Pilot Project II

Of the 650 rams entered in the Pilot Project, more than half are Merino. This indicates the clear benefits for Merino ram breeders from the genomics tests that provide information on a range of wool, meat and parasite traits for young rams. The high level of accuracies for predicting adult fleece weight and fibre diameter (over 0.7) are an advantage, particularly when these traits can be combined with additional information on growth rate and meat quality parameters.

This year breeders were encouraged to enter up to 10 sires for Terminal breeds and up to 20 for Merinos. These numbers of rams in the project have provided information for selecting a number of semen sires from the range of young rams tested. The use of genomic information alongside conventional classing and ASBVs provides a new dimension that is proving to be of practical value.

The CRC is working with Participants to evaluate new genomic testing systems that are likely to provide lower cost tests for the 2012-13 screening. Cheaper testing systems will provide a platform for the anticipated “commercial trial” in 2012-13. The basis of the ‘commercial trial’ will be DNA testing at a commercial rates - with no subsidy required. Further information on progress will be announced through the year.

To read background information click here.



March 2012 update

SNP-based Breeding Values for poll-horn status in Merinos

Based on CRC research, and data from the Information Nucleus program, a predictive breeding value for poll-horn status was released for rams entered in Genomics Pilot Project II and for rams in the Information Nucleus Program.

The breeding value reports that the animal has one of three possible genotypes:

  • PP – Polled
  • PH – Half poll
  • HH – Horned

 

The original test is based on a single SNP on the 50k SNP panel used in the Information Nucleus and Pilot Projects. It is now being incorporated into a new SNP-based parentage test.  The results and their interpretation, as explained below, will be exactly the same as for the Pilot Project results.

This SNP is not the direct marker, or the actual gene causing polled status. However, it is highly associated with polled and horn phenotypes, and is closely linked to the polled gene in this region, which has been independently confirmed in other studies.

This means that while using this SNP does not result in a simple ‘yes/no’ outcome, sires with the “PP” genotype will produce significantly more offspring with polled status than sires a ‘heterozygous’ “PH” genotype or the “HH” genotype.

As it is a predictive test, it is important to understand the probabilities of different outcomes when mating PP and HH rams to either horned or polled ewes. The table below summarises the probabilities of various poll-horn outcomes associated with the different status of sires and dams.

While not reported, outcomes for PH dams will lie somewhere between the probabilities shown for the PP and HH dams. Animals that have knobs or scurs are neither polled nor horned, and have not been included in the table.

Sire breeding values for horn status (Probability of progeny phenotype):


Animals with knobs or scurs have been classified as neither polled nor horned and probabilities do not add to 1.0.

Estimates are based on 2300 Merino progeny in the CRC Information Nucleus.



Results as at 24 November 2011

Horn/Poll gene – a measure of whether an animal carries a gene for polled, horned or both.

This new SNP test predicts the likelihood of whether an animal will be horned or polled. The test shows that sires with a “PP-polled” genotype will have significantly more offspring with polled status when mated to non-polled dams and their offspring are rarely horned. Sires with a “HH-horned” genotype can give between 1 and 79% horned offspring in males, depending on the dam population the sire is mated to. Breeding values of heterozygous sires (PH or HP) are intermediate. Results will also vary in line with the gene frequency in ewes.

Results show that:

  • animals with a “PP” genotype are mostly polled (>98%), and always not horned
  • animals with a “PH” genotype (having received a "P"-allele from the sire) gives often 'polled' in females (80%) and 'not polled' in male progeny (65%), and almost always 'not horned'.
  • animals with a “HP” genotype (having received a "P"-allele from the dam) gives usually 'polled' in males (74%) and almost always polled in females (97%) and almost always 'not horned' offspring.
  • animals with a “HH” genotype gives mostly "not polled', and males are mostly 'horned' (79%).

 

Results also suggest there is an imprinting effect, as receiving a “P” from the dam gives more often a “polled” status than receiving it from the sire. The effect is most visible in heterozygous males, who are generally less frequently polled than heterozygous females. This needs to be further investigated as imprinting effects could possibly be construed from the dam populations that are confounded with sites.

