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Summary of progress in Genomics & Genetics - 2012

Genomic Pilot Projects 2012

Between August 2012 and the end of April 2013, the Sheep CRC is offering three genomics tests as part of a pre-commercial pilot program.

As the genomic era gains momentum for the Australian sheep industry, the 2012 Genomic Pilot Projects represent an important development for everybody involved.  The Pilot Projects provide an opportunity for a wide cross-section of the sheep industry to trial DNA tests for poll, parentage, and full genotyping.  This is a chance to get first hand experience of each step of the process from sampling through to using the information in breeding decisions.

It is important that participants in these pilot projects understand that they are genuine ‘test runs’ that involve elements of research and the evaluation and streamlining of management systems for logistics and reporting. Please bear this in mind if there are any unpredicted delays or trouble shooting along the way. CLICK HERE for further information on  how to participate in the pilot projects and to place online orders.

General progress

The Sheep CRC is working closely with Sheep Genetics on a range of parallel and inter-related initiatives – all involving ram breeders throughout Australia. The assistance of these ram breeders is greatly appreciated and has added very significantly to the success of the program. There have been a number of questions about how each of the projects differ and how they fit together.

To watch the Channel 7 interview with Sam Gill, Sheep Genetics Manager click here.

To view the Landline program filmed in Armidale during July 2012 click here.

To watch Sheep CRC related video clips click here.



Finishing the Information Nucleus Program

This is the flagship CRC program that has been underway since early 2007. Each year approximately 100 young rams have been selected by the CRC’s genetics team on the basis of high levels of performance in at least one trait, a spread over a range of bloodlines/genotypes. Using AI, these rams were joined to 5000 ewes located at 8 sites throughout Australia. The progeny have been thoroughly measured for a comprehensive range of traits as well as ‘genotyping’ using a 50K SNP chip. The results have contributed to better understanding of genetic parameters, definition of new traits and utilisation of genomic information in predicting breeding values.

The last crop of lambs in this five-year program were born in 2011. Measurements of the progeny will continue to 2015 with a focus on reproductive performance and adult wool production. Many ram breeders have sold semen into the program at the discounted rate of $10/dose, and this contribution has been invaluable.

Genomics Pilot Project II (2011-2012)

The CRC is in the middle of our second pre-commercialisation pilot in collaboration with MLA and AWI. The Project aims to genotype young rams born in 2011 and use the results to assist with selection of sires for the 2012 breeding season. Genomics makes a particularly valuable contribution to selection of young rams for traits that are difficult to measure or only measurable later on in life. Data for the updated prediction of genomic breeding values largely comes the Information Nucleus program.

Ram breeders were invited to nominate up to 20 rams, for Merinos and 10 for other breeds, with a target for the whole project of 1,000 rams. This was an open call for all members of MERINOSELECT and LAMBPLAN. The cost of genotyping was subsidised with breeders paying $50/ram. Results have already been returned to breeders who submitted samples between September and November. These results are generating a lot of interest as they provide research breeding values for a wide range of traits considered to be very useful in ram selection decisions. There are also predictions for new traits such as horn-poll, intramuscular fat and dressing percent.

Industry sires with accurate ASBVs for NLW

Getting sufficient data on reproductive performance (number of lambs weaned - NLW) is a slow business. To try to speed up collection of data from which to develop genomic predictions for NLW, a number of ram breeders have been approached buy Sheep Genetics with a request to collect blood samples from rams with accurate ASBVs for NLW. We will use these samples to genotype the rams using the 50K SNP chip and include the data in future analyses in combination with the Information Nucleus data. There has been no cost to breeders in having these sires genotyped and Sheep Genetics been able to provide results to these breeders on the research breeding values outlined above for the Pilot Project.

Developing and testing a SNP-based parentage test

Sheep CRC and MLA are working together to develop a SNP-based DNA parentage test that will include prediction of horn-poll and pigmentation. A number of ram breeders with good parentage data collected through mothering up, pedigree matchmaker or other DNA tests have been asked to collect blood samples from progeny and parents to help validate an experimental version of the new test. Results of the evaluation will be available in February 2012 and it is anticipated that there will be pre-commercial testing of the new product for the 2012 lambing season.

Post-CRC Information Nucleus program 2012

The original Information Nucleus program, with its final lambing in 2011, was establish the value of the novel design in generating genetic and genomic information. The results have exceeded expectations. It is now clear that genomic technologies will deliver significant benefits to the sheep industry. It is also clear that the value of genomic predictions needs to be improved, and maintained, via an on-going Information Nucleus program. This is referred to as the post-CRC Information Nucleus program or Information Nucleus II (IN2). As for the original Information Nucleus program young rams are being selected for excellence and diversity with purchase of semen from cooperating breeders ($10/dose). While the focus of genotyping will be on the major breeds there will be inclusion of minor breeds in order to benchmark key difficult to measure phenotypic characteristics such as meat quality.

As implied by the title, the post-CRC Information Nucleus is beyond the scope of the CRC and will be largely funded by industry. Preparation of the ewes and the AI program, scheduled to commence March 2012, will be funded by MLA and AMPC. Decisions on longer term funding of the program will be made around March/April 2012.

Bringing it together

As more data is collected from all sources the genomic prediction of breeding values becomes more accurate and covers a wider range of traits. Whenever the predictive algorithms are updated then the results can be distributed for all rams that have been genotyped with the 50K SNP chip. A good example was the recent release in November 2011 of genomic breeding values for horn-poll as part of the Genomic Pilot Project II. The availability of this new information meant that results for rams in the entire Information Nucleus program, Pilot Project I and a wide range of industry sires received the update.

As the CRC and Sheep Genetics draws on the support and good will of collaborating breeders we are also focusing on how to return valuable new information to help breed better rams and accelerate genetic gain. Please let us know if there are ways we can improve the flow and nature of information.

Products & Training Resources Reports, Articles and Presentations

Products & Training Resources

ASBV Case Studies

Several case studies are available on the use and benefits of ASBVs - download the individual case studies below.

Australian Sheep Breeding Values - A guide for ram buyers

This guide is provided to help you understand the complexities of breeding profitable yet functional sheep that are right for your business.

Reports, Articles and Presentations

Sheep CRC Genomics Breakfast Workshop - LambEx 2012

During LambEx 2012 the Sheep CRC hosted a genomics breakfast workshop - download the papers from the workshop below.

SNP Chip - revolutionising genetics

This article appears courtesy of Meat & Livestock Australia (