Combined breed analysis for terminal sire sheep breeds

New approaches to extraction, defining breed (using PEB%), dominant breed, calculating heterosis, defining genetic groups and undertaking QA on mixed breed runs were all developed. Work on indexes was limited, but as trait definitions are changing this is acceptable. The first stage of this work didn’t result in findings that could be delivered directly to industry and there was limited thought on how to report them to Signet / clients – but this has been picked up in further work and has provided an excellent starting point. Further work is already planned, including dealing with the following:

Next Steps
Genetic issues

• Several breeds had extreme values
  • Genetic groups to be reviewed & RamCompare data to be assessed
• Lambing ease to be reviewed
• Mature weight to be reviewed with new parameters from Lambe / McLaren

Technical issues

• Link more flocks with two breeds on same holding
• Provide Signet access to the EBVs
• Provide PEB% and “Dominant breed” to Signet
• Review scan age criteria

Reporting mechanisms

• To get EBVs on BASCO Search
• To calculate breed specific percentiles

Building in new research

• Include RamCompare traits (stand alone at this stage) – Abbygail Moran
• Include new genetic parameters
  • New CT traits – spine length etc
  • Updated genetic parameters for all other weight adjusted traits

New index work

All indexes need to be reviewed, but the trait definition has changed with many traits becoming weight adjusted, not age adjusted – so advice in this area is being sort.

The Problem:

UK genetic evaluations of sheep have traditionally been undertaken within breeds. However, the UK sheep industry is a mostly stratified system with approximately 56% of ewes in the national flock being crossbred. This represents a 6% increase in the past decade. This shift has also been noticed in the rams that are used in the national flock. The recent sheep census (The breeding structure of the British sheep industry 2012) found that 5% of rams used in the national flock were crossbred. Increasingly, breeders are incorporating crossbred sheep into genetic improvement systems, and it is then not surprising that requests for across-breed Estimated Breeding Values (EBVs) from these cross-breeding flocks have also increased. These breeders could be serviced by moving the evaluation of terminal sire breeds to a “Combined Breed Analysis in a similar manner to the UK dairy evaluation.

Combined-breed genetic evaluation allows multiple breeds of sheep to be evaluated simultaneously and animals from different breeds to be compared directly via the resulting EBVs. The benefits of combined-breed evaluations are that they can accelerate genetic improvement as they increase the accuracy of EBVs (more data is included in the analysis) and allow more intense selection (as the gene-pool to select the next generation can be substantially widened as a result of combined-breed evaluation and the increased EBV accuracy). Rates of genetic improvement can also be increased indirectly by the ability to provide a more efficient service.

At the moment, genetic evaluations are run 3-4 times a year for individual breeds. In a combined-breed scenario only 1 genetic evaluation is required to service many breeds. Therefore, it will be possible to provide up-to-date genetic evaluations more frequently, meaning that breeders always have up-to-date information when they are making their selection decisions. This will help to engage more farmers in performance recording and result in farmers making better use of EBVs, ultimately improving the genetic progress of the national sheep industry.

Combined-breed sheep genetic evaluations are currently available in several countries including Ireland, New Zealand and Australia. However, the existing UK sheep genetic evaluations have been developed for purebred sheep and are not suitable for evaluation of cross-bred sheep. In order to expand the UK sheep genetic evaluation system to include multiple breeds and cross-bred data, the existing UK system needs to be modified to allow the methodology to be adapted such that it is applicable to a combined breed scenario.

The CBA concept was discussed at the Sheepbreeder’s Roundtable, November 2013 and over 95% of attendees voted in favour of such an approach for the UK sheep industry.

Aims & Objectives:

The new approach would:-

• Enable crossbred animals to be analysed accurately
• Take into account hybrid vigour in breeding value estimates
• Re-base the population to a common and more recent/relevant population of animals
• Enable a review of the genetic parameters and breeding indexes used
• Provide a mechanism for breed comparison in the future
• Improve genetic improved by potentially more accurate EBVs and a wider gene-pool for selection
• Enable a more efficient and frequent service to be delivered to industry

Approach:

Methodology

The data to undertake this evaluation is already held within the BASCO database. Research is now required to look at its structure and create robust new approaches to the extraction, analysis and reporting of this data.

The methodology required to enable the Sheepbreeder BLUP system to handle crossbred data is as follows:

1. An accurate knowledge of breed make- up. “Breed will be calculated on a Percentage of Each Breed basis (PEB). PEB procedures have already been formulated. Work is now required to automate & QA PEB values and populate BASCO
2. Assess the data structure to ascertain what pure-breeds and crosses are represented in the data and in what volume
3. Produce a test data extraction system from the BASCO database; the breeds to be included in this evaluation are; Texel, Suffolk, Charollais, Meatlinc, Hampshire Down, Beltex, Blue Texel, Bleu du Maine, Vendeen and Southdown
4. Develop the evaluation in Mix99 to produce EBVs
5. Produce post evaluation systems for EBVs to include “breed specific reporting, but allow flexibility in which groups of animals are reported together
6. Extensively test the resulting EBVs such that EGENES are confident and then you provide to industry from review
7. A review of breeding indexes and initial recommendations for the industry

Technical issues specific to the BLUP run will look at:

1. An investigation of “breed groups to determine the best way to account for heterosis and recombination effects
2. Determine which genetic parameters to use in the evaluation and what scaling is required to ensure fairness across the breeds. It may be required to undertake genetic parameter estimation to obtain suitable parameter estimates
3. Develop genetic group structures that reflect the breed make up and age structures (like existing genetic groups)