The following RBVs have shown significantly improved accuracy using Pilot II data:

  1. Adult greasy fleece weight – a measure of projected greasy fleece weight from sheep of over two years in age
  2. Adult fibre diameter - a measure of projected wool fibre diameter in sheep of over two years in age
  3. Adult staple strength - a measure of projected wool staple strength in sheep of over two years in age
  4. Intramuscular fat - a measure of the fat % in the loin muscle of a lamb (marbling). IMF has been shown to have a significant impact on the flavour, juiciness, tenderness and overall eating quality of lamb.
  5. Lean meat yield - a measure of the commercial yield of lean meat as a percentage of hot carcase weight
  6. Eye muscle depth - a measure of the eye muscle depth of the loin taken from a quartered carcase and reported in millimetres. This trait has been shown to influence lean meat yield and the weights of key muscles, particularly the loin muscle

Tables of Accuracies


DNA test development - Genomics Pilot Project II Background

The Sheep CRC is partnering with Sheep Genetics, MLA and AWI to further refine and develop the use of genomics to select the best young rams.

Following the ground-breaking Sheep Genomics Pilot Project I in 2010, a follow-up ‘Phase II’ is being conducted during 2011/12 to build on the learnings of first Pilot Project and test protocols that will form the basis of a future commercial DNA testing service for the Australian sheep industry. Sheep CRC Chief Executive, Prof James Rowe, says breeders are now invited to register their interest. “We’d like to include up to 1,000 young sires from the Merino, Border Leicester, Poll Dorset and White Suffolk breeds in this Pilot Project Phase II,” he said. “We have to limit our work – for the medium-term – to these major breeds as we now know that, with current technologies, we are not yet able to provide across-breed predictions and will not be able to develop sufficiently large data bases for the minor breeds.

“Letters, with nomination forms and background information, have now been sent to all Sheep Genetics clients who we hope can participate.” All ram breeders interested in participating should contact Sheep Genetics (see contact details below).

Prof Rowe explains that Phase II participants will be selected from breeders of these major breeds who use Sheep Genetics’ LAMBPLAN or MERINO SELECT, with preference for those involved in Pilot Project 1, and who have a minimum standard of ‘Bronze Data Quality’ data collection. These requirements are based on the fact that the genomic data has to be combined with pedigree and performance data to get real value from it, and currently, computational capability is only established for the LAMBPLAN and MERINOSELECT data bases. Genomic-based breeding values offer new opportunities for early selection decisions with young sires to achieve genetic improvement across a range of traits including new traits that breeders are unable to measure on-farm, such as intramuscular fat and shear force or tenderness.

Pilot Project I demonstrated that data from the 50k SNP-chip can be used in conjunction with conventional genetic parameters to predict breeding values with sufficient accuracies to be of value for early ram selection decisions, including long to measure traits such as adult fleece weight. The Pilot involved some 200 breeders and more than 360 young sires from across Australia having their DNA information incorporated with pedigree and performance data into Research Breeding Values, or RBVs. These RBVs have been produced for a range of existing and new LAMBPLAN -MERINOSELECT traits.

Pilot Project Phase II Manager, Dr Ken Geenty, says logistics and sample turnaround times will be improved compared to the first Pilot. “By using blood-cards for DNA tests and a more streamlined system for data analysis this year, we will be aiming to provide participants with more accurate predictions for a broader range of traits with RBVs within 12 weeks of receipt of a completed blood-card,” Dr Geenty said. “Because we are still developing and testing the process we consider that there is still an element of research involved in the Pilot Project and participants will, therefore, be offered a subsidised rate of $50 per genotyped sire.”

This second Genomics Pilot Project is the next step towards the Australian sheep industry being able to use genomic technologies, in conjunction with best practices, to improve genetic gain.

For further information contact Ken Geenty on 02 6773 1993 or Sheep Genetics on 02 6773 2948.



Practical Wisdom Notes / Fact Sheets

New Opportunities in Genetics and Genomics

PW4.1-01 Genomics and DNA testing: new tools for ram breeders to accelerate genetic gain

Using ASBVs

Products & Training Resources

ASBV Pocket Guide

Australian Sheep Breeding Values - A guide for ram buyers

Marketing your sheep with genetic data

Reports, Articles and Presentations

Getting Started with Sheep Genetics

Sheep CRC Genomics Breakfast Workshop - LambEx 2012

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