From the Homestead

The announcement earlier this month by Neogen (GeneSeek) to establish an Australian genotyping laboratory on the Gatton campus of the University of Queensland (UQ) is great news for the sheep industry.  Over the next few months, as the new laboratory is established, there will be a transition from overseas testing of sheep industry DNA samples to the local lab.  This change will mean faster turnaround time and address what has been recognised as a major impediment for large-scale adoption of genomic testing in the Australian sheep industry.

The Sheepmeat Council of Australia coordinate a planning workshop for the Sheep CRC’s Essential Participants and industry stakeholders in Canberra on 6 October 2017.  The purpose of the workshop was to identify the structures, processes and programs that may be needed to take the place of key functions currently performed by the Sheep CRC, once the CRC winds up in June 2019. 

A further activity planned to facilitate a smooth transition prior to termination of the CRC is the first meeting of a working group to oversee the transfer of CRC data and products in the MLA fields of genetics and meat science for ongoing management by MLA.  The first working group meeting will be on 16 October 2017. 

The Annual Report for the last financial year has been completed and, following review by the Board, will be available for distribution by the end of October.  This important summary of progress against Milestones and Commonwealth objectives has again documented good progress towards meeting our objectives and confirms that we are well placed to deliver the outcomes and impact that were anticipated when the Sheep CRC was established in 2014. 

The Sheep CRC’s Participants’ Forum and Annual General Meeting will be held on 15 November 2017 at the Stamford Plaza Sydney Airport.

Enhanced sheep wellbeing and productivity

There has been very useful feedback provided by users participating in the pre-commercialisation trial of ASKBILL.  The suggestions made by producers and service providers using the beta-version have been reviewed and collated into a prioritised work schedule.  The aim is to complete these upgrades and improvements prior to the launch of Version 1. 

The team has also been conducting a number of workshops with service providers to understand the particular needs of this sector.  These discussions and workshop sessions have been most helpful. 

Work continues on the user-interface, further investigation into new functionality and on the computational and data management components of the system.  There have been some delays in the availability of the long term climate forecasts.

Overall there is good progress in developing and evaluating ASKBILL and plans for the commercial launch and follow up activities are well advanced.

Quality-based sheepmeat value chains

An important development for the meat program was a meeting on 28 September with the MSA Lamb Taskforce.  This meeting provided an opportunity to review progress and accuracy in cuts-based MSA grading for lamb and is part of the process of achieving industry adoption of the results of our recent research to improve grading systems.

Methodology being investigated for the measurement of intramuscular fat is currently focusing on near-infrared technologies (NIR) and imaging systems using hyperspectral cameras.  During the last month three new cameras have been evaluated and their performance against chemical fat measurements will be analysed in the coming months.  There are also encouraging results from the new NIR measurement systems.

The sensory evaluation work being undertaken in the US is in full swing and results are expected before the end of the year. 

Faster, affordable genetic gain

Progress over the last quarter can be summarised by the fact that we have submitted six papers to the World Congress for Genetics Applied to Livestock Production.  This conference is held every four years and is the most important conference in animal breeding.  These papers are truly world class and document recent research achievements. 

  • Highly accurate imputation of 46,910 Australian sheep with lower density genotypes up to whole genome sequence (WGS) with 31,154,082 (30 million!) imputed DNA variants. The mean accuracy of imputation of sequence data was 0.97.
  • Identifying important gene regions to increase accuracy of through genome wide association study (GWAS) using these 30 million SNPs to detect important gene regions (QTL) for five key traits: carcass fat depth, intramuscular fat, post-weaning eye muscle depth and post-weaning body weight and shear force. We found that the WGS data provided more and clearer evidence of QTL regions, potentially resulting in more predictive SNPs and more detailed functional analysis of genes underlying these regions.
  • Improved genomic prediction accuracy
  • The improvement in accuracy of genomic prediction based on selected variants from imputed whole genome sequence was equal was between 6.2 and 4.1 percentage units for purebred and crossbred Merino sheep, respectively.
  • Genomic flock profiling: we developed a method to estimate breeding values for animals with genotype only by back-solving post analysis from the single step genomic BLUP model. In a test application it was found that flock genetic means for a range of key traits in Australian Merino sheep could be estimated with high accuracy from SNP genotypes from a sample of 20 animals (correlations usually exceeding 0.8). These results will form the basis of Gene Profiling, i.e. benchmarking of commercial flocks.
  • Single step analysis:  We described the single trait “single step” methods into full multiple trait single step analysis covering most traits evaluated. The new analyses has been shown to significantly improve the prediction of progeny performance across most traits.
  • Cost:benefit analysis of strategies to select for poll in a nucleus flock, and a cost:benefit analysis of measuring traits and genotyping in commercial flocks have been undertaken.