aotearoa projects. Two postdocs, managed across institutions, will be employed to build capability.


  • Novel approaches to imputation of large datasets to whole genome sequence
  • Identification of highly informative sequence variants from genome-wide association studies
  • New approaches to breeding value prediction using sequence variants
  • Effective co-operation between GA partners and industry stakeholders


  • Professor Dorian Garrick (Massey University) – co-lead researcher
  • Dr Michael Lee (University of Otago) – co-lead researcher
  • Dr Phil Wilcox (University of Otago)
  • Dr Shannon Clarke (AgResearch)
  • Dr Rudiger Brauning (AgResearch)
  • Dr David Chagne (Plant & Food)
  • Dr Christine Couldrey (LIC)
  • Dr Neville Jopson (AbacusBio)
  • Andrew Hess (AgResearch)
  • Yu Wang (Massey University and Livestock Improvement Corporation)
  • Brittany Jones (University of Otago)
  • Joshua Rich (University of Otago/AgResearch)