Genotyping and phenotyping for accelerated genetic improvement in northern Australia

This project aims to better describe the population genetics of three major tropically adapted beef cattle herds which will enable bull breeders and commercial producers to make better informed decisions regarding bull purchases and the genetic direction of their herd. This will be achieved by:

  • genotyping key industry sires to rapidly increase the accuracy of reproduction EBVs
  • recording high utility female reproduction phenotypes to drive increased rates of genetic gain
  • enhancing adoption of genomic influenced genetic evaluation for female reproduction traits

Queensland and Northern territory research station cow herds and industry sires will be used to achieve these goals. The research station herds will be used to intensively measure female reproduction traits on large numbers of females. These females will include the daughters (generated through AI) of highly influential sires of each breed. The research herds will provide phenotypes on the breeds run together thus also allowing for the development of genomic prediction and selection that will be effective across breeds. Genetic linkage will be generated across industry and research herds thus providing a way by which superior genetics identified within each breed can be directly compared and be readily available to industry.

The data generated from this project will increase our understanding of the genetics of reproduction, and allow improvements in trait definitions, use of correlated traits, better models and methods of genetic evaluation. Importantly, as our genetic evaluations move towards the use of genomic relationship matrices and single-step methodologies (Misztal et al. 2009) the data (and research) from this project will be pivotal in driving this new era of genetic evaluation in Australian beef cattle. While the Beef CRC genotyped and phenotyped a large number of tropically adapted cattle for female and male reproduction traits, these did not include Santa Gertrudis or Droughtmaster cattle, a gap which this projects is addressing. The project will put the northern breeding industry in a unique situation to take immediate advantage of this major change to the BREEDPLAN genetic evaluation system expected in the next 12 months.

The single-step procedure represents a seminal change in the evolution of the BREEDPLAN genetic evaluation system. Single-step evaluations allows simultaneous use of existing pedigree relationships (for the majority of animals) in conjunction with a genomic relationship matrix (GRM) of genotyped animals from high density SNP profiles (e.g. 20K or 50K). This simplifies, and is equivalent to, the use of genomic information currently using estimated genomic breeding values (GBV) derived from genomic prediction equations. However, the single-step procedure allows the evaluation to be continually updated as additional phenotypes and genotypes are added. Currently, the existing pedigree relationship matrix allows differences in phenotypic performance to be transmitted to relatives whereas the single-step (and GRM) will allow genetic differences between individuals to be influenced through their degree of genomic relationship. Therefore animals with large amounts of phenotypic information when genotyped will influence the EBVs and accuracies of any animal that is genotyped and genomically associated with this high accuracy individual.

The success of the project will be quantifiable by calculating the increased number of animals in the breeds with higher accuracies for reproduction EBVs as a direct result of the phenotypes and genotypes generated in this project. In addition, the amount of genetic variation described by the genomic information will be able to be determined from these data. The genetic trends, will also be a powerful tool to allow the herds to be benchmarked against each other and the breed allowing changes to be quantified, for not only reproduction traits, but all traits including overall genetic merit (i.e. $indexes).

When: October 2013 to December 2018

Where: Brian Pastures Research Station, Queensland; Douglas Daly Research Station, Northern Territory; Spyglass Research Station, Queensland

Contact: Dr. David Johnston E:, Tim Grant E:, Tim Schatz E:

Collaborators: AGBU, University of New England, Department of Agriculture and Fisheries, Northern Territory Department Primary Industry and Resources, University of Queensland

RD&E objectives: Enterprise viability: Increasing cost efficiency and productivity and profitability

Industry priority: Reproduction

Useful links: For more information about Beef CRC research, please visit the Beef CRC legacy website.